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[ { "content": "You will be shown a claim about public health and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\". If the abstract does not provide enough information to arrive at a verdict, write \"NEI\" (for \"not enough information\").\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract. If the verdict was \"NEI\", then return an empty array.\n\nFor instance, if the model were given the claim \"wearing masks can prevent the spread of COVID\", the output might be:\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that mass mask-wearing reduces the transmission rate for COVID-19.\"]\n}\n\nClaim: COVID May Trigger 'Cytokine Storm' in Some Cases\n\nAbstract:\nCytokine storm in COVID-19 is characterized by an excessive inflammatory response to SARS-CoV-2 that is caused by a dysregulated immune system of the host.\nWe are proposing a new hypothesis that SARS-CoV-2 mediated inflammation of nucleus tractus solitarius (NTS) may be responsible for the cytokine storm in COVID 19.\nThe inflamed NTS may result in a dysregulated cholinergic anti-inflammatory pathway and hypothalamic-pituitary-adrenal axis.", "role": "user" }, { "content": "{\"verdict\": \"SUPPORT\", \"evidence\": [\"Cytokine storm in COVID-19 is characterized by an excessive inflammatory response to SARS-CoV-2 that is caused by a dysregulated immune system of the host.\"]}", "role": "assistant" } ]

[ { "content": "You will be presented with a citation sentence from a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\nThe estimation of historical population parameters from mitochondrial (mt) DNA coalescent genealogies offers a unique way of understanding the effects of Pleistocene climate shifts on marine species (Avise, 2000).", "role": "user" }, { "content": "Background", "role": "assistant" } ]

[ { "content": "You will be shown the title of a chemistry paper, together with sections excerpted from the body of the paper. The paper sections may include HTML tags like `<p>` and `</p>`; please ignore these. Your task is to write an abstract for the paper. Your response should include the abstract and no other text.\n\nTitle:\nAddressable Terminally-Linked DNA-CNT Nanowires\n\nPaper sections:\n\n<p>The synthesis of well-defined hybrid carbon nanotubebiomaterials remains a significant challenge at the frontier of nanotechnology and nanoparticle constructs are having a major impact in bio-diagnostics.1 The regiospecific covalent functionalization of single walled carbon nanotubes (SWCNTs) with oligonucleotides could provide new hybrid materials with sensing and self-assembly properties for the precise positioning of biomolecules and nanoparticles. To date, most methods for the functionalization of SWCNTs with oligonucleotides have relied on non-covalent surface adsorption,2,3 and those using covalent attachment have suffered from a lack of regioselectivity due to defect sites on the SWCNT surface created during strong oxidation procedures.4,5,6 Furthermore, SWCNT aggregation/bundling3,4,6 and nonspecific surface absorption has also been a serious limitation that is seldom addressed in previous studies. Oligonucleotides have been shown to undergo adsorption to the surface of SWCNTs and this property has formed the basis for SWCNT purification methods.7–10 Previous studies have elegantly demonstrated that DNA detection can be performed at the single molecule level between two DNA linked CNT's however the use of ultrahigh resolution electron beam lithography and reproducibility are still major concerns for the mass production of reliable sensory devices.11,12 In this communication we report the synthesis of a new nanostructured material composed of unbundled SWCNTs that are regiospecifically and covalently linked at their termini with oligonucleotides of a defined sequence. By utilizing a SWCNT surface protection step we are able to simultaneously circumvent the problem of regiospecific SWCNT covalent attachment and non-specific surface adsorption/aggregation.13 Additionally, we show that the oligonucleotide junctions are addressable and can be used to position gold nanoparticles in a specific location along the nanostructures.</p><p>Figure 1 shows the reaction sequence for SWCNT oxidation, shielding, DNA conjugation, and gold nanoparticle targeting. In a typical experiment HiPco SWCNTs were acid treated in a mixture of concentrated sulfuric and nitric acid (3:1, 98% and 70%, respectively), subjected to sonication for 35 min. at 40 °C, and then oxidized with a mixture of concentrated sulfuric acid and hydrogen peroxide (4:1 98% and 30%, respectively, 30 min.) to give carboxylic acid functionalized nanotube ends and to remove extraneous carbon particles.14 In addition, studies have shown that under mild oxidation conditions the optical and electronic properties of CNTs can be preserved.15–18 For Raman spectra of CNTs before and after oxidation see figure S1. Previous studies have demonstrated that the chemical shortening of SWCNTs by mixtures of strong acids leads to oxidation at the nanotube ends and some sidewall defect sites.14 The oxidized nanotubes were incubated with Triton X-100/PEG (Mn = 10,000) in an aqueous solution and sonicated for 4 h in an ice bath. This process results in a stable dispersion of SWCNTs wrapped with surfactant and polymer to prevent unwanted functionalization of the nanotube sidewalls and non-specific surface adsorption.19,20 The oxidized termini of the shielded SWCNTs were then selectively coupled to the DNA strands (1) bearing a nucleophilic primary amine at the 5' and 3' ends. Efficient coupling was achieved using 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC) and N-hydroxysulfosuccinimide (sulfo-NHS) resulting in SWCNTs linked by DNA (1) at their termini in a nanowire configuration.13 Next, the resulting DNA-SWCNT nanowires were used to sequence specifically address gold nanoparticles to the DNA junctions connecting adjacent nanotubes.</p><p>Characterization of the DNA-SWCNT nanowires was performed using AFM and confocal Raman spectroscopy before and after gold nanoparticle hybridization (Figure 2 and 3). Oxidized shielded SWCNTs are dispersed and separated from adjacent nanotubes after sonication as evidenced by AFM, with average lengths of ~200 nm (Figure 2A). In contrast, DNA-SWCNT nanowires show the presence of contiguous nanotubes with terminal connections mediated by DNA junctions (1) and individual nanotube lengths of ~200 nm (Figure 2B,C). To confirm the nature of the nanowire DNA junctions we utilized DNA (2) and AuNP probes (3), which showed AuNPs bound at each DNA junction by AFM, confirming the presence of DNA-SWCNT nanowires (Figure 2D and Figure 3A). AuNP probes were chosen due to their large diameter (~30 nm) compared to shielded-SWCNTs (1–5 nm) providing an unambiguous probe for identification of the DNA junctions. Confocal Raman spectroscopy was performed on the mica deposited AFM samples and confirmed the presence of CNT's (Figure 3B). In addition, experiments were carried out with ~10 nm AuNP probes which showed similar results to the 30 nm particles above (See figure S2). Control experiments using non-complimentary DNA confirmed the sequence specificity of our AuNP targeting strategy (See figure S2).</p><p>The potential use of this new material for applications beyond gold nanoparticle addressing are considerable. The assembly of the SWCNT networks linked by oligonucleotides could serve as a novel sensing domain for applications such as DNA detection or biosensing and efforts in this area are underway. In addition to gold nanoparticles, the potential for addressing enzymes such as alkaline phosphatase, glucose oxidase or DNAzymes may provides many new avenues for the construction of hybrid biocatalytic-CNT devices. Importantly, this new material could have implications for the mass production of new bio-diagnostic sensory devices.</p>", "role": "user" }, { "content": "Despite many advances in carbon nanotube (CNT) research, several issues continue to plague the field with regard to the construction of well-defined hybrid CNT materials. Regiospecific covalent functionalization, non-specific surface absorption, and carbon nanotube aggregation/bundling present major difficulties when working with these materials. In this communication, we circumvent these problems and report a new addressable hybrid material composed of single-walled carbon nanotubes terminally linked by oligonucleotides into a nanowire motif. We show that the oligonucleotides junctions are addressable and can be targeted by gold nanoparticles.", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"RNA\", \"CellType\", \"CellLine\", \"Protein\", \"DNA\"].\n\nPlease return the output as a JSON object of the format: {\"DNA\" : [\"TAL1\", ...], \"RNA\": [\"mRNAs\", ...], \"CellLine\": [\"T cells\", ...], \"CellType\": [\"monocytes\", ...], \"Protein\": [\"IL-2\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nAlternative polyadenylation events contribute to the induction of NF-ATc in effector T cells. The transcription factor NF-ATc is synthesized in three prominent isoforms. These differ in the length of their C terminal peptides and mode of synthesis. Due to a switch from the use of a 3' polyA site to a more proximal polyA site, NF-ATc expression switches from the synthesis of the two longer isoforms in naive T cells to that of short isoform A in T effector cells. The relative low binding affinity of cleavage stimulation factor CstF-64 to the proximal polyA site seems to contribute to its neglect in naive T cells. These alternative polyadenylation events ensure the rapid accumulation of high concentrations of NF-ATc necessary to exceed critical threshold levels of NF-ATc for gene induction in effector T cells.", "role": "user" }, { "content": "{\"CellLine\": [], \"CellType\": [\"naive T cells\", \"effector T cells\", \"T effector cells\"], \"DNA\": [\"proximal polyA site\", \"3\\u0027 polyA site\"], \"Protein\": [\"cleavage stimulation factor\", \"transcription factor\", \"CstF - 64\", \"The transcription factor NF - ATc\", \"NF - ATc\", \"isoform A\", \"isoforms\"], \"RNA\": []}", "role": "assistant" } ]

[ { "content": "Given an abstract from a research paper, your task is to identify and label relationships between chemical compounds and genes mentioned in the abstract.\n\nThe relationship type must be one of ['DOWNREGULATOR', 'SUBSTRATE', 'INDIRECT-REGULATOR', 'PART-OF', 'MODULATOR-ACTIVATOR', 'REGULATOR', 'INHIBITOR', 'COFACTOR', 'UPREGULATOR', 'ACTIVATOR', 'ANTAGONIST', 'NOT', 'INDIRECT-DOWNREGULATOR', 'SUBSTRATE_PRODUCT-OF', 'INDIRECT-UPREGULATOR', 'AGONIST', 'PRODUCT-OF', 'MODULATOR', 'DIRECT-REGULATOR', 'UNDEFINED', 'AGONIST-INHIBITOR', 'AGONIST-ACTIVATOR', 'MODULATOR-INHIBITOR'].\n\nPlease format your output as a JSON array. Each entry in the array should express a single relation, formatted as [\"<Entity_A>\", \"<RELATION_A_B>\", \"<Entity_B>\"]. If no relations can be found, please output an empty JSON array [].\n\nAbstract:\n\nInteracting Glutamate Receptor-Like Proteins in Phloem Regulate Lateral Root Initiation in Arabidopsis. Molecular, genetic, and electrophysiological evidence indicates that at least one of the plant Glu receptor-like molecules, GLR3.4, functions as an amino acid-gated Ca (2 +) channel at the plasma membrane. The aspect of plant physiology, growth, or development to which GLR3.4 contributes is an open question. Protein localization studies performed here provide important information. In roots, GLR3.4 and the related GLR3.2 protein were present primarily in the phloem, especially in the vicinity of the sieve plates. GLR3.3 was expressed in most cells of the growing primary root but was not enriched in the phloem, including the sieve plate area. GLR3.2 and GLR3.4 physically interacted with each other better than with themselves as evidenced by a biophotonic assay performed in human embryonic kidney cells and Nicotiana benthamiana leaf cells. GLR3.3 interacted poorly with itself or the other two GLRs. Mutations in GLR3.2, GLR3.4, or GLR3.2 and GLR3.4 caused the same and equally severe phenotype, namely, a large overproduction and aberrant placement of lateral root primordia. Loss of GLR3.3 did not affect lateral root primordia. These results support the hypothesis that apoplastic amino acids acting through heteromeric GLR3.2/GLR3.4 channels affect lateral root development via Ca (2 +) signaling in the phloem.", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "You will be shown sections from a scientific research paper, together with a question about the paper. This is an extractive question-answering task, where you must find and extract relevant text spans directly from the paper to answer the question. Your response should strictly be a `json` object with two fields:\n\n\"answer\": An array of strings extracted directly from the paper which, collectively, answer the question.\n\"evidence\": An array of strings. Each should be an excerpt from the paper, in which one or more of the extracted answers can be found.\n\nFor example, for the question \"What baselines did the authors compare against?\", a sample response might be:\n{\n \"answer\": [\"BERT\", \"RoBERTa\"],\n \"evidence\": [\"In our experiments, we compare the performance of our model against BERT and RoBERTa.\"]\n}\n\nDo not include any text in your response other than the json.\n\nIf the question is unanswerable given the provided excerpts, respond with the single word \"null\".\n\nPaper: Duality Regularization for Unsupervised Bilingual Lexicon Induction\n\nUnsupervised bilingual lexicon induction naturally exhibits duality, which results from symmetry in back-translation. For example, EN-IT and IT-EN induction can be mutually primal and dual problems. Current state-of-the-art methods, however, consider the two tasks independently. In this paper, we propose to train primal and dual models jointly, using regularizers to encourage consistency in back translation cycles. Experiments across 6 language pairs show that the proposed method significantly outperforms competitive baselines, obtaining the best-published results on a standard benchmark.\n\nIntroduction\nUnsupervised bilingual lexicon induction (UBLI) has been shown to benefit NLP tasks for low resource languages, including unsupervised NMT BIBREF0, BIBREF1, BIBREF2, BIBREF3, BIBREF4, information retrieval BIBREF5, BIBREF6, dependency parsing BIBREF7, and named entity recognition BIBREF8, BIBREF9.\nRecent research has attempted to induce unsupervised bilingual lexicons by aligning monolingual word vector spaces BIBREF10, BIBREF11, BIBREF12, BIBREF13, BIBREF14, BIBREF15. Given a pair of languages, their word alignment is inherently a bi-directional problem (e.g. English-Italian vs Italian-English). However, most existing research considers mapping from one language to another without making use of symmetry. Our experiments show that separately learned UBLI models are not always consistent in opposite directions. As shown in Figure 1a, when the model of BIBREF11 Conneau18a is applied to English and Italian, the primal model maps the word “three” to the Italian word “tre”, but the dual model maps “tre” to “two” instead of “three”.\nWe propose to address this issue by exploiting duality, encouraging forward and backward mappings to form a closed loop (Figure 1b). In particular, we extend the model of BIBREF11 Conneau18a by using a cycle consistency loss BIBREF16 to regularize two models in opposite directions. Experiments on two benchmark datasets show that the simple method of enforcing consistency gives better results in both directions. Our model significantly outperforms competitive baselines, obtaining the best published results. We release our code at xxx.\n\nRelated Work\nUBLI. A typical line of work uses adversarial training BIBREF17, BIBREF10, BIBREF18, BIBREF11, matching the distributions of source and target word embeddings through generative adversarial networks BIBREF19. Non-adversarial approaches have also been explored. For instance, BIBREF15 Mukherjee18EMNLP use squared-loss mutual information to search for optimal cross-lingual word pairing. BIBREF13 and BIBREF20 exploit the structural similarity of word embedding spaces to learn word mappings. In this paper, we choose BIBREF11 Conneau18a as our baseline as it is theoretically attractive and gives strong results on large-scale datasets.\nCycle Consistency. Forward-backward consistency has been used to discover the correspondence between unpaired images BIBREF21, BIBREF22. In machine translation, similar ideas were exploited, BIBREF23, BIBREF24 and BIBREF25 use dual learning to train two “opposite” language translators by minimizing the reconstruction loss. BIBREF26 consider back-translation, where a backward model is used to build synthetic parallel corpus and a forward model learns to generate genuine text based on the synthetic output.\nCloser to our method, BIBREF27 jointly train two autoencoders to learn supervised bilingual word embeddings. BIBREF28 use sinkhorn distance BIBREF29 and back-translation to align word embeddings. However, they cannot perform fully unsupervised training, relying on WGAN BIBREF30 for providing initial mappings. Concurrent with our work, BIBREF31 build a adversarial autoencoder with cycle consistency loss and post-cycle reconstruction loss. In contrast to these works, our method is fully unsupervised, simpler, and empirically more effective.\n\nApproach\nWe take BIBREF11 as our baseline, introducing a novel regularizer to enforce cycle consistency. Let $X=\\lbrace x_1,...,x_n\\rbrace $ and $Y=\\lbrace y_1,...,y_m\\rbrace $ be two sets of $n$ and $m$ word embeddings for a source and a target language, respectively. The primal UBLI task aims to learn a linear mapping $\\mathcal {F}:X\\rightarrow Y$ such that for each $x_i$, $\\mathcal {F}(x_i)$ corresponds to its translation in $Y$. Similarly, a linear mapping $\\mathcal {G}:Y\\rightarrow X$ is defined for the dual task. In addition, we introduce two language discriminators $D_x$ and $D_y$, which are trained to discriminate between the mapped word embeddings and the original word embeddings.\n\nApproach ::: Baseline Adversarial Model\nBIBREF11 align two word embedding spaces through generative adversarial networks, in which two networks are trained simultaneously. Specifically, take the primal UBLI task as an example, the linear mapping $\\mathcal {F}$ tries to generate “fake” word embeddings $\\mathcal {F}(x)$ that look similar to word embeddings from $Y$, while the discriminator $D_y$ aims to distinguish between “fake” and real word embeddings from $Y$. Formally, this idea can be expressed as the minmax game min$_{\\mathcal {F}}$max$_{D{_y}}\\ell _{adv}(\\mathcal {F},D_y,X,Y)$, where\n$P_{D_y}(src|y_j)$ is a model probability from $D_y$ to distinguish whether word embedding $y_j$ is coming from the target language (src = 1) or the primal mapping $\\mathcal {F}$ (src = 0). Similarly, the dual UBLI problem can be formulated as min$_{\\mathcal {G}}$max$_{D_x}\\ell _{adv}(\\mathcal {G},D_x,Y,X)$, where $\\mathcal {G}$ is the dual mapping, and $D_x$ is a source discriminator.\nTheoretically, a unique solution for above minmax game exists, with the mapping and the discriminator reaching a nash equilibrium. Since the adversarial training happens at the distribution level, no cross-lingual supervision is required.\n\nApproach ::: Regularizers for Dual Models\nWe train $\\mathcal {F}$ and $\\mathcal {G}$ jointly and introduce two regularizers. Formally, we hope that $\\mathcal {G}(\\mathcal {F}(X))$ is similar to $X$ and $\\mathcal {F}(\\mathcal {G}(Y))$ is similar to $Y$. We implement this constraint as a cycle consistency loss. As a result, the proposed model has two learning objectives: i) an adversarial loss ($\\ell _{adv}$) for each model as in the baseline. ii) a cycle consistency loss ($\\ell _{cycle}$) on each side to avoid $\\mathcal {F}$ and $\\mathcal {G}$ from contradicting each other. The overall architecture of our model is illustrated in Figure FIGREF4.\nCycle Consistency Loss. We introduce\nwhere $\\Delta $ denotes the discrepancy criterion, which is set as the average cosine similarity in our model.\nFull objective. The final objective is:\n\nApproach ::: Model Selection\nWe follow BIBREF11, using an unsupervised criterion to perform model selection. In preliminary experiments, we find in adversarial training that the single-direction criterion $S(\\mathcal {F}, X, Y)$ by BIBREF11 does not always work well. To address this, we make a simple extension by calculating the weighted average of forward and backward scores:\nWhere $\\lambda $ is a hyperparameter to control the importance of the two objectives. Here $S$ first generates bilingual lexicons by learned mappings, and then computes the average cosine similarity of these translations.\n\nExperiments\nWe perform two sets of experiments, to investigate the effectiveness of our duality regularization in isolation (Section SECREF16) and to compare our final models with the state-of-the-art methods in the literature (Section SECREF18), respectively.\n\nExperiments ::: Experimental Settings\nDataset and Setup. Our datasets includes: (i) The Multilingual Unsupervised and Supervised Embeddings (MUSE) dataset released by BIBREF11 Conneau18a. (ii) the more challenging Vecmap dataset from BIBREF32 Dinu15 and the extensions of BIBREF33 Artetxe17ACL. We follow the evaluation setups of BIBREF11, utilizing cross-domain similarity local scaling (CSLS) for retrieving the translation of given source words. Following a standard evaluation practice BIBREF34, BIBREF35, BIBREF11, we report precision at 1 scores (P@1). Given the instability of existing methods, we follow BIBREF13 to perform 10 runs for each method and report the best and the average accuracies.\n\nExperiments ::: The Effectiveness of Dual Learning\nWe compare our method with BIBREF11 (Adv-C) under the same settings. As shown in Table TABREF12, our model outperforms Adv-C on both MUSE and Vecmap for all language pairs (except ES-EN). In addition, the proposed approach is less sensitive to initialization, and thus more stable than Adv-C over multiple runs. These results demonstrate the effectiveness of dual learning. Our method is also superior to Adv-C for the low-resource language pairs English $\\leftrightarrow $ Malay (MS) and English $\\leftrightarrow $ English-Esperanto (EO). Adv-C gives low performances on ES-EN, DE-EN, but much better results on the opposite directions on Vecmap. This is likely because the separate models are highly under-constrained, and thus easy to get stuck in poor local optima. In contrast, our method gives comparable results on both directions for the two languages, thanks to the use of information symmetry.\nTable TABREF13 shows the inconsistency rates of back translation between Adv-C and our method on MUSE. Compared with Adv-C, our model significantly reduces the inconsistency rates on all language pairs, which explains the overall improvement in Table TABREF12. Table TABREF14 gives several word translation examples. In the first three cases, our regularizer successfully fixes back translation errors. In the fourth case, ensuring cycle consistency does not lead to the correct translation, which explains some errors by our system. In the fifth case, our model finds a related word but not the same word in the back translation, due to the use of cosine similarity for regularization.\n\nExperiments ::: Comparison with the State-of-the-art\nIn this section, we compare our model with state-of-the-art systems, including those with different degrees of supervision. The baselines include: (1) Procrustes BIBREF11, which learns a linear mapping through Procrustes Analysis BIBREF36. (2) GPA BIBREF37, an extension of Procrustes Analysis. (3) GeoMM BIBREF38, a geometric approach which learn a Mahalanobis metric to refine the notion of similarity. (4) GeoMM$_{semi}$, iterative GeoMM with weak supervision. (5) Adv-C-Procrustes BIBREF11, which refines the mapping learned by Adv-C with iterative Procrustes, which learns the new mapping matrix by constructing a bilingual lexicon iteratively. (6) Unsup-SL BIBREF13, which integrates a weak unsupervised mapping with a robust self-learning. (7) Sinkhorn-BT BIBREF28, which combines sinkhorn distance BIBREF29 and back-translation. For fair comparison, we integrate our model with two iterative refinement methods (Procrustes and GeoMM$_{semi}$).\nTable TABREF15 shows the final results on Vecmap. We first compare our model with the state-of-the-art unsupervised methods. Our model based on procrustes (Ours-Procrustes) outperforms Sinkhorn-BT on all test language pairs, and shows better performance than Adv-C-Procrustes on most language pairs. Adv-C-Procrustes gives very low precision on DE-EN, FI-EN and ES-EN, while Ours-Procrustes obtains reasonable results consistently. A possible explanation is that dual learning is helpful for providing good initiations, so that the procrustes solution is not likely to fall in poor local optima. The reason why Unsup-SL gives strong results on all language pairs is that it uses a robust self-learning framework, which contains several techniques to avoid poor local optima.\nAdditionally, we observe that our unsupervised method performs competitively and even better compared with strong supervised and semi-supervised approaches. Ours-Procrustes obtains comparable results with Procrustes on EN-IT and gives strong results on EN-DE, EN-FI, EN-ES and the opposite directions. Ours-GeoMM$_{semi}$ obtains the state-of-the-art results on all tested language pairs except EN-FI, with the additional advantage of being fully unsupervised.\n\nConclusion\nWe investigated a regularization method to enhance unsupervised bilingual lexicon induction, by encouraging symmetry in lexical mapping between a pair of word embedding spaces. Results show that strengthening bi-directional mapping consistency significantly improves the effectiveness over the state-of-the-art method, leading to the best results on a standard benchmark.\n\nFigure 1: (a) Inconsistency between primal model F and the dual model G. (b) An ideal scenario.\n\nFigure 2: The proposed framework. (a)X → F(X)→ G(F(X))→ X; (b) Y → G(Y )→ F(G(Y ))→ Y .\n\nTable 1: Accuracy on MUSE and Vecmap.\n\nTable 4: Accuracy (P@1) on Vecmap. The best results are bolded. †Results as reported in the original paper. For unsupervised methods, we report the average accuracy across 10 runs.\n\nQuestion: What regularizers were used to encourage consistency in back translation cycles?", "role": "user" }, { "content": "{\"answer\": [\"an adversarial loss ($\\\\ell _{adv}$) for each model as in the baseline\", \"a cycle consistency loss ($\\\\ell _{cycle}$) on each side\"], \"evidence\": [\"We train $\\\\mathcal {F}$ and $\\\\mathcal {G}$ jointly and introduce two regularizers. Formally, we hope that $\\\\mathcal {G}(\\\\mathcal {F}(X))$ is similar to $X$ and $\\\\mathcal {F}(\\\\mathcal {G}(Y))$ is similar to $Y$. We implement this constraint as a cycle consistency loss. As a result, the proposed model has two learning objectives: i) an adversarial loss ($\\\\ell _{adv}$) for each model as in the baseline. ii) a cycle consistency loss ($\\\\ell _{cycle}$) on each side to avoid $\\\\mathcal {F}$ and $\\\\mathcal {G}$ from contradicting each other. The overall architecture of our model is illustrated in Figure FIGREF4.\"]}", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a materials science research paper. Your task is to extract all synthesis operations described in the abstract into a structured JSON format. Your output should be a JSON array. Each entry in the array should be a JSON object describing a single synthesis operation. Your output JSON object should have the following two fields:\n\n- \"trigger\": A verbal predicate indicating a synthesis operation. This should be a string extracted directly from the abstract.\n- \"arguments\": An array of arguments specifying aspects of the synthesis operation. Each entry in the array should be a length-2 array formatted as [<argument_text>, <argument_type>]. The `argument_text` should be a string extracted directly from the abstract. The `argument_type` should be one of the following types: [\"Recipe_Precursor\", \"Solvent_Material\", \"Atmospheric_Material\", \"Participant_Material\", \"Recipe_Target\"].\n\nFor instance, suppose an excerpt from the abstract reads:\n\nTetraethoxysilane (TEOS, 98%) and cetyltrimethylammonium bromide (CTAB, 98%) were purchased from Fluka. The MTTZ-siloxy derivative (triethoxysilyl-propyl-5-mercapto-1-methyl-tetrazole) was synthesized as previously described [38].\n\nThis excerpt includes two operations, which could be annotated as follows:\n\n[{\"arguments\": [[\"Tetraethoxysilane\", \"Recipe_Precursor\"], [\"cetyltrimethylammonium bromide\", \"Recipe_Precursor\"]], \"trigger\": \"purchased\"}, {\"arguments\": [[\"MTTZ-siloxy derivative\", \"Recipe_Target\"]], \"trigger\": \"synthesized\"}]\n\nIn your response, please include the JSON and no other text.\n\nAbstract:\n10.1016/j.jcat.2012.12.002\nCatalytic performance of sheet-like Fe/ZSM-5 zeolites for the selective oxidation of benzene with nitrous oxide\nFe/ZSM-5 zeolite nanosheets were prepared according to a literature procedure modified with the purpose of including Fe3+[25] and [26]. In a typical synthesis, 10.42 g of TEOS (tetraethylorthosilicate) was added to a solution containing 0.47 g of aluminum nitrate nonahydrate, 0.06 g of iron nitrate nonahydrate, and 20.0 g of distilled water. The mixture was stirred for 2 h. A solution containing 2.41 g of C16-6-6(Br)2 or C16-6-6(OH)2, 0.42 g sodium hydroxide (NaOH) and 15.7 g of demi-water was added to this mixture and shaken by hand for 5 min. After further stirring with a magnetic stirrer for 6 h at room temperature, the gel mixture was transferred to a Teflon-lined stainless-steel autoclave and heated at 140 degC for 9 days under tumbling (60 rpm). The zeolite product was filtered, washed with distilled water, and dried at 100 degC overnight. Using the OH form of the template, three different Si/Fe ratios were employed (Si/Fe = 84, 180 and 300). The as-synthesized zeolites were calcined at 580 degC for 4 h under a flow of air. The calcined samples were ion-exchanged into their ammonium form by triple ion-exchange with a 1 M aqueous solution of NH4NO3 at room temperature. The proton form of the zeolites was obtained by calcination at 550 degC under a flow of air for 4 h. The samples are denoted as Fe/ZSM-5-sheet(x, y) with x the anion of the template used (OH or Br) and y the Si/Fe ratio. Steam activation was carried out by heating an amount of sample in a flow of 10% water vapor (100 ml min-1) in artificial air at 700 degC for 3 h. The steamed samples are denoted by using the suffix \"-st.\" A reference Fe/ZSM-5 catalyst was prepared by controlled hydrolysis of TEOS in the presence of tetrapropylammonium hydroxide (TPAOH) according to a literature procedure [10].", "role": "user" }, { "content": "[{\"arguments\": [[\"Fe/ZSM-5\", \"Recipe_Target\"]], \"trigger\": \"prepared\"}, {\"arguments\": [[\"water\", \"Solvent_Material\"], [\"TEOS\", \"Recipe_Precursor\"], [\"iron nitrate nonahydrate\", \"Recipe_Precursor\"], [\"aluminum nitrate nonahydrate\", \"Recipe_Precursor\"]], \"trigger\": \"added\"}, {\"arguments\": [[\"mixture\", \"Participant_Material\"]], \"trigger\": \"stirred\"}, {\"arguments\": [[\"demi-water\", \"Solvent_Material\"], [\"C16-6-6(OH)2\", \"Participant_Material\"], [\"mixture\", \"Participant_Material\"], [\"sodium hydroxide\", \"Solvent_Material\"], [\"C16-6-6(Br)2\", \"Participant_Material\"]], \"trigger\": \"added\"}, {\"arguments\": [[\"gel mixture\", \"Participant_Material\"]], \"trigger\": \"transferred\"}, {\"arguments\": [[\"zeolite\", \"Participant_Material\"]], \"trigger\": \"filtered\"}, {\"arguments\": [[\"water\", \"Solvent_Material\"]], \"trigger\": \"washed\"}, {\"arguments\": [[\"air\", \"Atmospheric_Material\"], [\"zeolites\", \"Participant_Material\"]], \"trigger\": \"calcined\"}, {\"arguments\": [[\"NH4NO3\", \"Solvent_Material\"], [\"samples\", \"Participant_Material\"]], \"trigger\": \"ion-exchanged\"}, {\"arguments\": [[\"zeolites\", \"Participant_Material\"]], \"trigger\": \"obtained\"}, {\"arguments\": [[\"air\", \"Atmospheric_Material\"]], \"trigger\": \"calcination\"}, {\"arguments\": [[\"samples\", \"Participant_Material\"], [\"Fe/ZSM-5-sheet(x, y)\", \"Recipe_Target\"]], \"trigger\": \"denoted\"}, {\"arguments\": [[\"sample\", \"Participant_Material\"], [\"artificial air\", \"Atmospheric_Material\"], [\"water vapor\", \"Atmospheric_Material\"]], \"trigger\": \"heating\"}, {\"arguments\": [[\"samples\", \"Participant_Material\"]], \"trigger\": \"denoted\"}, {\"arguments\": [[\"Fe/ZSM-5\", \"Recipe_Target\"]], \"trigger\": \"prepared\"}]", "role": "assistant" } ]

[ { "content": "Below are the Abstract, Introduction, and Conclusion sections of a computer science research paper. Please summarize the main contribution of the work in a single sentence. Your response should include the summary sentence and no additional text.\n\nPaper text:\n\nWe propose an approach for sequence modeling based on autoregressive normalizing flows.\nEach autoregressive transform, acting across time, serves as a moving reference frame for modeling higher-level dynamics.\nThis technique provides a simple, general-purpose method for improving sequence modeling, with connections to existing and classical techniques.\nWe demonstrate the proposed approach both with standalone models, as well as a part of larger sequential latent variable models.\nResults are presented on three benchmark video datasets, where flow-based dynamics improve log-likelihood performance over baseline models.\nData often contain sequential structure, providing a rich signal for learning models of the world.\nSuch models are useful for learning self-supervised representations of sequences (Li & Mandt, 2018; Ha & Schmidhuber, 2018) and planning sequences of actions (Chua et al., 2018; Hafner et al., 2019) .\nWhile sequential models have a longstanding tradition in probabilistic modeling (Kalman et al., 1960) , it is only recently that improved computational techniques, primarily deep networks, have facilitated learning such models from high-dimensional data (Graves, 2013) , particularly video and audio.\nDynamics in these models typically contain a combination of stochastic and deterministic variables (Bayer & Osendorfer, 2014; Chung et al., 2015; Gan et al., 2015; Fraccaro et al., 2016) , using simple distributions (e.g. Gaussian) to directly model the likelihood of data observations.\nHowever, attempting to capture all sequential dependencies with relatively unstructured dynamics may make it more difficult to learn such models.\nIntuitively, the model should use its dynamical components to track changes in the input instead of simultaneously modeling the entire signal.\nRather than expanding the computational capacity of the model, we seek a method for altering the representation of the data to provide a more structured form of dynamics.\nTo incorporate more structured dynamics, we propose an approach for sequence modeling based on autoregressive normalizing flows (Kingma et al., 2016; Papamakarios et al., 2017) , consisting of one or more autoregressive transforms in time.\nA single transform is equivalent to a Gaussian autoregressive model.\nHowever, by stacking additional transforms or latent variables on top, we can arrive at more expressive models.\nEach autoregressive transform serves as a moving reference frame in which higher-level structure is modeled.\nThis provides a general mechanism for separating different forms of dynamics, with higher-level stochastic dynamics modeled in the simplified space provided by lower-level deterministic transforms.\nIn fact, as we discuss, this approach generalizes the technique of modeling temporal derivatives to simplify dynamics estimation (Friston, 2008 ).\nWe empirically demonstrate this approach, both with standalone autoregressive normalizing flows, as well as by incorporating these flows within more flexible sequential latent variable models.\nWhile normalizing flows have been applied in a few sequential contexts previously, we emphasize the use of these models in conjunction with sequential latent variable models.\nWe present experimental results on three benchmark video datasets, showing improved quantitative performance in terms of log-likelihood.\nIn formulating this general technique for improving dynamics estimation in the framework of normalizing flows, we also help to contextualize previous work.\nFigure 1: Affine Autoregressive Transforms.\nComputational diagrams for forward and inverse affine autoregressive transforms (Papamakarios et al., 2017) .\nEach y t is an affine transform of x t , with the affine parameters potentially non-linear functions of x <t .\nThe inverse transform is capable of converting a correlated input, x 1:T , into a less correlated variable, y 1:T .\nWe have presented a technique for improving sequence modeling based on autoregressive normalizing flows.\nThis technique uses affine transforms to temporally decorrelate sequential data, thereby simplifying the estimation of dynamics.\nWe have drawn connections to classical approaches, which involve modeling temporal derivatives.\nFinally, we have empirically shown how this technique can improve sequential latent variable models.", "role": "user" }, { "content": "We show how autoregressive flows can be used to improve sequential latent variable models.", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Chemical\", \"Protein\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\" : [\"Dexamethasone\", ...], \"Protein\" : [\"BRCA-1\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nRole of organic cation/carnitine transporter 1 in uptake of phenformin and inhibitory effect on complex I respiration in mitochondria.\nPhenformin causes lactic acidosis in clinical situations due to inhibition of mitochondrial respiratory chain complex I. It is reportedly taken up by hepatocytes and exhibits mitochondrial toxicity in the liver. In this study, uptake of phenformin and [(14)C]tetraethylammonium (TEA) and complex I inhibition by phenformin were examined in isolated liver and heart mitochondria. Uptake of phenformin into isolated rat liver mitochondria was higher than that into heart mitochondria. It was inhibited by several cat ionic compounds, which suggests the involvement of multispecific transport system(s). Similar characteristics were also observed for uptake of TEA; however, uptake of phenformin into mitochondria of organic cation/carnitine transporter 1 (OCTN1) knockout mice was lower than that in wild-type mice, whereas uptake of TEA was comparable between the two strains, suggesting the involvement of distinct transport mechanisms for these two cations in mitochondria. Inhibition by phenformin of oxygen consumption via complex I respiration in isolated rat liver mitochondria was greater than that in heart mitochondria, whereas inhibitory effect of phenformin on complex I respiration was similar in inside-out structured submitochondrial particles prepared from rat livers and hearts. Lactic acidosis provoked by iv infusion of phenformin was weaker in octn1(-/-) mice than that in wild-type mice. These observations suggest that uptake of phenformin into liver mitochondria is at least partly mediated by OCTN1 and functionally relevant to its inhibition potential of complex I respiration. This study was, thus, the first to demonstrate OCTN1-mediated mitochondrial transport and toxicity of biguanide in vivo in rodents.", "role": "user" }, { "content": "{\"Chemical\": [\"Phenformin\", \"oxygen\", \"phenformin\", \"carnitine\", \"[(14)C]tetraethylammonium\", \"TEA\"], \"Protein\": [\"OCTN1\", \"mitochondrial respiratory chain complex I\", \"complex I\", \"octn1\", \"organic cation/carnitine transporter 1\"]}", "role": "assistant" } ]

[ { "content": "You will be presented with a paragraph from a COVID-19 literature. Your task is to classify the topics of this piece of text by choosing from the following categories:\n\n- Epidemic Forecasting: The content relates to predictions about the spread of COVID-19.\n- Treatment: The paragraph discusses therapeutic methods or medication for COVID-19.\n- Prevention: The content covers measures to prevent the spread of COVID-19.\n- Mechanism: The paragraph explains the biological mechanisms of the virus.\n- Case Report: The content is a report of a COVID-19 case.\n- Transmission: The paragraph discusses how COVID-19 is transmitted.\n- Diagnosis: The content is about diagnosing COVID-19 in individuals.\n\nYour classification should be provided as an element within a JSON array. The array should be formatted with topics enclosed in double quotes and separated by commas, following the JSON format, for example: [\"Topic1\", \"Topic2\", ...]. Include all applicable categories within the array. \nYour output should be a valid JSON array, and no additional text should be included in your response.\n\nArticle:\n\nBACKGROUND: . The electrocardiographic (ECG) changes which may occur during hospitalization for COVID-19 have not yet been comprehensively assessed. PATIENTS AND METHODS: . We examined 50 patients admitted to hospital with proven COVID-19 pneumonia. At entry, all patients underwent a detailed clinical examination, 12-lead ECG, laboratory tests and arterial blood gas test. ECG was also recorded at discharge and in case of worsening clinical conditions. RESULTS: . Mean age of patients was 64 years and 72% were men. At baseline, 30% of patients had ST-T abnormalities, and 33% had left ventricular hypertrophy. During hospitalization, 26% of patients developed new ECG abnormalities which included atrial fibrillation, ST-T changes, tachy-brady syndrome, and changes consistent with acute pericarditis. One patient was transferred to intensive care unit for massive pulmonary embolism with right bundle branch block, and another for non-ST segment elevation myocardial infarction. Patients free of ECG changes during hospitalization were more likely to be treated with antiretrovirals (68% vs 15%, p = 0.001) and hydroxychloroquine (89% vs 62%, p = 0.026) versus those who developed ECG abnormalities after admission. Most measurable ECG features at discharge did not show significant changes from baseline (all p>0.05) except for a slightly decrease in Cornell voltages (13+/-6 vs 11+/-5 mm; p = 0.0001) and a modest increase in the PR interval. The majority (54%) of patients with ECG abnormalities had 2 prior consecutive negative nasopharyngeal swabs. ECG abnormalities were first detected after an average of about 30 days from symptoms' onset (range 12-51 days). CONCLUSIONS: . ECG abnormalities during hospitalization for COVID-19 pneumonia reflect a wide spectrum of cardiovascular complications, exhibit a late onset, do not progress in parallel with pulmonary abnormalities and may occur after negative nasopharyngeal swabs.", "role": "user" }, { "content": "[\"Diagnosis\"]", "role": "assistant" } ]

[ { "content": "You will be presented with a paragraph from a COVID-19 literature. Your task is to classify the topics of this piece of text by choosing from the following categories:\n\n- Epidemic Forecasting: The content relates to predictions about the spread of COVID-19.\n- Treatment: The paragraph discusses therapeutic methods or medication for COVID-19.\n- Prevention: The content covers measures to prevent the spread of COVID-19.\n- Mechanism: The paragraph explains the biological mechanisms of the virus.\n- Case Report: The content is a report of a COVID-19 case.\n- Transmission: The paragraph discusses how COVID-19 is transmitted.\n- Diagnosis: The content is about diagnosing COVID-19 in individuals.\n\nYour classification should be provided as an element within a JSON array. The array should be formatted with topics enclosed in double quotes and separated by commas, following the JSON format, for example: [\"Topic1\", \"Topic2\", ...]. Include all applicable categories within the array. \nYour output should be a valid JSON array, and no additional text should be included in your response.\n\nArticle:\n\nA 65-year-old known diabetic, hypertensive, and asthmatic patient was admitted for suspected coronavirus disease 19 (COVID-19) infection following complaints of breathlessness. He tested positive for COVID-19 and was put on ventilation. He developed severe follicular conjunctivitis of the right eye while on a ventilator, which was treated conservatively. The resolution of ocular signs was noted over 2 weeks without any complications. This case highlights the timeline of events and discusses the late ophthalmic manifestations in patients with COVID-19 infection.", "role": "user" }, { "content": "[\"Case Report\"]", "role": "assistant" } ]

