task33_gene_extraction_linnaeus_dataset.json

{
    "Contributors": [
        "Ishani Mondal"
    ],
    "Source": [
        "Linnaeus Corpus"
    ],
    "URL": [
        "https://huggingface.co/datasets/linnaeus"
    ],
    "Categories": [
        "Named Entity Recognition"
    ],
    "Reasoning": [],
    "Definition": [
        "In this task, you are given a sentence. You are expected to recognize the name of gene or protein. Although there might be several correct answers, you need to write one of them."
    ],
    "Input_language": [
        "English"
    ],
    "Output_language": [
        "English"
    ],
    "Instruction_language": [
        "English"
    ],
    "Domains": [
        "Medical Knowledge"
    ],
    "Positive Examples": [
        {
            "input": "Sox - 4 is important for very early B - cell differentiation , while TCF - 1 / LEF - 1 play a crucial role in early thymocyte development ",
            "output": "TCF - 1",
            "explanation": "The gene, TCF - 1 has been tagged as protein since it plays a crucial role in early thymocyte development."
        },
        {
            "input": "The NF - kappaB / Rel family represents one signal transduction pathway induced during such activation .",
            "output": "NF - kappaB",
            "explanation": "NF - kappaB, protein transcription factor, should be tagged."
        }
    ],
    "Negative Examples": [
        {
            "input": "Sox - 4 is important for very early B - cell differentiation , while TCF - 1 / LEF - 1 play a crucial role in early thymocyte development",
            "output": "thymocyte",
            "explanation": "Thymocytes are the immune cells present in the thymus, before it undergoes transformation into a T cell. Therefore, it should not be tagged as gene."
        },
        {
            "input": "O5257 shows homology with the SAS2 protein and another hypothetical protein from yeast .",
            "output": "protein",
            "explanation": "It is expected to return the entire phrase of SAS2 Protein as protein mention, instead of only protein."
        }
    ],
    "Instances": [
        {
            "id": "task1484-8bb108eef82148ec946b01a38bd8ef02",
            "input": " The ineffectiveness of tobramycin combination therapy in Streptococcus faecium endocarditis .",
            "output": [
                "Streptococcus faecium"
            ]
        },
        {
            "id": "task1484-d40de19ca28f49d2aa1825c1cceec6bc",
            "input": " A patient required mitral valve replacement following ineffective antibiotic treatment of enterococcal endocarditis caused by Streptococcus faecium .",
            "output": [
                "Streptococcus faecium"
            ]
        },
        {
            "id": "task1484-7e7d8944a7724bf1a864510da25eeb48",
            "input": " Against Streptococcus faecium Isolates from Blood Cultures",
            "output": [
                "Streptococcus faecium"
            ]
        },
        {
            "id": "task1484-9a0d80e6a2b04490a7e9800214a2ee9c",
            "input": " ' Wennersten C , Moellering RC Jr : Mechanism of resistance to penicillin - aminoglycoside synergism in Streptococcus faecium .",
            "output": [
                "Streptococcus faecium"
            ]
        },
        {
            "id": "task1484-e7b6364b822049a6b2177f025bf08646",
            "input": " defective Streptococcus faecium strains .",
            "output": [
                "Streptococcus faecium"
            ]
        },
        {
            "id": "task1484-561293e1951749bfa0f9772bf0f57ce8",
            "input": " Fifteen microliter binding reactions were prepared , each consisting of 20 000 c . p . m . radiolabeled DNA probe , 5 micro g of crude protein extract , non - specific competitor DNAs ( 0 . 3 micro g of yeast tRNA , 0 . 3 micro g of salmon sperm DNA and 0 . 5 micro g of E . coli DNA ) , 10 micro g of BSA , 10 mM Tris - HCl ( pH 8 . 0 ) , 10 mM MgCl2 and 8 % glycerol .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-4c6da2c268c94291b2592a73f3c5ef56",
            "input": " The E . coli RdgC protein is a potential negative regulator of the function of RecA ( 1 ) .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-c2e2fa82082f4febbedf486d56a4f27d",
            "input": " Sedimentation equilibrium data indicated that E . coli RdgC exists in solution as a mixture of oligomeric states in equilibrium , most likely monomers , dimers and tetramers ( 1 ) .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-2127e781e19f40fa8b55dc3b3a066e7d",
            "input": " Deletion of the E . coli rdgC gene alone causes no obvious phenotype but is highly deleterious in strains lacking certain enzymes involved in recombination and replication restart ( 2 , 3 ) .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-54ca371245564c138617820a7c18576e",
