instruction stringlengths 225 2.35k | input stringlengths 89 1.5k | response stringclasses 698
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<Instruct>: Given the context 'First identified in chicken, vigilin homologues have now been found in human (6), Xenopus laevis (7), Drosophila melanogaster (8), C.elegans (5) and Schizosaccharomyces pombe.', select the correct biomedical concept for each mention using the provided options. Answer by listing the select... | <Mentions>: [chicken; human; xenopus laevis; drosophila melanogaster]
<Options>: A: gallus sp.
B: avian (aka aves)
C: kingdom
D: gallus gallus (gallus gallus domesticus) (aka gallus gallus)
E: suborder
F: flies (aka diptera)
G: fruit fly (aka drosophila <flies,genus>)
H: human (aka homo sapiens)
I: xenopus <genus> (xen... | [D; H; N; P] |
<Instruct>: Given the context 'First identified in chicken, vigilin homologues have now been found in human (6), Xenopus laevis (7), Drosophila melanogaster (8), C.elegans (5) and Schizosaccharomyces pombe.', select the correct biomedical concept for each mention using the provided options. Answer by listing the select... | <Mentions>: [chicken; human; xenopus laevis; drosophila melanogaster]
<Options>: A: melanogaster group
B: fruit fly (aka drosophila melanogaster)
C: xenopus laevis tropicalis (aka xenopus tropicalis)
D: gallus gallus gallus (gallus gallus philippensis) (aka gallus gallus gallus)
E: drosophila (aka drosophila <flies,gen... | [M; P; I; B] |
<Instruct>: Given the context 'First identified in chicken, vigilin homologues have now been found in human (6), Xenopus laevis (7), Drosophila melanogaster (8), C.elegans (5) and Schizosaccharomyces pombe.', select the correct biomedical concept for each mention using the provided options. Answer by listing the select... | <Mentions>: [chicken; human; xenopus laevis; drosophila melanogaster]
<Options>: A: mammals (aka mammalia)
B: gallus gallus gallus (gallus gallus philippensis) (aka gallus gallus gallus)
C: clawed frog (aka xenopus laevis)
D: drosophila melanogaster (sophophora melanogaster) (aka drosophila melanogaster)
E: homo sapien... | [L; E; C; D] |
<Instruct>: Given the context 'First identified in chicken, vigilin homologues have now been found in human (6), Xenopus laevis (7), Drosophila melanogaster (8), C.elegans (5) and Schizosaccharomyces pombe.', select the correct biomedical concept for each mention using the provided options. Answer by listing the select... | <Mentions>: [chicken; human; xenopus laevis; drosophila melanogaster]
<Options>: A: animals (aka metazoa)
B: gallorhynchus
C: miletus gallus gallus
D: gallus
E: drosophila (aka drosophila <basidiomycete fungi>)
F: homo sapiens (human) (aka homo sapiens)
G: xenopus laevis laevis (bufo laevis laevis) (aka xenopus laevis ... | [J; F; K; N] |
<Instruct>: Given the context 'First identified in chicken, vigilin homologues have now been found in human (6), Xenopus laevis (7), Drosophila melanogaster (8), C.elegans (5) and Schizosaccharomyces pombe.', select the correct biomedical concept for each mention using the provided options. Answer by listing the select... | <Mentions>: [c.elegans; schizosaccharomyces pombe]
<Options>: A: caenorhabditis sp.