[ { "content": "You will be given an abstract from a computer science research paper. Given the abstract, your task is to extract all unique relationships between entities of the following, and ONLY the following, types:\n\n- \"USED-FOR\": For instance, \"Our method models user proficiency\" -> [\"method\", \"user proficiency\", \"USED-FOR\"].\n- \"EVALUATE-FOR\": For instance, \"We evaluate our method using F1-measure\" -> [\"F1-measure\", \"method\", \"EVALUATE-FOR\"].\n- \"FEATURE-OF\": For instance, \"prior knowledge of the model\" -> [\"prior knowledge\", \"model\", \"FEATURE-OF\"].\n- \"HYPONYM-OF\": For instance, \"TUIT is a software library\" -> [\"TUIT\", \"software library\", \"HYPONYM-OF\"].\n- \"PART-OF\": For instance, \"We incorporate NLU module into the system\" -> [\"NLU module\", \"system\", \"PART-OF\"].\n- \"COMPARE\": For instance, \"Unlike the quantitative prior, the qualitative prior is often ignored\" -> [\"quantitative prior\", \"qualitative prior\", \"COMPARE\"].\n- \"CONJUNCTION\": For instance, \"obtained from human expert or knowledge base\" -> [\"human expert\", \"knowledge base\", \"CONJUNCTION\"].\n\nFormat your output as a JSON array. Each entry in the array should express a single relation, formatted as [\"<Entity_A>\", \"<Entity_B>\", \"<RELATION_A_B>\"]. An example output might look like:\n\n[[\"neural networks\", \"classification\", \"USED-FOR\"], [\"neuron\", \"neural network\", \"PART-OF\"]].\n\nIf no relations are found, please return an empty JSON array \"[]\".\n\nAbstract:\n\nIn this paper, we address the problem of combining several language models (LMs). We find that simple interpolation methods, like log-linear and linear interpolation, improve the performance but fall short of the performance of an oracle. The oracle knows the reference word string and selects the word string with the best performance (typically, word or semantic error rate) from a list of word strings, where each word string has been obtained by using a different LM. Actually, the oracle acts like a dynamic combiner with hard decisions using the reference. We provide experimental results that clearly show the need for a dynamic language model combination to improve the performance further. We suggest a method that mimics the behavior of the oracle using a neural network or a decision tree. The method amounts to tagging LMs with confidence measures and picking the best hypothesis corresponding to the LM with the best confidence.", "role": "user" }, { "content": "[[\"decision tree\", \"method\", \"USED-FOR\"], [\"method\", \"LMs\", \"USED-FOR\"], [\"hard decisions\", \"dynamic combiner\", \"FEATURE-OF\"], [\"log-linear and linear interpolation\", \"interpolation methods\", \"HYPONYM-OF\"], [\"confidence measures\", \"method\", \"USED-FOR\"], [\"neural network\", \"method\", \"USED-FOR\"], [\"decision tree\", \"neural network\", \"CONJUNCTION\"]]", "role": "assistant" } ]

[ { "content": "You will be presented with a citation sentence from a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\nTo answer this research question, we develop an analysis tool, written in Rascal [27], that computes a set of metrics on the control corpus C0.", "role": "user" }, { "content": "Method", "role": "assistant" } ]

[ { "content": "You will be shown a claim about public health and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\". If the abstract does not provide enough information to arrive at a verdict, write \"NEI\" (for \"not enough information\").\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract. If the verdict was \"NEI\", then return an empty array.\n\nFor instance, if the model were given the claim \"wearing masks can prevent the spread of COVID\", the output might be:\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that mass mask-wearing reduces the transmission rate for COVID-19.\"]\n}\n\nClaim: taking vitamin D supplements could help boost the immune system, an essential piece of the puzzle in terms of how serious Covid-19 can be. \n\nAbstract:\nBACKGROUND The coronavirus disease 2019 (COVID-19) pandemic has affected almost 2.5 million people worldwide with almost 170 000 deaths reported to date.\nSo far, there is scarce evidence for the current treatment options available for COVID-19.\nVitamin C has previously been used for treatment of severe sepsis and septic shock.\nWe reviewed the feasibility of using vitamin C in the setting of COVID-19 in a series of patients.\nMETHODS We sequentially identified a series of patients who were requiring at least 30% of FiO2 or more who received IV vitamin C as part of the COVID-19 treatment and analyzed their demographic and clinical characteristics.\nWe compared inflammatory markers pre and post treatment including D-dimer and ferritin.\nRESULTS We identified a total of 17 patients who received IV vitamin C for COVID-19.\nThe inpatient mortality rate in this series was 12% with 17.6% rates of intubation and mechanical ventilation.\nWe noted a significant decrease in inflammatory markers, including ferritin and D-dimer, and a trend to decreasing FiO2 requirements, after vitamin C administration.\nCONCLUSION The use of IV vitamin C in patients with moderate to severe COVID-19 disease may be feasible.", "role": "user" }, { "content": "{\"verdict\": \"NEI\", \"evidence\": []}", "role": "assistant" } ]

[ { "content": "You will be shown a paragraph from a biomedical research article. Your task is to extract all drug combinations appearing in a specific sentence within the paragraph. Each drug combination should be assigned to one of the following three categories:\n\n- POS: Indicates a positive interaction between the drugs in the combination; for instance, drugs that have an additive or synergistic effect.\n- NEG: Indicates a negative interaction between the drugs in the combination; for instance, combining these drugs might result in adverse side effects, or might reduce their efficacy.\n- COMB: Indicates that the drugs are given in combination, but the type of interaction between the drugs cannot be determined based on the provided context.\n\nPlease format your answer as a JSON array. Each entry in the array should itself be an array formatted as [<drug_1>, <drug_2>, ..., <drug_n>, <category>] where <category> is one of the three categories listed above and <drug_1>, ..., <drug_n> are drug names copied verbatim from the input sentence. Different combinations may involve different numbers of drugs; in other words, the `n` in <drug_n> may vary.\n\nAs an example, the following output describes two extracted drug combinations; one between two drugs, and one between three drugs:\n\n[[\"artesunate\", \"artemether\", \"COMB\"], [\"Nifedipine\", \"Labetalol\", \"Prazosin\", \"POS\"]]\n\nThe paragraph and specific sentence are below. You should only extract relationships expressed in the specific sentence; the paragraph is provided for context.\n\nIn your output, return only the JSON array and no other text. If no drug combinations appear, return an empty array `[]`.\n\nparagraph: Pharmacologic myocardial protection in patients undergoing noncardiac surgery: a quantitative systematic review. A number of drugs have been tested in clinical trials to decrease cardiac complications in patients undergoing noncardiac surgery. To compare the results of these studies, we conducted a quantitative systematic review. Medline, Embase, and Cochrane databases were searched for randomized trials that assessed myocardial ischemia, myocardial infarction, 30-day cardiac mortality, and adverse effects. Data were combined using a fixed-effect model and expressed as Peto odds ratios (OR) with 95% confidence interval (CI) and as numbers-needed-to-treat/harm (NNT/H). Twenty-one trials involving 3646 patients were included : 11 trials using beta-blockers ( 6 drugs ; 866 patients ) , 6 clonidine or mivazerol ( 614 patients ) , 3 diltiazem or verapamil ( 121 patients ) , and 1 nitroglycerin ( 45 patients ) . All trials had an inactive control; there were no direct comparisons. beta-blockers decreased ischemic episodes during surgery (7.6% versus 20.2% with placebo; OR 0.32 [95% CI, 0.17-0.58]; NNT 8) and after surgery (15.2% versus 27.9% with control; OR 0.46 [95% CI, 0.26-0.81]; NNT 8). alpha(2)-agonists decreased ischemia during surgery only (19.4% versus 32.8%; OR 0.47 [95% CI, 0.33-0.68]; NNT 7). beta-blockers reduced the risk of myocardial infarction (0.9% versus 5.2%; OR 0.19 [95% CI, 0.08-0.48]; NNT 23) but only when 2 trials with high-risk patients were included. The effect of alpha(2)-agonists on myocardial infarction was not significant (6.1% versus 7.3%; OR 0.85 [95% CI, 0.62-1.14]). beta-blockers significantly decreased the risk of cardiac death from 3.9% to 0.8% (OR 0.25 [95% CI, 0.09-0.73], NNT 32). alpha(2)-agonists significantly decreased the risk of cardiac death from 2.3% to 1.1% (OR 0.50 [95% CI, 0.28-0.91], NNT 83). For calcium channel blockers and nitroglycerin, evidence of any benefit was lacking. The most common adverse effect was bradycardia, which occurred in 24.5% of patients receiving a beta adrenergic blocker versus 9.1% of controls (OR 3.76 [95% CI, 2.45-5.77], NNH 6).\n\nsentence: Twenty-one trials involving 3646 patients were included : 11 trials using beta-blockers ( 6 drugs ; 866 patients ) , 6 clonidine or mivazerol ( 614 patients ) , 3 diltiazem or verapamil ( 121 patients ) , and 1 nitroglycerin ( 45 patients ) .", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "You will be shown a claim about public health and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\". If the abstract does not provide enough information to arrive at a verdict, write \"NEI\" (for \"not enough information\").\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract. If the verdict was \"NEI\", then return an empty array.\n\nFor instance, if the model were given the claim \"wearing masks can prevent the spread of COVID\", the output might be:\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that mass mask-wearing reduces the transmission rate for COVID-19.\"]\n}\n\nClaim: It's important to remember, however, that people who recover from COVID-19 can still have some lingering symptoms, like difficulty breathing, fatigue, or a persistent cough or headache, William\n\nAbstract:\nThe novel Coronavirus disease 2019 (COVID-19) is an illness caused due to Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).\nThe World Health Organization (WHO) has declared this outbreak a global health emergency and as on April 24, 2020, it has spread to 213 countries, with 25,91,015 confirmed cases and 742,855 cases have been recovered from COVID-19.\nIn this dreadful situation our team has already published an article in the Science of the Total Environment, which elaborates the various aspects of the SARS-CoV-2 infection.\nIn this situation, it is imperative to understand the possible outcome of COVID-19 recovered patients and determine if they have any other detrimental illnesses by longitudinal analysis to safeguard their life in future.\nIt is necessary to follow-up these recovered patients and performs comprehensive assessments for detection and appropriate management towards their psychological, physical, and social realm.\nThis urges us to suggest that it is highly important to provide counselling, moral support as well as a few recommended guidelines to the recovered patients and society to restore to normalcy.\nEpidemiological, clinical and immunological studies from COVID-19 recovered patients are particularly important to understand the disease and to prepare better for potential outbreaks in the future.\nLongitudinal studies on a larger cohort would help us to understand the in-depth prognosis as well as the pathogenesis of COVID-19.\nAlso, follow-up studies will help us provide more information for the development of vaccines and drugs for these kinds of pandemics in the future.\nHence, we recommend more studies are required to unravel the possible mechanism of COVID-19 infection and the after-effects of it to understand the characteristics of the virus and to develop the necessary precautionary measures to prevent it.", "role": "user" }, { "content": "{\"verdict\": \"NEI\", \"evidence\": []}", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Chemical\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\": [\"Arsenic\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nEnzymatic synthesis of fructooligosaccharides by inulinases from Aspergillus niger and Kluyveromyces marxianus NRRL Y-7571 in aqueous-organic medium. This work is focused on the synthesis of the fructooligosaccharides (FOS) from sucrose and inulin, using free, immobilized and pre-treated immobilized inulinase from Kluyveromyces marxianus NRRL Y 7571 and Aspergillus niger in an aqueous-organic system. Initially, the influence of pre-treatment using four different gases, propane, n-butane, CO(2) and liquefied petroleum gas (LPG), was investigated towards FOS production and best results were found when both enzymes were previously treated with LPG. The best reaction yields were obtained when the immobilized enzymes were treated with LPG. Considering FOS synthesis using the enzyme from A. niger, yields of 26.62% of GF2 (kestose), 30.62% of GF3 (nystose) and 8.47% of GF4 (fructosyl nystose) were achieved using sucrose as substrate. Using inulinases from K. marxianus NRRL Y 7571, 11.89% of GF2 and 20.83% of GF3 were obtained, using inulin as substrate. However, promising results were achieved using the free form of inulinase from A. niger (77.19% of GF2; 14.03% of GF3 and 0.07% of GF4) using inulin as substrate.", "role": "user" }, { "content": "{\"Chemical\": [\"fructosyl nystose\", \"kestose\", \"CO(2)\", \"n-butane\", \"propane\", \"nystose\", \"sucrose\"]}", "role": "assistant" } ]

[ { "content": "You will be presented with a collection of medical randomized controlled trial (RCT) reports addressing a shared clinical question -- for instance, the efficacy of a medical intervention on a disease or condition. Given the titles and abstracts of these reports, your task is to generate the conclusion of the systematic review article synthesizing the key findings. Your conclusion should be a few sentences long. In your response, include only the conclusion and no other text. The RCT reports are below.\n\n\n\nTitle 1:\nA randomized study to assess the efficacy of the amniotic fluid index as a fetal admission test.\nAbstract 1:\nTo determine whether there is a difference in the incidence of abdominal delivery for presumed fetal distress in women who have an intrapartum fluid index assessment and those who do not.\n Over a 7-month period, parturients at 26-42 weeks' gestation and in early labor were randomized to the study (measured amniotic fluid index [AFI] on admission) or a control group (no sonographic assessment of amniotic fluid [AF] volume). The labor and delivery staff were aware of the AFI results of the study subjects. All patients had continuous electronic fetal monitoring, and none had an abnormal tracing on admission. Student t test or chi 2 was used for statistical analysis. P < .05 was considered significant.\n The study (N = 447) and control groups (N = 436) had similar maternal demographics as well as medical and obstetric complications. In the study group, the incidence of abdominal delivery for fetal distress (29 of 447) was significantly higher than among controls (14 of 436) (P = .02; relative risk 1.3, 95% confidence interval 1.1-1.7). Among parturients who had abdominal delivery for fetal distress, the decision-to-incision times (mean +/- standard deviation) were similar for parturients who had undergone assessment of AFI and those who had not (38.5 +/- 14.7 versus 32.5 +/- 14.7 minutes, respectively; P = .47). Mean birth weight, incidence of low birth weight, macrosomia, Apgar scores less than 7, and the number of admissions to the neonatal intensive care unit were not significantly different in the two groups.\n Patients having an intrapartum assessment of AFI as a fetal admission test are significantly more likely to have abdominal delivery for presumed fetal distress. However, the decision-to-incision time is not decreased and the perinatal outcome is not improved if the status of AF volume is known for patients in early labor.", "role": "user" }, { "content": "There is not enough evidence to support the use of admission tests other than cardiotocography for fetal assessment during labour. Appropriate randomised controlled trials with adequate sample size of admission tests other than cardiotocography for fetal assessment during labour are required.", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Disease\"].\n\nPlease return the output as a JSON object of the format: {\"Disease\": [\"COVID-19\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nNon-syndromic hearing loss associated with enlarged vestibular aqueduct is caused by PDS mutations. Enlarged vestibular aqueduct (EVA), known as the most common form of inner ear abnormality, has recently been of particular genetic interest because this anomaly is inherited in a recessive manner. The locus for non-syndromic sensorineural hearing loss with EVA has been mapped to the same chromosomal region, 7q31, as the Pendred syndrome locus. In the present study, seven mutations in the PDS gene (PDS), the gene responsible for Pendred syndrome, have been found in families of non-syndromic sensorineural hearing loss with EVA. One family is homozygous, three families are compound heterozygotes, and two families are heterozygous but with no other mutation detected. The present results provide evidence that mutations in PDS cause both syndromic and non-syndromic hearing loss..", "role": "user" }, { "content": "{\"Disease\": [\"Non-syndromic hearing loss\", \"Enlarged vestibular aqueduct\", \"non-syndromic sensorineural hearing loss\", \"syndromic and non-syndromic hearing loss\", \"PDS\", \"Pendred syndrome\", \"enlarged vestibular aqueduct\", \"EVA\", \"inner ear abnormality\"]}", "role": "assistant" } ]

[ { "content": "You will be shown sections from a scientific research paper, together with a question about the paper. This is an extractive question-answering task, where you must find and extract relevant text spans directly from the paper to answer the question. Your response should strictly be a `json` object with two fields:\n\n\"answer\": An array of strings extracted directly from the paper which, collectively, answer the question.\n\"evidence\": An array of strings. Each should be an excerpt from the paper, in which one or more of the extracted answers can be found.\n\nFor example, for the question \"What baselines did the authors compare against?\", a sample response might be:\n{\n \"answer\": [\"BERT\", \"RoBERTa\"],\n \"evidence\": [\"In our experiments, we compare the performance of our model against BERT and RoBERTa.\"]\n}\n\nDo not include any text in your response other than the json.\n\nIf the question is unanswerable given the provided excerpts, respond with the single word \"null\".\n\nPaper: Improving Visually Grounded Sentence Representations with Self-Attention\n\nSentence representation models trained only on language could potentially suffer from the grounding problem. Recent work has shown promising results in improving the qualities of sentence representations by jointly training them with associated image features. However, the grounding capability is limited due to distant connection between input sentences and image features by the design of the architecture. In order to further close the gap, we propose applying self-attention mechanism to the sentence encoder to deepen the grounding effect. Our results on transfer tasks show that self-attentive encoders are better for visual grounding, as they exploit specific words with strong visual associations.\n\nIntroduction\nRecent NLP studies have thrived on distributional hypothesis. More recently, there have been efforts in applying the intuition to larger semantic units, such as sentences, or documents. However, approaches based on distributional semantics are limited by the grounding problem BIBREF0 , which calls for techniques to ground certain conceptual knowledge in perceptual information.\nBoth NLP and vision communities have proposed various multi-modal learning methods to bridge the gap between language and vision. However, how general sentence representations can be benefited from visual grounding has not been fully explored yet. Very recently, BIBREF1 proposed a multi-modal encoder-decoder framework that, given an image caption, jointly predicts another caption and the features of associated image. The work showed promising results for further improving general sentence representations by grounding them visually. However, according to the model, visual association only occurs at the final hidden state of the encoder, potentially limiting the effect of visual grounding.\nAttention mechanism helps neural networks to focus on specific input features relevant to output. In the case of visually grounded multi-modal framework, applying such attention mechanism could help the encoder to identify visually significant words or phrases. We hypothesize that a language-attentive multi-modal framework has an intuitive basis on how humans mentally visualize certain concepts in sentences during language comprehension.\nIn this paper, we propose an enhanced multi-modal encoder-decoder model, in which the encoder attends to the input sentence and the decoders predict image features and the target sentence. We train the model on images and respective captions from COCO5K dataset BIBREF2 . We augment the state-of-the-art sentence representations with those produced by our model and conduct a series of experiments on transfer tasks to test the quality of sentence representations. Through detailed analysis, we confirm our hypothesis that self-attention help our model produce more feature-rich visually grounded sentence representations.\n\nRelated Work\nSentence Representations. Since the inception of word embeddings BIBREF3 , extensive work have emerged for larger semantic units, such as sentences and paragraphs. These works range from deep neural models BIBREF4 to log-bilinear models BIBREF5 , BIBREF6 . A recent work proposed using supervised learning of a specific task as a leverage to obtain general sentence representation BIBREF7 .\nJoint Learning of Language and Vision. Convergence between computer vision and NLP researches have increasingly become common. Image captioning BIBREF8 , BIBREF9 , BIBREF10 , BIBREF11 and image synthesis BIBREF12 are two common tasks. There have been significant studies focusing on improving word embeddings BIBREF13 , BIBREF14 , phrase embeddings BIBREF15 , sentence embeddings BIBREF1 , BIBREF16 , language models BIBREF17 through multi-modal learning of vision and language. Among all studies, BIBREF1 is the first to apply skip-gram-like intuition (predicting multiple modalities from langauge) to joint learning of language and vision in the perspective of general sentence representations.\nAttention Mechanism in Multi-Modal Semantics. Attention mechanism was first introduced in BIBREF18 for neural machine translation. Similar intuitions have been applied to various NLP BIBREF19 , BIBREF20 , BIBREF21 and vision tasks BIBREF8 . BIBREF8 applied attention mechanism to images to bind specific visual features to language. Recently, self-attention mechanism BIBREF21 has been proposed for situations where there are no extra source of information to “guide the extraction of sentence embedding”. In this work, we propose a novel sentence encoder for the multi-modal encoder-decoder framework that leverages the self-attention mechanism. To the best of our knowledge, such attempt is the first among studies on joint learning of language and vision.\n\nProposed Method\nGiven a data sample INLINEFORM0 , where INLINEFORM1 is the source caption, INLINEFORM2 is the target caption, and INLINEFORM3 is the hidden representation of the image, our goal is to predict INLINEFORM4 and INLINEFORM5 with INLINEFORM6 , and the hidden representation in the middle serves as the general sentence representation.\n\nVisually Grounded Encoder-Decoder Framework\nWe base our model on the encoder-decoder framework introduced in BIBREF1 . A bidirectional Long Short-Term Memory (LSTM) BIBREF22 encodes an input sentence and produces a sentence representation for the input. A pair of LSTM cells encodes the input sequence in both directions and produce two final hidden states: INLINEFORM0 and INLINEFORM1 . The hidden representation of the entire sequence is produced by selecting maximum elements between the two hidden states: INLINEFORM2 .\nThe decoder calculates the probability of a target word INLINEFORM0 at each time step INLINEFORM1 , conditional to the sentence representation INLINEFORM2 and all target words before INLINEFORM3 . INLINEFORM4 .\nThe objective of the basic encoder-decoder model is thus the negative log-likelihood of the target sentence given all model parameters: INLINEFORM0 .\n\nVisual Grounding\nGiven the source caption representation INLINEFORM0 and the relevant image representation INLINEFORM1 , we associate the two representations by projecting INLINEFORM2 into image feature space. We train the model to rank the similarity between predicted image features INLINEFORM3 and the target image features INLINEFORM4 higher than other pairs, which is achieved by ranking loss functions. Although margin ranking loss has been the dominant choice for training cross-modal feature matching BIBREF17 , BIBREF1 , BIBREF23 , we find that log-exp-sum pairwise ranking BIBREF24 yields better results in terms of evaluation performance and efficiency. Thus, the objective for ranking DISPLAYFORM0 \nwhere INLINEFORM0 is the set of negative examples and INLINEFORM1 is cosine similarity.\n\nVisual Grounding with Self-Attention\nLet INLINEFORM0 be the encoder hidden state at timestep INLINEFORM1 concatenated from two opposite directional LSTMs ( INLINEFORM2 is the dimensionality of sentence representations). Let INLINEFORM3 be the hidden state matrix where INLINEFORM4 -th column of INLINEFORM5 is INLINEFORM6 . The self-attention mechanism aims to learn attention weight INLINEFORM7 , i.e. how much attention must be paid to hidden state INLINEFORM8 , based on all hidden states INLINEFORM9 . Since there could be multiple ways to attend depending on desired features, we allow multiple attention vectors to be learned. Attention matrix INLINEFORM10 is a stack of INLINEFORM11 attention vectors, obtained through attention layers: INLINEFORM12 . INLINEFORM13 and INLINEFORM14 are attention parameters and INLINEFORM15 is a hyperparameter. The context matrix INLINEFORM16 is obtained by INLINEFORM17 . Finally, we compress the context matrix into a fixed size representation INLINEFORM18 by max-pooling all context vectors: INLINEFORM19 . Attended representation INLINEFORM20 and encoder-decoder representation INLINEFORM21 are concatenated into the final self-attentive sentence representation INLINEFORM22 . This hybrid representation replaces INLINEFORM23 and is used to predict image features (Section SECREF2 ) and target caption (Section SECREF1 ).\n\nLearning Objectives\nFollowing the experimental design of BIBREF1 , we conduct experiments on three different learning objectives: Cap2All, Cap2Cap, Cap2Img. Under Cap2All, the model is trained to predict both the target caption and the associated image: INLINEFORM0 . Under Cap2Cap, the model is trained to predict only the target caption ( INLINEFORM1 ) and, under Cap2Img, only the associated image ( INLINEFORM2 ).\n\nImplementation Details\nWord embeddings INLINEFORM0 are initialized with GloVe BIBREF25 . The hidden dimension of each encoder and decoder LSTM cell ( INLINEFORM1 ) is 1024. We use Adam optimizer BIBREF26 and clip the gradients to between -5 and 5. Number of layers, dropout, and non-linearity for image feature prediction layers are 4, 0.3 and ReLU BIBREF27 respectively. Dimensionality of hidden attention layers ( INLINEFORM3 ) is 350 and number of attentions ( INLINEFORM4 ) is 30. We employ orthogonal initialization BIBREF28 for recurrent weights and xavier initialization BIBREF29 for all others. For the datasets, we use Karpathy and Fei-Fei's split for MS-COCO dataset BIBREF10 . Image features are prepared by extracting hidden representations at the final layer of ResNet-101 BIBREF30 . We evaluate sentence representation quality using SentEval BIBREF7 , BIBREF1 scripts. Mini-batch size is 128 and negative samples are prepared from remaining data samples in the same mini-batch.\n\nEvaluation\nAdhering to the experimental settings of BIBREF1 , we concatenate sentence representations produced from our model with those obtained from the state-of-the-art unsupervised learning model (Layer Normalized Skip-Thoughts, ST-LN) BIBREF31 . We evaluate the quality of sentence representations produced from different variants of our encoders on well-known transfer tasks: movie review sentiment (MR) BIBREF32 , customer reviews (CR) BIBREF33 , subjectivity (SUBJ) BIBREF34 , opinion polarity (MPQA) BIBREF35 , paraphrase identification (MSRP) BIBREF36 , binary sentiment classification (SST) BIBREF37 , SICK entailment and SICK relatedness BIBREF38 .\n\nResults\nResults are shown in Table TABREF11 . Results show that incorporating self-attention mechanism in the encoder is beneficial for most tasks. However, original models were better in some tasks (CR, MPQA, MRPC), suggesting that self-attention mechanism could sometimes introduce noise in sentence features. Overall, utilizing self-attentive sentence representation further improves performances in 5 out of 8 tasks. Considering that models with self-attention employ smaller LSTM cells (1024) than those without (2048) (Section SECREF6 ), the performance improvements are significant. Results on COCO5K image and caption retrieval tasks (not included in the paper due to limited space) show comparable performances to other more specialized methods BIBREF10 , BIBREF39 .\n\nAttention Mechanism at Work\nIn order to study the effects of incorporating self-attention mechanism in joint prediction of image and language features, we examine attention vectors for selected samples from MS-COCO dataset and compare them to associated images (Figure FIGREF13 ). For example, given the sentence “man in black shirt is playing guitar”, our model identifies words that have association with strong visual imagery, such as “man”, “black” and “guitar”. Given the second sentence, our model learned to attend to visually significant words such as “cat” and “bowl”. These findings show that visually grounding self-attended sentence representations helps to expose word-level visual features onto sentence representations BIBREF1 .\n\nConclusion and Future Work\nIn this paper, we proposed a novel encoder that exploits self-attention mechanism. We trained the model using MS-COCO dataset and evaluated sentence representations produced by our model (combined with universal sentence representations) on several transfer tasks. Results show that the self-attention mechanism not only improves the qualities of general sentence representations but also guides the encoder to emphasize certain visually associable words, which helps to make visual features more prominent in the sentence representations. As future work, we intend to explore cross-modal attention mechanism to further intertwine language and visual information for the purpose of improving sentence representation quality.\n\nTable 1: Classification performance on transfer tasks. We report F1-score for MRPC, Pearson coefficient for SICK-R and accuracy for most others. All sentence representations have been concatenated with ST-LN embeddings. Note that the discrepancy between results reported in this paper and the referenced paper is likely due to differences in minor implementation details and experimental environment. Our models are denoted by †.\n\nFigure 1: Activated attention weights on two samples from MS-COCO dataset. Vertical axis shows attention vectors learned by our model (compressed due to space limit). Note how the sentence encoder learned to identify words with strong visual associations.\n\nQuestion: What baselines are the proposed method compared against?", "role": "user" }, { "content": "{\"answer\": [\"(Layer Normalized Skip-Thoughts, ST-LN) BIBREF31\", \"Cap2All, Cap2Cap, Cap2Img\"], \"evidence\": [\"Adhering to the experimental settings of BIBREF1 , we concatenate sentence representations produced from our model with those obtained from the state-of-the-art unsupervised learning model (Layer Normalized Skip-Thoughts, ST-LN) BIBREF31 . We evaluate the quality of sentence representations produced from different variants of our encoders on well-known transfer tasks: movie review sentiment (MR) BIBREF32 , customer reviews (CR) BIBREF33 , subjectivity (SUBJ) BIBREF34 , opinion polarity (MPQA) BIBREF35 , paraphrase identification (MSRP) BIBREF36 , binary sentiment classification (SST) BIBREF37 , SICK entailment and SICK relatedness BIBREF38 .\", \"Following the experimental design of BIBREF1 , we conduct experiments on three different learning objectives: Cap2All, Cap2Cap, Cap2Img. Under Cap2All, the model is trained to predict both the target caption and the associated image: INLINEFORM0 . Under Cap2Cap, the model is trained to predict only the target caption ( INLINEFORM1 ) and, under Cap2Img, only the associated image ( INLINEFORM2 ).\"]}", "role": "assistant" } ]

[ { "content": "You will be presented with a citation segment from the section of an NLP research paper, as well as the context surrounding that citation. Classify the intent behind this citation by choosing from one of the following categories:\n- Background: provides context or foundational information related to the topic.\n- Extends: builds upon the cited work.\n- Uses: applies the methods or findings of the cited work.\n- Motivation: cites the work as inspiration or rationale for the research.\n- CompareOrContrast: compares or contrasts the cited work with others.\n- FutureWork: cites the work as a direction for future research.\n\nYour answer should be a single word from the following list of options: [\"Background\", \"Extends\", \"Uses\", \"Motivation\", \"CompareOrContrast\", \"FutureWork\"]. Do not include any other text in your response.\n\nSection Title:\nintroduction\n\nContext before the citation:\nIn their Gaijin system, Veale and Way (1997) give a result of 63% accurate translations obtained for English −> German on a test set of 791 sentences from CorelDRAW manuals. On novel test sentences, he gives results of 72% correct translation. For English −> Urdu, Juola (1997, page 213) notes that “the system learned the original training corpus ... perfectly and could reproduce it without errors”; that is, it scored 100% accuracy when tested against the training corpus.\n\nCitation Sentence:\nIn their Gaijin system , Veale and Way ( 1997 ) give a result of 63 % accurate translations obtained for English − > German on a test set of 791 sentences from CorelDRAW manuals .\n\nContext after the citation:\nAs in METLA and Gaijin, we exploit lists of known marker words for each language to indicate the start and end of segments. For English, our source language, we use the sets of marker words in (13): <DET> {the, a, an, those, these, ... } <PREP> {in, on, out, with, from, to, under, ... } <QUANT> {all, some, few, many, ... } \u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000\u0000 A similar set (14) was produced for French, the target language in our wEBMT system: <DET> {le, la, l’, les, ce, ces, ceux, cet, ... } <PREP> {dans, sur, avec, de, `a, sous, ... } <QUANT> {tous, tout, toutes, certain, quelques, beaucoup, ... } <CONJ> {et, ou, ... } <POSS> {mon, ma, mes, ton, ta, tes, notre, nos, ... } <PRON> {je, j’, tu, il, elle, ... } In a preprocessing stage, the aligned (source, target) pairs in the phrasal lexicon are traversed word by word, and whenever any such marker word is encountered, a new chunk is begun, with the first word labeled with its marker category (<DET>, <PREP>, etc.). The example in (15) illustrates the results of running the marker hypothesis over the source phrase all uses of asbestos: \u0000\u0000\u0000\u0000", "role": "user" }, { "content": "CompareOrContrast", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a materials science research paper. Your task is to extract all synthesis operations described in the abstract into a structured JSON format. Your output should be a JSON array. Each entry in the array should be a JSON object describing a single synthesis operation. Your output JSON object should have the following two fields:\n\n- \"trigger\": A verbal predicate indicating a synthesis operation. This should be a string extracted directly from the abstract.\n- \"arguments\": An array of arguments specifying aspects of the synthesis operation. Each entry in the array should be a length-2 array formatted as [<argument_text>, <argument_type>]. The `argument_text` should be a string extracted directly from the abstract. The `argument_type` should be one of the following types: [\"Recipe_Precursor\", \"Solvent_Material\", \"Atmospheric_Material\", \"Participant_Material\", \"Recipe_Target\"].\n\nFor instance, suppose an excerpt from the abstract reads:\n\nTetraethoxysilane (TEOS, 98%) and cetyltrimethylammonium bromide (CTAB, 98%) were purchased from Fluka. The MTTZ-siloxy derivative (triethoxysilyl-propyl-5-mercapto-1-methyl-tetrazole) was synthesized as previously described [38].\n\nThis excerpt includes two operations, which could be annotated as follows:\n\n[{\"arguments\": [[\"Tetraethoxysilane\", \"Recipe_Precursor\"], [\"cetyltrimethylammonium bromide\", \"Recipe_Precursor\"]], \"trigger\": \"purchased\"}, {\"arguments\": [[\"MTTZ-siloxy derivative\", \"Recipe_Target\"]], \"trigger\": \"synthesized\"}]\n\nIn your response, please include the JSON and no other text.\n\nAbstract:\n10.1016/j.jpowsour.2016.01.014\nFacile synthesis of a MoO2-Mo2C-C composite and its application as favorable anode material for lithium-ion batteries\n\nAll chemical regents employed in this work were of analytical grade without further purification. A pretreated macroporous cinnamic anion-exchange resin (10 g) was first added into 100 mL of an aqueous solution containing 6.18 g ammonium molybdate tetrahydrate (AHM) and stirred in an ambient atmosphere at room temperature for 10 h. After the adsorption, the resin was filtered, washed several times with distilled water, and dried in air at 60 degC for 24 h. The resulting product was carbonized at 750 degC for 3 h under an argon atmosphere at a heating rate of 5 degC min-1. Finally, the black-colored product was further ground into tiny particles by ball milling and collected for further characterization. For comparison, pure carbon was prepared using the same method to calcine the bare resin without the addition of AHM. Mo2C was bought from Hunan Guangyuan Company and used without any further treatment.", "role": "user" }, { "content": "[{\"arguments\": [[\"resin\", \"Participant_Material\"], [\"ammonium molybdate tetrahydrate\", \"Recipe_Precursor\"]], \"trigger\": \"added\"}, {\"arguments\": [[\"resin\", \"Participant_Material\"]], \"trigger\": \"filtered\"}, {\"arguments\": [[\"water\", \"Solvent_Material\"]], \"trigger\": \"washed\"}, {\"arguments\": [[\"air\", \"Atmospheric_Material\"]], \"trigger\": \"dried\"}, {\"arguments\": [[\"argon\", \"Atmospheric_Material\"], [\"product\", \"Participant_Material\"]], \"trigger\": \"carbonized\"}, {\"arguments\": [[\"product\", \"Participant_Material\"], [\"particles\", \"Participant_Material\"]], \"trigger\": \"ground\"}]", "role": "assistant" } ]

[ { "content": "You are provided with the abstract of a scientific paper and the abstracts of the papers it references. Your task is to write a Related Work section for the main paper. This section should concisely summarize and integrate the key points from the cited abstracts, reflecting how they relate to the main paper's contributions and context. In your summary, use numerical citation markers like [1], [2], etc., to refer to the corresponding papers.\n\nMain Abstract:\nIn a recent conference paper, we have reported a rhythm transcription method based on a merged-output hidden Markov model (HMM) that explicitly describes the multiple-voice structure of polyphonic music. This model solves a major problem of conventional methods that could not properly describe the nature of multiple voices as in polyrhythmic scores or in the phenomenon of loose synchrony between voices. In this paper we present a complete description of the proposed model and develop an inference technique, which is valid for any merged-output HMMs for which output probabilities depend on past events. We also examine the influence of the architecture and parameters of the method in terms of accuracies of rhythm transcription and voice separation and perform comparative evaluations with six other algorithms. Using MIDI recordings of classical piano pieces, we found that the proposed model outperformed other methods by more than 12 points in the accuracy for polyrhythmic performances and performed almost as good as the best one for non-polyrhythmic performances. This reveals the state-of-the-art methods of rhythm transcription for the first time in the literature. Publicly available source codes are also provided for future comparisons.\n\nCited Abstract(s):\n[1]: We study indeterminacies in realization of ornaments and how they can be incorporated in a stochastic performance model applicable for music information processing such as score-performance matching. We point out the importance of temporal information, and propose a hidden Markov model which describes it explicitly and represents ornaments with several state types. Following a review of the indeterminacies, they are carefully incorporated into the model through its topology and parameters, and the state construction for quite general polyphonic scores is explained in detail. By analysing piano performance data, we find significant overlaps in inter-onset-interval distributions of chordal notes, ornaments, and inter-chord events, and the data is used to determine details of the model. The model is applied for score following and offline score-performance matching, yielding highly accurate matching for performances with many ornaments and relatively frequent errors, repeats, and skips.\n\n[2]: The capacity for real-time synchronization and coordination is a common ability among trained musicians performing a music score that presents an interesting challenge for machine intelligence. Compared to speech recognition, which has influenced many music information retrieval systems, music's temporal dynamics and complexity pose challenging problems to common approximations regarding time modeling of data streams. In this paper, we propose a design for a real-time music-to-score alignment system. Given a live recording of a musician playing a music score, the system is capable of following the musician in real time within the score and decoding the tempo (or pace) of its performance. The proposed design features two coupled audio and tempo agents within a unique probabilistic inference framework that adaptively updates its parameters based on the real-time context. Online decoding is achieved through the collaboration of the coupled agents in a Hidden Hybrid Markov semi-Markov framework, where prediction feedback of one agent affects the behavior of the other. We perform evaluations for both real-time alignment and the proposed temporal model. An implementation of the presented system has been widely used in real concert situations worldwide and the readers are encouraged to access the actual system and experiment the results.\n\n[3]: The automated discovery of recurrent patterns in music is a fundamental task in computational music analysis. This paper describes a new method for discovering patterns in the vertical and horizontal dimensions of polyphonic music. A formal representation of music objects is used to structure the musical surface, and several ideas for viewing pieces as successions of vertical structures are examined. A knowledge representation method is used to view pieces as sequences of relationships between music objects, and a pattern discovery algorithm is applied using this view of the Bach chorale harmonizations to find significant recurrent patterns. The method finds a small set of vertical patterns that occur in a large number of pieces in the corpus. Most of these patterns represent specific voice leading formulae within cadences.\n\n[4]: This paper discusses model-based rhythm and tempo analysis of music data in the MIDI format. The data is assumed to be obtained from a module performing multi-pitch analysis of music acoustic signals inside an automatic transcription system. In performed music, observed note lengths and local tempo fluctuate from the nominal note lengths and long-term tempo. Applying the framework of continuous speech recognition to rhythm recognition, we take a probabilistic top-down approach on the joint estimation of rhythm and tempo from the performed onset events in MIDI data. Short-term rhythm patterns are extracted from existing music samples and form a \"rhythm vocabulary.\" Local tempo is represented by a smooth curve. The entire problem is formulated as an integrated optimization problem to maximize a posterior probability, which can be solved by an iterative algorithm which alternately estimates rhythm and tempo. Evaluation of the algorithm through various experiments is also presented.", "role": "user" }, { "content": "The note HMM has been extended to handle polyphonic performances [4] . This is done by representing a polyphonic score as a linear sequence of chords or, more precisely, note clusters consisting of one or more notes. Such score representation is also familiarly used for music analysis [3] and score-performance matching [2] [1] . Chordal notes can be represented as self-transitions in the score model (Fig. ) and their IOIs can be described with a probability distribution with a peak at zero. Polyphonic extension of metrical HMMs is possible in the same way.", "role": "assistant" } ]