            "input": " RdgC is essential for the growth of an E . coli strain lacking PriA , indicating that it might affect replication fork progression or fork rescue ( 2 ) .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-b4c00a51afc1497cac7923095ed0c3f8",
            "input": " However , no detectable domains or nuclease activity could be identified for the E . coli RdgC protein ( 2 , 6 ) .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-e1b548e441c3485999daaedf7c4612eb",
            "input": " The complexes of E . coli RdgC with both linear and supercoiled circular plasmid DNA were imaged using atomic force microscopy ( 7 ) .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-8ba784b08efb4d4dab5c017312542a0c",
            "input": " The protein was expressed in E . coli C41 ( DE3 ) cells ( 9 ) .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-8d8513aa64564b17bd3a399f2d1a49ca",
            "input": " This observation is consistent with the results of previous gel filtration and sedimentation equilibrium experiments , which suggested the presence of dimeric species of E . coli RdgC in solution ( 1 , 2 ) .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-62c625b85e0f4686921a8dab8f521137",
            "input": " Electron microscopy showed that the E . coli RuvB protein , in the presence of ATP , forms a dodecamer on double - stranded DNA in which two stacked hexameric rings encircle the DNA and are oriented in opposite directions with D6 symmetry ( 33 ) .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-e2a4cd25a40a45c6a06818d05309dd28",
            "input": " RdgC was at its highest level during exponential phase , reaching its maximum of ~ 1000 dimers per E . coli cell .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-35b6ea78ba1145d48ef70984da156426",
            "input": " RdgC protein was shown to have a potent effect on RecA protein - promoted DNA strand exchange in E . coli ( 1 ) .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-87b3913d24cb495aa837d78c95c18370",
            "input": " Tetrameric species of E . coli RdgC , which started to form at around 2 micro M concentrations , were speculated to be the species with the most potent inhibitory effect , possibly by having a higher affinity for DNA ( 1 ) .",
            "output": [
                "E . coli"
            ]
        },
        {
            "id": "task1484-defd56a9234e4f5da702aceff1f8c5f9",
            "input": " The HML and HMR loci in Saccharomyces cerevisiae are silent chromatin domains ( 1 ) .",
            "output": [
                "Saccharomyces cerevisiae"
            ]
        },
        {
            "id": "task1484-1c59cbc74a3141cea5623b4b5987ed15",
            "input": " We performed initial cell , cytokine and complement depletion studies to investigate the possible role of these effectors in response to vaccination with heat - killed Burkholderia mallei in a susceptible BALB / c mouse model of infection .",
            "output": [
                "Burkholderia mallei"
            ]
        },
        {
            "id": "task1484-777ad3847405477ab7a0f16a486071ea",
            "input": " Burkholderia mallei , the etiologic agent of glanders , is a gram - negative , capsulated , non - motile , facultative intracelluar bacterium .",
            "output": [
                "Burkholderia mallei"
            ]
        },
        {
            "id": "task1484-e0b4f787833b47c6aa0521f2b28c35a2",
            "input": " For example , entering the gene ID 403437 results in downloading the Brca1 gene sequence for Canis familiaris .",
            "output": [
                "Canis familiaris"
            ]
        },
        {
            "id": "task1484-78c464ef7a39438dbb53a056967d9ecc",
            "input": " We describe a 64 - year - old man with S . faecium endocarditis in whom a six - week course of ampicillin and tobramycin , followed by additional courses of penicillin and other aminoglycosides , failed to eradicate the organism from the patient ' s mitral valve .",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-2d11f7ad19984aecbaae9b9a69949d36",
            "input": " This case is of interest because therapeutic failure of ampicillin and tobramycin in S . faecium endocarditis has not been reported previously , but might have been predicted on the basis of previous in vitro and in vivo studies [ 6 ] .",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-00cc327e04e7403eaed78ac2a22fe6b3",
            "input": " Although the need for both a penicillin derivative and an aminoglycoside in the therapy of enterococcal endocarditis is widely known , it is important to distinguish between the differing efficacies of penicillin - aminoglycoside combinations for treating various species of enterococci such as S . faecium .",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-347fcda9a6804097a35b27443e266925",
            "input": " Three separate morphologic colony variants were isolated from blood , each identified as S . faecium by Dr . R . R .",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-49525b15280a42689642472d3329d743",