B: enyo elegans (aka zodarion elegans)
C: schizosaccharomyces japonicus var. japonicus (aka schizosaccharomyces japonicus)
D: elegans subgroup (in: flies)
E: schizosaccharomycetes (archiascomycota) (aka schizosaccharomycetes)
F: schizos... | [G; J] |
<Instruct>: Given the context 'First identified in chicken, vigilin homologues have now been found in human (6), Xenopus laevis (7), Drosophila melanogaster (8), C.elegans (5) and Schizosaccharomyces pombe.', select the correct biomedical concept for each mention using the provided options. Answer by listing the select... | <Mentions>: [c.elegans; schizosaccharomyces pombe]
<Options>: A: caenorhabditis elegans (rhabditis elegans) (aka caenorhabditis elegans)
B: schizosaccharomyces
C: schizosaccharomycetales
D: fission yeast (aka schizosaccharomyces pombe)
E: gongylostoma elegans elegans (clausilia elegans elegans) (aka gongylostoma elegan... | [A; D] |
<Instruct>: Given the context 'For example, Kruse and colleagues reported from their work with human cells in culture that vigilin may be involved in the binding and transport of tRNA (9–11).', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one... | <Mentions>: [human]
<Options>: A: probles
B: mammals (aka mammalia)
C: human (aka homo sapiens)
D: placental mammals (aka eutheria)
E: kingdom
F: None of the above. | [C] |
<Instruct>: Given the context 'The goal of the present study was to begin elucidating the function of Scp160p in yeast by characterizing the subcellular distribution and macromolecular interactions of this protein.', select the correct biomedical concept for each mention using the provided options. Answer by listing th... | <Mentions>: [yeast]
<Options>: A: mycoderma cerevisiae (aka saccharomyces cerevisiae)
B: saccharomycodes
C: saccharomyceta
D: saccharomyces albicans (aka candida albicans)
E: saccharomyces cf. cerevisiae
F: None of the above. | [A] |
<Instruct>: Given the context 'These results indicate a role for Scp160p in mRNA metabolism in yeast, and by extension, support results seen with Xenopus vigilin in its interactions with mRNA.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, on... | <Mentions>: [yeast]
<Options>: A: saccharomyces sp.
B: saccharomyceta
C: saccharomyces cerevisiae or paradoxus (aka saccharomyces cf. cerevisiae/paradoxus)
D: saccharomyces cerevisiae (desm.) meyen ex e.c. hansen, 1883 (aka saccharomyces cerevisiae)
E: saccharomyces lactis (aka kluyveromyces lactis)
F: None of the abov... | [D] |
<Instruct>: Given the context 'To our knowledge, the data reported here demonstrate Scp160p to be the first example of a KH-domain protein that functions as a component of polyribosome-associated mRNP complexes in the yeast, S.cerevisiae.
MATERIALS AND METHODS
Plasmids, yeast strains and culture conditions
All recombi... | <Mentions>: [yeast; s.cerevisiae; e.coli]
<Options>: A: saccharomyces cf. cerevisiae
B: unspecified coliform bacterium
C: saccharomyces cerevisiae x saccharomyces mikatae
D: saccharomyces cerevisiae or paradoxus (aka saccharomyces cf. cerevisiae/paradoxus)
E: saccharomyceta
F: saccharomyces cerevisiae x saccharomyces p... | [G; G; L] |
<Instruct>: Given the context 'To our knowledge, the data reported here demonstrate Scp160p to be the first example of a KH-domain protein that functions as a component of polyribosome-associated mRNP complexes in the yeast, S.cerevisiae.
MATERIALS AND METHODS
Plasmids, yeast strains and culture conditions
All recombi... | <Mentions>: [yeast; s.cerevisiae; e.coli]
<Options>: A: saccharomyceta
B: escherichia coli k12 (aka escherichia coli k-12)
C: escherichia phage
D: escherichia/shigella coli (aka escherichia coli)
E: saccharomycetes (hemiascomycetes) (aka saccharomycetes)
F: saccharomyces cf. cerevisiae
G: enterobacteriales (aka enterob... | [J; J; D] |
<Instruct>: Given the context 'To our knowledge, the data reported here demonstrate Scp160p to be the first example of a KH-domain protein that functions as a component of polyribosome-associated mRNP complexes in the yeast, S.cerevisiae.
MATERIALS AND METHODS
Plasmids, yeast strains and culture conditions
All recombi... | <Mentions>: [yeast; s.cerevisiae; e.coli]
<Options>: A: saccharomyces cerevisiae x saccharomyces mikatae
B: 'escherichia faecalis' (aka escherichia faecalis)
C: saccharomyceta
D: prokaryotes (aka bacteria)
E: saccharomyces cerevisiae x saccharomyces uvarum
F: enterobacteria (aka enterobacteriaceae)
G: budding yeasts & ... | [J; J; M] |
<Instruct>: Given the context 'The yeast strain JFy1511, expressing FLAG–Scp160p, was derived by two-step gene replacement from strain yJJ52 (MATα gal7Δ102 ura3-52 trp1-289 ade1 lys1 leu2-3, 112; generously donated by Drs Mark Parthun and Judith Jaehning, University of Colorado Health Sciences Center), and confirmed by... | <Mentions>: [yeast]
<Options>: A: candida/saccharomycetales (aka candida/saccharomycales clade)
B: saccharomycetes (hemiascomycetes) (aka saccharomycetes)
C: saccharomyces sp.