[ { "content": "Write an abstract for the research paper below. Your response should only include the abstract and no additional text.\n\nArticle text:\nthe standard model ( sm ) of the electroweak interactions is confirmed with excellent accuracy by the existing results at lep , slc and tevatron\n. therefore only extensions which smoothly modify this theory are still conceivable .\nthe minimal supersymmetric standard model ( mssm ) is the most favorite .\nit solves the so - called hierarchy problem which is related to the presence of quadratic mass divergences due to scalar fields and it has an interesting property of decoupling . in the limit in which all the supersymmetric particles become heavy one recovers the sm with a light higgs .\nthis decoupling property however is not peculiar of the mssm only .\nin fact in my talk i will present a model for a strong electroweak sector sharing this property .\nmodels of dynamical breaking of the electroweak symmetry are based just on the symmetry structure , not taking into account the underlying theory which is responsible of the breaking and the corresponding chiral lagrangians are built using , as degrees of freedom , the goldstone bosons , the longitudinal components of @xmath0 and @xmath1 .\nexperiments , like the measurement of the @xmath2 parameter , suggests the existence of a custodial symmetry @xmath3 @xcite , which guarantees @xmath4 .\ntherefore chiral lagrangians can be built as a non linear @xmath5-model assuming the spontaneous breaking @xmath6 .\neffective lagrangians can be derived using the global symmetry @xmath7 and an expansion in the energy @xcite .\ngoldstones are described by a unitary field @xmath8 , transforming under @xmath9 as @xmath10 or @xmath11 .\nthe most general chiral lagrangian is a sum of infinite number of terms with an increasing number of derivatives or equivalently in terms of increasing powers of energy or momentum .\nthese lagrangians allow for a description of the physics below a cutoff scale @xmath12 , related to the new physics .\nvector resonances can be introduced in chiral lagrangians by following weinberg @xcite or in equivalent way by means of the hidden local symmetry approach @xcite .\nthe model so obtained when this technique is applied to the electroweak symmetry breaking sector is called bess @xcite .\nthe model we will review here is a model with new vector and axial vector bosons degenerate in mass .\nthese bosons correspond to the gauge bosons associated to a hidden symmetry , @xmath13 .\nthe symmetry group of the theory becomes @xmath14 .\nit breaks down spontaneously to @xmath15 , the diagonal subgroup of @xmath16 , and gives rise to nine goldstones .\nsix of these are absorbed by the vector and axial vector bosons .\nas soon as we perform the gauging of the subgroup @xmath17 , the three remaining goldstones disappear giving masses to the sm gauge bosons .\nthis general procedure for building models with vector and axial vector resonances is discussed in @xcite , while this special model has been proposed in @xcite .\nthis model has the nice property that all the deviations in the low energy parameters from their sm values are strongly suppressed .\nthis allows the existence of a strong electroweak sector at relatively low energies within the precision of electroweak tests , such that it may be accessible with accelerators designed for the near future . as such it offers possibilities of experimental tests even with future or existing machines of relatively low energy . in the following phenomenological implications at tevatron upgrade and lhc\nwill be discussed @xcite .\nthe model includes two new triplets of vector bosons ( @xmath18,@xmath19 ) and ( @xmath20,@xmath21 ) .\nthe parameters of the model are a new gauge coupling constant @xmath22 and a mass parameter @xmath23 , related to the scale of the underlying symmetry breaking sector . in the following we give approximate formulas in the limit @xmath24 and @xmath25 . for the numerical analysis\nthe exact formulas of @xcite were used . in the charged sector the fields @xmath20 are unmixed for any value of @xmath26 .\ntheir mass is given by : @xmath27 the charged fields @xmath28 and @xmath18 have the following masses : @xmath29 where @xmath30 , @xmath31 is the usual @xmath3 gauge coupling constant and @xmath32 . in the neutral sector\nwe have : @xmath33 where @xmath34 and @xmath35 is the usual @xmath36 gauge coupling constant .\nnotice that for small @xmath37 all the new vector resonances are degenerate in mass .\nthe charged part of the fermionic lagrangian is @xmath38 where @xmath39 apart from higher order terms and @xmath40 with @xmath41 .\nlet us notice that the @xmath42 are not coupled to the fermions . for the neutral part we get @xmath43z_\\mu\\nonumber\\\\ & + & \\left[c j_l^{(3)\\mu}+dj_{em}^\\mu \\right]l_{3\\mu}\\nonumber\\\\ & + & \\left[e j_l^{(3)\\mu}+fj_{em}^\\mu \\right]r_{3\\mu}\\big\\}\\end{aligned}\\ ] ] where @xmath44 in the preceeding formula is the photon field and again in the limit @xmath45 , @xmath46 , @xmath47 and @xmath48 , @xmath49 are the usual neutral currents . in fig\n[ fig1 ] @xmath50 c.l .\nupper bounds on @xmath51 versus @xmath23 from lep , tevatron and slc data are shown . the limits ( continuous line )\nare obtained calculating virtual effects up to order @xmath52 , and using the experimental data from ref .\nnote that in the low energy limit ( @xmath24 ) there are no deviations from the sm , thus allowing to consider light new resonances for the strong sector .\nwe will now study the detection of charged and neutral vector resonances from a strong electroweak sector at the upgrading of the fermilab tevatron @xcite .\nthe option we have chosen is the so called tev-33 , with a c.m .\nenergy of the collider of 2 tev and an integrated luminosity of @xmath53 .\nwe have considered the total cross - section @xmath54 and compared it with the sm background .\nthe events where simulated using pythia montecarlo @xcite .\nthe simulation was performed using the expected detector resolution , in particular a smearing of the energy of the leptons was done according to @xmath56 and the error on the 3-momentum determination was assumed to be between @xmath57 for a mass of the order of @xmath58 and @xmath59 for a mass of @xmath60 .\nwe have examined various cases with different choices of @xmath23 and @xmath51 ( taken inside the physical region shown in fig .\n1 ) to give an estimate of the sensitivity of the model to this option for the upgrading of the tevatron ( see table 1 for the charged case ) .\nfor each case we have selected cuts to maximize the statistical significance of the signal .\nwe see that the number of signal events decreases for increasing mass of the resonance .\nthe conclusion is that tevatron with the high luminosity option will be able to discover a strong electroweak resonant sector as described by the degenerate bess model for masses up to @xmath55 .\nit can be seen from the calculation of the statistical significance ( see @xcite ) that the charged process allows to push further the discovery limits of the new vector bosons with respect to the neutral process .\nhowever the experimental check of the model requires the proof of the existence of both neutral and charged vector bosons .\nnotice that the reconstruction of the resonance mass requires a careful study of the experimental setup , due to the smallness of the resonance width . in fig .\n[ fig2 ] we show the differential distribution of events at lhc of @xmath64 in the transverse mass of the new vector boson for @xmath65 and @xmath66 .\nthe following cuts have been applied : @xmath67 , @xmath68 .\nthe number of signal events per year is 469 , the corresponding background consists of 247 events . the energy of the muons was smeared by @xmath69 and the error in the 3-momentum increases with the momentum of the muon from @xmath57 to @xmath70 as stated in @xcite .\nthe statistical significance for some choices of the parameters is given in table 2 , showing that the discovery of a charged resonance up to @xmath71 with @xmath72 is well within the reach of lhc .\nthe limit of detection for a @xmath71 mass is reached for a value of @xmath73 .\nr. casalbuoni , a. deandrea , s. de curtis , d. dominici , f. feruglio , r. gatto and m. grazzini , _ phys .\n_ * b349 * , 533 ( 1995 ) ; r. casalbuoni , a. deandrea , s. de curtis , d. dominici , r. gatto and m. grazzini , _ phys .\n_ * d53 * , 5201 ( 1996 ) .", "role": "user" }, { "content": "i discuss the possible symmetries of effective theories for spinless and spin one bosons , to concentrate on a model with vector and axial vector strong interacting bosons possessing a discrete symmetry demanding degeneracy ( degenerate bess model , bess standing for breaking electroweak symmetry strongly ) . \n the phenomenology at future hadron colliders is also presented . * a strong electroweak sector + with decoupling at low energy * 1.0 cm d. dominici _ dipartimento di fisica universit di firenze _ _ \n i.n.f.n . sezione di firenze _ _ lgo e.fermi 2 , 50125 firenze , italia .", "role": "assistant" } ]

[ { "content": "You will be shown biomedical passages and your task is to answer the provided question. Provide a concise and accurate response and do not include any additional text in the response other than the answer.\n\nQuestion: Which is the E3 ubiquitin ligase which ubiquitinates IkB leading to its proteasomal degradation?\n\nContext: IKK activation and IκB degradation involve different ubiquitination modes; the latter is mediated by a specific E3 ubiquitin ligase SCF(β-TrCP) . The F-box component of this E3, β-TrCP, recognizes the IκB degron formed following phosphorylation by IKK and thus couples IκB phosphorylation to ubiquitination. SCF(β-TrCP) -mediated IκB ubiquitination and degradation is a very efficient process, often resulting in complete degradation of the key inhibitor IκBα within a few minutes of cell stimulation. In vivo ablation of β-TrCP results in accumulation of all the IκBs and complete NF-κB inhibition.\nSequence comparison analysis showed sequence motif identity between CLU and beta-transducin repeat-containing protein (beta-TrCP), a main E3 ubiquitin ligase involved in IkappaB-alpha degradation.\nIkappaB degradation is dependent upon its phosphorylation by the IkappaB kinase (IKK) complex and subsequent ubiquitination facilitated by beta-Trcp E3 ubiquitin ligase.\nHere we show that beta-catenin stabilizes the mRNA encoding the F-box protein betaTrCP1, and identify the RNA-binding protein CRD-BP (coding region determinant-binding protein) as a previously unknown target of beta-catenin/Tcf transcription factor. CRD-BP binds to the coding region of betaTrCP1 mRNA. Overexpression of CRD-BP stabilizes betaTrCP1 mRNA and elevates betaTrCP1 levels (both in cells and in vivo), resulting in the activation of the Skp1-Cullin1-F-box protein (SCF)(betaTrCP) E3 ubiquitin ligase and in accelerated turnover of its substrates including IkappaB and beta-catenin.\nThe multisubunit IkappaB kinase (IKK) responsible for inducible IkappaB phosphorylation is the point of convergence for most NF-kappaB-activating stimuli. IKK contains two catalytic subunits, IKKalpha and IKKbeta, both of which are able to correctly phosphorylate IkappaB. Gene knockout studies have shed light on the very different physiological functions of IKKalpha and IKKbeta. After phosphorylation, the IKK phosphoacceptor sites on IkappaB serve as an essential part of a specific recognition site for E3RS(IkappaB/beta-TrCP), an SCF-type E3 ubiquitin ligase, thereby explaining how IKK controls IkappaB ubiquitination and degradation.", "role": "user" }, { "content": "SCF beta-transducin repeat-containing protein (beta-TrCP)", "role": "assistant" } ]

[ { "content": "You are provided with the abstract of a scientific paper and the abstracts of the papers it references. Your task is to write a Related Work section for the main paper. This section should concisely summarize and integrate the key points from the cited abstracts, reflecting how they relate to the main paper's contributions and context. In your summary, use numerical citation markers like [1], [2], etc., to refer to the corresponding papers.\n\nMain Abstract:\nI study two privacy-preserving social network graphs to dis- close the types of relationships of connecting edges and provide flexible multigrained access control. To create such graphs, my schemes employ the concept of secretaries and types of relationships. It is significantly more efficient than those that using expensive cryptographic primitives. I also show how these schemes can be used for multigrained access control with various options. In addition, I describe how much these schemes are resilient to infer the types of connecting edges.\n\nCited Abstract(s):\n[1]: In this paper we introduce a novel scheme for key management in social networks that is a first step towards the creation of a private social network. A social network graph (i.e., the graph of friendship relationships) is private and social networks are often used to share content, which may be private, amongst its users. In the status quo, the social networking server has access to both this graph and to all of the content, effectively requiring that it is a trusted third party. The goal of this paper is to produce a mechanism through which users can control how their content is shared with other users, without relying on a trusted third party to manage the social network graph and the users' data. The specific access control model considered here is that users will specify access policies based on distance in the social network; for example some content is visible to friends only, while other content is visible to friends of friends, etc. This access control is enforced via key management. That is for each user, there is a key that only friends should be able to derive, there is a key that both friends of the user and friends of friends can derive, etc. The proposed scheme enjoys the following properties: i) the scheme is asynchronous in that it does not require users to be online at the same time, ii) the scheme provides key indistinguishability (that is if a user is not allowed to derive a key according to the access policy, then that key is indistinguishable from a random value), iii) the scheme is efficient in terms of server storage and key derivation time, and iv) the scheme is collusion resistant.", "role": "user" }, { "content": "Frikken and Srinivas [1] suggested a key management scheme in social networks without a trusted third party. With the derived keys, it protects user's content as well as enhances access control to a social network. A key for each user is derived based on the proximity of relationship between users. Suppose Alice, a friend of Bob, can access Bob's social network with her friendship of Bob's key and Carol, a friend of friend of Bob, can access Bob's social network with her friend of friend of Bob's key. Access can be controlled based on the those relationship keys that have different access policy of Bob's. This access control is done asynchronously, which means it does not require multiple users to be online simultaneously for the access control to allow access other users. For the social network graph protection, they encrypts destination nodes as well as edges in between. One drawback as the authors mentioned is that malicious users could access to the content of other unauthorized users by publishing other users' keys.", "role": "assistant" } ]

[ { "content": "Given a short query with keyphrases about a research idea in 2019 in the domain of artificial intelligence, recommend the relevant datasets to validate the research idea from the options provided. A short description of the datasets is also provided to help you.\n\nQuery: I want to understand how spatiotemporal representations are learned in two-stream networks for action recognition.\n\nKeyphrases: action recognition video\n\nDataset description:\nTVQA: The TVQA dataset is a large-scale vido dataset for video question answering. It is based on 6 popular TV shows (Friends, The Big Bang Theory, How I Met Your Mother, House M.D., Grey's Anatomy, Castle).\nMTL-AQA: A new multitask action quality assessment (AQA) dataset, the largest to date, comprising of more than 1600 diving samples; contains detailed annotations for fine-grained action recognition, commentary generation, and estimating the AQA score. Videos from multiple angles provided wherever available.\nUCF101: UCF101 dataset is an extension of UCF50 and consists of 13,320 video clips, which are classified into 101 categories. These 101 categories can be classified into 5 types (Body motion, Human-human interactions, Human-object interactions, Playing musical instruments and Sports).\nFineGym: FineGym is an action recognition dataset build on top of gymnasium videos. Compared to existing action recognition datasets, FineGym is distinguished in richness, quality, and diversity.\n\nOptions: A: TVQA B: MTL-AQA C: UCF101 D: FineGym", "role": "user" }, { "content": "UCF101", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"UnapprovedDrug\", \"Brand\", \"DrugGroup\", \"Drug\"].\n\nPlease return the output as a JSON object of the format: {\"Brand\": [\"Aspirin\", ...], \"DrugGroup\": [\"Salicylate\", ...], \"Drug\": [\"Phenobarbital\", ...], \"UnapprovedDrug\": [\"Heroin\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nImmediate and Extended Release Tablets The hypoglycemic action of sulfonylureas may be potentiated by certain drugs including nonsteroidal anti-inflammatory agents, some azoles and other drugs that are highly protein bound, salicylates, sulfonamides, chloramphenicol, probenecid, coumarins, monoamine oxidase inhibitors, and beta adrenergic blocking agents. When such drugs are administered to a patient receiving glipizide, the patient should be observed closely for hypoglycemia. When such drugs are withdrawn from a patient receiving glipizide, the patient should be observed closely for loss of control. In vitro binding studies with human serum proteins indicate that glipizide binds differently than tolbutamide and does not interact with salicylate or dicumarol. However, caution must be exercised in extrapolating these findings to the clinical situation and in the use of glipizide with these drugs. Certain drugs tend to produce hyperglycemia and may lead to loss of control. These drugs include the thiazides and other diuretics, corticosteroids, phenothiazines, thyroid products, estrogens, oral contraceptives, phenytoin, nicotinic acid, sympathomimetics, calcium channel blocking drugs, and isoniazid. When such drugs are administered to a patient receiving glipizide, the patient should be closely observed for loss of control. When such drugs are withdrawn from a patient receiving glipizide, the patient should be observed closely for hypoglycemia. A potential interaction between oral miconazole and oral hypoglycemic agents leading to severe hypoglycemia has been reported. Whether this interaction also occurs with the intravenous, topical, or vaginal preparations of miconazole is not known. The effect of concomitant administration of fluconazole and glipizide has been demonstrated in a placebo-controlled crossover study in normal volunteers. All subjects received glipizide alone and following treatment with 100 mg of fluconazole as a single daily oral dose for seven days. The mean percentage increase in the glipizide AUC after fluconazole administration was 56.9% (range: 35 to 81).", "role": "user" }, { "content": "{\"Brand\": [], \"Drug\": [\"glipizide\", \"tolbutamide\", \"miconazole\", \"fluconazole\", \"probenecid\", \"nicotinic acid\", \"dicumarol\", \"phenytoin\", \"chloramphenicol\", \"isoniazid\"], \"DrugGroup\": [\"coumarins\", \"corticosteroids\", \"estrogens\", \"sulfonylureas\", \"contraceptives\", \"monoamine oxidase inhibitors\", \"azoles\", \"calcium channel blocking drugs\", \"salicylates\", \"diuretics\", \"thyroid products\", \"thiazides\", \"sympathomimetics\", \"sulfonamides\", \"beta adrenergic blocking agents\", \"phenothiazines\", \"nonsteroidal anti-inflammatory agents\", \"hypoglycemic agents\", \"salicylate\"], \"UnapprovedDrug\": []}", "role": "assistant" } ]

[ { "content": "You will be presented with a citation sentence from a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\nEight empirically derived syndrome scales (syndrome scales) were built by exploratory and confirmatory factor analysis [4].", "role": "user" }, { "content": "Method", "role": "assistant" } ]

[ { "content": "You will be presented with a paragraph from a COVID-19 literature. Your task is to classify the topics of this piece of text by choosing from the following categories:\n\n- Epidemic Forecasting: The content relates to predictions about the spread of COVID-19.\n- Treatment: The paragraph discusses therapeutic methods or medication for COVID-19.\n- Prevention: The content covers measures to prevent the spread of COVID-19.\n- Mechanism: The paragraph explains the biological mechanisms of the virus.\n- Case Report: The content is a report of a COVID-19 case.\n- Transmission: The paragraph discusses how COVID-19 is transmitted.\n- Diagnosis: The content is about diagnosing COVID-19 in individuals.\n\nYour classification should be provided as an element within a JSON array. The array should be formatted with topics enclosed in double quotes and separated by commas, following the JSON format, for example: [\"Topic1\", \"Topic2\", ...]. Include all applicable categories within the array. \nYour output should be a valid JSON array, and no additional text should be included in your response.\n\nArticle:\n\nBACKGROUND: Shortly after its emergence in December 2019, the coronavirus disease 2019 (COVID-19) was declared as a pandemic by the World Health Organization. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the seventh member of the Coronaviridae family of viruses that causes disease in humans. THE PROBLEM: Despite the established role of molecular diagnostics, COVID-19 serodiagnosis remains a poorly discovered and enigmatic area. Although there are numerous commercial serological products available globally, there is a severe paucity of high-quality peer-reviewed literature on their true performance characteristics. That being said, publications including in-house developed serological tests started to shed light on the kinetics of the humoral response. SUMMARY: In spite of intense focus of assessing the performance characteristics of the commercially-available kits, the main issue remains rather invisible, that is, lack of solid science behind COVID-19 serology its clinical usefulness thereof. This short review summarizes the key points as to why COVID-19 is not jest ready to fly. PURPOSE OF REVIEW: Despite having been mentioned as a testing option, COVID-19 serology has significant shortcomings that needs discussing. This short review is meant to shed light on one of those aspects.", "role": "user" }, { "content": "[\"Treatment\", \"Diagnosis\"]", "role": "assistant" } ]

[ { "content": "Below are the Abstract, Introduction, and Conclusion sections of a computer science research paper. Please summarize the main contribution of the work in a single sentence. Your response should include the summary sentence and no additional text.\n\nPaper text:\n\nAttacks on natural language models are difficult to compare due to their different definitions of what constitutes a successful attack.\nWe present a taxonomy of constraints to categorize these attacks.\nFor each constraint, we present a real-world use case and a way to measure how well generated samples enforce the constraint.\nWe then employ our framework to evaluate two state-of-the art attacks which fool models with synonym substitution.\nThese attacks claim their adversarial perturbations preserve the semantics and syntactical correctness of the inputs, but our analysis shows these constraints are not strongly enforced.\nFor a significant portion of these adversarial examples, a grammar checker detects an increase in errors.\nAdditionally, human studies indicate that many of these adversarial examples diverge in semantic meaning from the input or do not appear to be human-written.\nFinally, we highlight the need for standardized evaluation of attacks that share constraints.\nWithout shared evaluation metrics, it is up to researchers to set thresholds that determine the trade-off between attack quality and attack success.\nWe recommend well-designed human studies to determine the best threshold to approximate human judgement.\nAdvances in deep learning have led to impressive performance on many tasks, but models still make mistakes.\nModels are particularly vulernable to adversarial examples, inputs designed to fool models (Szegedy et al., 2014) .\nGoodfellow et al. (2014) demonstrated that image classification models could be fooled by perturbations indistinguishable to humans.\nDue to the importance of natural language processing (NLP) tasks, a large body of research has focused on applying the concept of adversarial examples to text, including (Alzantot et al., 2018; Jin et al., 2019; Kuleshov et al., 2018; Zhang et al., 2019; Ebrahimi et al., 2017; Gao et al., 2018; Li et al., 2018; Samanta & Mehta, 2017; Jia & Liang, 2017; Iyyer et al., 2018; Papernot et al., 2016a) .\nThe importance of tasks such as spam and plagiarism detection highlights the need for robust NLP models.\nHowever, there are fundamental differences between image and text data.\nUnlike images, two different sequences of text are never entirely indistinguishable.\nThis raises the question: if indistinguishable perturbations aren't possible, what are adversarial examples in text?\nWe observe that each work from recent literature has a slightly different definition of what constitutes an adversarial example in natural language.\nComparing the success rate of two attacks is meaningless if the attacks use different methods to evaluate the same constraints or define different constraints altogether.\nIn this paper, we build on Gilmer et al. (2018) to introduce a taxonomy of constraints specific to adversarial examples in natural language.\nTo the best of our knowledge, our work provides the first comprehensive framework for categorizing and evaluating attack constraints in natural language.\nWe discuss use cases and propose standardized evaluation methods for each of these constraints.\nWe then apply our evaluation methods to the synonym-substitution based attacks of Jin et al. (2019) and Alzantot et al. (2018) .\nThese attacks claimed to preserve the syntax and semantics of the original sentence, while remaining non-suspicious to a human interpreter.\nHowever, we find that most of their adversarial examples contain additional grammatical errors, and human surveys reveal that many adversarial examples also change the meaning of the sentence and/or do not appear to be written by humans.\nThese results call into question the ubiquity of synonym-based adversarial examples and emphasize the need for more careful evaluation of attack approaches.\nLastly, we discuss how previous works rely on arbitrary thresholds to determine the semantic similarity of two sentences.\nThese thresholds can be tuned by the researcher to make their methods seem more successful with little penalty in quantitative metrics.\nThus, we highlight the importance of standardized human evaluations to approximate the true threshold value.\nAny method that introduces a novel approach to measure semantic similarity should support their choice of threshold with defensible human studies.\nThe three main contributions of this paper are:\n• We formally define and categorize constraints on adversarial examples in text, and introduce evaluation methods for each category.\n• Using these categorizations and evaluation methods, we quantitatively disprove claims that stateof-the-art synonym-based substitutions preserve semantics and grammatical correctness.\n• We show the sensitivity of attack success rate to changes in semantic similarity thresholds set by researchers.\nWe assert that perturbations which claim semantic similarity should use standardized human evaluation studies with precise wording to determine an appropriate threshold.\nWe introduced a framework for evaluating fulfillment of attack constraints in natural language.\nApplying this framework to synonym substitution attacks raised concerns about the semantic preservation, syntactic accuracy, and conspicuity of the adversarial examples they generate.\nFuture work may expand our hierarchy to categorize and evaluate different attack constraints in natural language.\nStandardized terminology and evaluation metrics will make it easier for defenders to determine which attacks they must protect themselves from-and how.\nIt remains to be seen how robust BERT is when subject to synonym attacks which rigorously preserve semantics and syntax.\nIt is up to future research to determine how prevalent adversarial examples are throughout the broader space of paraphrases.", "role": "user" }, { "content": "We present a framework for evaluating adversarial examples in natural language processing and demonstrate that generated adversarial examples are often not semantics-preserving, syntactically correct, or non-suspicious.", "role": "assistant" } ]

[ { "content": "You will be presented with a collection of medical randomized controlled trial (RCT) reports addressing a shared clinical question -- for instance, the efficacy of a medical intervention on a disease or condition. Given the titles and abstracts of these reports, your task is to generate the conclusion of the systematic review article synthesizing the key findings. Your conclusion should be a few sentences long. In your response, include only the conclusion and no other text. The RCT reports are below.\n\n\n\nTitle 1:\nThe AESOP robot system in laparoscopic surgery: increased risk or advantage for surgeon and patient?\nAbstract 1:\nThe aim of this study was to examine the advantages and risks of the Automated Endoscopic System for Optical Positioning (AESOP) 3000 robot system during uncomplicated laparoscopic cholecystectomies or laparoscopic hernioplasty.\n In a randomized study, we examined two groups of 120 patients each with the diagnosis cholecystolithiasis respectively the unilateral inguinal hernia. We worked with the AESOP 3000, a robotic arm system that is voice-controlled by the surgeon. The subjective and objective comfort of the surgeon as well as the course and length of the operation were measured.\n The robot-assisted operations required significantly longer preparation and operation times. With regard to the necessary commands and manual camera corrections, the assistant group was favored. The same was true for the subjective evaluation of the surgical course by the surgeon.\n Our study showed that the use of AESOP during laparoscopic cholecystectomy and hernioplasty is possible in 94% of all cases. The surgeon must accept a definite loss of comfort as well as a certain loss of time against the advantage of saving on personnel.\n\n\nTitle 2:\nZeus robot-assisted laparoscopic cholecystectomy in comparison with conventional laparoscopic cholecystectomy.\nAbstract 2:\nThe robotic surgical system overcomes many technological obstacles of conventional laparoscopic surgery, and possesses enormous clinical applied potential. The aim of this study was to compare the efficacy of Zeus robot-assisted laparoscopic cholecystectomy with conventional laparoscopic cholecystectomy.\n Forty patients undergoing elective cholecystectomy were randomly divided into two groups. Patients in group A (n=20) underwent Zeus robot-assisted laparoscopic cholecystectomy, and patients in group B (n=20) received conventional laparoscopic cholecystectomy. The parameters on operative field, operative time, the number of actions, the rate of operative errors and minimal trauma were evaluated and compared between the two groups.\n The number of clearing camera (1.1+/-1.0 times) and the time of adjusting the operative field (2.2+/-0.7 minutes) in group A were significantly less than those (4.5+/-1.5 times) and (7.5+/-1.2 minutes) in group B. The number of dissection actions (337+/-86 times) and the rate of operative errors (10%) in group A were less than those (389+/-94 times), (25%) in group B. The total operation time (104.9+/-20.5 minutes) and setup time (29.5+/-9.8 minutes) in group A were significantly longer than those (78.6+/-17.1 minutes), (12.6+/-2.5 minutes) in group B. Blood loss and postoperative hospitalization were similar. No postoperative complications occurred in both groups, and open cholecystectomy was performed in each group.\n Zeus robot-assisted cholecystectomy inherits the benefits of minimally invasive surgery. The Zeus robotic surgical system is better than conventional laparoscopic technique in controlling the operative field and can be manipulated precisely and stably though it requires more operative time.\n\n\nTitle 3:\nControlled trial of the introduction of a robotic camera assistant (EndoAssist) for laparoscopic cholecystectomy.\nAbstract 3:\nThe role of the human camera holder during laparoscopic surgery keeps valuable personnel from other duties. EndoAssist is a robotic camera-holding device controlled by the operator's head movements. This study assesses its introduction into clinical practice.\n Ninety-three patients undergoing laparoscopic cholecystectomy were randomized to have either the robotic (40) or a human (46) assistant. Seven patients converted to open operation were excluded. Six surgeons were evaluated. Operating time and subjective assessments were recorded. Learning curves were constructed.\n The mean operating time was less using the robotic assistant (66 min) than with human assistance (74 min) (p < 0.05, two-tailed t-test). The learning curves for operating time showed that within three operations surgeons were trained in using the robot. The device was safe in use.\n The EndoAssist operating device is a significant asset in laparoscopic surgery and a suitable substitute for a human assistant. Surgeons became competent in the use of the robot within three operations. The robot offers stability and good control of the television image in laparoscopic surgery.\n\n\nTitle 4:\nTime-action analysis of instrument positioners in laparoscopic cholecystectomy.\nAbstract 4:\nInstrument positioners can position and lock a laparoscopic instrument. This study uses time-action analysis to evaluate objectively whether IPs can substitute for a surgical assistant efficiently and safely.\n In four hospitals, 78 laparoscopic cholecystectomies were randomly assisted by a surgical assistant or an instrument positioner (AESOP and PASSIST) The efficiency and safety of laparoscopic cholecystectomies were analyzed with respect to time, number and type of actions, positioning accuracy, and peroperative complications. A questionnaire evaluated the difficulties for each operation and the comfort of instrument positioner use.\n The PASSIST and AESOP were able to replace the surgical assistant during laparoscopic cholecystectomies without significantly changing either the efficiency or the safety of the operation. The questionnaire showed that the surgeons preferred to operate with an instrument positioner.\n This study assessed objectively that instrument positioners can substitute for a surgical assistant efficiently and safely in elective laparoscopic cholecystectomies.", "role": "user" }, { "content": "Robot assisted laparoscopic cholecystectomy does not seem to offer any significant advantages over human assisted laparoscopic cholecystectomy. However, all trials had a high risk of systematic errors or bias (that is, risk of overestimation of benefit and underestimation of harm). All trials were small, with few or no outcomes. Hence, the risk of random errors (that is, play of chance) is high. Further randomised trials with low risk of bias or random errors are needed.", "role": "assistant" } ]

[ { "content": "Given an abstract from a research paper, your task is to identify and label relationships between chemical compounds and genes mentioned in the abstract.\n\nThe relationship type must be one of ['DOWNREGULATOR', 'SUBSTRATE', 'INDIRECT-REGULATOR', 'PART-OF', 'MODULATOR-ACTIVATOR', 'REGULATOR', 'INHIBITOR', 'COFACTOR', 'UPREGULATOR', 'ACTIVATOR', 'ANTAGONIST', 'NOT', 'INDIRECT-DOWNREGULATOR', 'SUBSTRATE_PRODUCT-OF', 'INDIRECT-UPREGULATOR', 'AGONIST', 'PRODUCT-OF', 'MODULATOR', 'DIRECT-REGULATOR', 'UNDEFINED', 'AGONIST-INHIBITOR', 'AGONIST-ACTIVATOR', 'MODULATOR-INHIBITOR'].\n\nPlease format your output as a JSON array. Each entry in the array should express a single relation, formatted as [\"<Entity_A>\", \"<RELATION_A_B>\", \"<Entity_B>\"]. If no relations can be found, please output an empty JSON array [].\n\nAbstract:\n\nBalancing societal needs and regulatory certainty: the case study of peramivir in Japan. Regulators must balance societal and medical requirements against the need for certainty about benefit and risk for new medicines. This is described in a case study of the expedited review and approval of peramivir, a novel neuraminidase inhibitor, in Japan in the context of the emergence of new strain of influenza in 2009. The case illustrates the importance of regulatory science and transparency in supporting such decision making.", "role": "user" }, { "content": "[[\"peramivir\", \"INHIBITOR\", \"neuraminidase\"]]", "role": "assistant" } ]

[ { "content": "Given an abstract from a research paper, your task is to identify and label relationships between chemical compounds and genes mentioned in the abstract.\n\nThe relationship type must be one of ['DOWNREGULATOR', 'SUBSTRATE', 'INDIRECT-REGULATOR', 'PART-OF', 'MODULATOR-ACTIVATOR', 'REGULATOR', 'INHIBITOR', 'COFACTOR', 'UPREGULATOR', 'ACTIVATOR', 'ANTAGONIST', 'NOT', 'INDIRECT-DOWNREGULATOR', 'SUBSTRATE_PRODUCT-OF', 'INDIRECT-UPREGULATOR', 'AGONIST', 'PRODUCT-OF', 'MODULATOR', 'DIRECT-REGULATOR', 'UNDEFINED', 'AGONIST-INHIBITOR', 'AGONIST-ACTIVATOR', 'MODULATOR-INHIBITOR'].\n\nPlease format your output as a JSON array. Each entry in the array should express a single relation, formatted as [\"<Entity_A>\", \"<RELATION_A_B>\", \"<Entity_B>\"]. If no relations can be found, please output an empty JSON array [].\n\nAbstract:\n\nPeptidyl-prolyl cis/trans-isomerase A1 (Pin1) is a target for modification by lipid electrophiles. Oxidation of membrane phospholipids is associated with inflammation, neurodegenerative disease, and cancer. Oxyradical damage to phospholipids results in the production of reactive aldehydes that adduct proteins and modulate their function. 4-Hydroxynonenal (HNE), a common product of oxidative damage to lipids, adducts proteins at exposed Cys, His, or Lys residues. Here, we demonstrate that peptidyl-prolyl cis/trans-isomerase A1 (Pin1), an enzyme that catalyzes the conversion of the peptide bond of pSer/pThr-Pro moieties in signaling proteins from cis to trans, is highly susceptible to HNE modification. Incubation of purified Pin1 with HNE followed by MALDI-TOF/TOF mass spectrometry resulted in detection of Michael adducts at the active site residues His-157 and Cys-113. Time and concentration dependencies indicate that Cys-113 is the primary site of HNE modification. Pin1 was adducted in MDA-MB-231 breast cancer cells treated with 8-alkynyl-HNE as judged by click chemistry conjugation with biotin followed by streptavidin-based pulldown and Western blotting with anti-Pin1 antibody. Furthermore, orbitrap MS data support the adduction of Cys-113 in the Pin1 active site upon HNE treatment of MDA-MB-231 cells. siRNA knockdown of Pin1 in MDA-MB-231 cells partially protected the cells from HNE-induced toxicity. Recent studies indicate that Pin1 is an important molecular target for the chemopreventive effects of green tea polyphenols. The present study establishes that it is also a target for electrophilic modification by products of lipid peroxidation.", "role": "user" }, { "content": "[[\"HNE\", \"REGULATOR\", \"peptidyl-prolyl cis/trans-isomerase A1\"], [\"8-alkynyl-HNE\", \"REGULATOR\", \"Pin1\"], [\"HNE\", \"REGULATOR\", \"Pin1\"], [\"polyphenols\", \"REGULATOR\", \"Pin1\"]]", "role": "assistant" } ]

[ { "content": "You have to answer a biomedical question in binary format, i.e., only yes and no are acceptable answers. A list of paragraphs is provided as context to help you answer the question.\n\nQuestion: Is acupotomy used to treat muscle stiffness?\n\nContext: All the included studies reviewed musculoskeletal disorders and reported a significantly higher total effective and cure rates in the acupotomy group for frozen shoulder, cervical spondylosis, third lumbar vertebrae transverse process syndrome, trigger finger, knee osteoarthritis, and lumbar spinal stenosis, compared to the other active control groups\nAcupotomy showed promising results for some musculoskeletal disorders; however, additional high-quality evidence is required to make clinical recommendations regarding this procedure.\nAcupotomy has been widely used to treat nerve entrapment syndrome\nTo evaluate the clinical efficacy and safety of acupotomy in treatment of knee osteoarthritis\nEffect and safety of acupotomy in treatment of knee osteoarthritis\nAcupotomy Therapy for Knee Osteoarthritis Pain: Systematic Review and Meta-Analysis.\nWe included only randomized controlled trials (RCTs) that used acupotomy therapy as the major intervention in adults with knee OA,\nAcupotomy, which involves the addition of a scalpel function to the conventional acupuncture treatment, has recently been applied as a conservative treatment method for lumbar disc herniation (LDH)\nLTS: The systematic review will provide high-quality evidence to assess the efficacy and safety of acupotomy for KOA by pain, stiffness, and dysfunction of knee joint, and quality of life, as well as adverse events.CONC\nAcupotomy has been widely used to treat KOA.\nAcupotomy, a biomechanical therapy guided by traditional Chinese medicine theory, alleviates cartilage degradation and is widely used in the clinic to treat KOA by correcting abnormal mechanics.\nBACKGROUND: Acupotomy has been widely used to treat nerve entrapment syndrome.\nAcupotomy has been widely used to treat calcaneodynia.\nThe aim of this study is to evaluate the efficacy and safety of the acupotomy treatment in patients with calcaneodynia.\notomy combined with rehabilitation was associated with significantly higher TER (RR 1.24, 95% CI 1.01-1.52, I = 77%) and gross motor function measure score (MD 12.62, 95% CI 11.75-13.49, I = 54%), and significantly lower muscle tone of gastrocnemius measured by the Ashworth scale or the modified Ashworth scale (MD -0.97, 95% CI -1.07 to -0.88, I = 0%) compared with rehabilitation alone. No\nBoth acupotomy and acupuncture have been widely used clinically to treat CSR in China with satisfied efficacy.\nGN AND METHODS: Total 75 patients were participated in acupotomy therapy and ultrasonic drug penetration to treat joint osteoarthritis. The\nAcupotomy Alleviates Energy Crisis at Rat Myofascial Trigger Points\nits in the acupotomy and EA groups underwent bilateral acupotomylysis intervention; those in the acupotomy-EA group underwent acupotomylysis and EA interventions. On the\nLTS: The systematic review will provide high-quality evidence to assess the efficacy and safety of acupotomy for KOA by pain, stiffness, and dysfunction of knee joint, and quality of life, as well as adverse events.CON\nAcupotomy for knee osteoarthritis: A systematic review protocol.\nThe aim of this study is to evaluate the efficacy and safety of acupotomy for the treatment of patients with KOA\nSION: The systematic review will provide evidence to assess the effectiveness and safety of acupotomy therapy for KOA patients.PROSP\ne systematic review will provide high-quality evidence to assess the efficacy and safety of acupotomy for KOA by pain, stiffness, and dysfunction of knee joint, and quality of life, as well as adverse events.CON\nThe aim of this study is to evaluate the efficacy and safety of acupotomy for the treatment of patients with KOA.M\nsystematic review will provide evidence to assess the effectiveness and safety of acupotomy therapy for KOA patients.PROS\nTo observe the clinical efficacy of minimally invasive acupotomy-injection technique with targeted three-point in the treatment of frozen shoulder.M\n[Percutaneous dynamic release in stress position by acupotomy in treating severe scapulohumeral periarthritis].\nTo investigate the clinical efficacy of acupotomy stress position percutaneous dynamic release for severe shoulder periarthritis.M\nl sequelae. Acupotomy, a modernized acupuncture form combining the effects of microsurgery and conventional acupuncture, may show specific benefits in the treatment of CP, especially with respect to\nBackground: Acupotomy, which involves the addition of a scalpel function to the conventional acupuncture treatment, has recently been applied as a conservative treatment method for lumbar disc herni\nhe methodological quality was medium-to-high in AMSTAR. All the included studies reviewed musculoskeletal disorders and reported a significantly higher total effective and cure rates in the acupotomy group for frozen shoulder, cervical spondylosis, third lumbar vertebrae transverse process syndrome, trigger finger, knee osteoarthritis, and lumbar spinal stenosis, compared to the other active control groups.CONCLUSION: Acupotomy showed promising results for some musculoskeletal disorders; however, additional high-quality evidence is", "role": "user" }, { "content": "no", "role": "assistant" } ]

[ { "content": "Below are the Abstract, Introduction, and Conclusion sections of a computer science research paper. Please summarize the main contribution of the work in a single sentence. Your response should include the summary sentence and no additional text.\n\nPaper text:\n\nThe driving force behind the recent success of LSTMs has been their ability to learn complex and non-linear relationships.\nConsequently, our inability to describe these relationships has led to LSTMs being characterized as black boxes.\nTo this end, we introduce contextual decomposition (CD), an interpretation algorithm for analysing individual predictions made by standard LSTMs, without any changes to the underlying model.\nBy decomposing the output of a LSTM, CD captures the contributions of combinations of words or variables to the final prediction of an LSTM.\nOn the task of sentiment analysis with the Yelp and SST data sets, we show that CD is able to reliably identify words and phrases of contrasting sentiment, and how they are combined to yield the LSTM's final prediction.\nUsing the phrase-level labels in SST, we also demonstrate that CD is able to successfully extract positive and negative negations from an LSTM, something which has not previously been done.\nIn comparison with simpler linear models, techniques from deep learning have achieved impressive accuracy by effectively learning non-linear interactions between features.\nHowever, due to our inability to describe the learned interactions, this improvement in accuracy has come at the cost of state of the art predictive algorithms being commonly regarded as black-boxes.\nIn the domain of natural language processing (NLP), Long Short Term Memory networks (LSTMs) BID2 have become a basic building block, yielding excellent performance across a wide variety of tasks (Sutskever et al., 2014) BID10 BID7 , while remaining largely inscrutable.In this work, we introduce contextual decomposition (CD), a novel interpretation method for explaining individual predictions made by an LSTM without any modifications to the underlying model.\nCD extracts information about not only which words contributed to a LSTM's prediction, but also how they were combined in order to yield the final prediction.\nBy mathematically decomposing the LSTM's output, we are able to disambiguate the contributions made at each step by different parts of the sentence.To validate the CD interpretations extracted from an LSTM, we evaluate on the problem of sentiment analysis.\nIn particular, we demonstrate that CD is capable of identifying words and phrases of differing sentiment within a given review.\nCD is also used to successfully extract positive and negative negations from an LSTM, something that has not previously been done.\nAs a consequence of this analysis, we also show that prior interpretation methods produce scores which have document-level information built into them in complex, unspecified ways.\nFor instance, prior work often identifies strongly negative phrases contained within positive reviews as neutral, or even positive.\nIn this paper, we have proposed contextual decomposition (CD), an algorithm for interpreting individual predictions made by LSTMs without modifying the underlying model.\nIn both NLP and general applications of LSTMs, CD produces importance scores for words (single variables in general), phrases (several variables together) and word interactions (variable interactions).\nUsing two sentiment analysis datasets for empirical validation, we first show that for information also produced by prior methods, such as word-level scores, our method compares favorably.\nMore importantly, we then show that CD is capable of identifying phrases of varying sentiment, and extracting meaningful word (or variable) interactions.\nThis movement beyond word-level importance is critical for understanding a model as complex and highly non-linear as LSTMs.\n6 APPENDIX Figure 4: Logistic regression coefficients versus coefficients extracted from an LSTM on SST.\nWe include a least squares regression line.\nStronger linear relationships in the plots correspond to better interpretation techniques.", "role": "user" }, { "content": "We introduce contextual decompositions, an interpretation algorithm for LSTMs capable of extracting word, phrase and interaction-level importance score", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Chemical\", \"Disease\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\": [\"Naloxone\", ...], \"Disease\": [\"Hypotensive\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nAcute bronchodilating effects of ipratropium bromide and theophylline in chronic obstructive pulmonary disease. The bronchodilator effects of a single dose of ipratropium bromide aerosol (36 micrograms) and short-acting theophylline tablets (dose titrated to produce serum levels of 10-20 micrograms/mL) were compared in a double-blind, placebo-controlled crossover study in 21 patients with stable, chronic obstructive pulmonary disease. Mean peak forced expiratory volume in 1 second (FEV1) increases over baseline and the proportion of patients attaining at least a 15% increase in the FEV1 (responders) were 31% and 90%, respectively, for ipratropium and 17% and 50%, respectively, for theophylline. The average FEV1 increases during the 6-hour observation period were 18% for ipratropium and 8% for theophylline. The mean duration of action was 3.8 hours with ipratropium and 2.4 hours with theophylline. While side effects were rare, those experienced after theophylline use did involve the cardiovascular and gastrointestinal systems. These results show that ipratropium is a more potent bronchodilator than oral theophylline in patients with chronic airflow obstruction.", "role": "user" }, { "content": "{\"Chemical\": [\"theophylline\", \"ipratropium\", \"ipratropium bromide\"], \"Disease\": [\"chronic obstructive pulmonary disease\", \"cardiovascular systems\", \"cardiovascular and gastrointestinal systems\", \"chronic airflow obstruction\", \"gastrointestinal systems\"]}", "role": "assistant" } ]