            "input": " S . faecium ( large colony morphotype , and poorly growing small colony morphotype ) grew from six sets of blood cultures obtained on admission .",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-5690642930e74be595fbace799f50ce7",
            "input": " Bacterial and fungal stains were negative but S . faecium grew from fragments of the resected valve .",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-44676017a99f48998b80105959cc013f",
            "input": " The minimum inhibitory and bactericidal concentrations of penicillin , ampicillin , and tobramycin against the S . faecium isolated from the patient ' s blood cultures",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-1f3d7480e994411196702cf83956f467",
            "input": " Organism Isolated MIC MIC MBC MIC MBC S . faecium , prior to ampicillin /",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-ef968ef2515f43a88843c99074fc8426",
            "input": " tobramycin therapy 3 / 17 / 81 2 1 2 > 32 > 32 S . faecium , after ampicillin /",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-ad72ebfb252c47d4946c38970758504c",
            "input": " Twenty - four hour time - kill curves for penicillin in combination with various aminoglycosides were performed by Dr . Robert Moellering on the S . faecium isolated from the patient ' s blood immediately prior to mitral valve excision and replacement ( Fig . 1 ) .",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-03e92f3112094fdb8257b4e2d7405907",
            "input": " Combinations of penicillin with kanamycin , tobramycin , sisomicin , and netilmicin have consistently failed to demonstrate synergistic killing of S . faecium in vitro [ 6 ] .",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-dde5f0ab3cfb417c9f58cd2e65e9adb2",
            "input": " Moellering et al . demonstrated in vivo , utilizing the rabbit model of endocarditis , that penicillin and netilmicin were not efficacious in the treatment of endocarditis caused by a low - level aminoglycoside - resistant strain of S . faecium [ 6 ] .",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-f135a4b3216b4b44a9f9f23afc5c5aee",
            "input": " In the present case , the recurrence of S . faecium endocarditis after six weeks of therapy with ampicillin and tobramycin confirms the therapeutic and clinical significance of their data , and emphasizes that tobramycin is not an aminoglycoside to be used for treatment of serious S . faecium infections .",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-720b09ebee8e45188f1b9c5e5c9cc926",
            "input": " MBCs were only slightly higher than MICs for the three S . faecium variants obtained from our patient , and they did not appear to be tolerant strains of S . faecium .",
            "output": [
                "S . faecium"
            ]
        },
        {
            "id": "task1484-a45685943cbf4fc09b6b7b3630e57f66",
            "input": " Lorian has also described the formation of numerous aberrant cross - walls by S . faecalis grown in the presence of subinhibitory concentrations of penicillin [ 15 ] .",
            "output": [
                "S . faecalis"
            ]
        },
        {
            "id": "task1484-a1c4324d17754d03abf6e71ce80a690d",
            "input": " gentamicin synergism in S . faecalis .",
            "output": [
                "S . faecalis"
            ]
        },
        {
            "id": "task1484-813587d5875141b5897634491f661de4",
            "input": " However , the lack of crossed recognition of cox2 promoters in wheat and potato is not a general situation since the A . thaliana cox2 gene is expressed and spliced when introduced into maize mitochondria , indicating that the Arabidopsis gene shares some signals with maize cox2 promoter that are sufficient for transcription ( 18 ) .",
            "output": [
                "A . thaliana"
            ]
        },
        {
            "id": "task1484-edf9e9a3864d454199b74b455198d266",
            "input": " The sites required for transcript initiation have been recently described in A . thaliana mitochondrial genes ( 28 ) .",
            "output": [
                "A . thaliana"
            ]
        },
        {
            "id": "task1484-229c06126a3a4b528d22e7ad2e774fc3",
            "input": " Turgor pressure measurements on leaf cells of T . voinierianum were difficult to perform because of the presence of mucilage .",
            "output": [
                "T . voinierianum"
            ]
        },
        {
            "id": "task1484-b2aef4bfad374787a04576242b63ed51",
            "input": " Experience collected with patch clamp pressure measurements on T . voinierianum and on preliminary results of other plants ( e . g . grapevines , bananas , Eucalyptus , and Arabidopsis ) showed that a smooth intercostal leaf area for clamping can readily be found .",
            "output": [
                "T . voinierianum"
            ]
        },
        {