[ { "content": "You will be presented with a sentence from biomedical research text. Extract all terms that correspond to chemical entities of biological interest (ChEBI).\nReturn your identified terms in a JSON array, formatted like this: [\"Entity1\", \"Entity2\", ...].\nIf no such entities are detected, respond by providing an empty JSON array [].\n\nBiomedical context:\nWeverifiedthesequencefromthemutatedplasmid,thendigesteditwithBamHIandEcoRI,toinsertinframeGFPsequencesfromaBamHI-EcoRIfragmentofplasmidphr-GFP-1(Stratagene).", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "You will be shown a paragraph from a biomedical research paper, followed by a question about the paper. Please extract text from the paragraph to answer the question. Do not include any text in your response other than the answer.\n\nParagraph: Text: 2019 Novel Coronavirus (2019-nCoV) is a novel respiratory disease first reported in Wuhan, Hubei Province, China in December 2019. 1 Chinese health officials were originally investigating a sudden increase in cases of pneumonia which were later determined to be linked to 2019-nCoV. While most cases originated within mainland China, the disease spread to neighboring countries including Taiwan, Thailand, South Korea, and Japan, and later to the United States, Europe, and Australia. A near real-time updated tracking website for cases and locations worldwide, along with reported deaths is available. 2 Chinese health authorities have sequenced 2019-nCoV and freely shared its genetic profile online. 3, 4 Additionally, on January 28, 2020, an Australian laboratory reported growing the virus from a patient sample. As of January 30, 2020, there have been at least 9,776 persons infected and 213 verified deaths. 2 These numbers are likely underestimates due to the limited information available regarding incubation time, transmissibility, and virus origin. The What was the research question? Investigators adapted the \"Identify, Isolate, Inform\" (3I) Tool for use in suspected cases of 2019-nCoV. What was the major finding of the study? A novel 2019-nCoV 3I Tool is designed for frontline clinicians in the management of suspected patients. This 2019-nCoV 3I adaptation will aid healthcare providers most likely to encounter the disease in the containment and effective treatment of patients. age distribution of these verified deaths is currently not available. One preliminary, small-scale study of 41 patients in Wuhan China, reported 6 deaths (15% mortality) with a median age of 49.0 years. 5 Additionally, transmission of the virus has reportedly occurred in healthcare facilities in Wuhan City, raising concerns of spread to healthcare workers, as was seen during prior outbreaks of the novel coronaviruses, Middle Eastern Respiratory Syndrome (MERS) and Severe Acute Respiratory Syndrome (SARS). Due to the dynamic nature of the outbreak, exposure criteria may change depending on where new cases of 2019-nCoV are detected, the degree of transmissibility, and when additional information regarding the origin of the virus is discovered and reported. On January 15, 2020 , the Centers for Disease Control and Prevention (CDC) confirmed the first known imported case of 2019-nCoV in the US state of Washington. The patient had recently returned from Wuhan City, where he likely contracted the disease. Chicago health authorities reported a second US case on January 24, 2020. This was quickly followed by additional imported cases reported in Orange and Los Angeles Counties, California on January 26, 2020. Additional suspected cases continue to be evaluated. On January 30, 2020, the CDC reported the first local transmission in the US between members in a household. On the same day, the World Health Organization declared 2019-nCoV to be a Public Health Emergency of International Concern (PHEIC). 6 On January 31, 2020, the US Department of Health and Human Services declared coronavirus a public health emergency. 7 Healthy individuals and those with mild illness may be asymptomatic, while others may have more pronounced symptoms of fever or lower respiratory illness. Upon identification of a suspected patient, that individual should immediately be isolated with airborne precautions. Further workup and laboratory confirmation can then proceed. Emergency physicians (EPs), emergency medical services (EMS) personnel, and other healthcare workers who encounter patients with suspected 2019-nCoV infection must inform the appropriate authorities, including but not limited to hospital infection control and local or state public health agencies. Healthcare workers must follow on-going developments related to the outbreak, especially new information concerning detection and management. 8, 9 The 3I Tool outlined in this paper is consistent with current US CDC guidelines and can be applied in a variety of settings such as those in emergency departments, urgent-care clinics, physicians' offices, and prehospital settings. This paper will first briefly review 2019-nCoV and then present the novel 2019-nCoV 3I Tool as modified from its initial conception for Ebola virus disease 10,11 and later adapted for measles, 12 MERS, 13 mumps, 14 Zika virus disease, 15 hepatitis A, 16 pertussis, 17 and scabies. 18 \n\nCoronavirus 2019-nCoV infection commonly presents with signs and symptoms of pneumonia or as a nonspecific lower respiratory illness, with coughing or difficulty breathing accompanied by fever. 5, 19, 20 Fever and cough constitute the most common presentations. However, patients may have other respiratory symptoms, sore throat, nasal congestion, malaise, myalgia, and headache. Bilateral infiltrates may be seen on chest X-ray. Severe cases may present with sepsis and even shock. Conversely, some patients may present as only mildly ill or asymptomatic altogether. 21 To date, patients with underlying medical conditions and the elderly are more likely to become severely ill, require hospitalization, and ultimately die. 22 Early predictions for incubation time are between 2 and 14 days, based on data from similar coronaviruses. The 14-day criterion for epidemiological risk assumes the longest estimated incubation time. 23 In addition, the World Health Organization (WHO) has created its own interim case definition. 24\n\nBy definition, the main features of a novel virus, for example, how it is transmitted, will not be immediately known. However, as with the development of any 3I Tool, it is essential to understand specific characteristics of the disease. In the case of a novel virus such as 2019-CoV, this is challenging since information is rapidly evolving and the science is not yet fully understood. It is possible that the virus will undergo mutations over time that could substantially change its\n\nThe Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus Koenig et al. features. Nevertheless, an appreciation of the key concepts that drive evidence-based management is beneficial (Table 1) . Management guidance will likely change over time. With the initial discovery of a new potential public health threat, it will likely be unclear how patients become sick. For example, rather than a contagion, there could be a contaminant or a toxin responsible for signs and symptoms. In this case, the possibility of an environmental toxin in the Wuhan Market was a consideration early on when limited to no human-tohuman transmission was reported. The mode of transmission has implications for the types of personal protective equipment (PPE) needed to protect healthcare providers in the prehospital, clinic, and hospital settings. 25 In addition, patients may need decontamination after exposure to certain toxins. 26 Another important consideration for application of the 3I Tool is whether the disease is contagious prior to symptom onset (like measles) or only after symptoms develop (like Ebola). A January 30, 2020 letter to the New England Journal of Medicine describes a purported confirmed instance of transmission from an asymptomatic individual. Researchers state that, before symptom onset, the primary case infected two individuals, one of which infected two additional colleagues. 27 Subsequent investigation suggested that the source patient did have mild symptoms and had taken an antipyretic, calling this reported asymptomatic transmission into question. While quarantine may not be feasible and can have unintended consequences, 28, 29, 30 it is a public health tool that can be considered in cases when disease is transmissible before symptom onset. 30 Conversely, if a disease is known not to be transmissible prior to symptom onset, asymptomatic exposed patients must be monitored, but do not require quarantine or isolation unless they develop symptoms. Initially, it may be unclear whether an infectious agent occurred naturally or was deliberately or accidentally released. In this case, a BSL-4 laboratory studying coronaviruses was located approximately 32 kilometers away from the market where initial exposures were felt to occur. 31 Recall that in 2001, the anthrax letter attacks were initially thought to be naturally occurring. Once determined to be bioterrorism, management of the event was similar to that for a chemical exposure with a sudden impact, defined scene, and need for a rapid response and decontamination on site. This differed from the WHO's modeling predicting an aerosolized release that would result in an incubation period with 100,000 or more persons exposed rather than the 22 people who contracted anthrax in 2001. 32 By understanding the key features of a novel disease, healthcare workers can take evidence-based measures to protect themselves, optimize individual patient management, and prevent further disease spread. It is currently unclear how 2019-nCoV is spread, but it is suspected to be transmitted through contact with infected respiratory secretions, like other known coronaviruses. There are instances of sustained human-to-human transmission across generations of cases, especially near the epicenter in Wuhan City. 21 Current evidence suggests that close contact with an infected person is a major factor in disease transmission. CDC defines \"close contact\" 33 as being in or within two meters of an area with a confirmed patient or being directly exposed to infectious secretions without appropriate PPE. Healthcare facilities in China have reported spread from person to person. In addition, some mildly ill or potentially even asymptomatic patients may have a higher chance of spreading the disease to others as they may be less likely to seek medical care. 34 The possibility that patients may be infectious prior to symptom onset further compounds the difficulty of containing the virus and effectively preventing transmission. The current majority of 2019-nCoV cases have been within China and its bordering countries. 2 Persons with recent travel (within 14 days) to Wuhan City or another region with widespread disease, or exposure to a patient under investigation, are considered to have an epidemiologic risk factor and should be assessed for signs and symptoms of a viral illness such as fever and respiratory symptoms. Coronavirus is a zoonotic virus\n\nThe Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus that is transmitted to humans via contact with infected animals. Preliminary reports suggest the disease may have originated in a seafood and live animal market in Wuhan City, but it is still unknown how or whether such transmission occurred. Clinicians working with local public health departments must arrange to have specimens from patients under investigation (PUIs) sent to the CDC laboratory. At this time, the CDC has the only laboratory that can definitively test for 2019-nCoV, though laboratory testing capacity is being rapidly expanded. Polymerase chain reaction (PCR) assays conducted on samples from a patient's upper and lower respiratory tracts will be used to confirm potential cases. In addition, serum antibody titers can be analyzed for confirmation of infection or evidence of immunity. Up-to-date information about the needed specimens and handling requirements to test for 2019-nCoV are available on the CDC website. 35\n\nLike other related coronaviruses, patients with 2019-nCoV frequently present with non-specific symptoms resembling that of influenza. Physicians may consider differential diagnoses related to a wide variety of respiratory infections. In order to relate these symptoms to 2019-nCoV, it is imperative that the identification of a potential exposure event (epidemiologic risk factor) within 14 days of symptom onset is made so that a more focused work-up for 2019-nCoV can be completed. Although the likelihood of coinfection of 2019-nCoV and another respiratory virus is thought to be low, a positive finding of another respiratory pathogen does not exclude the diagnosis of 2019-nCoV. Many commercially available respiratory panels include \"coronavirus\" in the results, but neither a positive nor a negative finding on these panels should be used to include or exclude a diagnosis of 2019-nCoV. Supportive care with appropriate infection control is the mainstay of current CDC treatment guidelines for 2019-nCoV. There are not yet any approved antiviral treatments for 2019-nCoV. Emergency Use Authorizations (EUA) for compassionate use cases may be forthcoming from the US federal government for normally unapproved treatments. Supportive treatment predominantly includes respiratory support, hydration, and antipyretics. General treatment for severe cases should focus on the preservation of vital organ function. In the future, antiviral medications may be available. If a secondary bacterial infection such as pneumonia develops, targeted antibiotics are indicated. Prevention of 2019-nCoV transmission, like any other infectious agent, involves minimizing risk of exposure. Vaccines are under accelerated development and may be useful in the future for post-exposure prophylaxis. Healthcare personnel are at increased risk and should practice standard, droplet, and airborne precautions when encountering an infected person, a PUI, or any symptomatic close contacts. Healthcare workers handling specimens should also adhere to CDC guidelines and should not attempt to perform any virus isolation or characterization. Fever screening has been implemented at numerous airports, including major international hubs within Asia and the US. The efficacy of this intervention is not well documented, however, as some infected persons may be afebrile and disease transmission might occur prior to symptom onset. 27 In addition, people can artificially lower their temperature readings, e.g., by applying ice to their foreheads. As outlined above, admission criteria for 2019-nCoV are similar to that of other patients. If patients do not meet medical criteria for hospitalization, they may be discharged home with isolation precautions and continued observation. EPs must notify local public health authorities so appropriate monitoring and community protective measures can be instituted. The Identify-Isolate-Inform (3I) Tool was initially developed for Ebola virus disease 10,11 and later adapted for measles, 12 MERS, 13 mumps, 14 Zika virus disease, 15 hepatitis A, 16 pertussis, 17 and scabies. 18 This novel tool for suspected 2019-nCoV patients ( Figure 1 ) provides frontline clinicians with a simple algorithm to manage an emerging disease. Identification of exposed patients with an epidemiologic risk factor within 14 days of symptom onset is a crucial first step. An automatic prompt in the electronic health record can be useful in assisting clinicians with early identification of patients at risk. Case definitions promulgated by the WHO 24 and CDC 33 provide useful comprehensive definitions that have been incorporated into the 3I Tool. The 2019-nCoV Tool provides an accurate, summarized algorithm to immediately, and effectively manage suspected patients until additional resources can be consulted. Patients who do not have an exposure risk or any symptoms may be triaged normally. However, before making patient contact, providers must first apply the Vital Sign Zero concept. 36 Vital Sign Zero is a preliminary, non-contact assessment (i.e., performed prior to touching a patient to take traditional vital signs) to first determine whether specific PPE is indicated before the examination commences. By taking the additional time to complete this assessment, risk of exposure and further transmission can be minimized. while in the treatment facility should be started and maintained to assist with the possibility of contact tracing.\n\nQuestion: When was the first case of COVID19 confirmed in the USA?", "role": "user" }, { "content": "January 15, 2020", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Chemical\", \"Protein\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\" : [\"Dexamethasone\", ...], \"Protein\" : [\"BRCA-1\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nProhormone convertase-1 will process prorelaxin, a member of the insulin family of hormones.\nRelaxin is a polypeptide hormone involved in remodeling of the birth canal during parturition. It is synthesized as a preprohormone precursor, which undergoes specific processing to form the mature two-chain disulfide-linked active species that is secreted by the cell. A major part of this processing requires endoproteolytic cleavage at specific pairs of basic amino acid residues, an event necessary for the maturation of a variety of important biologically active proteins, such as insulin and nerve growth factor. Human type 2 preprorelaxin was coexpressed in human kidney 293 cells with the candidate prohormone convertase-processing enzymes mPC1 or mPC2, both cloned from the mouse pituitary tumor AtT-20 cell line, or with the yeast kex2 alpha-mating factor-converting enzyme from Saccharomyces cerevisiae. Prorelaxin expressed alone in 293 cells was secreted into the culture medium unprocessed. Transient coexpression with mPC1 or kex2, but not with mPC2, resulted in the secretion of a low mol wt species with an electrophoretic mobility very similar, if not identical, to that of authentic mature relaxin purified from human placenta. This species was precipitable by monoclonal antibodies specific for relaxin and had a retention time on reverse phase HPLC comparable to that of relaxin. Its analysis by both electrospray and fast atom bombardment mass spectrometry generated mass data that were consistent only with mature relaxin. The basic residues required for mPC1-dependent cleavage of prorelaxin are defined by site-directed mutagenesis.", "role": "user" }, { "content": "{\"Chemical\": [\"amino acid\", \"disulfide\"], \"Protein\": [\"mPC2\", \"mPC1\", \"Prohormone convertase-1\", \"prohormone convertase-processing enzymes\", \"kex2\", \"relaxin\", \"Human type 2 preprorelaxin\", \"insulin\", \"nerve growth factor\", \"yeast kex2\", \"prorelaxin\", \"alpha-mating factor-converting enzyme\", \"Prorelaxin\", \"Relaxin\"]}", "role": "assistant" } ]

[ { "content": "You will be shown an excerpt from a computer science research paper, followed by a question about the paper. Please answer the question given the context. Do not include any text in your response other than the answer.\n\nContext: Given a dataset of parallel text containing N input-output sequencepairs, denoted \\mathcal{D}\\equiv\\left\\{(X^{(i)},Y^{*(i)})\\right\\}_{i=1}^{N},standard maximum-likelihood training aims at maximizing the sum of logprobabilities of the ground-truth outputs given the correspondinginputs,\\mathcal{O}_{\\mathrm{ML}}(\\bm{\\mathbf{\\theta}})=\\sum_{i=1}^{N}\\log{P}_{\\theta}(Y^{*(i)}\\mid X^{(i)})~{}.(7)The main problem with this objective is that it does not reflect thetask reward function as measured by the BLEU score in translation. Further,this objective does not explicitly encourage a ranking among incorrectoutput sequences – where outputs with higher BLEU scores should still obtainhigher probabilities under the model – since incorrect outputs are neverobserved during training. In other words, using maximum-likelihoodtraining only, the model will not learn to be robust to errors made duringdecoding since they are never observed, which is quite a mismatch betweenthe training and testing procedure.\n\nQuestion: Does the task reward function in this context mean the translation task-related reward function?", "role": "user" }, { "content": "Yes, author's concerns are translation tasks.", "role": "assistant" } ]

[ { "content": "You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should only include the abstract and no additional text.\n\nPaper text:\napproximately one in 1,000 children is affected by severe or profound hearing loss at birth or during early childhood , which is defined as pre - lingual deafness ( 1 ) .\nabout one half of childhood hearing loss is thought to have a genetic etiology , the majority of which is non - syndromic and not associated with abnormalities of other organ systems .\nestimates from clinical and epidemiological studies suggest that 80 - 85% of hereditary , non - syndromic , pre - lingual deafness is autosomal recessive ( 1 , 2 ) . pendred syndrome phenotypes are associated with enlargement of the vestibular aqueduct ( eva ) as detected by radiological imaging of the temporal bones ( 3 ) .\nwe present a case of profound sensorineural hearing loss during early childhood with homozygous h723r mutation for slc26a4 associated with bilateral evas .\nthe proband , a 3-yr - old boy , visited our clinic because of poor response to sound after head injury two months ago . after the accident\nhowever , his mother reported he had been able to speak two - word combination and telegraphic sentences before head injury .\nand other findings of physical examination were unremarkable . a sedated auditory brainstem response ( abr ) revealed no identifiable wave v peak at 90 db in both ears . and distortion - product otoacoustic emission ( dpoae ) were absent in both ears .\nto obtain frequency - specific information and to check any residual hearing for fitting hearing aid , auditory steady state response ( assr ) was performed .\ntemporal bone computed tomography showed bilateral eva with no anomaly in the middle and inner ear ( fig .\nwe recommended bilateral fitting of hearing aids and auditory rehabilitation prior to the decision to have cochlear implanation .\neven though he was improved in the detection of sound and language with hearing aid , his performance was not satisfactory to follow the normal course of language development .\nafter 6 months rehabilitation with hearing aids , cochlear implantation was done on his left side .\npreoperatively , repeated abr revealed no identifiable wave at 90 db in the both ears .\nafter 24 months of rehabilitation with bimodal binaural stimulation with ci and hearing aid , the hearing threshold in the free field was 27 db a and the percentage of open - set monosyllabic word recognition was 92% in audio - visual ( av ) condition and 64% in auditory only ( ao ) condition at 55 db a. the genetic study showed h723r heterozygous mutation for all other family members , except the proband who showed h723r homozygous ( fig .\nthyroid function tests were performed to evaluate any possible thyroid dysfunction related with slc26a4 mutation .\nthe thyroid function tests showed thyroid - stimulating hormone ( tsh ) of 1.11 mu / l ( normal range , 0.93 to 1.7 ) , free triiodothyronine ( ft3 ) of 4.0 pg / ml ( normal range , 1.4 to 4.4 ) , free thyroxine ( ft4 ) of 1.84 ng / dl ( normal range , 0.27 to 4.2 ) , and thyroglobulin antigen of 33.6 ng / ml ( normal range , 0 to 70 ) .\nmutations were detected by a combination of intronic polymerase chain reaction ( pcr ) amplification , using primers flanking each exon , and sequencing of the amplification products .\nexons 1 - 21 of the slc26a4 gene were amplified from a genomic dna samples by pcr .\namplification was carried out in a perkin - elmer thermal cycler using the following conditions : 5-min denaturation at 95 , 37 three - step cycles ( 95 for 30 sec , 55 for 1 min , 72 for 1 or 3 min ) , 72 for 10 min , and ending with a holding period at 4. the pcr products were directly sequenced after removal of unincorporated dntps and primers by incubation of 50 - 100 ng pcr product at 37 for 30 min with 0.1 l exonuclease i ( amersham life science , cleveland , usa ) and 1 l shrimp alkaline phosphatase ( american life science ) .\nan aliquot of 6 pmol of either the forward or the reverse primer was used in standard cycle sequencing reactions with abi big dye terminators , and run on an abi 377 sequencer .\nmutations were detected by a combination of intronic polymerase chain reaction ( pcr ) amplification , using primers flanking each exon , and sequencing of the amplification products .\nexons 1 - 21 of the slc26a4 gene were amplified from a genomic dna samples by pcr .\namplification was carried out in a perkin - elmer thermal cycler using the following conditions : 5-min denaturation at 95 , 37 three - step cycles ( 95 for 30 sec , 55 for 1 min , 72 for 1 or 3 min ) , 72 for 10 min , and ending with a holding period at 4. the pcr products were directly sequenced after removal of unincorporated dntps and primers by incubation of 50 - 100 ng pcr product at 37 for 30 min with 0.1 l exonuclease i ( amersham life science , cleveland , usa ) and 1 l shrimp alkaline phosphatase ( american life science ) .\nan aliquot of 6 pmol of either the forward or the reverse primer was used in standard cycle sequencing reactions with abi big dye terminators , and run on an abi 377 sequencer .\noverall , slc26a4 mutations may account for between 5 and 10% of patients with prelingual hearing loss ( 4 ) .\nthe gene is located on chromosome 7q22-q31 and encodes a chloride - iodide transporter that is expressed in the thyroid , inner ear , and kidney .\nthe gene has 21 exons that encode a 780 amino acid protein called pendrin , a 86 kda glycoprotein with 11 or 12 transmembrane domains ( 5 ) .\neach ethnic population has its own distinctive , diverse series of slc26a4 mutant alleles which includes one or a few prevalent founder alleles ( 6 ) . in caucasoid populations , the mutations ivs8\n+ 1g > a , l236p , and t416p account for nearly half of all slc26a4 mutation alleles ( 7 ) .\non the other hand , h723r , ivs7 - 2a > g , and ivs9 + 3a > gare common alleles and account for the majority of slc26a4 mutations in east asian populations ( 6 ) .\nespecially , the mutation h723r accounts for 40% of slc26a4 mutation in korean ( 8) and 53% in japanese patients ( 9 ) and is the most frequently detected mutation in both korean and japanese populations , as a result of a common founder effect ( 6 ) .\nthe frequency of h723r heterozygote detection among normal korean control is reported as 1.6% ( 6 ) .\nthe pendred syndrome is characterized by congenital sensorineural hearing loss and goiter ( 10 ) .\nhowever , the infrequent detection of goiter may reflect reduced diagnostic sensitivity of manual palpation , or the young ages of the probands , considering the tendency for goiter in pendred syndrome to begin around the time of puberty .\nphenotypic variability has also been reported in two families carrying the same pds missense mutation ( 11 ) .\nrecent study reported that some missens pendrin product , hypofunctional slc26a4 alleles , affected transport activity of pendrin ( 12 ) . a modifier gene , hypo - functional slc26a4 variants , or environmental factor ( iodine uptake , nutrition , etc .\nwe successfully performed a cochlear implant on a patient with eva . in the absence of syndromic features to guide genetic diagnosis , a detailed knowledge of the distribution of mutant alleles at specific loci for individual populations is required for more efficient diagnosis .", "role": "user" }, { "content": "recessive mutations of the slc26a4 ( pds ) gene on chromosome 7q31 can cause sensorineural deafness with goiter ( pendred syndrome , omim 274600 ) or nsrd with goiter ( at the dfnb4 locus , omim 600791 ) . \n h723r ( 2168a > g ) is the most commonly reported slc26a4 mutations in korean and japanese and known as founder mutation . \n we recently experienced one patient with enlarged vestibular aqueduct syndrome . \n the genetic study showed h723r homozygous in the proband and h723r heterozygous mutation in his family members . \n the identification of a disease - causing mutation can be used to establish a genotypic diagnosis and provide important information to both families and their physicians .", "role": "assistant" } ]

[ { "content": "You will be presented with a citation segment from the section of an NLP research paper, as well as the context surrounding that citation. Classify the intent behind this citation by choosing from one of the following categories:\n- Background: provides context or foundational information related to the topic.\n- Extends: builds upon the cited work.\n- Uses: applies the methods or findings of the cited work.\n- Motivation: cites the work as inspiration or rationale for the research.\n- CompareOrContrast: compares or contrasts the cited work with others.\n- FutureWork: cites the work as a direction for future research.\n\nYour answer should be a single word from the following list of options: [\"Background\", \"Extends\", \"Uses\", \"Motivation\", \"CompareOrContrast\", \"FutureWork\"]. Do not include any other text in your response.\n\nSection Title:\nNone\n\nContext before the citation:\nFor HMMs (footnote 11), Ti is the familiar trellis, and we would like this computation of ti to reduce to the forwardbackward algorithm (Baum, 1972). • In many cases of interest, Ti is an acyclic graph.20 Then Tar an’s method computes w0j for each j in topologically sorted order, thereby finding ti in a linear number of ⊕ and ⊗ operations. Efficient hardware implementation is also possible via chip-level parallelism (Rote, 1985).\n\nCitation Sentence:\nFor HMMs ( footnote 11 ) , Ti is the familiar trellis , and we would like this computation of ti to reduce to the forwardbackward algorithm ( Baum , 1972 ) .\n\nContext after the citation:\nBut notice that it has no backward pass. In place of pushing cumulative probabilities backward to the arcs, it pushes cumulative arcs (more generally, values in V ) forward to the probabilities. This is slower because our ⊕ and ⊗ are vector operations, and the vectors rapidly lose sparsity as they are added together. We therefore reintroduce a backward pass that lets us avoid ⊕ and ⊗ when computing ti (so they are needed only to construct Ti).", "role": "user" }, { "content": "Background", "role": "assistant" } ]

[ { "content": "You will be presented with a citation sentence from a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\n, 2012), and other studies have indicated that the fornix is affected in Pick’s disease, FTD with tau mutation, or TAR-DNA-binding protein43 type C pathology, but not for FTD caused by a progranulin mutation or with fused-in-sarcoma protein accumulation (Rohrer et al., 2011; Hornberger et al., 2012).", "role": "user" }, { "content": "Result", "role": "assistant" } ]

[ { "content": "You are provided with a research question, keyphrases about the question, a description of candidate datasets and dataset options. Read the description of popular datasets provided below and select the ones that can be used to validate the following research question. Use your knowledge of machine learning datasets to make the best judgement.\nYour response should be formatted as a `json` array. For instance, for the query \"Semi supervised image classification\", a sample response might be: [\"CIFAR-10\", \"CIFAR-100\"]. Do not include any extra text in the response other than the answer array.\n\nQuery: Instance mask projection is an end-to-end trainable operator that projects instance\n\nKeyphrases: semantic segmentation images top-view grid map sequences autonomous driving\n\nDataset description:\nCOCO: The MS COCO (Microsoft Common Objects in Context) dataset is a large-scale object detection, segmentation, key-point detection, and captioning dataset. The dataset consists of 328K images.\nCityscapes: Cityscapes is a large-scale database which focuses on semantic understanding of urban street scenes. It provides semantic, instance-wise, and dense pixel annotations for 30 classes grouped into 8 categories (flat surfaces, humans, vehicles, constructions, objects, nature, sky, and void).\nISBDA: Consists of user-generated aerial videos from social media with annotations of instance-level building damage masks. This provides the first benchmark for quantitative evaluation of models to assess building damage using aerial videos.\nKnowledgeNet: KnowledgeNet is a benchmark dataset for the task of automatically populating a knowledge base (Wikidata) with facts expressed in natural language text on the web. KnowledgeNet provides text exhaustively annotated with facts, thus enabling the holistic end-to-end evaluation of knowledge base population systems as a whole, unlike previous benchmarks that are more suitable for the evaluation of individual subcomponents (e.g., entity linking, relation extraction).\nTHEODORE: Recent work about synthetic indoor datasets from perspective views has shown significant improvements of object detection results with Convolutional Neural Networks(CNNs). In this paper, we introduce THEODORE: a novel, large-scale indoor dataset containing 100,000 high- resolution diversified fisheye images with 14 classes.\nPKU-MMD: The PKU-MMD dataset is a large skeleton-based action detection dataset. It contains 1076 long untrimmed video sequences performed by 66 subjects in three camera views.\n\nOptions:- A: COCO B: Cityscapes C: ISBDA D: KnowledgeNet E: THEODORE F: PKU-MMD", "role": "user" }, { "content": "[\"COCO\", \"Cityscapes\"]", "role": "assistant" } ]

[ { "content": "You will be presented with a citation sentence from a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\nFGF23 induces hypertrophic growth of cardiac myocytes in vitro and LVH in rodents through a direct FGFR-dependent mechanism, but independently of a-klotho, which is not expressed in cardiac myocytes (Faul et al., 2011).", "role": "user" }, { "content": "Background", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Chemical\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\": [\"Arsenic\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nSingle-molecule surface-enhanced Raman spectroscopy: a perspective on the current status. This perspective presents an overview of single-molecule surface-enhanced Raman scattering (sm-SERS). Our overview is organized as a brief theoretical background, discussion of the factors that enhance SERS, various experimental preparations for inserting a single molecule in a hot spot, recent sm-SERS experiments, and a perspective. Although, there have been numerous review papers on sm-SERS, we mainly concentrated on the logical development of sm-SERS on the basis of the fundamental concepts and their physical significance, so that readers outside this field can understand the motivation and the underlying physics when describing current sm-SERS measurements. Indeed, understanding such current sm-SERS experiments conducted by representative groups would be very helpful for readers to answer for themselves the fundamental and practical questions surrounding sm-SERS: (1) what information can sm-SERS provide? (2) Which factors based on the SERS mechanism should be considered to significantly amplify the SERS signal? (3) What kinds of related microscopy techniques could be combined with sm-SERS to attain more meaningful results? (4) Which statistical approaches can be used and how they can be applied to properly analyze sm-SERS data? We hope that this review article can help readers answer these questions.", "role": "user" }, { "content": "{\"Chemical\": []}", "role": "assistant" } ]

[ { "content": "Given a short query with keyphrases about a research idea in 2011 in the domain of artificial intelligence, recommend the relevant datasets to validate the research idea from the options provided. A short description of the datasets is also provided to help you.\n\nQuery: I want to study cancer biology using high-throughput technologies.\n\nKeyphrases: cancer biology gene expression proteomic data\n\nDataset description:\nBreakHis: The Breast Cancer Histopathological Image Classification (BreakHis) is composed of 9,109 microscopic images of breast tumor tissue collected from 82 patients using different magnifying factors (40X, 100X, 200X, and 400X). It contains 2,480 benign and 5,429 malignant samples (700X460 pixels, 3-channel RGB, 8-bit depth in each channel, PNG format).\nBioGRID: BioGRID is a biomedical interaction repository with data compiled through comprehensive curation efforts. The current index is version 4.2.192 and searches 75,868 publications for 1,997,840 protein and genetic interactions, 29,093 chemical interactions and 959,750 post translational modifications from major model organism species.\nNuCLS: The NuCLS dataset contains over 220,000 labeled nuclei from breast cancer images from TCGA. These nuclei were annotated through the collaborative effort of pathologists, pathology residents, and medical students using the Digital Slide Archive.\nSNIPS: The SNIPS Natural Language Understanding benchmark is a dataset of over 16,000 crowdsourced queries distributed among 7 user intents of various complexity: SearchCreativeWork (e.g. Find me the I, Robot television show), GetWeather (e.g.\n\nOptions: A: BreakHis B: BioGRID C: NuCLS D: SNIPS", "role": "user" }, { "content": "BioGRID", "role": "assistant" } ]

[ { "content": "You will be presented with a sentence from biomedical research text. Extract all terms that correspond to chemical entities of biological interest (ChEBI).\nReturn your identified terms in a JSON array, formatted like this: [\"Entity1\", \"Entity2\", ...].\nIf no such entities are detected, respond by providing an empty JSON array [].\n\nBiomedical context:\nAnanimalmodelforMCADdeficiencyisessentialtobetterunderstandthepathogenesisofMCADdeficiencyandtodevelopbettermanagementregimensforhumanpatients.", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Gene\"].\n\nPlease return the output as a JSON object of the format: {\"Gene\": [\"IGF\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nMetalloprotease-disintegrin ADAM12 actively promotes the stem cell-like phenotype in claudin-low breast cancer. BACKGROUND: ADAM12 is upregulated in human breast cancers and is a predictor of chemoresistance in estrogen receptor-negative tumors. ADAM12 is induced during epithelial-to-mesenchymal transition, a feature associated with claudin-low breast tumors, which are enriched in cancer stem cell (CSC) markers. It is currently unknown whether ADAM12 plays an active role in promoting the CSC phenotype in breast cancer cells. METHODS: ADAM12 expression was downregulated in representative claudin-low breast cancer cell lines, SUM159PT and Hs578T, using siRNA transfection or inducible shRNA expression. Cell characteristics commonly associated with the CSC phenotype in vitro (cell migration, invasion, anoikis resistance, mammosphere formation, ALDH activity, and expression of the CD44 and CD24 cell surface markers) and in vivo (tumor formation in mice using limiting dilution transplantation assays) were evaluated. RNA sequencing was performed to identify global gene expression changes after ADAM12 knockdown. RESULTS: We found that sorted SUM159PT cell populations with high ADAM12 levels had elevated expression of CSC markers and an increased ability to form mammospheres. ADAM12 knockdown reduced cell migration and invasion, decreased anoikis resistance, and compromised mammosphere formation. ADAM12 knockdown also diminished ALDEFLUOR(+) and CD44(hi)/CD24(-/lo) CSC-enriched populations in vitro and reduced tumorigenesis in mice in vivo. RNA sequencing identified a significant overlap between ADAM12- and Epidermal Growth Factor Receptor (EGFR)-regulated genes. Consequently, ADAM12 knockdown lowered the basal activation level of EGFR, and this effect was abolished by batimastat, a metalloproteinase inhibitor. Furthermore, incubation of cells with exogenously added EGF prevented the downregulation of CD44(hi)/CD24(-/lo) cell population by ADAM12 knockdown. CONCLUSIONS: These results indicate that ADAM12 actively supports the CSC phenotype in claudin-low breast cancer cells via modulation of the EGFR pathway.", "role": "user" }, { "content": "{\"Gene\": [\"CD44\", \"CD24\", \"Metalloprotease-disintegrin\", \"Epidermal Growth Factor Receptor\", \"claudin\", \"EGFR\", \"ADAM12\", \"estrogen receptor\", \"ALDH\"]}", "role": "assistant" } ]

[ { "content": "You will be shown biomedical passages and your task is to answer the provided question. Provide a concise and accurate response and do not include any additional text in the response other than the answer.\n\nQuestion: Which enzyme is targeted by the drug Imetelstat?\n\nContext: Imetelstat (a telomerase antagonist) exerts off‑target effects on the cytoskeleton.\nimetelstat sodium (GRN163L), is a 13-mer oligonucleotide N3'→P5' thio-phosphoramidate lipid conjugate, which represents the latest generation of telomerase inhibitors targeting the template region of the human functional telomerase RNA (hTR) subunit. In preclinical trials, this compound has been found to inhibit telomerase activity in multiple cancer cell lines, as well as in vivo xenograft mouse models.\nIn addition to the inhibition of telomerase activity in cancer cell lines, GRN163L causes morphological cell rounding changes, independent of hTR expression or telomere length.\nWe sought to evaluate the potential of the thio-phosphoramidate oligonucleotide inhibitor of telomerase, imetelstat, as a drug candidate for treatment of esophageal cancer. Our results showed that imetelstat inhibited telomerase activity in a dose-dependent manner in esophageal cancer cells\nFurthermore, long-term treatment with imetelstat decreased cell growth of esophageal cancer cells with different kinetics regarding telomere lengths\nTelomerase extension is less processive during the first few weeks following the reversal of long-term treatment with the telomerase inhibitor Imetelstat (GRN163L), a time when Cajal bodies fail to deliver telomerase RNA to telomeres.\nThe role of telomerase as an immunotherapy, as a gene therapy approach using telomerase promoter driven oncolytic viruses and as a small oligonucleotide targeted therapy (Imetelstat) will be discussed\nWe then tested the efficacy of the telomerase inhibitor Imetelstat on propagation and self-renewal capacity of TIC and normal stem cells in vitro and in vivo. R\ne telomerase inhibitor imetelstat depletes cancer stem cells in breast and pancreatic cancer cell lines\nIn this study, we investigated the effects of imetelstat (GRN163L), a potent telomerase inhibitor, on both the bulk cancer cells and putative CSCs. When breast and pancreatic cancer cell lines were treated with imetelstat in vitro, telomerase activity in the bulk tumor cells and CSC subpopulations were inhibited.\nTelomerase activity is required for the maintenance of normal adult stem cells, and we examined the activity of the telomerase inhibitor imetelstat against MM CSC.\nHuman MM CSC were isolated from cell lines and primary clinical specimens and treated with imetelstat, a specific inhibitor of the reverse transcriptase activity of telomerase. Two weeks of exposure to imetelstat resulted in a significant reduction in telomere length and the inhibition of clonogenic MM growth both in vitro and in vivo.\nShort oligonucleotide N3'-->P5' thio-phosphoramidate conjugated to 5'-palmitoyl group, designated as GRN163L (Imetelstat), was recently introduced as a potent human telomerase inhibitor\netelstat (GRN163L)--telomerase-based cancer therapy.\nImetelstat (GRN163L) is a potent and specific telomerase inhibitor and so far the only drug of its class in clinical trials.\ne telomerase antagonist, imetelstat, efficiently targets glioblastoma tumor-initiating cells leading to decreased proliferation and tumor growth.\nThe effects of a novel human telomerase antagonist, imetelstat, on primary human glioblastoma (GBM) tumor-initiating cells were investigated in vitro and in vivo.\nImetelstat treatment produced a dose-dependent inhibition of telomerase (IC(50) 0.45 micromol/L). Long-term imetelstat treatment led to progressive telomere shortening, reduced rates of proliferation, and eventually cell death in GBM tumor-initiating cells.\nWe have found that prostate TICs have significant telomerase activity which is inhibited by imetelstat sodium (GRN163L), a new telomerase antagonist that is currently in Phase I/II clinical trials for several hematological and solid tumor malignancies. Prostate TICs telomeres were of similar average length to the telomeres of the main population of cells and significant telomere shortening was detected in prostate TICs as a result of imetelstat treatment.\nTelomerase activation was countered by co-treatment with Imetelstat (GRN163L), a potent telomerase inhibitor.", "role": "user" }, { "content": "Human Telomerase", "role": "assistant" } ]

[ { "content": "Write an abstract for the research paper below. Your response should only include the abstract and no additional text.\n\nArticle text:\nstate - of - the - art quantum technology can trap and experiment with individual atoms , image brains as well as generate structural and dynamical information of biological macromolecules .\nnumerous applications arising from such emerging techniques involve controlling a large quantum ensemble , e.g. , on the order of avogadro number ( @xmath0 ) , by use of the same control field @xcite . in many cases ,\nthe elements of the ensemble show variations in the values of parameters characterizing the system dynamics , and hence the system hamiltonians of different elements of the ensemble are distinct .\nthis phenomenon results in a dispersion in the system dynamics .\nfor example , in magnetic resonance experiments , the spins of an ensemble may have large dispersions in their natural frequencies ( larmor dispersion ) , strength of the applied radio frequency ( rf ) field ( rf inhomogeneity ) , and the dissipation rates of the spins @xcite . in solid state nmr spectroscopy of powder\n, the random distribution of the orientations of internuclear vectors of coupled spins within an ensemble leads to a distribution of coupling strengths @xcite .\na canonical problem among these applications is to develop excitations ( control signals ) that will steer such an ensemble of systems with different dynamics from an initial state to a desired final state in finite time using a time - varying electromagnetic pulse . from the perspective of mathematical control theory\n, this is a very challenging state transfer problem because it requires steering a continuum of dynamical systems between points of interest in an infinite dimensional state space with the same control function .\nthis motivates the study of * ensemble control * and the notion of ensemble controllability @xcite described as follows .\nconsider a parameterized family of control systems @xmath1 where @xmath2 is a smooth function of its arguments and @xmath3 is a compact subset of @xmath4 .\ndifferent values of the parameter @xmath5 in ( [ eq : dxs ] ) correspond distinct members of the ensemble @xmath6 showing variations , but we are constrained to use the same open - loop control @xmath7 to steer the whole ensemble .\nthe existence of such a control raises fundamental questions of _ ensemble controllability_. the formal definition will be given in section [ sec : basics ] . in practice ,\nsuch control designs are called _ compensating pulse sequences _ as they can compensate for or are insensitive to the dispersion in system dynamics .\ntypical applications include the design of excitation and inversion pulses in nmr spectroscopy in the presence of larmor dispersion and rf inhomogeneity @xcite , the transfer of coherence between a coupled spin ensemble with variations in the coupling strengths @xcite , and the construction of slice selective pulses in mri , where some spins of the ensemble are excited or inverted while the others remain unaffected @xcite .\npractical considerations , such as power constraints and signal or information losses due to relaxation effects , make it desirable to construct pulses that achieve a desired level of compensation with minimum energy or in the shortest possible time .\nthese considerations give rise to problems in _ optimal control of ensembles_. these pulse design problems are widely studied in nmr spectroscopy on the subject of composite pulses that correct the dispersion in system dynamics @xcite .\nhowever , a systematic study of the design of compensating pulse sequences has been missing .\nthe research in ensemble control will give explicit answers to the questions of when a compensation for the system dynamics is possible and how , if possible , to achieve the desired level of compensation .\nmore generally , ensemble control provides a framework to devise open - loop controls that are robust to parameter uncertainties , namely , they are insensitive to parameters . in many control applications ,\nan accurate model is not available and systems have unknown parameters .\nthey either have some level of uncertainty or are not deterministic , however , there are instead bounds or distributions that describe these parameters .\nfor example , systems biology models have numerous parameters , such as kinetic constants , which are unknown or only weakly constrained by existing experimental knowledge @xcite . in chaotic dynamics , the problem of parameter uncertainties is unavoidable in synchronizing chaotic systems @xcite . in such scenarios ,\none aims to design controllers that are robust to these parameter uncertainties .\nsubjects on robust control theory and sliding mode control are well studied to design controllers that can control or stabilize such systems using `` feedback '' @xcite .\nwhile effective , these controllers are closed - loop and dependent on measurement of the system state - at times a difficult , or impossible requirement .\nensemble control , rather , provides a systematic framework for the design of open - loop controls that are immune to parameters and robust to uncertainties .\nthis paper is organized as follows . in the following section , we review ensemble control problems and the notion of ensemble controllability .\nwe summarize our previous work of steering an ensemble of systems evolving on so(3 ) to highlight the basics of ensemble control .\nsimple examples of ensemble control of linear systems are addressed to motivate the need of developing ensemble controllability conditions . in section\n[ sec : theory ] , we present our main results of necessary and sufficient controllability conditions for ensemble control of finite - dimensional time - varying linear systems . finally , we study optimal control of an ensemble of harmonic oscillators as a demonstration of our main results as well as provide an insight of how ensemble control framework can be adopted to deal with systems with parameter uncertainties .\nwe show that this system is ensemble controllable and the optimal control of such a system is pertinent to the study of time - frequency limited signals and prolate spheroidal wave functions ( pswf ) .\nwe present both analytical and numerical solutions .\nin this section , we review the basics of the ensemble control and the notion of ensemble controllability @xcite .\nensemble control involves problems of simultaneously manipulating a continuum of dynamical systems with different internal and external dynamics by use of the same open - loop control input .\nthe general form of an ensemble control system is shown as in ( [ eq : dxs ] ) , and standard linear and bilinear ensemble control systems are of the respective forms @xmath8x(t , s).\\end{aligned}\\ ] ] the investigation of what kind of dispersions @xmath5 in the system dynamics can and can not be corrected is a subject of fundamental and practical importance .\nthis raises interesting questions of ensemble controllability .\n[ cols=\"^,^ \" , ] as a result , the model described in ( [ eq : consnew ] ) is a convex optimization problem with a unique global minimum .\nwe solve this problem numerically as a discrete quadratic optimization problem of the form @xmath9 where @xmath10 , @xmath11 , @xmath12 , and @xmath13,\\,\\ , q=\\left[\\begin{array}{c}\\frac{\\sin(t_{1})}{t_{1}}\\\\ \\frac{\\sin(t_{2})}{t_{2}}\\\\ \\vdots\\\\ \\frac{\\sin(t_{n})}{t_{n}}\\end{array}\\right ] , \\nonumber\\end{aligned}\\ ] ] some simulation results of problem [ prob : bounded ] for various values of @xmath14 are shown in figure [ fig : constrained ] , where we assume @xmath15 and @xmath16 .\nwe consider 51 harmonic oscillators ( @xmath17 ) with their frequencies uniformly distributed in @xmath18 $ ] .\nthe optimal control laws with square wave forms are illustrated in figure [ fig : constrained](a ) .\nfigure [ fig : constrained](b ) shows the @xmath19 distance between the final state and the origin of each harmonic oscillator following the corresponding designed control laws .\nin this paper , we studied ensemble control of general time - varying linear systems and derived the necessary and sufficient controllability conditions .\nthe key idea of understanding controllability relies on investigating the solvability of the integral equation associated with the system dynamics , and it is of fredholm equations of the first kind .\nwe highlighted the role of singular systems and spectral theorem in designing ensemble control laws , and an analytical optimal control is provided .\nthe work on computing singular values and eigenfunctions of operators will be pursued .\nanother interesting topic is to characterize the researchable set for the system under the constrained controls , i.e. , @xmath20 .\nwe plan to continue working on extending and generalizing our current results towards the goal of developing a theory of ensemble control .\nwe believe the study of ensemble control problems will foster further developments in control and systems theory with broader applications such as systems with parameter uncertainties as well as system identification .\nlet @xmath26\\times [ 0,t])$ ] be the vector space of all those matrix valued functions @xmath27 whose elements @xmath28 , @xmath29 , @xmath30 , are lebesgue measurable on @xmath31\\times [ 0,t]$ ] and for which @xmath32 with the inner product for @xmath33 defined by @xmath34 @xmath35 is a hilbert space .\n[ lem : basis ] suppose that @xmath43 and @xmath44 are orthonormal bases for @xmath45 and @xmath46 , respectively , and @xmath47 for @xmath48\\times [ 0,t ] , ( i , j)\\in\\mathbb{n}\\times\\mathbb{n}$ ] .\nthen , @xmath49 is an orthonormal basis of @xmath35 .\n_ for @xmath50 , @xmath51 \\left[\\psi_m(s)\\phi_n(t)^{\\dagger}\\right]^{\\dagger } dtds\\\\ & = tr\\int_{s_1}^{s_2}\\psi_j(s)\\left[\\int_0^t\\phi_k(t)^{\\dagger}\\phi_n(t)dt\\right]\\psi_m(s)^{\\dagger}ds\\\\ & = \\delta_{kn}\\left[tr\\int_{s_1}^{s_2}\\psi_j(s)\\psi_m(s)^{\\dagger}ds\\right]\\\\ & = \\delta_{kn}\\left[\\int_{s_1}^{s_2}\\psi_m(s)^{\\dagger}\\psi_j(s)ds\\right]\\\\ & = \\delta_{kn}\\delta_{mj},\\end{aligned}\\ ] ] so that @xmath49 is an orthonormal set in @xmath35 .\nnow , suppose that @xmath52 be such that @xmath53 for all @xmath54 .\ncorresponding to this @xmath55 , let @xmath56 be defined by @xmath57 then , we have for all @xmath54 @xmath58^{\\dagger}dtds\\\\ & = tr\\int_{s_1}^{s_2}\\left[\\int_0^t k(s , t)\\phi_j(t)dt\\right]\\psi_i(s)^{\\dagger}ds\\\\ & = tr\\int_{s_1}^{s_2}(k\\phi_j)\\psi_i(s)^{\\dagger}ds\\\\ & = \\int_{s_1}^{s_2}\\psi_i(s)^{\\dagger}(k\\phi_j)ds\\\\ & = \\\n< \\psi_i , k\\phi_j\\>_{\\h_2}.\\end{aligned}\\ ] ] since @xmath59 is an orthonormal basis of @xmath46 and @xmath60 is an orthonormal basis of @xmath45 , it follows that @xmath61 consequently , @xmath62 a.e . and\nhence @xmath49 is an orthonormal basis for @xmath63 .\n@xmath64 according to lemma [ lem : basis ] , @xmath69 can be represented as @xmath70 .\ndefine @xmath71 then , @xmath72 let @xmath73 be the integral operator defined on @xmath45 by @xmath74 now @xmath73 is a bounded linear operator of finite rank since @xmath75 , and hence @xmath73 is compact\n. by ( [ eq : lbdd ] ) and ( [ eq : h - hn ] ) applied to @xmath76 , @xmath77 this follows @xmath38 is compact by theorem [ thm : compactseq ] .\nnote that the compactness of @xmath38 can also be shown by using the properties of hilbert - schmidt operators @xcite .\n@xmath64 t. e. skinner , t. reiss , b. luy , n. khaneja and s. j. glaser , application of optimal control theory to the design of broadband excitation pulses for high resolution nmr \" , _ j. magn\n8 - 15 , 2003 .", "role": "user" }, { "content": "in this article , we investigate the problem of simultaneously steering an uncountable family of finite dimensional time - varying linear systems . \n we call this class of control problems ensemble control , a notion coming from the study of spin dynamics in nuclear magnetic resonance ( nmr ) spectroscopy and imaging ( mri ) . \n this subject involves controlling a continuum of parameterized dynamical systems with the same open - loop control input . from a viewpoint of mathematical control theory , this class of problems is challenging because it requires steering a continuum of dynamical systems between points of interest in an infinite dimensional state space by use of the same control function . \n the existence of such a control raises fundamental questions of ensemble controllability . \n we derive the necessary and sufficient controllability conditions and an accompanying analytical optimal control law for ensemble control of time - varying linear systems . \n we show that ensemble controllability is in connection with singular values of the operator characterizing the system dynamics . \n in addition , we study the problem of optimal ensemble control of harmonic oscillators to demonstrate our main results . \n we show that the optimal solutions are pertinent to the study of time - frequency limited signals and prolate spheroidal wave functions \n . a systematic study of ensemble control systems has immediate applications to systems with parameter uncertainties as well as to broad areas of quantum control systems as arising in coherent spectroscopy and quantum information processing . \n the new mathematical structures appearing in such problems are an excellent motivation for new developments in control theory . \n time varying ; ensemble control ; nmr ; mri ; lie brackets ; linear operators ;", "role": "assistant" } ]

[ { "content": "You will be shown a claim related to the COVID-19 pandemic, and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\".\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract.\n\nFor instance, if the model were given the claim \"the COVID vaccine is safe for healthy adults\", the output might be:\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that the risks of severe COVID vaccine side effects are low for healthy adults.\"]\n}\n\nClaim: A granulocytic signature identifies covid-19 and its species\n\nAbstract:\nBACKGROUND: An unbiased approach to SARS-CoV-2-induced immune dysregulation has not been undertaken so far.\nWe aimed to identify previously unreported immune markers able to discriminate COVID-19 patients from healthy controls and to predict mild and severe disease.\nMETHODS: An observational, prospective, multicentric study was conducted in patients with confirmed mild/moderate (n = 7) and severe (n = 19) COVID-19.\nImmunophenotyping of whole-blood leukocytes was performed in patients upon hospital ward or intensive care unit admission and in healthy controls (n = 25).\nClinically relevant associations were identified through unsupervised analysis.\nRESULTS: Granulocytic (neutrophil, eosinophil, and basophil) markers were enriched during COVID-19 and discriminated between patients with mild and severe disease.\nIncreased counts of CD15+CD16+ neutrophils, decreased granulocytic expression of integrin CD11b, and Th2-related CRTH2 downregulation in eosinophils and basophils established a COVID-19 signature.\nSeverity was associated with emergence of PD-L1 checkpoint expression in basophils and eosinophils.\nThis granulocytic signature was accompanied by monocyte and lymphocyte immunoparalysis.\nCorrelation with validated clinical scores supported pathophysiological relevance.\nCONCLUSIONS: Phenotypic markers of circulating granulocytes are strong discriminators between infected and uninfected individuals as well as between severity stages.\nCOVID-19 alters the frequency and functional phenotypes of granulocyte subsets with emergence of CRTH2 as a disease biomarker.", "role": "user" }, { "content": "{\"verdict\": \"CONTRADICT\", \"evidence\": [\"Increased counts of CD15+CD16+ neutrophils, decreased granulocytic expression of integrin CD11b, and Th2-related CRTH2 downregulation in eosinophils and basophils established a COVID-19 signature.\"]}", "role": "assistant" } ]

[ { "content": "You will be shown a claim related to the COVID-19 pandemic, and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\".\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract.\n\nFor instance, if the model were given the claim \"the COVID vaccine is safe for healthy adults\", the output might be:\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that the risks of severe COVID vaccine side effects are low for healthy adults.\"]\n}\n\nClaim: Immunal profiling reveals trpm5-expressing cells involved in viral infection in the olfactory epithelium\n\nAbstract:\nBACKGROUND: Understanding viral infection of the olfactory epithelium is essential because the olfactory nerve is an important route of entry for viruses to the central nervous system.\nSpecialized chemosensory epithelial cells that express the transient receptor potential cation channel subfamily M member 5 (TRPM5) are found throughout the airways and intestinal epithelium and are involved in responses to viral infection.\nRESULTS: Herein we performed deep transcriptional profiling of olfactory epithelial cells sorted by flow cytometry based on the expression of mCherry as a marker for olfactory sensory neurons and for eGFP in OMP-H2B::mCherry/TRPM5-eGFP transgenic mice (Mus musculus).\nWe find profuse expression of transcripts involved in inflammation, immunity and viral infection in TRPM5-expressing microvillous cells compared to olfactory sensory neurons.\nCONCLUSION: Our study provides new insights into a potential role for TRPM5-expressing microvillous cells in viral infection of the olfactory epithelium.\nWe find that, as found for solitary chemosensory cells (SCCs) and brush cells in the airway epithelium, and for tuft cells in the intestine, the transcriptome of TRPM5-expressing microvillous cells indicates that they are likely involved in the inflammatory response elicited by viral infection of the olfactory epithelium.\nSUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07528-y.", "role": "user" }, { "content": "{\"verdict\": \"CONTRADICT\", \"evidence\": [\"Specialized chemosensory epithelial cells that express the transient receptor potential cation channel subfamily M member 5 (TRPM5) are found throughout the airways and intestinal epithelium and are involved in responses to viral infection.\"]}", "role": "assistant" } ]

[ { "content": "You will be presented with a collection of medical randomized controlled trial (RCT) reports addressing a shared clinical question -- for instance, the efficacy of a medical intervention on a disease or condition. Given the titles and abstracts of these reports, your task is to generate the conclusion of the systematic review article synthesizing the key findings. Your conclusion should be a few sentences long. In your response, include only the conclusion and no other text. The RCT reports are below.\n\n\n\nTitle 1:\nTooth-color assessment after orthodontic treatment: a prospective clinical trial.\nAbstract 1:\nINTRODUCTION Our aim was to prospect ively assess in-vivo color alterations of natural teeth associated with fixed orthodontic treatment . METHODS Twenty-six consecutive patients were treated with fixed appliances bonded with a chemically cured or a light-cured resin with a split-mouth design . The spectrophotometric data of a st and ardized labial circular area of all teeth were recorded , before bracket bonding and after debonding and cleaning procedures . The color parameters of the Commission Internationale de l'Eclairage-L∗ , a∗ , and b∗ ( lightness , red/green , and blue/yellow)-were measured for each adhesive and type of tooth , and the corresponding color differences ( ΔE ) between the interval groups were calculated . The effect of these parameters on color was assessed with 3-way mixed analysis of variance ( ANOVA ) and the Bonferroni comparisons test ( α < 0.05 ) . RESULTS Orthodontic treatment was associated with changes in color parameters . The L∗ values decreased ( P < 0.001 ) , whereas the a∗ and b∗ values increased ( P < 0.001 ) at the end of treatment . All measured types of teeth demonstrated significant color changes ( ΔE ) ; their mean differences ranged from 2.12 to 3.61 ΔE units . Chemically cured resin was associated with greater color changes than light-cured composite . CONCLUSIONS The color of natural teeth is changed in various ways after fixed orthodontic treatment\n\n\nTitle 2:\nOrthodontic bracket removal using conventional and ultrasonic debonding techniques, enamel loss, and time requirements.\nAbstract 2:\nThe purpose of this study was to examine the effects of ultrasonic orthodontic bracket removal and cleanup and compare them with conventional debonding and cleaning of the enamel surfaces with burs and polishing disks . The amount of enamel loss and time for bracket removal and clean-up were also addressed . Thirty extracted human premolars were collected . The teeth were r and omly placed in one of the three debonding groups : debonding with orthodontic pliers and enamel clean-up with finishing burs and polishing disks ( group 1 ) , debonding with orthodontic pliers and ultrasonic clean-up of the enamel surface ( group 2 ) , and ultrasonic debonding enamel clean-up ( group 3 ) . The teeth were stored for 48 hours in 100 % humidity before bracket removal . All brackets were then removed . Polyvinyl siloxane impressions were made before and after bracket removal . Direct measurements of the teeth in micrometers were made at all steps . An additional 30 teeth were similarly prepared , and the brackets were debonded and cleaned-up as in the three groups previously described . The total time for bracket removal and enamel clean-up for each group was recorded in seconds . ( ABSTRACT TRUNCATED AT 250 WORDS\n\n\nTitle 3:\nEnamel colour changes at debonding and after finishing procedures using five different adhesives.\nAbstract 3:\nThe purpose of this study was to evaluate enamel colour alteration of five different orthodontic bonding adhesives by means of digital measurements after exposure to photoageing in order to simulate discolouration of adhesives in vivo . Seventy-five non-carious premolars were r and omly divided into five equal groups . The brackets were bonded with five different adhesives ( Transbond XT , Eagle Bond , Light Bond , Blugloo , Unite ) and subjected to artificial accelerated photoageing for 24 hours . The enamel surfaces were colourimetrically evaluated before bonding , following debonding and cleaning with a tungsten carbide bur , after polishing with Stainbuster , and after photoageing of the debonded enamel surface . The Commission Internationale de l'Eclairage(CIE ) colour parameters ( L*a*b * ) were recorded and colour differences ( DeltaE ) were calculated . The results were statistically analyzed using the Kruskall-Wallis test . Further investigation among subgroups was performed using Dunn 's multiple correlation test ( P < 0.05 ) . The clinical detection threshold for DeltaE value was set at 3.7 units . DeltaE values between the first and second measurements showed an increase in the Transbond XT , Eagle Bond , and Light Bond groups . The highest DeltaE value was 1.51 + /- 1.15 in the Transbond XT group . No clinical ly significant DeltaE value was observed . Colour changes of orthodontic bonding systems induced by photoageing can not be clinical ly observed . Polishing with Stainbuster eliminates enamel surface roughness , which may improve light reflection", "role": "user" }, { "content": "The studies review ed suggested that orthodontic treatment alters the original color of enamel , and both adhesive systems and resin-removal methods can contribute to this change .\nConclusion There is no strong evidence from this review that orthodontic treatment with fixed appliances alters the original color of enamel .", "role": "assistant" } ]

[ { "content": "You have to answer a biomedical question in binary format, i.e., only yes and no are acceptable answers. A list of paragraphs is provided as context to help you answer the question.\n\nQuestion: Is Pim-1 a protein phosphatase?\n\nContext: Pim-1 proto-oncogene, serine/threonine kinase (PIM-1) phosphorylates a series of substrates to exert its oncogenic function in numerous malignancies.\nThe Pim1 serine/threonine kinase is associated with multiple cellular functions including proliferation, survival, differentiation, apoptosis, tumorigenesis, immune regulation and inflammation in vertebrates.", "role": "user" }, { "content": "no", "role": "assistant" } ]

[ { "content": "You will be shown a question, followed by excerpts from biomedical research papers. Please answer the question based on the provided context. Do not include any text in your response other than the answer.\n\nQuestion: What is known as Calcium Induced Calcium Release (CICR) and its role in cardiomyocyte contractility?\n\nContext: Cardiomyocyte contraction depends on rapid changes in intracellular Ca(2+). In mammals, Ca(2+) influx as L-type Ca(2+) current (ICa) triggers the release of Ca(2+) from sarcoplasmic reticulum (SR) and Ca(2+)-induced Ca(2+) release (CICR) is critical for excitation-contraction coupling.\nRelease of calcium (Ca(2+)) from the sarcoplasmic reticulum (SR) induced by Ca(2+) influx through voltage-dependent sarcolemmal L-type Ca(2+) channels (CICR) in cardiac muscle cells has been implicated as a potential target contributing to anesthetic-induced myocardial depression.\nIt is well known that calcium-induced calcium-release in cardiac myocytes takes place in spatially restricted regions known as dyads, where discrete patches of junctional sarcoplasmic reticulum tightly associate with the t-tubule membrane.\nCalcium (Ca(2+))-induced Ca(2+) release (CICR) is widely accepted as the principal mechanism linking electrical excitation and mechanical contraction in cardiac cells. The CICR mechanism has been understood mainly based on binding of cytosolic Ca(2+) with ryanodine receptors (RyRs) and inducing Ca(2+) release from the sarcoplasmic reticulum (SR).\nWaves of calcium-induced calcium release occur in a variety of cell types and have been implicated in the origin of cardiac arrhythmias.\nCalcium-induced calcium release (CICR) has been observed in cardiac myocytes as elementary calcium release events (calcium sparks) associated with the opening of L-type Ca(2+) channels. In heart cells, a tight coupling between the gating of single L-type Ca(2+) channels and ryanodine receptors (RYRs) underlies calcium release.\nL-type Ca(2+) channels activate RYRs to produce CICR in smooth muscle cells in the form of Ca(2+) sparks and propagated Ca(2+) waves.\nthe importance of Ca-induced Ca release in excitation-contraction coupling in the heart.\nCalcium-induced calcium release (CICR) is an inherently regenerative process due to the Ca(2+)-dependent gating of ryanodine receptors (RyRs) in the sarco/endoplasmic reticulum (SR) and is critical for cardiac excitation-contraction coupling.\nPURPOSE: Release of calcium (Ca(2+)) from the sarcoplasmic reticulum (SR) induced by Ca(2+) influx through voltage-dependent sarcolemmal L-type Ca(2+) channels (CICR) in cardiac muscle cells has been implicated as a potential target contributing to anesthetic-induced myocardial depression.\nThe Ca(2+)-induced Ca(2+) release (CICR) process that governs cardiac contractility is defective in hypertrophy/heart failure, but the molecular mechanisms remain elusive.\nThe Ca(2+)-induced Ca(2+) release (CICR) process that governs cardiac contractility is defective in hypertrophy/heart failure, but the molecular mechanisms remain elusive\nThe majority of contractile calcium in cardiac muscle is released from stores in the sarcoplasmic reticulum (SR), by a process of calcium-induced calcium release (CICR) through ryanodine receptors", "role": "user" }, { "content": "the cicr mechanism has been understood mainly based on binding of cytosolic ca(2+) with ryanodine receptors (ryrs) and inducing ca(2+) release from the sarcoplasmic reticulum (sr). l-type ca(2+) channels activate ryrs to produce cicr in smooth muscle cells in the form of ca(2+) sparks and propagated ca(2+) waves. in heart cells, a tight coupling between the gating of single l-type ca(2+) channels and ryanodine receptors (ryrs) underlies calcium release. the importance of ca-induced ca release in excitation-contraction coupling in the heart. waves of calcium-induced calcium release occur in a variety of cell types and have been implicated in the origin of cardiac arrhythmias. in mammals, ca(2+) influx as l-type ca(2+) current (ica) triggers the release of ca(2+) from sarcoplasmic reticulum (sr) and ca(2+)-induced ca(2+) release (cicr) is critical for excitation-contraction coupling.", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"RNA\", \"CellType\", \"CellLine\", \"Protein\", \"DNA\"].\n\nPlease return the output as a JSON object of the format: {\"DNA\" : [\"TAL1\", ...], \"RNA\": [\"mRNAs\", ...], \"CellLine\": [\"T cells\", ...], \"CellType\": [\"monocytes\", ...], \"Protein\": [\"IL-2\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nThe Epstein-Barr virus latency BamHI-Q promoter is positively regulated by STATs and Zta interference with JAK / STAT activation leads to loss of BamHI-Q promoter activity. In Epstein-Barr virus (EBV) -associated tumors in nonimmunocompromised patients, EBV gene expression is highly restricted. EBV-encoded nuclear antigen (EBNA) -1 is expressed, whereas the immunogenic and proliferative EBNAs are not. This pattern of EBNA expression is generated by usage of the BamHI-Q promoter (Qp). We have determined that the JAK / STAT pathway positively regulates Qp activity. In transient-transfection assays, a Qp-CAT reporter was activated by cotransfected JAK-1 and by treatment of cells with the cytokine IL-6. The ability of Qp to bind signal transducer and activator of transcription (STAT) proteins was directly demonstrated by electrophoretic mobility-shift assay, and mutation of potential STAT-binding sites reduced Qp responsiveness to Janus kinase (JAK) -1. Consistent with a role for STATs in Qp function, Qp using Burkitt 's lymphoma Rael cells and cultured nasopharyngeal carcinoma (NPC) cells contained nuclear STAT protein. We investigated whether the inability to maintain EBV-positive NPC cell lines in culture was related to Qp activity. Passaging of the NPC cell line HK666 led to activation of expression of BZLF1, which encodes Zta and loss of Qp function. Transient expression assays linked Zta expression to the down-regulation of Qp. Cotransfection of Zta reduced Qp activity in reporter assays. This negative regulation required Zta DNA-binding activity. We provide evidence that Zta up-regulation of p53 leads to p53-mediated interference with JAK / STAT activation of Qp. The data imply that JAK / STAT signaling has a role in EBV-associated malignancies.", "role": "user" }, { "content": "{\"CellLine\": [\"Burkitt \\u0027s lymphoma Rael cells\", \"NPC cell line HK666\", \"EBV - positive NPC cell lines\"], \"CellType\": [\"cultured nasopharyngeal carcinoma (NPC) cells\"], \"DNA\": [\"BamHI - Q promoter\", \"Epstein - Barr virus latency BamHI - Q promoter\", \"BZLF1\", \"Qp - CAT reporter\", \"Qp\", \"STAT - binding sites\"], \"Protein\": [\"EBNA\", \"Zta\", \"JAK\", \"p53\", \"EBV - encoded nuclear antigen (EBNA) - 1\", \"IL - 6\", \"signal transducer and activator of transcription (STAT) proteins\", \"/ STAT\", \"STAT protein\", \"EBNAs\", \"JAK - 1\", \"cytokine\", \"Janus kinase (JAK) - 1\", \"STATs\"], \"RNA\": []}", "role": "assistant" } ]

[ { "content": "You will be shown a paragraph from a biomedical research article. Your task is to extract all drug combinations appearing in a specific sentence within the paragraph. Each drug combination should be assigned to one of the following three categories:\n\n- POS: Indicates a positive interaction between the drugs in the combination; for instance, drugs that have an additive or synergistic effect.\n- NEG: Indicates a negative interaction between the drugs in the combination; for instance, combining these drugs might result in adverse side effects, or might reduce their efficacy.\n- COMB: Indicates that the drugs are given in combination, but the type of interaction between the drugs cannot be determined based on the provided context.\n\nPlease format your answer as a JSON array. Each entry in the array should itself be an array formatted as [<drug_1>, <drug_2>, ..., <drug_n>, <category>] where <category> is one of the three categories listed above and <drug_1>, ..., <drug_n> are drug names copied verbatim from the input sentence. Different combinations may involve different numbers of drugs; in other words, the `n` in <drug_n> may vary.\n\nAs an example, the following output describes two extracted drug combinations; one between two drugs, and one between three drugs:\n\n[[\"artesunate\", \"artemether\", \"COMB\"], [\"Nifedipine\", \"Labetalol\", \"Prazosin\", \"POS\"]]\n\nThe paragraph and specific sentence are below. You should only extract relationships expressed in the specific sentence; the paragraph is provided for context.\n\nIn your output, return only the JSON array and no other text. If no drug combinations appear, return an empty array `[]`.\n\nparagraph: Management of Adverse Events Following Treatment With Anti-Programmed Death-1 Agents. : Immune checkpoint inhibitors have emerged as a mainstay of melanoma therapy and are playing an increasingly important role in the treatment of other tumor types. The clinical benefit afforded by these treatments can be accompanied by a unique spectrum of adverse events, called immune-related adverse events (irAEs), which reflect the drug's immune-based mechanism of action. IrAEs typically originate in the skin, gastrointestinal tract, liver, and endocrine system, although other organ systems may also be affected. This article provides an overview of irAEs associated with anti-programmed death-1 (anti-PD-1) antibodies (nivolumab and pembrolizumab) as monotherapy or in combination with anti-cytotoxic T-lymphocyte antigen-4 inhibition (ipilimumab), followed by a discussion of irAEs of special clinical interest based on the potential for morbidity, frequent steroid use, and inpatient admission. We review clinical trial data and provide recommendations on how to manage irAEs associated with anti-PD-1 agents based on clinical experience and established management guidelines. We further illustrate the practical considerations of managing irAEs by presenting three cases of immune-related toxicity in melanoma patients treated with nivolumab or pembrolizumab . A better understanding of the identification and management of irAEs will help inform health care providers about the risks associated with anti-PD-1 treatment, to ensure the safe and appropriate use of these important new treatments. ### Implications For Practice Immune checkpoint inhibitors have demonstrated significant clinical benefit in advanced melanoma and other tumor types. These treatments are associated with immune-related adverse events (irAEs), which most commonly affect the skin and gastrointestinal tract, and, to a lesser extent, the liver, endocrine system, and other organs. This review focuses on the management of irAEs after treatment with anti-programmed death-1 (anti-PD-1) antibodies (nivolumab or pembrolizumab) as monotherapy or in combination with anti-cytotoxic T-lymphocyte antigen-4 inhibition (ipilimumab) in patients with advanced melanoma. A better understanding of the management of irAEs will help ensure the safe and appropriate use of anti-PD-1 agents in melanoma and other tumor types.\n\nsentence: We further illustrate the practical considerations of managing irAEs by presenting three cases of immune-related toxicity in melanoma patients treated with nivolumab or pembrolizumab .", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "You will be shown inclusion or exclusion criteria for a clinical trial. Given these criteria, your task is to extract all unique entities of the following types: [\"Person\", \"Condition\", \"Value\", \"ReferencePoint\", \"Temporal\", \"Qualifier\", \"Observation\", \"Visit\", \"Measurement\", \"Mood\", \"Device\", \"Scope\", \"Negation\", \"Drug\", \"Procedure\", \"Multiplier\"].\n\nPlease return the output as a JSON object of the format: {\"Condition\": [\"breast cancer\", ...], \"Device\": [\"ports\", ...], \"Drug\": [\"Atenolol\", ...], \"Measurement\": [\"blood pressure\", ...], \"Mood\": [\"suspected\", ...], \"Multiplier\": [\"more than two\", ...], \"Negation\": [\"no\", ...], \"Observation\": [\"history\", ...], \"Person\": [\"male\", ...], \"Procedure\": [\"surgery\", ...], \"Qualifier\": [\"severe\", ...], \"ReferencePoint\": [\"enrollment\", ...], \"Scope\": [\"infection\", ...], \"Temporal\": [\"one day\", ...], \"Value\": [\"50%\", ...], \"Visit\": [\"ICU\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nPregnancy and lactation \nPatients with diabetes, Ischemic heart disease (IHD), stroke, malignancy and psychiatric diseases are excluded from study. \nThe patients receiving vitamin supplements or who had clinical evidence for an acute illness, renal dysfunction, thyroid dysfunction, chronic inflammatory diseases, inborn errors of homocysteine, cobalamin or folate metabolism, or any other condition known to interfere with homocysteine metabolism will be excluded \nPatients who are already involved in any other trial. \nPatients not willing to fill consent/ assent form are also excluded from study.", "role": "user" }, { "content": "{\"Condition\": [\"renal dysfunction\", \"inborn errors of folate metabolism\", \"chronic inflammatory diseases\", \"malignancy\", \"thyroid dysfunction\", \"stroke\", \"acute illness\", \"diabetes\", \"condition known to interfere with homocysteine metabolism\", \"lactation\", \"Pregnancy\", \"clinical evidence for an acute illness\", \"inborn errors of homocysteine metabolism\", \"Ischemic heart disease (IHD)\", \"inborn errors of cobalamin metabolism\", \"psychiatric diseases\"], \"Device\": [], \"Drug\": [\"vitamin supplements\"], \"Measurement\": [], \"Mood\": [], \"Multiplier\": [], \"Negation\": [], \"Observation\": [], \"Person\": [], \"Procedure\": [], \"Qualifier\": [], \"ReferencePoint\": [], \"Scope\": [], \"Temporal\": [], \"Value\": [], \"Visit\": []}", "role": "assistant" } ]

[ { "content": "You are provided with the abstract of a scientific paper and the abstracts of the papers it references. Your task is to write a Related Work section for the main paper. This section should concisely summarize and integrate the key points from the cited abstracts, reflecting how they relate to the main paper's contributions and context. In your summary, use numerical citation markers like [1], [2], etc., to refer to the corresponding papers.\n\nMain Abstract:\nWe study computational aspects of three prominent voting rules that use approval ballots to elect multiple winners. These rules are satisfaction approval voting, proportional approval voting, and reweighted approval voting. We first show that computing the winner for proportional approval voting is NP-hard, closing a long standing open problem. As none of the rules are strategyproof, even for dichotomous preferences, we study various strategic aspects of the rules. In particular, we examine the computational complexity of computing a best response for both a single agent and a group of agents. In many settings, we show that it is NP-hard for an agent or agents to compute how best to vote given a fixed set of approval ballots from the other agents.\n\nCited Abstract(s):\n[1]: We consider approval voting elections in which each voter votes for a (possibly empty) set of candidates and the outcome consists of a set of k candidates for some parameter k, e.g., committee elections. We are interested in the min-imax approval voting rule in which the outcome represents a compromise among the voters, in the sense that the maximum distance between the preference of any voter and the outcome is as small as possible. This voting rule has two main drawbacks. First, computing an outcome that minimizes the maximum distance is computationally hard. Furthermore, any algorithm that always returns such an outcome provides incentives to voters to misreport their true preferences. In order to circumvent these drawbacks, we consider approximation algorithms, i.e., algorithms that produce an outcome that approximates the minimax distance for any given instance. Such algorithms can be considered as alternative voting rules. We present a polynomial-time 2-approximation algorithm that uses a natural linear programming relaxation for the underlying optimization problem and deterministically rounds the fractional solution in order to compute the outcome; this result improves upon the previously best known algorithm that has an approximation ratio of 3. We are furthermore interested in approximation algorithms that are resistant to manipulation by (coalitions of) voters, i.e., algorithms that do not motivate voters to misreport their true preferences in order to improve their distance from the outcome. We complement previous results in the literature with new upper and lower bounds on strategyproof and group-strategyproof algorithms.\n\n[2]: A new voting procedure for electing committees, called the minimax procedure, is described. Based on approval balloting, it chooses the committee that minimizes the maximum Hamming distance to voters’ ballots, where these ballots are weighted by their proximity to other voters’ ballots. This minimax outcome may be diametrically opposed to the outcome obtained by aggregating approval votes in the usual manner, which minimizes the sum of the Hamming distances and is called the minisum outcome. The manipulability of these procedures, and their applicability when election outcomes are restricted in various ways, are also investigated.\n\n[3]: CLOSEST STRING is one of the core problems in the field of consensus word analysis with particular importance for computational biology. Given k strings of the same length and a nonnegative integer d , find a center string'' s such that none of the given strings has the Hamming distance greater than d from s . CLOSEST STRING is NP-complete. In biological applications, however, d is usually very small. We show how to solve CLOSEST STRING in linear time for fixed d —the exponential growth in d is bounded by O(dd) . We extend this result to the closely related problems d -MISMATCH and DISTINGUISHING STRING SELECTION. Moreover, we also show that CLOSEST STRING is solvable in linear time when k is fixed and d is arbitrary. In summary, this means that CLOSEST STRING is fixed-parameter tractable with respect to parameter d and with respect to parameter k . Finally, the practical usefulness of our findings is substantiated by some experimental results.", "role": "user" }, { "content": "The Handbook of Approval Voting discusses various approval-based multi-winner rules including @math , @math and @math . Another prominent multi-winner rule in the Handbook is [2] . Each agent's approval ballot and the winning set can be seen as a binary vector. Minimax approval voting selects the set of @math candidates that minimizes the maximum Hamming distance from the submitted ballots. Although minimax approval voting is a natural and elegant rule, showed that computing the winner set is unfortunately NP-hard. Strategic issues and approximation questions for minimax approval voting are covered in [1] and [3] where the problem is known as the closest string problem.''", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Finding\", \"Bacterium\", \"ProfessionalOrOccupationalGroup\", \"InjuryOrPoisoning\", \"Eukaryote\", \"BodySystem\", \"Virus\", \"ResearchActivity\", \"BodySubstance\", \"PopulationGroup\", \"Chemical\", \"AnatomicalStructure\", \"SpatialConcept\", \"HealthCareActivity\", \"Organization\", \"BiomedicalOccupationOrDiscipline\", \"Food\", \"ClinicalAttribute\", \"MedicalDevice\", \"BiologicFunction\", \"IntellectualProduct\"].\n\nPlease return the output as a JSON object of the format: {\"Virus\": [\"HIV\", ...], \"Bacterium\": [\"MRSA\", ...], \"AnatomicalStructure\": [\"Lung\", ...], \"BodySystem\": [\"CNS\", ...], \"BodySubstance\": [\"Serum\", ...], \"Finding\": [\"Headache\", ...], \"InjuryOrPoisoning\": [\"Fracture\", ...], \"BiologicFunction\": [\"Death\", ...], \"HealthCareActivity\": [\"Biopsy\", ...], \"ResearchActivity\": [\"Clinical trial\", ...], \"MedicalDevice\": [\"Lenses\", ...], \"SpatialConcept\": [\"Camps\", ...], \"BiomedicalOccupationOrDiscipline\": [\"Forensic medicine\", ...], \"Organization\": [\"WHO\", ...], \"ProfessionalOrOccupationalGroup\": [\"Provider\", ...], \"PopulationGroup\": [\"Swimmers\", ...], \"Chemical\": [\"Gold\", ...], \"Food\": [\"Rice\", ...], \"IntellectualProduct\": [\"RPAM\", ...], \"ClinicalAttribute\": [\"Biomarker\", ...], \"Eukaryote\": [\"Dogs\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nImmunoassays for riboflavin and flavin mononucleotide using antibodies specific to d-ribitol and d-ribitol-5-phosphate Riboflavin (vitamin B2), a water-soluble vitamin, plays a key role in maintaining human health. Though, numerous methods have been reported for the determination of total riboflavin (TRF) content in foods and biological samples, very few methods are reported for quantifying riboflavin and its coenzymes [flavin mononucleotide (FMN); flavin adenine dinucleotide (FAD)] individually. Recently, we have demonstrated that antibodies specific to d-ribitol and d-ribitol-5-phosphate also recognize riboflavin and FMN, respectively, and not vice-versa. In this study, we have evaluated these two antibodies for the analysis of riboflavin and FMN by indirect competitive ELISA (icELISA) in selected foods and pharmaceuticals. Under the optimal assay conditions, 50% inhibition concentration (IC50) and limit of detection (LOD, IC10) were 3.41ng/mL and 0.02ng/mL for riboflavin, and 7.84ng/mL and 0.24ng/mL for FMN, respectively, with detectable concentration range between 0.1 and 100ng of analytes and <0.1% cross-reactivity with other water-soluble vitamins. The amounts of TRF in food samples, as analyzed by icELISA using ribitol antibody, were 90-95% of the reported values in the literature or label values. Quantification of individual flavins (riboflavin and FMN) from the same food samples showed variation in their values compared to TRF, and were in good agreement with values obtained from HPLC and AOAC methods. Further, spiking and recovery analysis of food samples and pharmaceuticals showed no significant matrix effects. The immunoassays were validated in terms of accuracy and precision using inter- and intra-assays. The immunoassays developed in this study are sensitive and appears feasible for screening a large number of samples in the quantification of riboflavin and FMN in various biological samples, pharmaceuticals and natural / processed foods.", "role": "user" }, { "content": "{\"AnatomicalStructure\": [], \"Bacterium\": [], \"BiologicFunction\": [\"competitive\", \"cross-reactivity\"], \"BiomedicalOccupationOrDiscipline\": [], \"BodySubstance\": [], \"BodySystem\": [], \"Chemical\": [\"pharmaceuticals\", \"FAD\", \"Riboflavin\", \"flavins\", \"flavin mononucleotide\", \"water-soluble vitamin\", \"matrix\", \"TRF\", \"antibodies\", \"vitamin B2\", \"d-ribitol\", \"antibody\", \"coenzymes\", \"d-ribitol-5-phosphate\", \"riboflavin\", \"ribitol\", \"FMN\", \"water-soluble vitamins\", \"flavin adenine dinucleotide\"], \"ClinicalAttribute\": [\"detectable\"], \"Eukaryote\": [\"human\"], \"Finding\": [\"IC10\", \"no significant\"], \"Food\": [\"foods\", \"processed foods\"], \"HealthCareActivity\": [\"determination\", \"intra-assays\", \"ELISA\", \"Immunoassays\", \"total riboflavin (TRF) content\", \"evaluated\", \"icELISA\", \"HPLC\", \"inter-\", \"screening\", \"AOAC\", \"immunoassays\", \"assay\"], \"InjuryOrPoisoning\": [], \"IntellectualProduct\": [\"agreement\", \"reported\", \"literature\", \"methods\"], \"MedicalDevice\": [], \"Organization\": [], \"PopulationGroup\": [], \"ProfessionalOrOccupationalGroup\": [], \"ResearchActivity\": [\"analysis\", \"study\", \"analyzed\"], \"SpatialConcept\": [], \"Virus\": []}", "role": "assistant" } ]