            "id": "task1484-331e4a459c2642ee99a51cd54e483676",
            "input": " 4A and B , restoration of full turgescence in T . voinierianum was faster than the preceding turgor pressure loss if the lianas were well - watered .",
            "output": [
                "T . voinierianum"
            ]
        },
        {
            "id": "task1484-297d70d725cc4919852625265f97ac10",
            "input": " Even though more work is required , the present study shows that the leaf patch clamp pressure probe is a promising tool to elucidate short - and long - distance water transport in T . voinierianum and other plants .",
            "output": [
                "T . voinierianum"
            ]
        },
        {
            "id": "task1484-64e020a95f934540b9bbd9ae85bbfcd6",
            "input": " Here , we have determined the crystal structure of RdgC from Pseudomonas aeruginosa .",
            "output": [
                "Pseudomonas aeruginosa"
            ]
        },
        {
            "id": "task1484-9748473e2445439e9a6c0f516fa5feef",
            "input": " Pseudomonas aeruginosa is a ubiquitous environmental Gram - negative bacterium that belongs to the gamma subdivision of the Proteobacteria .",
            "output": [
                "Pseudomonas aeruginosa"
            ]
        },
        {
            "id": "task1484-f4b096dc2d35401bb7f3d4c37de18cee",
            "input": " In S . cerevisiae , there is evidence that Sir3p ( hence the SIR complex ) has much higher affinity to unacetylated histone H4 than acetylated H4 ( 5 ) .",
            "output": [
                "S . cerevisiae"
            ]
        },
        {
            "id": "task1484-6b6b9473cd3e429fb264ebbc4ebaa90c",
            "input": " Recently , sequences that could block the spread of silent chromatin have been discovered in S . cerevisiae ( 7 , 8 ) .",
            "output": [
                "S . cerevisiae"
            ]
        },
        {
            "id": "task1484-7f7638cd2e1d4a22a1f003d34cdbd0b1",
            "input": " in Streptococcus Faecium Endocarditis",
            "output": [
                "Streptococcus Faecium"
            ]
        },
        {
            "id": "task1484-6c584de9a97e4e70b752fbaced322854",
            "input": " Non - commercial antibodies used were : BC2 , a mouse monoclonal to the MUC1 - EX ( gift of Dr McGuckin , Queensland University , Queensland , Australia ) , and CT2 , an Armenian hamster monoclonal to the MUC1 - CT developed in our lab [ 12 ] .",
            "output": [
                "Armenian hamster"
            ]
        },
        {
            "id": "task1484-111d49e6f3aa416ebf81cc00e4034261",
            "input": " Rosevalt tubers and T . aestivum var Fortal seeds were used .",
            "output": [
                "T . aestivum"
            ]
        },
        {
            "id": "task1484-3269365054cd4ead8ee80d4c17c4a1af",
            "input": " The potato rps10 gene controlled by a T . aestivum promoter ( Figure 1A ) was transcribed as a 1204 nt precursor in wheat mitochondria , but no traces of mature RNA were observed .",
            "output": [
                "T . aestivum"
            ]
        },
        {
            "id": "task1484-aa2d4014c8d849c0bc938041450a62ad",
            "input": " In Arabidopsis thaliana 456 C - to - U editing events have been described ( 6 ) .",
            "output": [
                "Arabidopsis thaliana"
            ]
        },
        {
            "id": "task1484-a9c9ab2e3d0246f38404a58032e14be1",
            "input": " To challenge the ability of mitochondrial gene expression machinery to recognize genetic information which has been lost during evolution , we decided to introduce the S . tuberosum non - cognate rps10 gene into wheat mitochondria .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-fc8b39f6b1c5419797410321e8865c8f",
            "input": " To test this hypothesis , it was necessary to set up the conditions for electroporation of foreign DNA into S . tuberosum mitochondria .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-0e2d62dc013c4c869fe1855b51b63ec1",
            "input": " S . tuberosum cox2 gene , including a 727 bp non - coding upstream region , was isolated by PCR from total DNA using the primer A designed from partial sequences reported by L o essl et al .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-75396a2d006643e6bb762110a354f261",
            "input": " The complete sequence of the S . tuberosum cox2 was determined ( accession no . DQ18064 ) .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-f2620f3e9169427f817dc27b2ab14db1",
            "input": " To generate the plasmid pCOXIISt containing the S . tuberosum cox2 gene , a KpnI / SpeI fragment containing the 727 bp upstream region and the complete coding region was used to replace the wheat gene from pCOXII .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-f5ca6c491dfa41eda1679c6c193fbc06",