[ { "content": "Below are the Abstract, Introduction, and Conclusion sections of a computer science research paper. Please summarize the main contribution of the work in a single sentence. Your response should include the summary sentence and no additional text.\n\nPaper text:\n\nWe investigate multi-task learning approaches which use a shared feature representation for all tasks.\nTo better understand the transfer of task information, we study an architecture with a shared module for all tasks and a separate output module for each task.\nWe study the theory of this setting on linear and ReLU-activated models.\nOur key observation is that whether or not tasks' data are well-aligned can significantly affect the performance of multi-task learning.\nWe show that misalignment between task data can cause negative transfer (or hurt performance) and provide sufficient conditions for positive transfer.\nInspired by the theoretical insights, we show that aligning tasks' embedding layers leads to performance gains for multi-task training and transfer learning on the GLUE benchmark and sentiment analysis tasks; for example, we obtained a 2.35% GLUE score average improvement on 5 GLUE tasks over BERT LARGE using our alignment method.\nWe also design an SVD-based task re-weighting scheme and show that it improves the robustness of multi-task training on a multi-label image dataset.\nMulti-task learning has recently emerged as a powerful paradigm in deep learning to obtain language (Devlin et al. (2018) ; Liu et al. (2019a; b) ) and visual representations (Kokkinos (2017) ) from large-scale data.\nBy leveraging supervised data from related tasks, multi-task learning approaches reduce the expensive cost of curating the massive per-task training data sets needed by deep learning methods and provide a shared representation which is also more efficient for learning over multiple tasks.\nWhile in some cases, great improvements have been reported compared to single-task learning (McCann et al. (2018) ), practitioners have also observed problematic outcomes, where the performances of certain tasks have decreased due to task interference (Alonso and Plank (2016) ; Bingel and Søgaard (2017) ).\nPredicting when and for which tasks this occurs is a challenge exacerbated by the lack of analytic tools.\nIn this work, we investigate key components to determine whether tasks interfere constructively or destructively from theoretical and empirical perspectives.\nBased on these insights, we develop methods to improve the effectiveness and robustness of multi-task training.\nThere has been a large body of algorithmic and theoretical studies for kernel-based multi-task learning, but less is known for neural networks.\nThe conceptual message from the earlier work (Baxter (2000) ; Evgeniou and Pontil (2004) ; Micchelli and Pontil (2005) ; Xue et al. (2007) ) show that multi-task learning is effective over \"similar\" tasks, where the notion of similarity is based on the single-task models (e.g. decision boundaries are close).\nThe work on structural correspondence learning (Ando and Zhang (2005) ; Blitzer et al. (2006) ) uses alternating minimization to learn a shared parameter and separate task parameters.\nZhang and Yeung (2014) use a parameter vector for each task and learn task relationships via l 2 regularization, which implicitly controls the capacity of the model.\nThese results are difficult to apply to neural networks: it is unclear how to reason about neural networks whose feature space is given by layer-wise embeddings.\nTo determine whether two tasks interfere constructively or destructively, we investigate an architecture with a shared module for all tasks and a separate output module for each task (Ruder (2017) ).\nSee Figure 1 for an illustration.\nOur motivating observation is that in addition to model similarity which affects the type of interference, task data similarity plays a second-order effect after controlling model similarity.\nTo illustrate the idea, we consider three tasks with the same number of data samples where task 2 and 3 have the same decision boundary but different data distributions (see Figure 2 for an illustration).\nWe observe that training task 1 with task 2 or task 3 can either improve or hurt task 1's performance, depending on the amount of contributing data along the decision boundary!\nThis observation shows that by measuring the similarities of the task data and the models separately, we can analyze the interference of tasks and attribute the cause more precisely.\nMotivated by the above observation, we study the theory of multi-task learning through the shared module in linear and ReLU-activated settings.\nOur theoretical contribution involves three components: the capacity of the shared module, task covariance, and the per-task weight of the training procedure.\nThe capacity plays a fundamental role because, if the shared module's capacity is too large, there is no interference between tasks; if it is too small, there can be destructive interference.\nThen, we show how to determine interference by proposing a more fine-grained notion called task covariance which can be used to measure the alignment of task data.\nBy varying task covariances, we observe both positive and negative transfers from one task to another!\nWe then provide sufficient conditions which guarantee that one task can transfer positively to another task, provided with sufficiently many data points from the contributor task.\nFinally, we study how to assign per-task weights for settings where different tasks share the same data but have different labels.\nOur theory leads to the design of two algorithms with practical interest.\nFirst, we propose to align the covariances of the task embedding layers and present empirical evaluations on well-known benchmarks and tasks.\nOn 5 tasks from the General Language Understanding Evaluation (GLUE) benchmark (Wang et al. (2018b) ) trained with the BERT LARGE model by Devlin et al. (2018) , our method improves the result of BERT LARGE by a 2.35% average GLUE score, which is the standard metric for the benchmark.\nFurther, we show that our method is applicable to transfer learning settings; we observe up to 2.5% higher accuracy by transferring between six sentiment analysis tasks using the LSTM model of Lei et al. (2018) .\nSecond, we propose an SVD-based task reweighting scheme to improve multi-task training for settings where different tasks have the same data but different labels.\nOn the ChestX-ray14 image classification dataset, we compare our method to the unweighted scheme and observe an improvement of 5.6 AUC score for all tasks.\nIn conclusion, these evaluations confirm that our theoretical insights are applicable to a broad range of settings and applications.\nIn this work, we studied the theory of multi-task learning in linear and ReLU-activated settings.\nWe verified our theory and its practical implications through extensive synthetic and real world experiments.\nOur work opens up many interesting future questions.\nFirst, could we extend the guarantees for choosing optimization schemes to non-linear settings?\nSecond, a limitation of our SVD-based optimization scheduler is that it only applies to settings with the same data.\nCould we extend the method for heterogeneous task data?\nMore broadly, we hope our work inspires further studies to better understand multi-task learning in neural networks and to guide its practice.\nHard parameter sharing vs soft parameter sharing.\nThe architecture that we study in this work is also known as the hard parameter sharing architecture.\nThere is another kind of architecture called soft parameter sharing.\nThe idea is that each task has its own parameters and modules.\nThe relationships between these parameters are regularized in order to encourage the parameters to be similar.\nOther architectures that have been studied before include the work of Misra et al. (2016), where the authors explore trainable architectures for convolutional neural networks.\nDomain adaptation.\nAnother closely related line of work is on domain adaptation.\nThe acute reader may notice the similarity between our study in Section 2.3 and domain adaptation.\nThe crucial difference here is that we are minimizing the multi-task learning objective, whereas in domain adaptation the objective is typically to minimize the objective on the target task.\nSee Ben", "role": "user" }, { "content": "A Theoretical Study of Multi-Task Learning with Practical Implications for Improving Multi-Task Training and Transfer Learning", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Chemical\", \"Disease\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\": [\"Naloxone\", ...], \"Disease\": [\"Hypotensive\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nKetamine sedation for the reduction of children's fractures in the emergency department. BACKGROUND: There recently has been a resurgence in the utilization of ketamine, a unique anesthetic, for emergency-department procedures requiring sedation. The purpose of the present study was to examine the safety and efficacy of ketamine for sedation in the treatment of children's fractures in the emergency department. METHODS: One hundred and fourteen children (average age, 5.3 years; range, twelve months to ten years and ten months) who underwent closed reduction of an isolated fracture or dislocation in the emergency department at a level-I trauma center were prospectively evaluated. Ketamine hydrochloride was administered intravenously (at a dose of two milligrams per kilogram of body weight) in ninety-nine of the patients and intramuscularly (at a dose of four milligrams per kilogram of body weight) in the other fifteen. A board-certified emergency physician skilled in airway management supervised administration of the anesthetic, and the patients were monitored by a registered nurse. Any pain during the reduction was rated by the orthopaedic surgeon treating the patient according to the Children's Hospital of Eastern Ontario Pain Scale (CHEOPS). RESULTS: The average time from intravenous administration of ketamine to manipulation of the fracture or dislocation was one minute and thirty-six seconds (range, twenty seconds to five minutes), and the average time from intramuscular administration to manipulation was four minutes and forty-two seconds (range, sixty seconds to fifteen minutes). The average score according to the Children's Hospital of Eastern Ontario Pain Scale was 6.4 points (range, 5 to 10 points), reflecting minimal or no pain during fracture reduction. Adequate fracture reduction was obtained in 111 of the children. Ninety-nine percent (sixty-eight) of the sixty-nine parents present during the reduction were pleased with the sedation and would allow it to be used again in a similar situation. Patency of the airway and independent respiration were maintained in all of the patients. Blood pressure and heart rate remained stable. Minor side effects included nausea (thirteen patients), emesis (eight of the thirteen patients with nausea), clumsiness (evident as ataxic movements in ten patients), and dysphoric reaction (one patient). No long-term sequelae were noted, and no patients had hallucinations or nightmares. CONCLUSIONS: Ketamine reliably, safely, and quickly provided adequate sedation to effectively facilitate the reduction of children's fractures in the emergency department at our institution. Ketamine should only be used in an environment such as the emergency department, where proper one-on-one monitoring is used and board-certified physicians skilled in airway management are directly involved in the care of the patient.", "role": "user" }, { "content": "{\"Chemical\": [\"ketamine\", \"Ketamine\", \"Ketamine hydrochloride\"], \"Disease\": [\"fracture\", \"clumsiness\", \"hallucinations\", \"fractures\", \"ataxic movements\", \"emesis\", \"dysphoric reaction\", \"trauma\", \"pain\", \"dislocation\", \"nausea\", \"Pain\"]}", "role": "assistant" } ]

[ { "content": "You will be presented with a citation sentence from a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\nIn patients with insulin resistance, production of NH3 from proximal tubules is reduced and ammonia excretion is also reduced accordingly, resulting in low urine pH.[27] In addition, in patients with insulin resistance, sodium absorption is increased because of hyperinsulinemia, which also lowers urine pH.", "role": "user" }, { "content": "Background", "role": "assistant" } ]

[ { "content": "You will be shown a question, followed by excerpts from biomedical research papers. Please answer the question based on the provided context. Do not include any text in your response other than the answer.\n\nQuestion: What is the function of emergency granulopoiesis?\n\nContext: During 'emergency' situations such as infections, host defense requires rapid mobilization of bone marrow granulocyte progenitors\nThese data suggest a critical function for C/EBPbeta in emergency granulopoiesis, which demands both differentiation and proliferation of granulocyte precursors.\nEmergency granulopoiesis promotes neutrophil-dendritic cell encounters that prevent mouse lung allograft acceptance\nOur findings identify granulopoiesis-mediated augmentation of alloimmunity as a novel link between innate and adaptive immune responses after organ transplantation.\nGranulopoiesis is tightly regulated to meet host demands during both \"steady-state\" and \"emergency\" situations, such as infections\nAfter the induction of candidemia, rapid mobilization of mature granulocytes and an increase in early granulocyte precursors accompanied by cell cycle acceleration was followed by a gradual increase in granulocytes originating from the immature populations\nEmergency granulopoiesis is a component of the innate immune response that is induced in response to infectious or inflammatory challenge.\nFailed emergency granulopoiesis in Fancc(-/-) mice was associated with excess apoptosis of HSCs and progenitor cells in the bone marrow and impaired HSC function.\nSystemic bacterial infection induces a hematopoietic response program termed \"emergency granulopoiesis\" that is characterized by increased de novo bone marrow (BM) neutrophil production\nOur studies demonstrate a previously undescribed role for HoxA10 in terminating emergency granulopoiesis, suggesting an important contribution by Hox proteins to the innate immune response.\nHowever, if microbial infection cannot be controlled locally, and consequently develops into a life-threatening condition, neutrophils are used up in large quantities and the haematopoietic system has to rapidly adapt to the increased demand by switching from steady-state to emergency granulopoiesis.\nThis involves the markedly increased de novo production of neutrophils, which results from enhanced myeloid precursor cell proliferation in the bone marrow\nEmergency granulopoiesis refers to the increased production of neutrophils in bone marrow and their release into circulation induced by severe infection.\nEmergency granulopoiesis is a very important strategy to supply efficient neutrophil number in response to infection.\nWe previously showed that C/EBPβ, which is a transcription factor required for emergency granulopoiesis, plays a pivotal role at the level of hematopoietic stem/progenitor cells under stress conditions.\nIn fact, emergency granulopoiesis (EG), a process regulating neutrophil homeostasis in inflammatory conditions and infections, may occur improperly in leukemic conditions, leading to reduced neutrophil counts.\nInterferon consensus sequence-binding protein (Icsbp) is required for terminating emergency granulopoiesis, an episodic event responsible for granulocyte production in response to infections and a key component of the innate immune response\nGranulocyte colony-stimulating factor (G-CSF) mediates \"emergency\" granulopoiesis during infection, a process that is mimicked by clinical G-CSF use, yet we understand little about the intracellular signaling cascades that control demand-driven neutrophil production.\nIn addition, embryos, where pax9 was functionally disrupted by injecting morpholinos, failed to increase the number of neutrophils in response to pathogenic bacteria, suggesting that Pax9 is not only essential for developmental granulopoiesis but also emergency granulopoiesis.\nEmergency granulopoiesis is a hematopoietic program of stem cell-driven neutrophil production used to counteract immune cell exhaustion following infection.\nInfections and inflammation trigger neutrophilias that are supported by a hematopoietic program of accelerated granulopoiesis known as emergency granulopoiesis\nEmergency granulopoiesis is the enhanced production of neutrophils by hematopoietic stem and progenitor cells (HSPCs) upon infection and is widely considered a homoeostatic mechanism for replacing exhausted leukocytes.\nWe show that stem cell-driven neutrophil production occurs in response to Shigella infection and requires macrophage-independent signaling by granulocyte colony-stimulating factor (Gcsf).\nEmergency granulopoiesis promotes neutrophil-dendritic cell encounters that prevent mouse lung allograft acceptance.", "role": "user" }, { "content": "Emergency granulopoiesis refers to the increased production of neutrophils in bone marrow and their release into circulation induced by severe infection. Emergency granulopoiesis is a component of the innate immune response that is induced in response to infectious or inflammatory challenge. During 'emergency' situations such as infections, host defense requires rapid mobilization of bone marrow granulocyte progenitors.", "role": "assistant" } ]

[ { "content": "You are provided with a research question, keyphrases about the question, a description of candidate datasets and dataset options. Read the description of popular datasets provided below and select the ones that can be used to validate the following research question. Use your knowledge of machine learning datasets to make the best judgement.\nYour response should be formatted as a `json` array. For instance, for the query \"Semi supervised image classification\", a sample response might be: [\"CIFAR-10\", \"CIFAR-100\"]. Do not include any extra text in the response other than the answer array.\n\nQuery: A method for retinal vessel segmentation.\n\nKeyphrases: retinal vessel segmentation images\n\nDataset description:\nSTARE: The STARE (Structured Analysis of the Retina) dataset is a dataset for retinal vessel segmentation. It contains 20 equal-sized (700×605) color fundus images.\nORVS: The ORVS dataset has been newly established as a collaboration between the computer science and visual-science departments at the University of Calgary. This dataset contains 49 images (42 training and seven testing images) collected from a clinic in Calgary-Canada.\nROSE: Retinal OCTA SEgmentation dataset (ROSE) consists of 229 OCTA images with vessel annotations at either centerline-level or pixel level.\nDRIVE: The Digital Retinal Images for Vessel Extraction (DRIVE) dataset is a dataset for retinal vessel segmentation. It consists of a total of JPEG 40 color fundus images; including 7 abnormal pathology cases.\nCHASE_DB1: CHASE_DB1 is a dataset for retinal vessel segmentation which contains 28 color retina images with the size of 999×960 pixels which are collected from both left and right eyes of 14 school children. Each image is annotated by two independent human experts.\n\nOptions:- A: STARE B: ORVS C: ROSE D: DRIVE E: CHASE_DB1", "role": "user" }, { "content": "[\"STARE\", \"DRIVE\"]", "role": "assistant" } ]

[ { "content": "You have to answer a biomedical question in binary format, i.e., only yes and no are acceptable answers. A list of paragraphs is provided as context to help you answer the question.\n\nQuestion: Does epidural anesthesia for pain management during labor affect the Apgar score of the the infant?\n\nContext: We retrospectively analyzed 93 consecutive single-pregnancy patients who underwent cesarean section with combined spinal-epidural anesthesia. The patients were divided into two groups, depending on the use of 6% HES 130/0.4: group A (461 ± 167 ml of saline-based HES was administered; 43 patients) and group B (HES not administered; 50 patients). The major outcome was umbilical cord chloride level at delivery. The volume infused from operating room admission until delivery was not significantly different between groups. The umbilical cord chloride level at delivery was statistically significantly higher in group A than in group B, but clinically similar (108 ± 2 vs. 107 ± 2 mmol/l, P = 0.02). No differences were observed in the Apgar score or other umbilical cord laboratory data at delivery (Na+, K+, pH, base excess)\nCONCLUSION Subarachnoid or epidural sufentanil, in the doses used in this study, associated with local anesthetics, had the same effect on the duration of labor after analgesia and in the Apgar score of newborns.\nCONCLUSION Subarachnoid or epidural sufentanil, in the doses used in this study, associated with local anesthetics, had the same effect on the duration of labor after analgesia and in the Apgar score of newborns.", "role": "user" }, { "content": "no", "role": "assistant" } ]

[ { "content": "You will be presented with a citation sentence from a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\nby the ICMJE [16], and none limited inclusion to trials completed after the 2007 U.", "role": "user" }, { "content": "Method", "role": "assistant" } ]

[ { "content": "You are provided with a research question, keyphrases about the question, a description of candidate datasets and dataset options. Read the description of popular datasets provided below and select the ones that can be used to validate the following research question. Use your knowledge of machine learning datasets to make the best judgement.\nYour response should be formatted as a `json` array. For instance, for the query \"Semi supervised image classification\", a sample response might be: [\"CIFAR-10\", \"CIFAR-100\"]. Do not include any extra text in the response other than the answer array.\n\nQuery: I want to train a method that predicts the age of an image with high accuracy.\n\nKeyphrases: age estimation images\n\nDataset description:\nMORPH: MORPH is a facial age estimation dataset, which contains 55,134 facial images of 13,617 subjects ranging from 16 to 77 years old.\nAbalone: Predicting the age of abalone from physical measurements. The age of abalone is determined by cutting the shell through the cone, staining it, and counting the number of rings through a microscope -- a boring and time-consuming task.\nCOVERAGE: COVERAGE contains copymove forged (CMFD) images and their originals with similar but genuine objects (SGOs). COVERAGE is designed to highlight and address tamper detection ambiguity of popular methods, caused by self-similarity within natural images.\nI-HAZE: The I-Haze dataset contains 25 indoor hazy images (size 2833×4657 pixels) training. It has 5 hazy images for validation along with their corresponding ground truth images.\nCelebA: CelebFaces Attributes dataset contains 202,599 face images of the size 178×218 from 10,177 celebrities, each annotated with 40 binary labels indicating facial attributes like hair color, gender and age.\nACDC: The goal of the Automated Cardiac Diagnosis Challenge (ACDC) challenge is to: compare the performance of automatic methods on the segmentation of the left ventricular endocardium and epicardium as the right ventricular endocardium for both end diastolic and end systolic phase instances; compare the performance of automatic methods for the classification of the examinations in five classes (normal case, heart failure with infarction, dilated cardiomyopathy, hypertrophic cardiomyopathy, abnormal right ventricle). The overall ACDC dataset was created from real clinical exams acquired at the University Hospital of Dijon.\n\nOptions:- A: MORPH B: Abalone C: COVERAGE D: I-HAZE E: CelebA F: ACDC", "role": "user" }, { "content": "[\"MORPH\", \"CelebA\"]", "role": "assistant" } ]

[ { "content": "You will be shown a claim about public health and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\". If the abstract does not provide enough information to arrive at a verdict, write \"NEI\" (for \"not enough information\").\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract. If the verdict was \"NEI\", then return an empty array.\n\nFor instance, if the model were given the claim \"wearing masks can prevent the spread of COVID\", the output might be:\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that mass mask-wearing reduces the transmission rate for COVID-19.\"]\n}\n\nClaim: Can you boost your immune system to fight COVID-19? This is the question on everyone's mind as we face a worldwide crisis.\n\nAbstract:\nThe WHO has declared SARS-CoV-2 outbreak a public health emergency of international concern.\nHowever, to date, there was hardly any study in characterizing the immune responses, especially adaptive immune responses to SARS-CoV-2 infection.\nIn this study, we collected blood from COVID-19 patients who have recently become virus-free and therefore were discharged, and analyzed their SARS-CoV-2-specific antibody and T cell responses.\nWe observed SARS-CoV-2-specific humoral and cellular immunity in the patients.\nBoth were detected in newly discharged patients, suggesting both participate in immune-mediated protection to viral infection.\nHowever, follow-up patients (2 weeks post discharge) exhibited high titers of IgG antibodies, but with low levels of virus-specific T cells, suggesting that they may enter a quiescent state.\nOur work has thus provided a basis for further analysis of protective immunity to SARS-CoV-2, and understanding the pathogenesis of COVID-19, especially in the severe cases.\nIt has also implications in designing an effective vaccine to protect and treat SARS-CoV-2 infection.", "role": "user" }, { "content": "{\"verdict\": \"NEI\", \"evidence\": []}", "role": "assistant" } ]

[ { "content": "Write an abstract for the research paper below. Your response should only include the abstract and no additional text.\n\nArticle text:\nin this paper we are concerned with _ perfect forms _ , which are _ real positive definite quadratic forms _ @xmath4 = \\sum_{i , j=1}^d q_{ij } x_i x_j\\ ] ] in @xmath0 variables @xmath5 , determined uniquely by their _\narithmetical minimum _ @xmath6\\ ] ] and _ its representations _ @xmath7 = \\lambda(q ) \\}.\\ ] ] the study of perfect forms goes back to the work of korkin and zolotarev @xcite .\nthey observed that perfection is necessary for positive definite quadratic forms in order to give a local maximum of the _ hermite invariant _\n@xmath8 such forms are called _\nextreme_. as briefly reviewed in section [ sec : quadforms ] , finding the global maximum of the hermite invariant , or equivalently the densest lattice sphere packing is a widely studied problem . in this article\nwe describe the only known algorithmic solution of this problem which works in principle in every dimension .\nit is based on the classification respectively enumeration of perfect forms .\nwe refer to @xcite , @xcite , @xcite , @xcite and @xcite for further reading . based on perfect forms , voronoi @xcite developed a polyhedral reduction theory , which was later found to have several applications in other contexts .\nit has for example been used for compactification of moduli spaces ( cf .\nfor example @xcite , @xcite , @xcite ) , for computing the cohomology of @xmath9 and of congruence subgroups , as well as for computing algebraic @xmath10-groups @xmath11 for small @xmath0 and up to small torsion ( cf .\n@xcite , @xcite and the appendix in @xcite ) .\na basic task in these computations is the enumeration of perfect forms . in some of the applications it is also necessary to understand more of the structure of the _ ryshkov polyhedron _ ( to be defined in section [ sec : ryshkov ] ) whose vertices are perfect forms . in this article\nwe explain voronoi s theory based on the ryshkov polyhedron .\nwe provide complete proofs for all of its required properties .\nwe think that this view is more accessible than the usual dual viewpoint , originally taken by voronoi and by most other authors subsequently .\nvoronoi s algorithm can be simply described as a traversal search on the graph consisting of vertices and edges of the ryshkov polyhedron .\nthis viewpoint allows in particular a very simple and direct generalization to so called @xmath1-perfect forms : intersecting a linear subspace @xmath1 with the ryshkov polyhedron yields a lower dimensional ryshkov polyhedron whose vertices are @xmath1-perfect forms .\nvoronoi s theory immediately generalizes .\nthe article is organized as follows . in section [ sec : quadforms ] we review some necessary background and notations . in section\n[ sec : ryshkov ] we define the ryshkov polyhedron and prove that it is `` locally finite '' .\nthis yields the grounds for voronoi s algorithm to be described in section [ sec : voronoi ] .\nhere we put special emphasis on practical issues related to running voronoi s algorithm on a computer . in section [ sec : extremality ] we briefly explain how to determine extreme forms .\nsection [ sec : symmetries ] contains some informations on automorphism groups and their computation and in section [ sec : tperfect ] we explain the `` @xmath1-theory '' , when restricting to a linear subspace @xmath1 . as examples of linear subspaces that contain forms invariant with respect to a finite group of automorphisms , we consider in section [ sec : examples ] forms with a _ gaussian _ , _ eisenstein _ or _ hurwitz quaternionic _ structure .\nwe obtain several new classification results .\nin this section we review basically from scratch some of the historical background and notations used in the remaining of the article .\nthe reader familiar with most of this background may simply skip this section .\nwe consider real quadratic forms in @xmath0 variables as in , hence with coefficients @xmath12 . by assuming @xmath13 without loss of generality\n, we simply identify the quadratic form @xmath14 with the real symmetric matrix @xmath15 .\nthe space of all real quadratic forms in @xmath0 variables is identified with the space [ not : sd ] @xmath16 of real symmetric @xmath17 matrices . using matrix notation we have @xmath18 = { x}^t q { x}$ ] .\nendowed with the inner product @xmath19 @xmath20 becomes a @xmath21-dimensional euclidean space .\ntwo quadratic forms @xmath22 are called _ arithmetically ( or integrally ) equivalent _ , if there exists a matrix @xmath23 in the group @xmath24 such that @xmath25 note that @xmath26= q'[{\\mathbb z}^d]$ ] for arithmetical equivalent @xmath14 and @xmath27 , but the opposite may not hold .\na quadratic form @xmath28 is _ positive definite _ , if @xmath18>0 $ ] for all @xmath29 .\nthe set of all positive definite quadratic forms ( pqfs from now on ) is denoted by @xmath30 .\nit is not hard to see that @xmath30 is an open ( full dimensional ) _ convex cone _ in @xmath20 with apex @xmath31 . in particular for @xmath32 , the _ open ray _\n@xmath33 is contained in @xmath30 as well .\nonly for pqfs the arithmetical minimum defined in is greater than @xmath31 .\na pqf @xmath14 defines a real valued strictly convex function on @xmath34 and for @xmath35 @xmath36 \\leq \\lambda \\}\\ ] ] is a non - empty _ ellipsoid _ with center @xmath37 , providing a geometric interpretation of a pqf .\nthe arithmetical minimum is the smallest number @xmath35 for which the ellipsoid @xmath38 contains an integral point aside of @xmath37 .\nthe integral points @xmath39 in @xmath40 ( see ) lie on the boundary of the ellipsoid @xmath41 .\nhermite , who initiated the systematic arithmetic study of quadratic forms in @xmath0 variables found in particular an upper bound of the arithmetical minimum in terms of the _ determinant _ @xmath42 of @xmath14 : [ thm : hermite ] @xmath43 hermite s theorem implies in particular the existence of _\nhermite s constant _\n@xmath44 hermite s constant and generalizations have been extensively studied , e.g. in the context of algebraic number theory and differential geometry .\nwe refer to @xcite , @xcite , @xcite and @xcite for further reading .\nthe following _ lattice sphere packing _ interpretation is due to minkowski : using a _ cholesky decomposition _\n@xmath45 of a pqf @xmath14 , with @xmath46 , the set @xmath47 is a _ ( point ) lattice _ , that is , a discrete subgroup of @xmath34 .\nthe column vectors of the matrix @xmath48 are referred to as a _ basis _ of\nthe maximum radius of non overlapping solid spheres around lattice points of @xmath49 is @xmath50 the so called _ packing radius _ of @xmath49 . denoting the solid _ unit sphere _ by @xmath51 ,\nthe _ sphere packing density _ @xmath52 of a lattice @xmath49 is defined as the portion of space covered by solid spheres of radius @xmath53 , hence @xmath54 note that @xmath55 is invariant with respect to isometries and scalings of the lattice @xmath49 .\nthe supremum of possible lattice packing densities @xmath56 is , up to a constant factor , equal to a power of hermite s constant .\ntable [ tab : sphere - packing - results ] lists the dimensions in which @xmath56 respectively hermite s constant @xmath57 is known .\n.known values of hermite s constant .\n[ cols=\"^,^,^,^,^\",options=\"header \" , ] the situation becomes more interesting in dimension @xmath3 ( cf .\ntable [ tab : hurwitz ] ) . by our computations , there are precisely eight classes of @xmath58-perfect forms , as previously observed by jaquet - chiffelle and sigrist ( cf .\n@xcite ) . figure [ fig : hurwitz ] uses their labeling .\nthe data of our computations can be obtained from our webpage . or @xmath3 .\n] note that all @xmath58-perfect forms are also perfect in the classical sense . a quite interesting consequence of the classification in dimension @xmath3 is the possibility to derive of a sharp bound for the largest possible sphere packing density among hurwitz quaternionic forms in dimension @xmath59 , as shown by vance @xcite using a mordell type inequality .\nshe shows that the barnes - wall lattice @xmath60 has the largest density among lattices with a hurwitz quaternionic structure in dimension @xmath59 .\na very nice example of a human - computer - interacted proof !\nthe author likes to thank henry cohn , rainer schulze - pillot , mathieu dutour sikiri , francois sigrist , jacques martinet and stephanie vance for helpful comments and communications .\nd. bremner , m. dutour sikiri , and a. schrmann , _ polyhedral representation conversion up to symmetries _ , proceedings of the 2006 crm workshop on polyhedral computation ( d. bremner d. avis and a. deza , eds . ) , crm proceedings & lecture notes , ams , providence , 2009 , to appear , preprint at http://arxiv.org/abs/math/0702239[arxiv:math/0702239 ] .\nr. coulangeon , _\nvorono theory over algebraic number fields _ , rseaux euclidiens , designs sphriques et formes modulaires , monogr .\n37 , enseignement math . ,\ngeneva , 2001 , pp .\n147162 . c. hermite , _ extraits de lettres de m.ch . hermite\n m. jacobi sur diffrents objets de la thorie des nombres , deuxime lettre _ , j. reine .\nangew . math .\n* 40 * ( 1850 ) , 279290 , in oeuvres de charles hermite i , 100121 ; letter is dated to aug .\n6th 1845 .\nm. mcconnell , _ generalizations of voronoi i to symmetric spaces and arithmetic groups _ , voronoi s impact on modern science ( ed .\np engel et .\nal . ) , proc .\nukraine , vol .\n21 , institute of math . ,\nkyiv , 1998 , pp .\n155185 .\nh. minkowski , _ ber die positiven quadratischen formen und ber kettenbruchhnliche algorithmen _\n, j. reine angew . math .\n* 107 * ( 1891 ) , 278297 , reprint in _ gesammelte abhandlungen _ , band i , teubner , leipzig , 1911 .\nj. opgenorth , _ ph.d .\nthesis : normalisatoren und bravaismannigfaltigkeiten endlicher unimodularer gruppen _ , technical university of aachen , 1995 , also in aachener beitrge zur mathematik . 16 .\n, verlag der augustinus buchh . ,\naachen , 1996 .\nvoronoi , _ nouvelles applications des paramtres continus la thorie des formes quadratiques .\npremier mmoire .\nsur quelques proprits des formes quadratiques positives parfaites _ ,\nj. reine angew . math .\n* 133 * ( 1907 ) , 97178 .\nt. watanabe , _ a survey and a complement of fundamental hermite constants _ , algebraic and arithmetic theory of quadratic forms , contemp .\n344 , amer .\nsoc . , providence , ri , 2004 , pp .", "role": "user" }, { "content": "a positive definite quadratic form is called perfect , if it is uniquely determined by its arithmetical minimum and the integral vectors attaining it . in this self - contained survey \n we explain how to enumerate perfect forms in @xmath0 variables up to arithmetical equivalence and scaling . \n we put an emphasis on practical issues concerning computer assisted enumerations . for the necessary theory of voronoi we provide complete proofs based on ryshkov polyhedra . \n this allows a very natural generalization to @xmath1-perfect forms , which are perfect with respect to a linear subspace @xmath1 in the space of quadratic forms . \n important examples include gaussian , eisenstein and hurwitz quaternionic perfect forms , for which we present new classification results in dimensions @xmath2 and @xmath3 .", "role": "assistant" } ]

[ { "content": "You will be presented with a citation sentence from a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\nReceptors of virtually every type have been shown to stimulate the production of the phosphoinositides phosphatidylinositol-3,4,5-trisphosphate (PtdIns-3,4,5-P3) and PtdIns-3,4-P2 (Auger et al., 1989; Serunian et al., 1991; Gold and Aebersold, 1994; Gold et al., 1994; Okada et al., 1996).", "role": "user" }, { "content": "Method", "role": "assistant" } ]

[ { "content": "You have to answer a biomedical question in binary format, i.e., only yes and no are acceptable answers. A list of paragraphs is provided as context to help you answer the question.\n\nQuestion: Is there high nucleotide diversity in the Drosophila suzukii species?\n\nContext: Native to Asia, the soft-skinned fruit pest Drosophila suzukii has recently invaded the United States and Europe. The eastern United States represents the most recent expansion of their range, and presents an opportunity to test alternative models of colonization history. Here, we investigate the genetic population structure of this invasive fruit fly, with a focus on the eastern United States. We sequenced six X-linked gene fragments from 246 individuals collected from a total of 12 populations. We examine patterns of genetic diversity within and between populations and explore alternative colonization scenarios using approximate Bayesian computation. Our results indicate high levels of nucleotide diversity in this species and suggest that the recent invasions of Europe and the continental United States are independent demographic events.", "role": "user" }, { "content": "yes", "role": "assistant" } ]

[ { "content": "You will be presented with a citation sentence from a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\nTherefore, we generated a yeast strain in which Scp160p expression is under control of a repressible Tet-off operator, which allows rapid depletion of the protein on addition of doxycyclin (11,25).", "role": "user" }, { "content": "Method", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"RNA\", \"CellType\", \"CellLine\", \"Protein\", \"DNA\"].\n\nPlease return the output as a JSON object of the format: {\"DNA\" : [\"TAL1\", ...], \"RNA\": [\"mRNAs\", ...], \"CellLine\": [\"T cells\", ...], \"CellType\": [\"monocytes\", ...], \"Protein\": [\"IL-2\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nGender and vascular reactivity. Estrogen receptors are found on vascular endothelial and smooth muscle cells; their expression is influenced by exposure to the hormone. Estrogen receptors influence non-genomic events, which are rapid in onset and genomic events, which are longer acting responses. Estrogens affect vascular tone indirectly by modulating release of endothelium-derived vasoactive factors and directly by modulating intracellular calcium in vascular smooth muscle cells. Estrogens indirectly affect thrombotic events and inflammation by altering platelet aggregation and leukocyte adherence and migration, respectively. Estrogens also influence production of mitogens which, when released at sites of vascular injury, affect vascular remodeling. Although estrogens initiate vascular responses, genomic sex may influence and / or limit expression of estrogen receptors and therefore actions of sex steroid hormones throughout the vasculature.", "role": "user" }, { "content": "{\"CellLine\": [], \"CellType\": [\"leukocyte\", \"platelet\", \"vascular endothelial and smooth muscle cells\", \"vascular smooth muscle cells\"], \"DNA\": [], \"Protein\": [\"estrogen receptors\", \"endothelium - derived vasoactive factors\", \"Estrogen receptors\"], \"RNA\": []}", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Chemical\", \"Disease\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\": [\"Naloxone\", ...], \"Disease\": [\"Hypotensive\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nCompression neuropathy of the radial nerve due to pentazocine-induced fibrous myopathy. Fibrous myopathy is a common, well-known side effect of repeated pentazocine injection. However, compression neuropathy due to fibrotic muscle affected by pentazocine-induced myopathy has not previously been reported. In a 37-year-old woman with documented pentazocine-induced fibrous myopathy of triceps and deltoid muscles bilaterally and a three-week history of right wrist drop, electrodiagnostic examination showed a severe but partial lesion of the right radial nerve distal to the branches to the triceps, in addition to the fibrous myopathy. Surgery revealed the right radial nerve to be severely compressed by the densely fibrotic lateral head of the triceps. Decompression and neurolysis were performed with good subsequent recovery of function.", "role": "user" }, { "content": "{\"Chemical\": [\"pentazocine\"], \"Disease\": [\"fibrous myopathy\", \"neuropathy of the radial nerve\", \"Fibrous myopathy\", \"compression neuropathy\", \"Compression neuropathy\", \"myopathy\", \"Compression neuropathy of the radial nerve\"]}", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Chemical\", \"Disease\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\": [\"Naloxone\", ...], \"Disease\": [\"Hypotensive\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nSafety and side-effects of alprazolam. Controlled study in agoraphobia with panic disorder. BACKGROUND: The widespread use of benzodiazepines has led to increasing recognition of their unwanted effects. The efficacy of alprazolam and placebo in panic disorder with agoraphobia, and the side-effect and adverse effect profiles of both drug groups were measured. METHOD: In London and Toronto 154 patients who met DSM-III criteria for panic disorder with agoraphobia were randomised to alprazolam or placebo. Subjects in each drug group also received either exposure or relaxation. Treatment was from weeks 0 to 8 and was then tapered from weeks 8 to 16. RESULTS: Mean alprazolam dose was 5 mg daily. Compared with placebo subjects, alprazolam patients developed more adverse reactions (21% v. 0%) of depression, enuresis, disinhibition and aggression; and more side-effects, particularly sedation, irritability, impaired memory, weight loss and ataxia. Side-effects tended to diminish during treatment but remained significant at week 8. Despite this, the drop-out rate was low. CONCLUSIONS: Alprazolam caused side-effects and adverse effects during treatment but many patients were willing to accept these.", "role": "user" }, { "content": "{\"Chemical\": [\"alprazolam\", \"Alprazolam\", \"benzodiazepines\"], \"Disease\": [\"weight loss\", \"enuresis\", \"aggression\", \"agoraphobia\", \"impaired memory\", \"depression\", \"panic disorder\", \"irritability\", \"ataxia\"]}", "role": "assistant" } ]

[ { "content": "You will be shown a claim about public health and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\". If the abstract does not provide enough information to arrive at a verdict, write \"NEI\" (for \"not enough information\").\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract. If the verdict was \"NEI\", then return an empty array.\n\nFor instance, if the model were given the claim \"wearing masks can prevent the spread of COVID\", the output might be:\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that mass mask-wearing reduces the transmission rate for COVID-19.\"]\n}\n\nClaim: 5G has no causal connection to COVID-19\n\nAbstract:\nObjective@#To analyze application fields of 5G communication technology in Corona Virus Disease 2019 (COVID-19) epidemic prevention and control, and build a 5G intelligent medical service system for COVID-19 epidemic prevention and control in China.@*Methods@#We collected and analyzed 5G technology application cases used in the fight against COVID-19 from December 2019 to February 2020: 5G + telemedicine application cases, 5G + negative pressure ambulance cases, 5G + remote monitoring cases, 5G + artificial intelligence cases, 5G + infrared thermography temperature detection cases, 5G + big data analysis cases for epidemic prevention and control.@*Results@#Through the analysis of 5G application cases in COVID-19 epidemic prevention and control, we found out the key elements of 5G intelligent medical service system in COVID-19 epidemic prevention and control.\nBy optimizing and upgrading the internal service mode of the hospital, breaking the internal and external barriers, integrating internal and external resources, and strengthening 5G intelligent medical security, we can form a 5G intelligent medical service system for COVID-19 epidemic prevention and control, including application layer, technical service layer, network support layer and security system layer.@*Conclusion@#5G communication technology has the characteristics of faster speed, shorter time delay and denser capacity.\nIn COVID-19 epidemic prevention and control work, it can further improve the efficiency of doctors&apos; diagnosis, improve patients&apos; medical experience, realize the remote sharing of high-quality medical resources and real-time information exchange, effectively block the spread of epidemic, alleviate the shortage of medical resources and medical staff, and make the epidemic prevention and control more efficient.", "role": "user" }, { "content": "{\"verdict\": \"SUPPORT\", \"evidence\": [\"In COVID-19 epidemic prevention and control work, it can further improve the efficiency of doctors&apos; diagnosis, improve patients&apos; medical experience, realize the remote sharing of high-quality medical resources and real-time information exchange, effectively block the spread of epidemic, alleviate the shortage of medical resources and medical staff, and make the epidemic prevention and control more efficient.\"]}", "role": "assistant" } ]