            "input": " The coding region was isolated from total S . tuberosum DNA by PCR using primers D1 and D2 containing the restriction sites NsiI and SpeI , respectively .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-f25ad20a77c847ff893f450e66d2067e",
            "input": " S . tuberosum cv .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-6ff858527f4c401f9e43cfff5f0b42f0",
            "input": " S . tuberosum rps10 transcripts are not processed in wheat mitochondria",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-3b55f798cdc647a2bd938b5402c1e791",
            "input": " The S . tuberosum rps10 construct under control of a wheat cox2 promoter ( Figure 1A ) was incorporated into purified wheat mitochondria by electroporation as indicated in Materials and Methods .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-8c24b65bd52946d2916691a981f67264",
            "input": " Electroporation of S . tuberosum mitochondria",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-78618c8c586444bdbdf7490b44b709da",
            "input": " Since two important post - transcriptional processes , RNA editing and splicing , were inoperative when S . tuberosum rps10 was expressed in wheat mitochondria , we decided to verify whether the negative results were inherent to the rps10 chimeric constructs or due to the lack of trans - recognition elements in wheat mitochondria .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-f9f74b3fc45b460ca500746d419d99b1",
            "input": " For this purpose , it was necessary to set up an electroporation protocol adapted to S . tuberosum mitochondria .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-a74ffd447e294daca6f9a5abe0963960",
            "input": " S . tuberosum mitochondria does not recognize the wheat cox2 promoter",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-2900b0bda0c04b95843f5b4305ad82e3",
            "input": " The construct expressing potato rps10 under the control of potato cox2 promoter was introduced into S . tuberosum isolated mitochondria .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-b7a0f2251d6a43ed83446f0f3f9a775d",
            "input": " The analogous MAb and ME6b constructs , containing the S . tuberosum cox2 promoter and the C259 region inserted into rps10 exon 1 and intron were used to electroporate potato mitochondria .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-c1c1bb1d13db4dc08c211457af1bad8c",
            "input": " To best evaluate the expression of rps10 in the non - cognate mitochondria , it was necessary to set up electroporation conditions for introducing foreign DNA into S . tuberosum mitochondria .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-9b47e00e812a462cb0d433f138967df9",
            "input": " Based on the canonical structure of group II mitochondrial introns ( 21 ) , two editing sites , C2 located at the Intron Binding Site 2 ( IBS2 ) and C3 located in the intron , nine residues downstream from the end of exon 1 in S . tuberosum rps10 are of particular interest .",
            "output": [
                "S . tuberosum"
            ]
        },
        {
            "id": "task1484-b05669ed7c004275971453b005864614",
            "input": " The power function Tf = f ( Pc ) theoretically derived was experimentally confirmed by concomitant Pp and Pc measurements on intact leaflets of the liana Tetrastigma voinierianum under greenhouse conditions .",
            "output": [
                "Tetrastigma voinierianum"
            ]
        },
        {
            "id": "task1484-50fc5fca55274dff870daf7f8f16205a",
            "input": " This could be verified by combined turgor pressure probe and leaf patch clamp pressure probe measurements on leaflets of the liana Tetrastigma voinierianum .",
            "output": [
                "Tetrastigma voinierianum"
            ]
        },
        {
            "id": "task1484-23aff3ddc68c44f88333481f45846bab",
            "input": " Experiments were performed on two specimens of the liana Tetrastigma voinierianum , growing in the c .",
            "output": [
                "Tetrastigma voinierianum"
            ]
        },
        {
            "id": "task1484-34f0b1d72c954c518840964d37ad8795",
            "input": " Most known members of the Burkholderiaceae are resident in the soil ; however , B . mallei is thought to be an obligate mammalian pathogen .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-eca30ff40a104980bf76108ea119541f",
            "input": " Naturally acquired human infection with B . mallei , although not seen in the United States since 1945 , has occurred rarely and sporadically among laboratory workers and those in direct contact with infected animals [ 2 ] .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-96a828bd408b4d83af58f75b3aa1e6f1",
            "input": " Inhalation of aerosol or dust containing B . mallei can lead to septicemic , pulmonary , or chronic infections of the muscle , liver and spleen .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-1df558b3b5f2472cbcf6a3821f326e86",
            "input": " Previous studies with B . mallei and the host response have shown that a mixed immune response consisting of both Th1 and Th2 - associated cytokines with a predominant IgG1 subclass does not correlate with protection [ 4 ] .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-4466c70c2e624b7ab392a311005a2e39",
            "input": " Additional studies with passive transfer of monoclonal antibodies specific for B . mallei have correlated with early protection from infection [ 5 ] .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-ea07cd3e982c4dd8b5fd784ef25cd8eb",
            "input": " Recent studies have also shown the Th1 cytokine IL - 12 to mediate partial protection to non - viable B . mallei - vaccinated mice [ 6 ] .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-58ec4811d53b4dd79ba341fac2aa9143",
            "input": " Thus , full correlates of protection mediated by the adaptive immune system against B . mallei remain to be fully elucidated .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-983d2235c0c741d7b09e927ddc3bbc64",
            "input": " Heat killed bacteria were used as a model of vaccination to allow evaluation of B . mallei specific immune responses .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-588b3ffa44fd419c8966fe66a3473c73",
            "input": " Heat - killed B . mallei vaccination mediates partial protection from lethal challenge",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-808cc7539b7141a497b6f8b95300da62",
            "input": " The administration of vaccines for B . mallei during an outbreak would mandate relatively rapid onset of protection for human or veterinary use .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-f59c3bc758094bf1880175301bdad41b",
            "input": " Our results indicate that HK vaccination can afford partial protection to an otherwise lethal challenge of B . mallei by the i . p . route .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-0e2bd5bbf6bd4063af5147b048855de4",
            "input": " To further evaluate the host TNF - alpha response during an established B . mallei chronic infection , we infected 12 BALB / c mice by the i . p . route with 1 x 106 CFU B . mallei .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-31b1c22c8a334c73bc01f0e1c09a75d2",
            "input": " Results indicated enhanced bacterial uptake in J774A . 1 phagocytes inoculated with serum treated B . mallei ( p = . 0082 ) , compared to B . mallei alone , while heat - inactivated serum produced uptake percentages similar to those prior to serum addition ( Fig . 6 ) .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-1b5c01ec37de41a4a7bd7fb3dbe3e3dc",
            "input": " Thus , loss or reduction of TNF - alpha and IFN - gamma levels result in significantly reduced survival rates , substantiating previous reports of the role of these factors in protection against B . mallei [ 7 ] .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-a6206673d65a4057aa71afd59b0d4b03",
            "input": " Moreover , we demonstrate a role for sustained TNF - alpha production in the maintenance of host survival throughout the course of B . mallei infection .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-005644cfd7cd46ada6fdc292b2532786",
            "input": " Mice with an established B . mallei chronic infection rapidly lost the ability to control the growth of the bacillus upon neutralization of TNF - alpha .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-d133d696061c4df397dbbd329a18caa0",
            "input": " Additional studies are underway to determine more precisely the role of TNF - alpha in host protection to B . mallei .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-7b39a315241a43a7b2bae09768668f95",
            "input": " Multiple innate and adaptive cell types may contribute to the production of IFN - gamma in response to infection with B . mallei following vaccination .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-21b25147cb554f6b99effddc78496da6",
            "input": " The effector role for IFN - gamma in mediating protection against B . mallei may include both immunoregulatory and non - regulatory functions .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-e9dc1b061c5744feab1921eda59d88f3",
            "input": " Regardless , the requirement of IFN - gamma , as demonstrated by administration of neutralizing antibody prior to infection , indicates that stimulation of IFN - gamma response is a desirable goal for a B . mallei vaccine .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-a5cb8a513f2049208bcb918f49d1ede5",
            "input": " Similarly , B220 - positive cells appear to play a role in protection following vaccination with heat - killed B . mallei .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-a530e5fb1da64c9eaab5121a0b6d83e9",