[ { "content": "You will be presented with a collection of medical randomized controlled trial (RCT) reports addressing a shared clinical question -- for instance, the efficacy of a medical intervention on a disease or condition. Given the titles and abstracts of these reports, your task is to generate the conclusion of the systematic review article synthesizing the key findings. Your conclusion should be a few sentences long. In your response, include only the conclusion and no other text. The RCT reports are below.\n\n\n\nTitle 1:\nMixture of Arnebia euchroma and Matricaria chamomilla (Marhame-Mafasel) for pain relief of osteoarthritis of the knee - a two-treatment, two-period crossover trial.\nAbstract 1:\nOsteoarthritis is the most prevalent chronic non-infective joint arthritis. Because of its chronic disease nature, local drugs are preferred due to lower complications. In the present study, the new herbal pomade Marhame-Mafasel for knee osteoarthritis was used in a double-blind crossover trial. The aim of the study was to assess the efficacy and safety of Marhame-Mafasel pomade, which consists of several medical herbs including Arnebia euchroma and Matricaria chamomilla, in osteoarthritis of the knee.\n This study was a placebo-controlled double-blind crossover trial. Forty-two patients with pain associated with osteoarthritis of the knee (diagnosed by criteria of the European League against Rheumatism and physical examination) were drawn from patients attending the Clinic of Mostafa-Khomeini Hospital. In this study we assessed efficacy (analgesic effect and improved function) of herbal pomade Marhame-Mafasel, which was used locally in patients with primary osteoarthritis of the knee over three weeks. The instrument of the study was the Western Ontario and McMaster Universities (WOMAC) LK3.1 standard questionnaires.\n The participants in each group were 21 patients; 30 (71.4%) were women and 12 (28.6%) of them were men. The participants were between 40 and 76 years old. Six patients had mild arthritis, 15 had moderate arthritis and 21 had severe arthritis. The positive analgesic effect of the herbal pomade Marhame-Mafasel in primary knee osteoarthritis was proven. The herbal joint pomade Marhame-Mafasel had a significantly greater mean change in score compared to the placebo group for osteoarthritis severity (p < 0.05).\n Herbal pomade Marhame-Mafasel in comparison to placebo has more effect on reduction of pain of primary knee osteoarthritis.\n\n\nTitle 2:\nChoosing between NSAID and arnica for topical treatment of hand osteoarthritis in a randomised, double-blind study.\nAbstract 2:\nThe use of topical preparations for symptom relief is common in osteoarthritis. The effects of ibuprofen (5%) and arnica (50 g tincture/100 g, DER 1:20), as gel preparations in patients with radiologically confirmed and symptomatically active osteoarthritis of interphalangeal joints of hands, were evaluated in a randomised, double-blind study in 204 patients, to ascertain differences in pain relief and hand function after 21 days' treatment. Diagnosis was according to established criteria; primary endpoints were pain intensity and hand function; statistical design was as per current regulatory guidelines for testing topical preparations. There were no differences between the two groups in pain and hand function improvements, or in any secondary end points evaluated. Adverse events were reported by six patients (6.1%) on ibuprofen and by five patients (4.8%) on arnica. Our results confirm that this preparation of arnica is not inferior to ibuprofen when treating osteoarthritis of hands.\n\n\nTitle 3:\nNettle sting for chronic knee pain: a randomised controlled pilot study.\nAbstract 3:\nNon-pharmacological interventions for chronic knee pain are increasingly requested by patients and are recommended in current treatment guidelines. An intervention that has been used for many years for pain relief is nettle sting.\n To explore the feasibility of a definitive RCT of nettle sting for chronic knee pain, in particular the acceptability of the research to GPs and patients, and the optimal methods for recruitment and outcome measurement.\n Patient blinded pilot RCT, set in two inner city primary care practices in Plymouth, UK. Potential participants were identified from practice computerised databases using three different approaches: age and analgesic use, age and appropriate Read code, or age alone. Patients had to be aged between 55 and 80 years with knee pain and a presumptive clinical diagnosis of OA knee, with a baseline WOMAC pain subscale score of more than 4. They were randomised to receive either treatment with Urtica dioica, or placebo intervention with Urtica galeopsifolia daily for 1 week. The main outcome measure for the treatment effect was the WOMAC pain subscale; other outcomes included quantitative and qualitative data to inform the design of a future study.\n Out of 45 patients who were eligible, 42 were recruited. Invitations targeted at patients who were both currently receiving repeat prescriptions for non-steroidal or analgesic drugs and had relevant Read codes proved most efficient for recruitment. Mean baseline WOMAC pain subscale scores were 9.2 (S.D. 3.4) and 7.9 (2.3) in the two groups. The mean reduction in pain score at the end of treatment in the nettles group was 1.7 (95% confidence interval 0.6, 2.9) and in the controls 1.6 (CI 0.5, 2.7). All GP practices, and all patients approached, were willing to be involved in the research. Patients liked the treatment mostly because it was 'natural'. The sting was acceptable and viewed as a minor irritation.\n Research into nettle sting is acceptable to patients and GPs, and patients do not find the treatment more than a minor irritation. Larger rigorous studies are justified to determine the effectiveness of this ancient therapy.\n\n\nTitle 4:\nEfficacy of symptomatic control of knee osteoarthritis with 0.0125% of capsaicin versus placebo.\nAbstract 4:\nKnee osteoarthritis (OA) is prevalent and associated with both pain and functional disability. Current treatments aim to alleviate mild to moderate symptoms by various methods. Topical capsaicin (0.075% and 0.05%) has been evaluated for the treatment of the painful joints. A burning sensation was the most common side effect at these strengths. Therefore, the authors aimed to evaluate the efficacy of 0.0125% capsaicin gel (Capsika gel) compared to a placebo (the vehicle gel) in patients with symptomatic OA knee.\n This was a cross-over; double blinded, randomized, controlled trial of 100 patients with mild to moderate knee OA. All of the patients received either capsaicin gel or placebo gel applied to the affected knee, three times daily for 4 weeks with one week washout period after which the treatment switched to either capsaicin gel or placebo gel for the next 4 weeks. A blinded examiner used the visual analog scale (VAS) and WOMAC score to do weekly assessments.\n Subjects averaged 61 years of age (range, 44 to 82). During the enrollment phase, only female farmers presented. Mean body weight and height was 62.97 +/- 10.25 kg and 1.54 +/- 0.053 m, respectively The respective baseline VAS and WOMAC score was 6.40 +/- 1.64 and 51.65 +/- 13.3. The severity of OA, according to the KL criteria was: 83 patients with grade 2 and 16 with grade 3. The respective mean difference of VAS and total WOMAC score in the capsaicin group vs. the placebo group was statistically significant (p < 0.05). The mean difference of the WOMAC pain, stiffness and functional subscales in the capsaicin vs. the placebo group was also significant (p < 0.05). The only adverse event reported was a burning sensation. During the 4-week treatment with capsaicin, approximately 67% of patients had a burning sensation but none withdrew for this reason.\n 0.0125% capsaicin gel was an effective treatment in mildly to moderately painful OA knees. The burning sensation reported by patients in the capsaicin group was less disturbing than in previous studies and none of the present patients withdrew for this reason.\n\n\nTitle 5:\nEfficacy of a comfrey root (Symphyti offic. radix) extract ointment in the treatment of patients with painful osteoarthritis of the knee: results of a double-blind, randomised, bicenter, placebo-controlled trial.\nAbstract 5:\nThis randomised, double-blind, bicenter, placebo-controlled clinical trial investigated the effect of a daily application of 6g Kytta-Salbe f (3 x 2 g) over a 3 week period with patients suffering from painful osteoarthritis of the knee. The two hundred and twenty patients examined consisted of 153 women and 67 men of an average age of 57.9 years. On average, the complaints relating to osteoarthritis of the knee had persisted for 6.5 years. Two hundred and twenty patients were included in the Full Analysis Set (FAS) and safety collective, 186 (84.5%) in the Valid Case Analysis Set (VCAS) collective. In the course of the trial, the visual analog scale (VAS) total score (primary target value) in the verum group dropped by 51.6 mm (54.7%) and in the placebo group by 10.1 mm (10.7%). The average difference between the groups of 41.5 mm (95% confidence interval=34.8 to 48.2 mm) or 44.0% is significant (p<0.001). The significance is confirmed through the evaluation of the diary, the VCAS evaluation and the separate assessment of the two centres. This also applies to the separate assessment of the VAS total score following pain at rest and on movement. The WOMAC (Western Ontario and McMaster Universities) total score (secondary target value) also improved similar to the VAS total score. At the end of the trial, a reduction by 60.4 mm (58.0%) was recorded for the verum group and a reduction of 14.7 mm (14.1%) for the placebo group. The average group difference of 45.7 mm (95% confidence interval=37.1 to 54.3 mm) or 43.9% is significant (p<0.001). The difference between the treatment groups increased systematically and significantly, in parallel with the duration of the treatment. Thus, the superiority of the treatment with Kytta-Salbe f over that with the placebo is proven, even by means of the multi-factorial multivariate analysis for repetitive measurements. In respect of the explorative secondary target values SF-36 (quality of life), angle measurement (mobility of the knee), CGI (clinical global impression) and global assessment of efficacy by the physician and the patient, a significant superiority (p<0.001 each) of the verum group over the placebo group was also proven. The results suggest that the comfrey root extract ointment is well suited for the treatment of osteoarthritis of the knee. Pain is reduced, mobility of the knee improved and quality of life increased.\n\n\nTitle 6:\nRandomized controlled trial of nettle sting for treatment of base-of-thumb pain.\nAbstract 6:\nThere are numerous published references to use of nettle sting for arthritis pain but no randomized controlled trials have been reported. We conducted a randomized controlled double-blind crossover study in 27 patients with osteoarthritic pain at the base of the thumb or index finger. Patients applied stinging nettle leaf (Urtica dioica) daily for one week to the painful area. The effect of this treatment was compared with that of placebo, white deadnettle leaf (Lamium album), for one week after a five-week washout period. Observations of pain and disability were recorded for the twelve weeks of the study. After one week's treatment with nettle sting, score reductions on both visual analogue scale (pain) and health assessment questionnaire (disability) were significantly greater than with placebo (P = 0.026 and P = 0.0027).", "role": "user" }, { "content": "Although the mechanism of action of the topical medicinal plant products provides a rationale basis for their use in the treatment of osteoarthritis, the quality and quantity of current research studies of effectiveness are insufficient. Arnica gel probably improves symptoms as effectively as a gel containing non-steroidal anti-inflammatory drug, but with no better (and possibly worse) adverse event profile. Comfrey extract gel probably improves pain, and Capsicum extract gel probably will not improve pain or function at the doses examined in this review. Further high quality, fully powered studies are required to confirm the trends of effectiveness identifed in studies so far.", "role": "assistant" } ]

[ { "content": "You will be presented with a sentence from biomedical research text. Extract all terms that correspond to chemical entities of biological interest (ChEBI).\nReturn your identified terms in a JSON array, formatted like this: [\"Entity1\", \"Entity2\", ...].\nIf no such entities are detected, respond by providing an empty JSON array [].\n\nBiomedical context:\nAfterE9,embryoswereremovedfromtheirmembranesandembeddedseparately.", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Finding\", \"Bacterium\", \"ProfessionalOrOccupationalGroup\", \"InjuryOrPoisoning\", \"Eukaryote\", \"BodySystem\", \"Virus\", \"ResearchActivity\", \"BodySubstance\", \"PopulationGroup\", \"Chemical\", \"AnatomicalStructure\", \"SpatialConcept\", \"HealthCareActivity\", \"Organization\", \"BiomedicalOccupationOrDiscipline\", \"Food\", \"ClinicalAttribute\", \"MedicalDevice\", \"BiologicFunction\", \"IntellectualProduct\"].\n\nPlease return the output as a JSON object of the format: {\"Virus\": [\"HIV\", ...], \"Bacterium\": [\"MRSA\", ...], \"AnatomicalStructure\": [\"Lung\", ...], \"BodySystem\": [\"CNS\", ...], \"BodySubstance\": [\"Serum\", ...], \"Finding\": [\"Headache\", ...], \"InjuryOrPoisoning\": [\"Fracture\", ...], \"BiologicFunction\": [\"Death\", ...], \"HealthCareActivity\": [\"Biopsy\", ...], \"ResearchActivity\": [\"Clinical trial\", ...], \"MedicalDevice\": [\"Lenses\", ...], \"SpatialConcept\": [\"Camps\", ...], \"BiomedicalOccupationOrDiscipline\": [\"Forensic medicine\", ...], \"Organization\": [\"WHO\", ...], \"ProfessionalOrOccupationalGroup\": [\"Provider\", ...], \"PopulationGroup\": [\"Swimmers\", ...], \"Chemical\": [\"Gold\", ...], \"Food\": [\"Rice\", ...], \"IntellectualProduct\": [\"RPAM\", ...], \"ClinicalAttribute\": [\"Biomarker\", ...], \"Eukaryote\": [\"Dogs\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nRole of endoscopy in primary sclerosing cholangitis: European Society of Gastrointestinal Endoscopy (ESGE) and European Association for the Study of the Liver (EASL) Clinical Guideline 1 ESGE / EASL recommend that, as the primary diagnostic modality for PSC, magnetic resonance cholangiography (MRC) should be preferred over endoscopic retrograde cholangiopancreatography (ERCP). Moderate quality evidence, strong recommendation. 2 ESGE / EASL suggest that ERCP can be considered if MRC plus liver biopsy is equivocal or contraindicated in patients with persisting clinical suspicion of PSC. The risks of ERCP have to be weighed against the potential benefit with regard to surveillance and treatment recommendations. Low quality evidence, weak recommendation. 6 ESGE / EASL suggest that, in patients with an established diagnosis of PSC, MRC should be considered before therapeutic ERCP. Weak recommendation, low quality evidence. 7 ESGE / EASL suggest performing endoscopic treatment with concomitant ductal sampling (brush cytology, endobiliary biopsies) of suspected significant strictures identified at MRC in PSC patients who present with symptoms likely to improve following endoscopic treatment. Strong recommendation, low quality evidence. 9 ESGE / EASL recommend weighing the anticipated benefits of biliary papillotomy / sphincterotomy against its risks on a case-by-case basis. Strong recommendation, moderate quality evidence. Biliary papillotomy / sphincterotomy should be considered especially after difficult cannulation. Strong recommendation, low quality evidence. 16 ESGE / EASL suggest routine administration of prophylactic antibiotics before ERCP in patients with PSC. Strong recommendation, low quality evidence. 17 EASL / ESGE recommend that cholangiocarcinoma (CCA) should be suspected in any patient with worsening cholestasis, weight loss, raised serum CA19-9, and/or new or progressive dominant stricture, particularly with an associated enhancing mass lesion. Strong recommendation, moderate quality evidence. 19 ESGE / EASL recommend ductal sampling (brush cytology, endobiliary biopsies) as part of the initial investigation for the diagnosis and staging of suspected CCA in patients with PSC. Strong recommendation, high quality evidence.", "role": "user" }, { "content": "{\"AnatomicalStructure\": [\"ductal\", \"stricture\", \"strictures\"], \"Bacterium\": [], \"BiologicFunction\": [\"cholestasis\", \"CCA\", \"weight loss\", \"primary sclerosing cholangitis\", \"PSC\", \"suspected\", \"cholangiocarcinoma\"], \"BiomedicalOccupationOrDiscipline\": [], \"BodySubstance\": [\"serum\"], \"BodySystem\": [], \"Chemical\": [], \"ClinicalAttribute\": [], \"Eukaryote\": [], \"Finding\": [\"diagnosis\", \"symptoms\", \"improve\", \"contraindicated\", \"suspicion\"], \"Food\": [], \"HealthCareActivity\": [\"investigation\", \"treatment\", \"ERCP\", \"biliary papillotomy\", \"sphincterotomy\", \"endoscopic\", \"magnetic resonance cholangiography\", \"staging\", \"CA19-9\", \"Biliary papillotomy\", \"cannulation\", \"endoscopy\", \"diagnostic\", \"therapeutic\", \"MRC\", \"endoscopic retrograde cholangiopancreatography\", \"liver biopsy\", \"surveillance\", \"routine administration\"], \"InjuryOrPoisoning\": [], \"IntellectualProduct\": [\"Clinical Guideline\"], \"MedicalDevice\": [], \"Organization\": [\"European Society of Gastrointestinal Endoscopy\", \"European Association for the Study of the Liver\", \"EASL\", \"ESGE\"], \"PopulationGroup\": [], \"ProfessionalOrOccupationalGroup\": [], \"ResearchActivity\": [], \"SpatialConcept\": [], \"Virus\": []}", "role": "assistant" } ]

[ { "content": "You will be shown a claim about public health and the abstract of a biomedical research paper. Each sentence from the abstract will be on a separate line. Your task is to return a JSON object with two fields:\n\n- \"verdict\": The fact-checking verdict. If the information in the abstract supports the claim, write \"SUPPORT\". If the abstract contradicts the claim, write \"CONTRADICT\". If the abstract does not provide enough information to arrive at a verdict, write \"NEI\" (for \"not enough information\").\n- \"evidence\": An array of sentences providing evidence for the verdict. Please copy all relevant sentences verbatim from the abstract. If the verdict was \"NEI\", then return an empty array.\n\nFor instance, if the model were given the claim \"wearing masks can prevent the spread of COVID\", the output might be:\n{\n \"verdict\": \"SUPPORT\",\n \"evidence\": [\"Our findings indicate that mass mask-wearing reduces the transmission rate for COVID-19.\"]\n}\n\nClaim: Some cancer treatments such as chemotherapy can weaken your immune system (cause you to be immunocompromised) and may increase your risk for severe illness from COVID-19.\n\nAbstract:\nBACKGROUND: The 2019 novel coronavirus has caused the outbreak of the acute respiratory disease in Wuhan, Hubei Province of China since December 2019.\nThis study was performed to analyze the clinical characteristics of patients who succumbed to and who recovered from 2019 novel coronavirus disease (COVID-19).\nMETHODS: Clinical data were collected from two tertiary hospitals in Wuhan.\nA retrospective investigation was conducted to analyze the clinical characteristics of fatal cases of COVID-19 (death group) and we compare them with recovered patients (recovered group).\nContinuous variables were analyzed using the Mann-Whitney U test.\nCategorical variables were analyzed by &#967; test or Fisher exact test as appropriate.\nRESULTS: Our study enrolled 109 COVID-19 patients who died during hospitalization and 116 recovered patients.\nThe median age of the death group was older than the recovered group (69 [62, 74] vs. 40 [33, 57] years, Z = 9.738, P < 0.001).\nMore patients in the death group had underlying diseases (72.5% vs. 41.4%, &#967; = 22.105, P < 0.001).\nPatients in the death group had a significantly longer time of illness onset to hospitalization (10.0 [6.5, 12.0] vs. 7.0 [5.0, 10.0] days, Z = 3.216, P = 0.001).\nOn admission, the proportions of patients with symptoms of dyspnea (70.6% vs. 19.0%, &#967; = 60.905, P < 0.001) and expectoration (32.1% vs. 12.1%, &#967; = 13.250, P < 0.001) were significantly higher in the death group.\nThe blood oxygen saturation was significantly lower in the death group (85 [77, 91]% vs. 97 [95, 98]%, Z = 10.625, P < 0.001).\nThe white blood cell (WBC) in death group was significantly higher on admission (7.23 [4.87, 11.17] vs. 4.52 [3.62, 5.88] ×10/L, Z = 7.618, P < 0.001).\nPatients in the death group exhibited significantly lower lymphocyte count (0.63 [0.40, 0.79] vs. 1.00 [0.72, 1.27] ×10/L, Z = 8.037, P < 0.001) and lymphocyte percentage (7.10 [4.45, 12.73]% vs. 23.50 [15.27, 31.25]%, Z = 10.315, P < 0.001) on admission, and the lymphocyte percentage continued to decrease during hospitalization (7.10 [4.45, 12.73]% vs. 2.91 [1.79, 6.13]%, Z = 5.242, P < 0.001).\nAlanine transaminase (22.00 [15.00, 34.00] vs. 18.70 [13.00, 30.38] U/L, Z = 2.592, P = 0.010), aspartate transaminase (34.00 [27.00, 47.00] vs. 22.00 [17.65, 31.75] U/L, Z = 7.308, P < 0.001), and creatinine levels (89.00 [72.00, 133.50] vs. 65.00 [54.60, 78.75] µmol/L, Z = 6.478, P < 0.001) were significantly higher in the death group than those in the recovered group.\nC-reactive protein (CRP) levels were also significantly higher in the death group on admission (109.25 [35.00, 170.28] vs. 3.22 [1.04, 21.80] mg/L, Z = 10.206, P < 0.001) and showed no significant improvement after treatment (109.25 [35.00, 170.28] vs. 81.60 [27.23, 179.08] mg/L, Z = 1.219, P = 0.233).\nThe patients in the death group had more complications such as acute respiratory distress syndrome (ARDS) (89.9% vs. 8.6%, &#967; = 148.105, P < 0.001), acute cardiac injury (59.6% vs. 0.9%, &#967; = 93.222, P < 0.001), acute kidney injury (18.3% vs. 0%, &#967; = 23.257, P < 0.001), shock (11.9% vs. 0%, &#967; = 14.618, P < 0.001), and disseminated intravascular coagulation (DIC) (6.4% vs. 0%, &#967; = 7.655, P = 0.006).\nCONCLUSIONS: Compared to the recovered group, more patients in the death group exhibited characteristics of advanced age, pre-existing comorbidities, dyspnea, oxygen saturation decrease, increased WBC count, decreased lymphocytes, and elevated CRP levels.\nMore patients in the death group had complications such as ARDS, acute cardiac injury, acute kidney injury, shock, and DIC.", "role": "user" }, { "content": "{\"verdict\": \"NEI\", \"evidence\": []}", "role": "assistant" } ]

[ { "content": "You will be shown sections from a scientific research paper, together with a question about the paper. This is an extractive question-answering task, where you must find and extract relevant text spans directly from the paper to answer the question. Your response should strictly be a `json` object with two fields:\n\n\"answer\": An array of strings extracted directly from the paper which, collectively, answer the question.\n\"evidence\": An array of strings. Each should be an excerpt from the paper, in which one or more of the extracted answers can be found.\n\nFor example, for the question \"What baselines did the authors compare against?\", a sample response might be:\n{\n \"answer\": [\"BERT\", \"RoBERTa\"],\n \"evidence\": [\"In our experiments, we compare the performance of our model against BERT and RoBERTa.\"]\n}\n\nDo not include any text in your response other than the json.\n\nIf the question is unanswerable given the provided excerpts, respond with the single word \"null\".\n\nPaper: Towards Detection of Subjective Bias using Contextualized Word Embeddings\n\nSubjective bias detection is critical for applications like propaganda detection, content recommendation, sentiment analysis, and bias neutralization. This bias is introduced in natural language via inflammatory words and phrases, casting doubt over facts, and presupposing the truth. In this work, we perform comprehensive experiments for detecting subjective bias using BERT-based models on the Wiki Neutrality Corpus(WNC). The dataset consists of $360k$ labeled instances, from Wikipedia edits that remove various instances of the bias. We further propose BERT-based ensembles that outperform state-of-the-art methods like $BERT_{large}$ by a margin of $5.6$ F1 score.\n\nIntroduction\nIn natural language, subjectivity refers to the aspects of communication used to express opinions, evaluations, and speculationsBIBREF0, often influenced by one's emotional state and viewpoints. Writers and editors of texts like news and textbooks try to avoid the use of biased language, yet subjective bias is pervasive in these texts. More than $56\\%$ of Americans believe that news sources do not report the news objectively , thus implying the prevalence of the bias. Therefore, when presenting factual information, it becomes necessary to differentiate subjective language from objective language.\nThere has been considerable work on capturing subjectivity using text-classification models ranging from linguistic-feature-based modelsBIBREF1 to finetuned pre-trained word embeddings like BERTBIBREF2. The detection of bias-inducing words in a Wikipedia statement was explored in BIBREF1. The authors propose the \"Neutral Point of View\" (NPOV) corpus made using Wikipedia revision history, containing Wikipedia edits that are specifically designed to remove subjective bias. They use logistic regression with linguistic features, including factive verbs, hedges, and subjective intensifiers to detect bias-inducing words. In BIBREF2, the authors extend this work by mitigating subjective bias after detecting bias-inducing words using a BERT-based model. However, they primarily focused on detecting and mitigating subjective bias for single-word edits. We extend their work by incorporating multi-word edits by detecting bias at the sentence level. We further use their version of the NPOV corpus called Wiki Neutrality Corpus(WNC) for this work.\nThe task of detecting sentences containing subjective bias rather than individual words inducing the bias has been explored in BIBREF3. However, they conduct majority of their experiments in controlled settings, limiting the type of articles from which the revisions were extracted. Their attempt to test their models in a general setting is dwarfed by the fact that they used revisions from a single Wikipedia article resulting in just 100 instances to evaluate their proposed models robustly. Consequently, we perform our experiments in the complete WNC corpus, which consists of $423,823$ revisions in Wikipedia marked by its editors over a period of 15 years, to simulate a more general setting for the bias.\nIn this work, we investigate the application of BERT-based models for the task of subjective language detection. We explore various BERT-based models, including BERT, RoBERTa, ALBERT, with their base and large specifications along with their native classifiers. We propose an ensemble model exploiting predictions from these models using multiple ensembling techniques. We show that our model outperforms the baselines by a margin of $5.6$ of F1 score and $5.95\\%$ of Accuracy.\n\nBaselines and Approach\nIn this section, we outline baseline models like $BERT_{large}$. We further propose three approaches: optimized BERT-based models, distilled pretrained models, and the use of ensemble methods for the task of subjectivity detection.\n\nBaselines and Approach ::: Baselines\nFastTextBIBREF4: It uses bag of words and bag of n-grams as features for text classification, capturing partial information about the local word order efficiently.\nBiLSTM: Unlike feedforward neural networks, recurrent neural networks like BiLSTMs use memory based on history information to learn long-distance features and then predict the output. We use a two-layer BiLSTM architecture with GloVe word embeddings as a strong RNN baseline.\nBERT BIBREF5: It is a contextualized word representation model that uses bidirectional transformers, pretrained on a large $3.3B$ word corpus. We use the $BERT_{large}$ model finetuned on the training dataset.\n\nBaselines and Approach ::: Proposed Approaches\nOptimized BERT-based models: We use BERT-based models optimized as in BIBREF6 and BIBREF7, pretrained on a dataset as large as twelve times as compared to $BERT_{large}$, with bigger batches, and longer sequences. ALBERT, introduced in BIBREF7, uses factorized embedding parameterization and cross-layer parameter sharing for parameter reduction. These optimizations have led both the models to outperform $BERT_{large}$ in various benchmarking tests, like GLUE for text classification and SQuAD for Question Answering.\nDistilled BERT-based models: Secondly, we propose to use distilled BERT-based models, as introduced in BIBREF8. They are smaller general-purpose language representation model, pre-trained by leveraging distillation knowledge. This results in significantly smaller and faster models with performance comparable to their undistilled versions. We finetune these pretrained distilled models on the training corpus to efficiently detect subjectivity.\nBERT-based ensemble models: Lastly, we use the weighted-average ensembling technique to exploit the predictions made by different variations of the above models. Ensembling methodology entails engendering a predictive model by utilizing predictions from multiple models in order to improve Accuracy and F1, decrease variance, and bias. We experiment with variations of $RoBERTa_{large}$, $ALBERT_{xxlarge.v2}$, $DistilRoBERTa$ and $BERT$ and outline selected combinations in tab:experimental-results.\n\nExperiments ::: Dataset and Experimental Settings\nWe perform our experiments on the WNC dataset open-sourced by the authors of BIBREF2. It consists of aligned pre and post neutralized sentences made by Wikipedia editors under the neutral point of view. It contains $180k$ biased sentences, and their neutral counterparts crawled from $423,823$ Wikipedia revisions between 2004 and 2019. We randomly shuffled these sentences and split this dataset into two parts in a $90:10$ Train-Test split and perform the evaluation on the held-out test dataset.\nFor all BERT-based models, we use a learning rate of $2*10^{-5}$, a maximum sequence length of 50, and a weight decay of $0.01$ while finetuning the model. We use FastText's recently open-sourced automatic hyperparameter optimization functionality while training the model. For the BiLSTM baseline, we use a dropout of $0.05$ along with a recurrent dropout of $0.2$ in two 64 unit sized stacked BiLSTMs, using softmax activation layer as the final dense layer.\n\nExperiments ::: Experimental Results\ntab:experimental-results shows the performance of different models on the WNC corpus evaluated on the following four metrics: Precision, Recall, F1, and Accuracy. Our proposed methodology, the use of finetuned optimized BERT based models, and BERT-based ensemble models outperform the baselines for all the metrics.\nAmong the optimized BERT based models, $RoBERTa_{large}$ outperforms all other non-ensemble models and the baselines for all metrics. It further achieves a maximum recall of $0.681$ for all the proposed models. We note that DistillRoBERTa, a distilled model, performs competitively, achieving $69.69\\%$ accuracy, and $0.672$ F1 score. This observation shows that distilled pretrained models can replace their undistilled counterparts in a low-computing environment.\nWe further observe that ensemble models perform better than optimized BERT-based models and distilled pretrained models. Our proposed ensemble comprising of $RoBERTa_{large}$, $ALBERT_{xxlarge.v2}$, $DistilRoBERTa$ and $BERT$ outperforms all the proposed models obtaining $0.704$ F1 score, $0.733$ precision, and $71.61\\%$ Accuracy.\n\nConclusion\nIn this paper, we investigated BERT-based architectures for sentence level subjective bias detection. We perform our experiments on a general Wikipedia corpus consisting of more than $360k$ pre and post subjective bias neutralized sentences. We found our proposed architectures to outperform the existing baselines significantly. BERT-based ensemble consisting of RoBERTa, ALBERT, DistillRoBERTa, and BERT led to the highest F1 and Accuracy. In the future, we would like to explore document-level detection of subjective bias, multi-word mitigation of the bias, applications of detecting the bias in recommendation systems.\n\nTable 1: Experimental Results for the Subjectivity Detection Task\n\nQuestion: What is the baseline for the experiments?", "role": "user" }, { "content": "{\"answer\": [\"FastText\", \"BiLSTM\", \"BERT\"], \"evidence\": [\"FastTextBIBREF4: It uses bag of words and bag of n-grams as features for text classification, capturing partial information about the local word order efficiently.\", \"BiLSTM: Unlike feedforward neural networks, recurrent neural networks like BiLSTMs use memory based on history information to learn long-distance features and then predict the output. We use a two-layer BiLSTM architecture with GloVe word embeddings as a strong RNN baseline.\", \"BERT BIBREF5: It is a contextualized word representation model that uses bidirectional transformers, pretrained on a large $3.3B$ word corpus. We use the $BERT_{large}$ model finetuned on the training dataset.\"]}", "role": "assistant" } ]

[ { "content": "You are provided with a research question, keyphrases about the question, a description of candidate datasets and dataset options. Read the description of popular datasets provided below and select the ones that can be used to validate the following research question. Use your knowledge of machine learning datasets to make the best judgement.\nYour response should be formatted as a `json` array. For instance, for the query \"Semi supervised image classification\", a sample response might be: [\"CIFAR-10\", \"CIFAR-100\"]. Do not include any extra text in the response other than the answer array.\n\nQuery: We propose a scene-debiasing strategy for learning representations for video action classification. We augment the\n\nKeyphrases: action classification video\n\nDataset description:\nUASOL: The UASOL an RGB-D stereo dataset, that contains 160902 frames, filmed at 33 different scenes, each with between 2 k and 10 k frames. The frames show different paths from the perspective of a pedestrian, including sidewalks, trails, roads, etc.\nFreiHAND: FreiHAND is a 3D hand pose dataset which records different hand actions performed by 32 people. For each hand image, MANO-based 3D hand pose annotations are provided.\nUCF101: UCF101 dataset is an extension of UCF50 and consists of 13,320 video clips, which are classified into 101 categories. These 101 categories can be classified into 5 types (Body motion, Human-human interactions, Human-object interactions, Playing musical instruments and Sports).\nHMDB51: The HMDB51 dataset is a large collection of realistic videos from various sources, including movies and web videos. The dataset is composed of 6,766 video clips from 51 action categories (such as “jump”, “kiss” and “laugh”), with each category containing at least 101 clips.\nBDD100K: Datasets drive vision progress, yet existing driving datasets are impoverished in terms of visual content and supported tasks to study multitask learning for autonomous driving. Researchers are usually constrained to study a small set of problems on one dataset, while real-world computer vision applications require performing tasks of various complexities.\nKinetics-600: The Kinetics-600 is a large-scale action recognition dataset which consists of around 480K videos from 600 action categories. The 480K videos are divided into 390K, 30K, 60K for training, validation and test sets, respectively.\nA2D: A2D (Actor-Action Dataset) is a dataset for simultaneously inferring actors and actions in videos. A2D has seven actor classes (adult, baby, ball, bird, car, cat, and dog) and eight action classes (climb, crawl, eat, fly, jump, roll, run, and walk) not including the no-action class, which we also consider.\n\nOptions:- A: UASOL B: FreiHAND C: UCF101 D: HMDB51 E: BDD100K F: Kinetics-600 G: A2D", "role": "user" }, { "content": "[\"UCF101\", \"HMDB51\"]", "role": "assistant" } ]

[ { "content": "You will be presented with a collection of medical randomized controlled trial (RCT) reports addressing a shared clinical question -- for instance, the efficacy of a medical intervention on a disease or condition. Given the titles and abstracts of these reports, your task is to generate the conclusion of the systematic review article synthesizing the key findings. Your conclusion should be a few sentences long. In your response, include only the conclusion and no other text. The RCT reports are below.\n\n\n\nTitle 1:\nThe development of effective behaviour change interventions to support the use of malaria rapid diagnostic tests by Tanzanian clinicians\nAbstract 1:\nBackground Parasitological confirmation is now recommended for all cases of suspected malaria . The roll-out of rapid diagnostic tests ( RDTs ) is hoped to enable this goal in low re source setting s through point of care testing . However , simply making RDTs available has not led to high uptake of the tests or adherence to results by clinicians , with malaria continuing to be overdiagnosed in many setting s. We undertook to design an evidence -based intervention package that would be sufficient to support the introduction of RDTs at dispensaries in Tanzania , to be evaluated through the Targeting Artemisinin Combination Therapy ( TACT ) cluster r and omised controlled trial . Methods We describe five steps in our intervention design : formative research , review of existing evidence and theory , a workshop to define the intervention approach and content and results of formative research , engagement with behaviour change theory and literature , detailed design of intervention material s and piloting and pretesting of intervention material s. This involved fieldwork with a total of 19 health workers and 212 community members in northeast Tanzania . Results The formative research suggested that RDTs were a potential source of conflict in the health worker-patient interaction , but that health workers used various techniques to resolve this , including provision of antimalarial drugs for RDT-negative patients . Our review s showed that evidence was mixed regarding the effectiveness of different methods and theories to support change in prescribing practice . Our design process is presented , drawing from this collective evidence . We describe the final TACT intervention package ( including interactive small group workshops , feedback text messages , motivational text messages and patient information leaflets and posters ) in terms of its programme theory and implementation theory . Conclusions Our study suggests that evidence -based design of complex interventions is possible . The use of formative research to underst and malaria overdiagnosis in context was central to the design of the intervention as well as empirical research to test material s and methods prior to implementation . The TACT interventions may be appropriate for other setting s where clinicians face similar challenges with malaria diagnostics . Trial registration NCT01292707\n\n\nTitle 2:\nImproving prescribing of antihypertensive and cholesterol-lowering drugs: a method for identifying and addressing barriers to change\nAbstract 2:\nBackground We describe a simple approach we used to identify barriers and tailor an intervention to improve pharmacological management of hypertension and hypercholesterolaemia . We also report the results of a post hoc exercise and survey we carried out to evaluate our approach for identifying barriers and tailoring interventions . Methods We used structured reflection , search ed for other relevant trials , surveyed general practitioners and talked with physicians during pilot testing of the intervention . The post hoc exercise was carried out as focus groups of international research ers in the field of quality improvement in health care . The post hoc survey was done by telephone interviews with physicians allocated to the experimental group of a r and omised trial of our multifaceted intervention . Results A wide range of barriers was identified and several interventions were suggested through structured reflection . The survey led to some adjustments . Study ing other trials and pilot testing did not lead to changes in the design of the intervention . Neither the post hoc focus groups nor the post hoc survey revealed important barriers or interventions that we had not considered or included in our tailored intervention . Conclusions A simple approach to identifying barriers to change appears to have been adequate and efficient . However , we do not know for certain what we would have gained by using more comprehensive methods and we do not know whether the result ing intervention would have been more effective if we had used other methods . The effectiveness of our multifaceted intervention is under evaluation in a r and omised controlled trial\n\n\nTitle 3:\nIdentification of randomized controlled trials in systematic reviews: accuracy and reliability of screening records.\nAbstract 3:\nA study was conducted to estimate the accuracy and reliability of review ers when screening records for relevant trials for a systematic review . A sensitive search of ten electronic bibliographic data bases yielded 22 571 records of potentially relevant trials . Records were allocated to four review ers such that two review ers examined each record and so that identification of trials by each review er could be compared with those identified by each of the other review ers . Agreement between review ers was assessed using Cohen 's kappa statistic . Ascertainment intersection methods were used to estimate the likely number of trials missed by review ers . Full copies of reports were obtained and assessed independently by two research ers for eligibility for the review . Eligible reports formed the ' gold st and ard ' against which an assessment was made about the accuracy of screening by review ers . After screening , 301 of 22 571 records were identified by at least one review er as potentially relevant . Agreement was ' almost perfect ' ( kappa>0.8 ) within two pairs , ' substantial ' ( kappa>0.6 ) within three pairs and ' moderate ' ( kappa>0.4 ) within one pair . Of the 301 records selected , 273 complete reports were available . When pairs of review ers agreed on the potential relevance of records , 81 per cent were eligible ( range 69 to 91 per cent ) . If review ers disagreed , 22 per cent were eligible ( range 12 to 45 per cent ) . Single review ers missed on average 8 per cent of eligible reports ( range 0 to 24 per cent ) , whereas pairs of review ers did not miss any ( range 0 to 1 per cent ) . The use of two review ers to screen records increased the number of r and omized trials identified by an average of 9 per cent ( range 0 to 32 per cent ) . Review ers can reliably identify potentially relevant records when screening thous and s of records for eligibility . Two review ers should screen records for eligibility , whenever possible , in order to maximize ascertainment of relevant trials", "role": "user" }, { "content": "Conclusions There is an agreement across methods of four tasks that need to be completed when design ing individual-level interventions : identifying barriers , selecting intervention components , using theory , and engaging end-users .", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Finding\", \"Bacterium\", \"ProfessionalOrOccupationalGroup\", \"InjuryOrPoisoning\", \"Eukaryote\", \"BodySystem\", \"Virus\", \"ResearchActivity\", \"BodySubstance\", \"PopulationGroup\", \"Chemical\", \"AnatomicalStructure\", \"SpatialConcept\", \"HealthCareActivity\", \"Organization\", \"BiomedicalOccupationOrDiscipline\", \"Food\", \"ClinicalAttribute\", \"MedicalDevice\", \"BiologicFunction\", \"IntellectualProduct\"].\n\nPlease return the output as a JSON object of the format: {\"Virus\": [\"HIV\", ...], \"Bacterium\": [\"MRSA\", ...], \"AnatomicalStructure\": [\"Lung\", ...], \"BodySystem\": [\"CNS\", ...], \"BodySubstance\": [\"Serum\", ...], \"Finding\": [\"Headache\", ...], \"InjuryOrPoisoning\": [\"Fracture\", ...], \"BiologicFunction\": [\"Death\", ...], \"HealthCareActivity\": [\"Biopsy\", ...], \"ResearchActivity\": [\"Clinical trial\", ...], \"MedicalDevice\": [\"Lenses\", ...], \"SpatialConcept\": [\"Camps\", ...], \"BiomedicalOccupationOrDiscipline\": [\"Forensic medicine\", ...], \"Organization\": [\"WHO\", ...], \"ProfessionalOrOccupationalGroup\": [\"Provider\", ...], \"PopulationGroup\": [\"Swimmers\", ...], \"Chemical\": [\"Gold\", ...], \"Food\": [\"Rice\", ...], \"IntellectualProduct\": [\"RPAM\", ...], \"ClinicalAttribute\": [\"Biomarker\", ...], \"Eukaryote\": [\"Dogs\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nCinobufagin Modulates Human Innate Immune Responses and Triggers Antibacterial Activity The traditional Chinese medicine Chan-Su is widely used for treatment of cancer and cardiovascular diseases, but also as a remedy for infections such as furunculosis, tonsillitis and acute pharyngitis. The clinical use of Chan-Su suggests that it has anti-infective effects, however, the mechanism of action is incompletely understood. In particular, the effect on the human immune system is poorly defined. Here, we describe previously unrecognized immunomodulatory activities of cinobufagin (CBG), a major bioactive component of Chan-Su. Using human monocyte-derived dendritic cells (DCs), we show that LPS - induced maturation and production of a number of cytokines was potently inhibited by CBG, which also had a pro-apoptotic effect, associated with activation of caspase-3. Interestingly, CBG triggered caspase-1 activation and significantly enhanced IL-1β production in LPS - stimulated cells. Finally, we demonstrate that CBG upregulates gene expression of the antimicrobial peptides (AMPs) hBD-2 and hBD-3 in DCs, and induces secretion of HNP1 - 3 and hCAP-18/LL-37 from neutrophils, potentiating neutrophil antibacterial activity. Taken together, our data indicate that CBG modulates the inflammatory phenotype of DCs in response to LPS, and triggers an antibacterial innate immune response, thus proposing possible mechanisms for the clinical effects of Chan-Su in anti-infective therapy.", "role": "user" }, { "content": "{\"AnatomicalStructure\": [\"dendritic cells\", \"monocyte-derived\", \"neutrophil\", \"DCs\", \"cells\", \"neutrophils\"], \"Bacterium\": [], \"BiologicFunction\": [\"gene expression\", \"Antibacterial Activity\", \"infections\", \"secretion\", \"antibacterial activity\", \"furunculosis\", \"tonsillitis\", \"acute pharyngitis\", \"activation\", \"upregulates\"], \"BiomedicalOccupationOrDiscipline\": [], \"BodySubstance\": [], \"BodySystem\": [\"immune system\"], \"Chemical\": [\"Cinobufagin\", \"cytokines\", \"caspase-3\", \"Chan-Su\", \"medicine\", \"cinobufagin\", \"CBG\", \"antimicrobial peptides\", \"AMPs\", \"3\", \"HNP1\", \"antibacterial\", \"hBD-3\", \"hBD-2\", \"hCAP-18/LL-37\", \"IL-1\\u03b2\", \"LPS\", \"caspase-1\"], \"ClinicalAttribute\": [\"Triggers\", \"triggers\"], \"Eukaryote\": [\"human\", \"Human\"], \"Finding\": [], \"Food\": [], \"HealthCareActivity\": [\"immunomodulatory\", \"cardiovascular diseases\", \"anti-infective therapy\", \"treatment of cancer\"], \"InjuryOrPoisoning\": [], \"IntellectualProduct\": [], \"MedicalDevice\": [], \"Organization\": [], \"PopulationGroup\": [], \"ProfessionalOrOccupationalGroup\": [], \"ResearchActivity\": [], \"SpatialConcept\": [\"Modulates\", \"modulates\", \"Chinese\"], \"Virus\": []}", "role": "assistant" } ]