            "input": " Although CD8 - / - C57BL / 6 demonstrated no decreased survival in our HK - vaccinated model , a lack of potential endogenous protein production by HK B . mallei may have contributed to limited MHC - I presentation .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-3771d1133b51400790644b35fd07a67a",
            "input": " Complement associated studies revealed increased J774A . 1 uptake of serum - treated B . mallei .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-dfc198631ff0400ab59916249d2bda9d",
            "input": " Previous studies have demonstrated that a polysaccharide capsule is present in B . mallei , [ 14 , 15 ] although in the present study enhanced uptake with serum - treated B . mallei was observed .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-a290dfe7168e41a98b2cdf133af2c27e",
            "input": " Previous reports have demonstrated the ability of B . mallei to survive within macrophage without the aid of serum coating organisms [ 16 ] .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-717193081f144d6f9de1253c93ee1329",
            "input": " The current results suggest that cobra venom factor treatment may affect the modulation of the immune response to B . mallei infection through B cell activation and / or memory B cell generation .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-6e9420c7e7294ef28d0fcf461ffa71e5",
            "input": " Understanding and defining the role of B cells in adaptive B . mallei immunity will likely be fundamental to the design of an efficacious vaccine and important goals of future research .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-192d081458544373a53ba765956e1fd5",
            "input": " B . mallei strain ATCC 23344 ( China 7 ) was cultured on Luria - Bertani agar supplemented with 4 % glycerol ( LB + 4 % G ) agar plates for 48 h at 37 degrees C .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-edad50c906a344959db3f16e34b04d85",
            "input": " The absence of live B . mallei organisms in the HK preparations was confirmed after plating 10 % of the total inoculums ( v / v ) and incubating these at 37 degrees C for 48 h .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-789b8c45356b472aafeb3c5e3d9ada5f",
            "input": " BALB / c and C57BL / 6 mice were grouped and vaccinated with 0 . 5 mu g of HK B . mallei ( without adjuvant ) by i . p . injection using a 25 - gauge syringe .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-34917bf69121464a83e614b8e854f162",
            "input": " Two weeks post HK vaccination mice were injected i . p . with 2 x 107 CFU / 100 mu l of live B . mallei ( ~ 20 LD50 ) [ 18 ] .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-69fd1c135b9e4010a601e9980e88ed65",
            "input": " Mice , six to seven per group , were vaccinated i . p . with 1 x 105 CFU of nonviable B . mallei cell preparation in a total volume of 0 . 1 ml .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-30aa97fb56964262a10ade471d73e005",
            "input": " B . mallei J774A . 1 uptake assays",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-24dfc59a88134a8b9826f9ba754a4f95",
            "input": " B . mallei antigen was diluted in 0 . 1 M carbonate buffer ( pH 9 . 5 ) and 50 mu l of diluted cells placed into wells .",
            "output": [
                "B . mallei"
            ]
        },
        {
            "id": "task1484-951bc17aca074e788409cd00ea1b9b88",
            "input": " Gene expression studies in isolated mitochondria : Solanum tuberosum rps10 is recognized by cognate potato but not by the transcription , splicing and editing machinery of wheat mitochondria",
            "output": [
                "Solanum tuberosum"
            ]
        },
        {
            "id": "task1484-56bdbb12b5c64bd8a3ee9e1caece8fcf",
            "input": " Of particular interest is the situation of the small ribosomal protein 10 gene ( rps10 ) , a group II intron - bearing gene which is encoded in Solanum tuberosum mitochondrial DNA but is absent from the wheat mitochondrial genome ( 20 ) .",
            "output": [
                "Solanum tuberosum"
            ]
        },
        {
            "id": "task1484-48ec21ee094245de890abaf3e3b90743",
            "input": " Here , we report the crystal structure of P . aeruginosa RdgC as determined by the multiwavelength anomalous diffraction ( MAD ) method of X - ray crystallography .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-a23afeae8bee4baa9e1d67bafbc22a62",
            "input": " The rdgC gene ( PA3263 ) was amplified by the polymerase chain reaction ( PCR ) using the genomic DNA of P . aeruginosa strain PAO1 as a template .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-6fd131f817d94fe2b135a5609ebeec07",
            "input": " The structure of P . aeruginosa RdgC was solved using two sets of MAD data collected from a crystal of the selenomethionine ( SeMet ) - substituted protein and from a mercury derivative crystal of the native protein ( Supplementary Table 1 ) .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-9a3d5d46eb214fadbca304329f6f58fc",
            "input": " The P . aeruginosa RdgC monomer is J - shaped and has approximate dimensions of 72 A x 60 A x 40 A ( Figure 1 ) .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-28badf80e3e942e9aa88ffd394b298ee",
            "input": " When we searched for structural similarity against the Protein Data Bank database using the program DALI ( 18 ) , the P . aeruginosa RdgC monomer showed no significant similarity with a Z score above 5 .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-4709a9dd0bdb4416880a521bdd3ad20f",
            "input": " When we elaborated the structural comparisons with individual domains of P . aeruginosa RdgC , only the center domain gave a Z score above 5 .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-0c27c3f2a96d433b9e9320cc2cc4813f",
            "input": " Using the center domain ( residues 1 - 73 and 121 - 167 ) alone , the highest structural similarity is found with the human beta 2 - adaptin appendage domain ( PDB code 1E42 , Z score = 7 . 1 , r . m . s . deviation = 2 . 5 A for 85 structurally aligned residues , residues 1 - 12 , 14 - 30 , 44 - 47 , 58 - 72 , 122 - 133 and 135 - 160 of P . aeruginosa RdgC chain A and residues 838 - 841 , 848 - 880 , 885 - 906 and 912 - 967 of the human beta 2 - adaptin appendage domain chain A ) ( 19 ) .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-51dd8f90b85447bb965e29253896801d",
            "input": " The next highest similarity is found with the yeast TATA - box - binding protein ( PDB code 1YTB , Z score = 5 . 7 , r . m . s . deviation = 2 . 6 A for 79 structurally aligned residues , residues 4 - 12 , 14 - 19 , 21 - 27 , 56 - 70 , 124 - 132 and 134 - 166 of P . aeruginosa RdgC chain A and residues 69 - 96 , 100 - 126 and 132 - 155 of TATA - box - binding protein , N - terminal half of chain A ) ( 20 ) .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-ba1d013d75da4ac6b4b3401cda202842",
            "input": " Using the tip domain ( residues 74 - 120 ) alone , the ATPase domain of bovine Hsc70 chaperone shows highest structural similarity ( PDB code 1BA1 , Z score = 4 . 8 , r . m . s . deviation = 1 . 7 A for 45 structurally aligned residues , residues 76 - 120 of P . aeruginosa RdgC chain A and residues 230 - 253 and 256 - 276 of the Hsc70 ATPase domain ) ( 21 ) .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-f2fa5d5e079944308265b01b22fd1e49",
            "input": " However , the tip domain of P . aeruginosa RdgC protein does not have such a sequence motif , and the loop in the RdgC tip domain is much more extended than that of the HhH motifs .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-c61fe85d3ecc4982a086d097f0ad7be7",
            "input": " With the base domain ( residues 168 - 306 ) alone , the highest similarity is found with P . aeruginosa isochorismate - pyruvate lyase ( unpublished deposition ; PDB code 2H9C , Z score = 4 . 0 , r . m . s . deviation = 4 . 8 A for 51 structurally aligned residues , residues 186 - 191 , 237 - 240 , 257 - 272 and 274 - 298 of P . aeruginosa RdgC chain A and residues 36 - 41 , 50 - 53 , 55 - 66 and 68 - 96 of P . aeruginosa isochorismate - pyruvate lyase chain A ) .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-875b6845da1c4b7cbd6361b8e75ab9fd",
            "input": " The 101 - residue chain of P . aeruginosa isochorismate - pyruvate lyase is folded into three alpha - helices , two of which overlap with two alpha - helices ( alpha 2 and alpha 3 ) of the base domain of RdgC .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-537ab3a04397489da7c01d7e6ff165b3",
            "input": " Our structure reveals that P . aeruginosa RdgC forms a ring - shaped dimer of approximate 2 - fold symmetry in the crystal ( Figure 1 ) .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-20642cb9685a4b86b68e65cca362a2c6",
            "input": " The net charge of P . aeruginosa RdgC is highly negative , since each monomer contains 12 aspartate , 13 glutamate , 10 lysine , 9 arginine and 2 histidine residues .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-8cc3bd2da8a64dcda069e73f43320906",
            "input": " ATP was not required for dsDNA binding by P . aeruginosa RdgC , either ( Supplementary Figure 2 ) .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-f941113466da449e884daecb4b159d6d",
            "input": " In P . aeruginosa RdgC , the inner surface of the ring - shaped dimer is largely formed by beta - strands , while the outer surface of the ring is mostly formed by alpha - helices ( Figure 5 ) .",
            "output": [
                "P . aeruginosa"
            ]
        },
        {
            "id": "task1484-68a2bf6d45cb45d78d2bbd8fe63b4ed3",
            "input": " The predicted DNA - binding site of P . aeruginosa RdgC dimer is primarily formed by beta - strands and loops .",
            "output": [
                "P . aeruginosa"
            ]
        }
    ],
    "Instance License": [
        "Unknown"
    ]
}