[ { "content": "You will be presented with a sentence from biomedical research text. Extract all terms that correspond to chemical entities of biological interest (ChEBI).\nReturn your identified terms in a JSON array, formatted like this: [\"Entity1\", \"Entity2\", ...].\nIf no such entities are detected, respond by providing an empty JSON array [].\n\nBiomedical context:\nConclusion", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "You will be presented with a paragraph from a COVID-19 literature. Your task is to classify the topics of this piece of text by choosing from the following categories:\n\n- Epidemic Forecasting: The content relates to predictions about the spread of COVID-19.\n- Treatment: The paragraph discusses therapeutic methods or medication for COVID-19.\n- Prevention: The content covers measures to prevent the spread of COVID-19.\n- Mechanism: The paragraph explains the biological mechanisms of the virus.\n- Case Report: The content is a report of a COVID-19 case.\n- Transmission: The paragraph discusses how COVID-19 is transmitted.\n- Diagnosis: The content is about diagnosing COVID-19 in individuals.\n\nYour classification should be provided as an element within a JSON array. The array should be formatted with topics enclosed in double quotes and separated by commas, following the JSON format, for example: [\"Topic1\", \"Topic2\", ...]. Include all applicable categories within the array. \nYour output should be a valid JSON array, and no additional text should be included in your response.\n\nArticle:\n\nNecessary procedures during the COVID-19 pandemic include electroconvulsive therapy (ECT). Providing ECT has been considered an essential service during COVID-19 in the Singapore healthcare system, not least to contribute to disease control within a society in part due to the nature of the ECT patient population. There is limited evidence-based scientific information available regarding a procedural framework for ECT during a respiratory pandemic, when much attention in the healthcare system is focused on different areas of clinical care. This article attempts to describe such a framework for ECT procedures acknowledging limited solid scientific evidence at this time and being mindful of future changes to these suggestions as testing, immunization, and treatment options develop. This approach can be adopted in whole or in part to assist practitioners to protect the patient and themselves during the procedure.", "role": "user" }, { "content": "[\"Prevention\"]", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Chemical\"].\n\nPlease return the output as a JSON object of the format: {\"Chemical\": [\"Arsenic\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nNovel iontophoretic administration method for local therapy of breast cancer. Ductal drug therapy is a novel therapeutic approach for primary breast cancers, particularly those involving ductal carcinoma in situ lesions. Total or partial mastectomy with or without radiotherapy is the standard local therapy for primary breast cancer. Here, we propose a novel drug administration method for ductal drug therapy based on a drug delivery system (DDS) for primary breast cancer. This DDS was designed to deliver miproxifen phosphate (TAT-59), an antiestrogen drug, to ductal lesions via the milk duct, where carcinomas originate, more efficiently than systemic administration, using an iontophoretic technique applied to the nipple (IP administration). Autoradiography imaging confirmed that TAT-59 was directly delivered to the milk duct using IP administration. The plasma concentrations of TAT-59 and its active metabolite DP-TAT-59 were quite low with IP administration. The area under the curve value of DP-TAT-59 in the mammary tissue was approximately 3 times higher with IP administration than with oral administration, at a 6-fold lower dose, indicating higher availability of the drug delivered via DDS than via systemic administration. The low plasma concentrations would limit adverse effects to minor ones. These characteristics show that this DDS is suitable for the delivery of active DP-TAT-59 to ductal lesions.", "role": "user" }, { "content": "{\"Chemical\": [\"miproxifen phosphate\", \"DP-TAT-59\", \"TAT-59\"]}", "role": "assistant" } ]

[ { "content": "You will be presented with a sentence from biomedical research text. Extract all terms that correspond to chemical entities of biological interest (ChEBI).\nReturn your identified terms in a JSON array, formatted like this: [\"Entity1\", \"Entity2\", ...].\nIf no such entities are detected, respond by providing an empty JSON array [].\n\nBiomedical context:\n(AandB)WholemountskeletonsfromE13.5embryosthatarestainedwithalcianblue.", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: [\"Gene\"].\n\nPlease return the output as a JSON object of the format: {\"Gene\": [\"SSX\", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].\n\nOnly output the JSON object and do not include any additional text.\n\nAbstract:\n\nThe eukaryotic UDP-N-acetylglucosamine pyrophosphorylases. Gene cloning, protein expression, and catalytic mechanism. A search of the yeast data base for a protein homologous to Escherichia coli UDP-N-acetylglucosamine pyrophosphorylase yielded UAP1 (UDP-N-acetylglucosamine pyrophosphorylase), the Saccharomyces cerevisiae gene for UDP-N-acetylglucosamine pyrophosphorylase. The Candida albicans and human homologs were also cloned by screening a C. albicans genomic library and a human testis cDNA library, respectively. Sequence analysis revealed that the human UAP1 cDNA was identical to previously reported AGX1. A null mutation of the S. cerevisiae UAP1 (ScUAP1) gene was lethal, and when expressed under the control of ScUAP1 promoter, both C. albicans and Homo sapiens UAP1 (CaUAP1 and HsUAP1) rescued the ScUAP1-deficient S. cerevisiae cells. All the recombinant ScUap1p, CaUap1p, and HsUap1p possessed UDP-N-acetylglucosamine pyrophosphorylase activities in vitro. The yeast Uap1p utilized N-acetylglucosamine-1-phosphate as the substrate, and together with Agm1p, it produced UDP-N-acetylglucosamine from N-acetylglucosamine-6-phosphate. These results demonstrate that the UAP1 genes indeed specify eukaryotic UDP-GlcNAc pyrophosphorylase and that phosphomutase reaction precedes uridyltransfer. Sequence comparison with other UDP-sugar pyrophosphorylases revealed that amino acid residues, Gly112, Gly114, Thr115, Arg116, Pro122, and Lys123 of ScUap1p are highly conserved in UDP-sugar pyrophosphorylases reported to date. Among these amino acids, alanine substitution for Gly112, Arg116, or Lys123 severely diminished the activity, suggesting that Gly112, Arg116, or Lys123 are possible catalytic residues of the enzyme.", "role": "user" }, { "content": "{\"Gene\": [\"HsUAP1\", \"CaUap1p\", \"Agm1p\", \"ScUAP1\", \"HsUap1p\", \"UDP-GlcNAc pyrophosphorylase\", \"UAP1\", \"Uap1p\", \"UDP-N-acetylglucosamine pyrophosphorylase\", \"UDP-N-acetylglucosamine pyrophosphorylases\", \"CaUAP1\", \"ScUap1p\", \"AGX1\"]}", "role": "assistant" } ]

[ { "content": "You have to answer a biomedical question in binary format, i.e., only yes and no are acceptable answers. A list of paragraphs is provided as context to help you answer the question.\n\nQuestion: Does gepotidacin activate bacterial topoisomerase?\n\nContext: GSK2140944 is a novel bacterial topoisomerase inhibitor in development for the treatment of bacterial infections.", "role": "user" }, { "content": "no", "role": "assistant" } ]

[ { "content": "You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should only include the abstract and no additional text.\n\nPaper text:\nthe word hemovigilance is derived from the greek word haema which means blood and the latin word vigilans which means watchful .\nhemovigilance as defined by faber is a set of surveillance procedures covering the whole transfusion chain ( from the donation of blood and its components to the follow - up of recipients of transfusion ) , intended to collect and assess information on unexpected or undesirable effects resulting from the therapeutic use of labile blood products and to prevent the occurrence or recurrence of such incidents . \nthe need for safe blood transfusion was felt as early as 1980 's and 1990 's when many hemophilia patients in the uk , france , canada , japan , and usa contracted hcv and hiv from blood transfusions and factor concentrates .\nthe work on hemovigilance was first initiated in france in 1991 , with the setup of monitoring systems by blood transfusion committees followed by the inception of centre national dhemovigilance in 1992 .\na complete french hemovigilance system was in place by 1994 , followed by the serious hazards of transfusion launched by the uk .\na similar voluntary scheme called the transfusion transmitted injuries surveillance system was introduced by the public health agency of canada .\ncurrently , on a global scale an international hemovigilance network ( ihn ) is functional , which evolved from the european hemovigilance network established in 1998 . to further augment the safety of blood transfusion an international database - international surveillance of transfusion associated reactions and events has been formed to share hemovigilance data across the globe .\nblood transfusion safety systems may be managed either by regulators ( e.g. france , germany , and switzerland ) , blood manufacturers ( e.g. japan , singapore , and south africa ) , medical societies ( e.g. netherlands , uk ) or public health authorities ( e.g. canada ) .\nhemovigilance has evolved from pharmacovigilance , which aims to collect and assess information related to medicinal products , most importantly adverse drug reactions in human beings .\npharmacovigilance in transfusion medicine deals with plasma derivatives : clotting factor concentrates immunoglobulins , albumin , and other fractionated products .\nhemovigilance , as the name suggests , is responsible for blood components : whole blood , erythrocytes concentrates , thrombocytes concentrates , and fresh frozen plasma .\nthe information obtained through hemovigilance is imperative to make necessary changes in transfusion policies , for amendments in transfusion practices in hospitals and blood services , to enhance transfusion standards , to help in formulating transfusion guidelines and to improve quality and safety of entire transfusion process .\nthe ultimate goal is to improve the overall safety of blood transfusion by detecting and analyzing all untoward effects of blood transfusion to correct their cause and to prevent recurrence . as per the ministry of health and family welfare , government of india\n, there are 2545 authorized blood banks in india which emphasise the need of a centralized hemovigilance system in india .\nhemovigilance program of india was launched at the national level on december 10 , 2012 , as a fundamental component of the pharmacovigilance program of india ( pvpi ) .\nthe hemovigilance program is functional through a core group and an advisory committee , which coordinate the activities of hemovigilance between medical colleges and the national coordinating centre and also provide an expert opinion for analysis of the information generated .\nthe advisory committee also provides insights helpful in linking hemovigilance program of india with the ihn .\nthe transfusion reaction reporting form ( trrf ) and the software ( hemovigil ) for reporting were also designed under the guidance of the advisory committee .\nhemovigil software was uplinked on national institute of biologicals ( nib ) website on january 24 , 2013 , and can be assessed from http://nib.gov.in/haephp/haemovigilance_login.php .\nit is launched by the nib in collaboration with the indian pharmacopoeia commission ( ipc ) .\nthe data from the medical colleges ( department of transfusion medicine or the blood bank ) in case of any adverse reaction related to blood transfusion or blood product administration is collected .\ninformation obtained is filled in the trrf and forwarded to the national coordinating centre at nib through hemovigil software .\nthe recommendations based on the collected data will be forwarded to the national coordinating centre ipc for further transmission to drugs controller general ( india ) , central drugs standard control organization .\nthe safety regulatory guidelines will be formulated and modified from time to time by cdsco based on the inputs from trrf , which will be implemented by health care professionals and blood banks for the benefit of patients .\nflow chart of transfer of information under hemovigilance program of india about 765 adverse reports were submitted via hemovigil software by centers to nib .\nof 735 reports submitted between february to november 2013 , 364 ( 49.7% ) were febrile nonhemolytic transfusion reactions and 167 ( 22.8% ) were allergic reactions .\nthe type and number of reaction reports generated under the hemovigilance program of india have been shown in figure 2 .\nnot a single case of transfusion - related acute lung injury were reported which may be a result of under - diagnosis as well as under - reporting . despite being active ,\nthere is overall under - reporting of adverse reactions associated with blood transfusion . who identified that the fragmented blood transfusion systems , lack of government commitment , lack of understanding among clinicians , lack of culture of reporting , fear of punishment , lack of expertise and regulatory framework on hemovigilance , lack of computerized management system might be challenges for the implementation of hemovigilance program in the world .\ntad transfusion associated dyspnea , taco transfusion associated circulatory load , ta - gvhd transfusion associated graft versus host disease\nhemovigilance is an essential component of quality management in a blood system and is needed for the continual enhancement of quality and safety of blood products and transfusion process by monitoring and safeguarding the adverse events associated with the use of blood products .", "role": "user" }, { "content": "hemovigilance plays an essential role in ensuring patient safety with regard to blood transfusions . \n the data generated through the hemovigilance system helps in framing important changes in the whole blood transfusion process which are useful for better patient safety . \n this article briefly describes the history of hemovigilance , why the need of hemovigilance was felt and also illustrates about the hemovigilance program of india .", "role": "assistant" } ]

[ { "content": "You will be presented with a citation sentence from a research paper. Classify the intent behind this citation by choosing from one of the following categories:\n\n- Method: Cites the paper for its methodology or procedure.\n- Background: Cites the paper to provide background information.\n- Result: Cites the paper for its findings or results.\n\nYour answer should be a single word from the following list of options: [\"Method\", \"Background\", \"Result\"]. Do not include any other text in your response.\n\nCitation sentence:\n\nStatic Single Assignment (SSA) [2] is a standard program representation used in modern optimizing compilers.", "role": "user" }, { "content": "Background", "role": "assistant" } ]

[ { "content": "You will be shown the title of a chemistry paper, together with sections excerpted from the body of the paper. The paper sections may include HTML tags like `<p>` and `</p>`; please ignore these. Your task is to write an abstract for the paper. Your response should include the abstract and no other text.\n\nTitle:\nPhosphoramidate derivates as controlled-release prodrugs of l-Dopa\n\nPaper sections:\n\n<p>Parkinson's disease (PD) is a progressive neurodegenerative disorder of the central nervous system (CNS) that affects the motor system.1,2 It is the 2nd-most common neurodegenerative disease, affecting about 1% of the population above the age of 65.3 Though a definite etiology has yet to be identified, the main pathological characteristics of PD are the continual loss of dopamine-secreting neurons in the substantia nigra pars compacta and the accumulation of Lewy bodies in many of the remaining neurons. The markedly low secretion of dopamine in the midbrain leads to the motor dysfunctions and non-motor related symptoms.3</p><p>Levodopa (l-Dopa) was first used to treat PD in the 1960s and remains the primary treatment option to elevate dopamine level in the CNS.4 However, l-Dopa suffers from poor pharmacokinetic properties as both the gastrointestinal absorption and brain uptake of l-Dopa at these sites compete with endogeneous amino acid substrates for transporters.5,6 Furthermore, it is extensively metabolized by peripheral Dopa decarboxylase (DCC), catechol-O-methyltransferase (COMT) and monoamine oxidase-B (MOA-B), and cleared rapidly from circulation leading to a short circulating half-life (approximately 1 h). Inhibitors of DCC (e.g. carbidopa), COMT (e.g. entacopone, tolcapone) and MOA-B (e.g. selegiline, rasagiline) are routinely co-administered with l-Dopa to help increase its circulation half-life, but it is only extended by an additional 30–90 min.7 Collectively, the erratic absorption and premature metabolism of l-Dopa result in waning and fluctuating levels in the brain, giving rise to the intermittent stimulation of dopaminergic neurons upon its conversion to dopamine. This pulsatile neuronal stimulation contributes to the development of disabling dyskinesias and motor fluctuations in patients after long-term use of l-Dopa.8,9 It is believed that approaches that maintain a steady therapeutic level of l-Dopa in systemic circulation, and hence continuous dopaminergic stimulation, could significantly reduce or delay the incidence of motor complications.9</p><p>We recently reported a novel phosphoramidate scaffold that can be tuned for the controlled and pH-triggered release of amine-containing drugs.10,11 With this scaffold, control over the release of the drug was dependent upon the proximity of a neighboring acidic group (e.g. carboxylic acid or pyridinium) to the phosphorus center (Figure 1). In this present study, we hypothesized that a prodrug of l-Dopa based on a phosphoramidate scaffold could be developed for the controlled and sustained release l-Dopa at physiological conditions. Thus, the focus of this proof-of-concept study was aimed at developing a library of l-Dopa prodrugs 1, and representative ethyl ester l-Dopa double-prodrugs 2, to identify compounds with desirable properties for the controlled release of l-Dopa.</p><p>The synthesis of l-Dopa phosphoramidates was achieved via a parallel synthetic methodology, which was amenable to late stage diversification (Scheme 1). Alcohols (3 and 4) were prepared from commercially available amino acids. The protected H-phosphonates (5 and 6) and phosphoramidate intermediates (7 and 8) were synthesized as previously described11 with minor modifications (see Supplemental Information). Global deprotection via Pd/C-catalyzed hydrogenolysis yielded the final l-Dopa prodrugs 1 and 2.</p><p>Once prepared, the stability of the l-Dopa prodrugs 1a-e and 2a-c at pH 3.0 and 7.4 were monitored by 31P NMR over 16 h (see representative example in Figure 2A) and referenced to an internal standard (triphenylphoshine oxide, TPPO). With the exception of the compounds that were stable, the rate of hydrolysis for these l-Dopa prodrugs followed first-order kinetics (see representative example in Figure 2B) as we have observed previously for simple model systems. Stability data for the complete library of compounds at pH 3.0 and 7.4 is shown in Figure 3.</p><p>Consistent with our previous findings,10,11 all of the prodrugs 1a – 1e were relatively unstable at pH 3 compared to pH 7.4. Also similar to our earlier observations with a model phosphoramidate linker platform, the hydrolysis rates of the l-Dopa phosphoramidates in this study were influenced by the presence of a carboxylic acid moiety and its proximity to the phosphorus center.11 For example, the half-life of prodrug 1b was observed to be approximately 10 h at pH 7.4 while the analogous compound 1e, which lacked a proximal carboxylate, was stable. Similarly, it was observed that the hydrolytic stability of compounds 1a-1c was considerably enhanced when the carboxylates were protected as the ethyl esters (2a-2c). This enhanced stability of 2a-2c at pH 3 may be sufficient for oral administration of these l-Dopa prodrugs, thus providing sustained release of l-Dopa in vivo.</p><p>It is interesting to note that compound 1c, which lacked the amide motif, was unstable compared to 1b suggesting that the amide of the serine residue of 1b attenuated the effect of the proximal carboxylate on the phosphoramidate P–N bond. Our initial studies on this phosphoramidate platform, suggested that the hydrolysis of the P–N bond may proceed through intramolecular general-acid mechanism (Scheme 2). Based on Taft σ* constants,12 the presence of the proximal amide in 1b should decrease the pKa of the serine carboxylic acid thereby diminishing its effect on the hydrolysis of the phoshoramidate P–N bond. Therefore, it is likely that the pKa of the carboxylic acid in serine, and consequently the hydrolytic stability of the P–N bond, could be further tuned with substituted benzamides on the N-terminus of serine instead of the acetamide used in this study. In addition, it is apparent that the carboxylic acid moiety of l-Dopa itself exerts only a modest effect on the hydrolysis of the P–N bond as evidenced by comparing 1b (t1/2 = 9.9 h) to 1b' (t1/2 = 12.1 h). Again based on Taft σ* constants,12 it is likely that the zwitterionic nitrogen (Scheme 2) has a stabilizing effect on the alpha carboxylate of l-Dopa, thereby reducing its pKa and diminishing its effect on the hydrolytic stability of the P–N bond. In addition to alterations of the pKa and proximity of the carboxylic acid to the phosphoramidate center, we also observed rate enhancement for hydrolysis of the P–N bond presumably due to the Thorpe-Ingold effect. For example, the threonine analog 1a was considerably less stable than the serine analog 1b, which is consistent with our previous observations with phosphoramidates of simple amines.11</p><p>In summary, we have demonstrated that various l-Dopa phosphoramidate-based prodrugs can be prepared to possess a wide range of stabilities for the controlled release of l-Dopa. The controlled release of l-Dopa, or other amine-containing drugs, from this phosphoramidate prodrug platform is tunable, as predicted by Taft σ* constants, and in all likelihood could be attenuated further by conveniently selecting suitably substituted benzamides of serine or threonine instead of the N-terminus acetamide used in this study. The ester-based double-prodrugs such as compounds 2a-2c demonstrate sufficient stability at pH 3 to support the feasibility of oral administration. The choice of particular esters in such compounds could provide an additional level of control based on rates of esterase-mediated hydrolysis. Such investigations are currently underway and will be reported in due course.</p>", "role": "user" }, { "content": "l-Dopa has continued to be a mainstay in the symptomatic treatment of Parkinson\\xe2\\x80\\x99s disease (PD). However, extensive peripheral metabolism, a short systemic circulation half-life and development of motor complications called dyskinesia prevents its long-term utilization as a PD therapeutic. Herein, we report a series of phosphoramidate derivatives of l-Dopa and controlled release of l-Dopa at pH 7.4 and 3. The kinetic data for the release of l-Dopa support our hypothesis that a proximal carboxylic acid can promote the pH-triggered hydrolysis of the phosphoramidate P\\xe2\\x80\\x93N bond. As expected, esterification of the proximal carboxylic acid protects the scaffold from rapid release at low pH. This latter observation is particularly noteworthy as it suggests that the phosphoramidate-based l-Dopa\\xe2\\x80\\x93conjugate scaffold can be adapted for oral administration as an ester prodrug.", "role": "assistant" } ]

[ { "content": "Write an abstract for the research paper below. Your response should only include the abstract and no additional text.\n\nArticle text:\nthe nature of the contact to a semiconductor at point breakdowns in ultrathin oxides , is not well understood .\nan important observed feature of these contacts is that they can have a high minority carrier injection ratio .\nthere have been a number of attempts to model point breakdowns in ultrathin oxides on silicon @xcite .\nthese models concentrate on the physics at the contact interface and attempt to derive the current vs voltage ( @xmath0 ) characteristic . however , in many physical devices the main contribution to the @xmath0 characteristic is due to the conduction in the bulk of the semiconductor .\ntherefore , one should include a model of the bulk conductivity in an explanation of point contact behavior . in this paper ,\nsuch a model is developed using standard semiconductor equations solved for point contacts with minority carrier injection .\nthis problem has the same geometry as the spreading resistance problem .\nthe difference is that the spreading resistance problem assumes an ohmic contact and only majority carrier conduction . in the point contact problem\narbitrary levels of minority carrier injection will be included .\nthis calculation will assume high - level injection , which implies that there is charge neutrality in the bulk .\nthis means that the number of excess holes ( beyond the equilibrium concentration ) is equal to the number of excess electrons .\nsince the bulk is neutral , the laplace equation can be used to find the electric field , @xmath1 the remaining equations needed to describe conduction in a semiconductor are the continuity equations for holes and electrons along with expressions for the hole and electron current in terms of drift and diffusion @xcite . for high - level injection , as in the case of high forward bias of a pn junction @xcite\n, these equations reduce to @xmath2 for holes and electrons .\n@xmath3 ( @xmath4 ) is the total hole ( electron ) concentration , @xmath5 ( @xmath6 ) is the excess hole ( electron ) concentration , and @xmath7 ( @xmath8 ) is the equilibrium hole ( electron ) concentration , so that @xmath9 ( @xmath10 ) .\n@xmath11 is the high - level diffusion length , @xmath12 , where @xmath13 and @xmath14 are hole and electron mobilities , @xmath15 is the hole diffusion constant , and @xmath16 is the hole lifetime . a similar equation can be written for @xmath17 . since @xmath18 and @xmath19 , then @xmath20 .\nthese equations must be solved for the boundary conditions of the contact .\na semi - infinite structure will be used , where the surface of the semiconductor is on the @xmath21-@xmath22 plane and the bulk of the semiconductor extends in the positive @xmath23 direction to infinity .\nthe potential at infinity will be taken as 0 .\nthere are mixed boundary conditions on the @xmath21-@xmath22 plane .\nsimilar mixed boundary conditions , for the laplace equation , are used in the solution of the usual spreading resistance problem @xcite . outside the contact radius @xmath24 ,\nthe current through the surface and the perpendicular component of the electric field are 0 .\nthe boundary conditions on the contact are given by specifying the hole and electron currents through the contact .\nthese conditions are set on the semiconductor side of the contact in order to avoid the physics of the contact interface .\nthe problem is cylindrically symmetric about the @xmath23-axis which is perpendicular to the center of the contact .\nequation ( [ eq : pcont ] ) can be written ( ignoring the @xmath25 dependence ) in cylindrical coordinates , @xmath26 this is the helmholtz equation .\nit can be solved by separating variables . using the boundary condition that the potential is zero for @xmath27 , @xmath23 at infinity ,\nthe solution for excess hole concentration is @xmath28^{\\frac{1}{2}}\\,z ) } \\mathrm{d}\\lambda.\\ ] ] @xmath29 is a bessel function of order 0 .\nthe function @xmath30 must be found using the remaining boundary conditions .\na similar solution for the electron density can be written .\nan analytic solution can be found if @xmath30 is chosen to be @xmath31 where @xmath32 is a bessel function of order 1 , @xmath33 is a constant , and @xmath34 . with this choice , the current density over the area of the contact is approximately constant for @xmath35 .\nthe electric field at the contact must be consistent with the current , which implies that the on the area of the contact the @xmath23 component of the field is @xmath36 where @xmath37 is a constant . since , in the high - level injection case , @xmath38 , the solutions can be equated and values of @xmath33 and @xmath37 determined for any given values of total hole current , @xmath39 , and electron current , @xmath40 .\nthe potential at the center of the contact can be found from the solution of the laplace equation and thus the @xmath41 vs @xmath42 curve can be calculated .\nthe numerical results below use typical values of parameters for silicon .\nthe solution for @xmath37 and the resistance can be approximated as @xmath46 @xmath47 is somewhat dependent on @xmath24 , but is approximately equal to @xmath48 .\nit is seen that as the electron current gets large , the electric field coefficient tends to a constant .\nthis is opposed to the normal ohm s law behavior where the electric field is proportional to current .\nthe resistance of the contact actually decreases as @xmath49 as opposed to the ohmic behavior of a constant resistance .\na single point breakdown device was fabricated by opening a 100 nm square window in a thick ( 20 nm ) sio@xmath50 insulating layer on a 6@xmath51 cm p - type silicon wafer . a thin sio@xmath50 layer ( 2 nm )\nwas grown in this opening and an indium tin oxide top electrode was deposited on top of this @xcite .\nthe device was voltage stressed to create a hard breakdown .\niv data of this breakdown site is presented in figure [ iv - a5b ] .\ntheoretical @xmath0 curves were calculated assuming a constant electron injection ratio .\na constant voltage was added to model the voltage drop across the contact interface for large current .\nthe experimental current is more than 10 times larger than the calculated current for only hole injection . considering the curvature at low currents ,\nthe best fit is for @xmath44 nm and an electron injection of 74% . with smaller values of @xmath24\nthe theoretical curve is not straight and can not fit the measured data .\na reasonable fit can be obtained for a range of contact size , however it is clear that the electron injection ratio is between 70% and 75% .\nthis demonstrates that a large minority injection ratio exists for these devices .\n99 e. miranda and j. su , _ microelectron .\n_ * 44 * , 1 ( 2004 ) .\nallen nussbaum , _ semiconductor device physics _ ,\n( prentice - hall , inc .\n, englewood cliffs , n.j . , 1962 ) .\ns. m. sze , _ physics of semiconductor devices _ ,\n2nd ed . , ( wiley , new york , 1981 ) . c. j. tranter , _ integral transforms in mathematical physics _\n, 2nd ed . , ( methuen and co. ltd . ,\nlondon , 1956 ) .\nm. w. denhoff , _ j. phys .\nphys . _ * 39 * , 1761 ( 2006 ) .\nj. g. mihaychuk , m. w. denhoff , s. p. mcalister , and w. r. mckinnon , _ j. appl .\nphys . _ * 98 * , 054502 ( 2005 ) .", "role": "user" }, { "content": "the standard equations for semiconductor device analysis were solved by specifying the electron and hole current injected at a small contact , assuming high - level injection . \n calculated current - voltage characteristics were fit to measurements of a single point breakdown in an ultrathin dielectric . it was found that the minority carrier injection level was about 70% .", "role": "assistant" } ]

[ { "content": "You are presented with multiple paper abstracts, a literature review title, and a specific chapter title. Your task is to write a focused literature review chapter that aligns with the given chapter title. The review should synthesize the content from the provided abstracts, draw connections between different works, highlight major findings, and identify any gaps in the existing research.\nLiterature Review Title: Giant Magnetoresistance Sensors: A Review on Structures and Non-Destructive Eddy Current Testing Applications \nChapter Title: Giant Magnetoresistance Spin Valve Sensor \n1. Abstract of Cited Paper (BIB001): Abstract This paper demonstrates spin valve sensor applications as read elements in storage systems, or, when in a Wheatstone bridge configuration, as rotational speed control devices (for ABS systems), high current monitoring devices for power lines, and positioning control devices in robotic systems. For recording heads, shielded spin valve sensors are adequate for high linear density recording. A tape head was fabricated with output 400 μV per micron of trackwidth, with a D50 value of 100 kfci, and signal loss of −0.34 dB/kfci. For rotational speed measurement, spin valve bridge sensors with flux guides were used, yielding a 400-mVpp amplitude, and square wave output with rise/fall times below 70 μs, when excited by a magnetized wheel. Amplitude is independent of speed (0–3000 rpm), and of sensor to wheel separation (0.5–2.0 mm). For power line applications, currents up to 2100 A (at 50 Hz) could be measured with a sensitivity of 35 μVrms/A and deviations from linearity of ±1.5%. In robot position control, a maximum error of ±9 μm over a ±0.5-mm span was obtained. In the two last cases, bridges without flux guides are used to maximize linear response. \n2. Abstract of Cited Paper (BIB002): The arrangement of spins at interfaces in a layered magnetic material often has an important effect on the properties of the material. One example of this is the directional coupling between the spins in an antiferromagnet and those in an adjacent ferromagnet, an effect first discovered in 1956 and referred to as exchange bias. Because of its technological importance for the development of advanced devices such as magnetic read heads and magnetic memory cells, this phenomenon has received much attention. Despite extensive studies, however, exchange bias is still poorly understood, largely due to the lack of techniques capable of providing detailed information about the arrangement of magnetic moments near interfaces. Here we present polarization-dependent X-ray magnetic dichroism spectro-microscopy that reveals the micromagnetic structure on both sides of a ferromagnetic-antiferromagnetic interface. Images of thin ferromagnetic Co films grown on antiferromagnetic LaFeO3 show a direct link between the arrangement of spins in each material. Remanent hysteresis loops, recorded for individual ferromagnetic domains, show a local exchange bias. Our results imply that the alignment of the ferromagnetic spins is determined, domain by domain, by the spin directions in the underlying antiferromagnetic layer.\n\nLiterature Review:", "role": "user" }, { "content": "The term \"spin valve magnetoresistance\" was introduced by Dieny et al. BIB001 . They introduced a GMR sensor structure consisting of two ferromagnetic layers separated by a thin layer of non-ferromagnetic material (NM). The ferromagnetic (FM) layer is a permanent magnetization and soft layer. The soft layer structure has an electron orientation that is easily manipulated by applying an external magnetic field. The orientation of electrons in the ferromagnetic material can be changed from parallel and non-parallel or vice versa by change the coercive field in the ferromagnetic layer. Thus, the resistance between these layers depends on the orientation of electron carriers in the layer of the material structure. In the 1950s, the exchange of anisotropy that is caused by the direct exchange of electrons between a ferromagnetic and antiferromagnetic material layer in the GMR structure was studied by Dieny et al. BIB001 . Prinz [15] described the physical origin of the spin valve magnetoresistance by using two principles. He explained that the principles of the GMR sensor are due to the different numbers of spin up and spin down electrons in the conduction band of the GMR sensor material structure. This phenomenon occurs because of an imbalance of electrons on the Fermi energy level and scattering of the spin electrons caused by collisions with impurities in the GMR material structure. The spin valve principle is based on the orientation of electrons. When the ferromagnetic layers have the same magnetization direction, only one type of electrons (spin down) scatter strongly, which makes a low resistivity material. Conversely, when the GMR sensor layer magnetization directions are opposite to each other, the two types of electrons (spin up and spin down) are scattered significantly which makes the resistivity of the material high. Nogues et al. explained that anisotropy and exchange bias occur on the surface layer between ferromagnetic and antiferromagnetic (AFM/FM) in the GMR structure. When the magnetic field applied to the GMR structure is in the temperature range between the Neel and Curie temperatures (TN <T <TC), the electron spin in FM materials is aligned with the magnetic field while the electron spin in the AFM remains scattered, as shown in Figure 3 (i). When the temperature is reduced to T < TN electron spin in an AFM layer is parallel to the direction of the electron spin in the FM layer. This interaction causes the effective electromagnetic field on the surface of the FM/AFM layer to be zero as shown in Figure 3 (ii). If a magnetic field is applied to the GMR structure in opposite directions, the electron spin in the FM layer starts rotating while the electron spin in the AFM layer remained unchanged (Figure 3(iii) ). In the mid-1990s, Freitas et al. BIB002 introduced the linear spin valve sensor design as shown in Figure 4 . Length and width of the magnet dimensions are W and h. A material layer of scattered electrons is arranged in a longitudinal orientation. When an excitation magnetic field is applied opposite the spin electrons' orientation, electron spin in the material will rotate and be parallel to the direction of the applied magnetic field. The scattering angle rotation of electron spins is dependent on the position of electron spins along the surface layer material. Nolting et al. BIB003 studied the effect arrangement of electron spin structure on the surface multilayer GMR structure. Electron spin in the surface layer has a big impact on the material properties. Direct coupling between the electron spin in the antiferromagnetic layer and the electron spin in ferromagnetic materials becomes very important in the development of magnetic read heads and magnetic memory cells. There are various types of multi-layer GMR spin valve. The spin valves that most attract the interest of researchers in this field are the top spin valve, the bottom valve and the symmetric spin valve. The differences in this type of spin valve are based on the fabrication process, the material layers used and the structure of the layers.", "role": "assistant" } ]

[ { "content": "You will be presented with the abstract, introduction, and discussion section from a biomedical research article. Your task is to create a summary that a layperson can understand, capturing the essence of the research article. Keep essential scientific terms, but ensure that the language remains clear and the concepts are explained in an uncomplicated manner.\n\nTitle: Oxidized Calmodulin Kinase II Regulates Conduction Following Myocardial Infarction: A Computational Analysis\nArticle:\nAbstract:\nCalmodulin kinase II( CaMKII) mediates critical signaling pathways responsible for divergent functions in the heart including calcium cycling, hypertrophy and apoptosis. Dysfunction in the CaMKII signaling pathway occurs in heart disease and is associated with increased susceptibility to life-threatening arrhythmia. Furthermore, CaMKII inhibition prevents cardiac arrhythmia and improves heart function following myocardial infarction. Recently, a novel mechanism for oxidative CaMKII activation was discovered in the heart. Here, we provide the first report of CaMKII oxidation state in a well-validated, large-animal model of heart disease. Specifically, we observe increased levels of oxidized CaMKII in the infarct border zone( BZ). These unexpected new data identify an alternative activation pathway for CaMKII in common cardiovascular disease. To study the role of oxidation-dependent CaMKII activation in creating a pro-arrhythmia substrate following myocardial infarction, we developed a new mathematical model of CaMKII activity including both oxidative and autophosphorylation activation pathways. Computer simulations using a multicellular mathematical model of the cardiac fiber demonstrate that enhanced CaMKII activity in the infarct BZ, due primarily to increased oxidation, is associated with reduced conduction velocity, increased effective refractory period, and increased susceptibility to formation of conduction block at the BZ margin, a prerequisite for reentry. Furthermore, our model predicts that CaMKII inhibition improves conduction and reduces refractoriness in the BZ, thereby reducing vulnerability to conduction block and reentry. These results identify a novel oxidation-dependent pathway for CaMKII activation in the infarct BZ that may be an effective therapeutic target for improving conduction and reducing heterogeneity in the infarcted heart.\nIntroduction:\nCalmodulin kinase II( CaMKII) mediates diverse roles in the heart, including excitation-contraction coupling, sinus node automaticity, apoptosis, hypertrophy, and gene transcription[1],[2]. Mounting experimental evidence demonstrates an important role for CaMKII in heart disease and arrhythmias. Specifically, CaMKII overexpression occurs in human heart failure[3] and transgenic mice overexpressing CaMKII develop dilated cardiomyopathy[4],[5]. Conversely, transgenic inhibition of CaMKII prevents structural remodeling and improves heart function following myocardial infarction( MI)[6] while knockout mice lacking the predominant cardiac CaMKII isoform( CaMKIIδ) are resistant to development of pressure overload-induced hypertrophy and/or heart failure[7],[8]. Finally, CaMKII inhibition prevents arrhythmias in several different mouse models of heart disease[9],[10]. CaMKII is activated by binding of Ca2+/calmodulin and may undergo inter-subunit autophosphorylation that allows the kinase to retain activity even upon dissociation of Ca2+/calmodulin( autonomy)[11]. Recently, a novel CaMKII activation pathway was identified where oxidation at specific methionine residues in the CaMKII regulatory subunit results in persistent activity independent of autophosphorylation[12]. While oxidative-dependent CaMKII activation has been shown to mediate apoptosis in response to chronic AngII treatment in the mouse[12] as well as arrhythmogenic afterdepolarizations in isolated cardiomyocytes treated with hydrogen peroxide[13], nothing is known about its role in large animal models of heart disease. Considering that levels of reactive oxygen species( ROS) such as H2O2 and superoxide are elevated following myocardial infarction[14], we hypothesized that oxidation of CaMKII represents an important pathway for CaMKII activation in the infarct border zone( BZ) that may provide a mechanistic link between increased ROS production, Na+ channel remodeling and conduction slowing following MI. In this study, we describe a dramatic increase in levels of oxidized CaMKII in a well-validated large animal model of arrhythmias following MI[15]–[22]. To investigate a role for oxidized CaMKII in regulating refractoriness and conduction in the infarct BZ, we develop a novel mathematical model of CaMKII activity that includes oxidation and autophosphorylation activation pathways. Our computer simulations show that enhanced CaMKII activity in the BZ, due primarily to increased oxidation, leads to slowed conduction, prolonged refractory periods and increased vulnerability to conduction block at the BZ margin( a prerequisite for reentry initiation). Our results identify oxidation-dependent CaMKII activation as a potential link between oxidative stress and electrical remodeling after myocardial infarction. Furthermore, our findings support CaMKII inhibition as a potential therapy for reducing susceptibility to ventricular tachycardia by improving conduction and reducing refractory gradients in the infarcted heart. Finally, it is important to note the oxidative activation of CaMKII allows for independent regulation of the kinase by a host of unique upstream activators and signaling partners( e. g. oxidases/reductases) with great potential relevance to human disease. As details emerge regarding regulation of the kinase by this newly identified pathway, they may be incorporated into our model to study electrophysiological consequences of CaMKII activation via this independent signaling pathway.\nDiscussion:\nWhile our mathematical model accounts for central aspects of the newly identified oxidation-dependent pathway for CaMKII activation, it has important limitations based on the available experimental data. Many questions remain to be answered regarding the function of CaMKII oxidation in the normal and diseased heart. For example, how do oxidation and autophosphorylation of CaMKII interact to control regulation of the holoenzyme? Do these pathways interact synergistically to activate the kinase and what are the unique/shared targets for each activation pathway? Finally, what is the relative importance of oxidized versus autophosphorylated CaMKII in normal and diseased hearts? Answers to these questions will not only facilitate the development of more comprehensive models but also will provide critical information necessary to design novel cell-specific therapies for regulating cardiac excitability. It is important to note that CaMKII in the model detects a subspace pool of Ca2+ that reaches concentrations somewhere between cytosolic and dyadic concentrations( peak concentration 10–20 µM). Previous modeling studies have shown that the dynamic response of CaMKII may vary greatly between dyadic and cytosolic pools based on variability in concentrations of Ca2+ and CaM[27]. Consistent with previous studies[27], we found that cytosolic Ca2+ transients do not significantly activate CaMKII activity at baseline or even in the presence of 1 µM H2O2( <1% maximal activity, not shown). However 10 µM H2O2 was able to activate CaMKII( 25% maximal), suggesting that a sufficiently high level of oxidative stress may be able to activate even cytosolic CaMKII. Clearly, local regulation of CaMKII in well-defined subcellular domains is an exciting area for future research with important implications for human disease. As we learn more about CaM and CaMKII signaling in the vicinity of Na+ channels, it will be important to incorporate these data into the model.", "role": "user" }, { "content": "Calmodulin kinase II ( CaMKII ) is a multifunctional serine/threonine kinase that regulates diverse functions in heart . Recently , a novel pathway for CaMKII activation was discovered where oxidation of the kinase at specific methionine residues produces persistent activity . This alternative oxidation-dependent pathway has important implications for heart disease where oxidative stress is increased ( e . g . , heart failure and following myocardial infarction ) . We hypothesized that myocardial infarction caused by occlusion of a coronary artery would increase levels of oxidized CaMKII . Moreover , we hypothesized that oxidative CaMKII activation represents an important mechanistic link between increased oxidative stress and life-threatening heart rhythm disturbances ( arrhythmias ) in heart disease . We report a dramatic increase in levels of oxidized CaMKII following myocardial infarction in the canine . Based on these experimental data , we developed a novel mathematical model of CaMKII activity to study the role of oxidation-dependent CaMKII activation in regulating cardiac cell excitability . Our findings identify a novel role for oxidation-dependent CaMKII activation following myocardial infarction and provide a mechanistic link between oxidative stress and lethal cardiac arrhythmias in heart disease .", "role": "assistant" } ]

[ { "content": "You have to answer a biomedical question in binary format, i.e., only yes and no are acceptable answers. A list of paragraphs is provided as context to help you answer the question.\n\nQuestion: Are there any functional differences between Mfd and its human Cocaine syndrome protein B (CSB) homolog?\n\nContext: In humans, the TCR coupling factor, CSB, plays a critical role in restoring transcription following both UV-induced and oxidative DNA damage. It also contributes indirectly to the global repair of some forms of oxidative DNA damage. The Escherichia coli homolog, Mfd, is similarly required for TCR of UV-induced lesions.\nMfd may be functionally distinct from its human CSB homolog in that it does not detectably contribute to the recovery of gene expression or global repair following oxidative damage.\nCSB has an ATPase activity that is stimulated strongly by DNA; however, it neither acts as a helicase nor does it dissociate stalled RNA polymerase II, suggesting a coupling mechanism in humans different from that in prokaryotes.\nIn addition, these findings imply that Mfd may be functionally distinct from its human CSB homolog in that it does not detectably contribute to the recovery of gene expression or global repair following oxidative damage.\nIn addition, these findings imply that Mfd may be functionally distinct from its human CSB homolog in that it does not detectably contribute to the recovery of gene expression or global repair following oxidative damage.\nIn contrast, no difference was detected in the rate of transcription recovery in mfd, uvrA, fpg, nth, or polB dinB umuDC mutants relative to wild-type cells following oxidative damage", "role": "user" }, { "content": "yes", "role": "assistant" } ]