D: saccharomyces lactis (aka kluyveromyces lactis)
E: brewer's yeast (aka saccharomyces cerevisiae)
F: None of the above. | [E] |
<Instruct>: Given the context 'The N-terminally HA-tagged allele of BFR1 was generated by PCR-amplifiction of the BFR1 locus from wild-type (W303) yeast genomic DNA using the primers BFR1HAF1 (5′-CCGCGGATCCATGTACC-CATACGACGTCCCAGACTACGCTATGTCCTCCCAAC-AACACAA-3′) and BFR1HINDR1 (5′-CCGCAAGCTTGTCG-ACTATTTCATATGCCACAGGAAA... | <Mentions>: [yeast]
<Options>: A: saccharomyces cf. cerevisiae/paradoxus (saccharomyces cerevisiae or paradoxus) (aka saccharomyces cf. cerevisiae/paradoxus)
B: saccharomyces cerevisiae x saccharomyces mikatae
C: baker's yeast (aka saccharomyces cerevisiae)
D: saccharomyces hansenii (aka debaryomyces hansenii)
E: sacch... | [C] |
<Instruct>: Given the context 'Finally, the HA–BFR1 allele was substituted into the yeast genome in place of the native allele using linearization with SphI and standard two-step gene replacement techniques.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selec... | <Mentions>: [yeast]
<Options>: A: candida/saccharomycetales (aka candida/saccharomycales clade)
B: saccharomyces cf. cerevisiae
C: saccharomycetes (hemiascomycetes) (aka saccharomycetes)
D: saccharomyces cerevisiae x saccharomyces mikatae
E: baker's yeast (aka saccharomyces cerevisiae)
F: None of the above. | [E] |
<Instruct>: Given the context 'All yeast transformations and culture manipulations were performed according to standard protocols as described elsewhere (19).
', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each mention, separated by... | <Mentions>: [yeast]
<Options>: A: saccharomyces cf. cerevisiae/paradoxus (saccharomyces cerevisiae or paradoxus) (aka saccharomyces cf. cerevisiae/paradoxus)
B: candida/saccharomycetales (aka candida/saccharomycales clade)
C: true yeasts (aka saccharomycotina)
D: saccharomyces hansenii (aka debaryomyces hansenii)
E: my... | [E] |
<Instruct>: Given the context 'Confirmation of genomic integrations
All genomic integrations were confirmed by PCR amplifications from purified yeast genomic DNA.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each mention, separated ... | <Mentions>: [yeast]
<Options>: A: candida/saccharomycetales (aka candida/saccharomycales clade)
B: true yeasts (aka saccharomycotina)
C: saccharomyces albicans (aka candida albicans)
D: saccharomyces cf. cerevisiae
E: brewer's yeast (aka saccharomyces cerevisiae)
F: None of the above. | [E] |
<Instruct>: Given the context 'Confirmation of genomic integrations
All genomic integrations were confirmed by PCR amplifications from purified yeast genomic DNA.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each mention, separated ... | <Mentions>: [yeast]
<Options>: A: saccharomyces albicans (aka candida albicans)
B: true yeasts (aka saccharomycotina)
C: saccharomyces cf. cerevisiae
D: candida/saccharomycetales (aka candida/saccharomycales clade)
E: None of the above. | [E] |
<Instruct>: Given the context 'In brief, a 100 ml culture of yeast was grown in either YEPD or Hartwell synthetic medium, to early-log phase (OD600 = 1.0), at which time cyclohexamide (Sigma) was added directly to the culture to a final concentration of 100 µg/ml.', select the correct biomedical concept for each mentio... | <Mentions>: [yeast]
<Options>: A: saccharomyces cerevisiae (saccharomyces cerevisiae (desm.) meyen ex e.c. hansen, 1883) (aka saccharomyces cerevisiae)
B: saccharomyces lactis (aka kluyveromyces lactis)
C: saccharomycodes
D: saccharomyces cf. cerevisiae
E: saccharomyces cf. cerevisiae/paradoxus (saccharomyces cerevisia... | [A] |
<Instruct>: Given the context 'The column had been calibrated previously using the following molecular weight standards (Sigma): blue dextran (2000 kDa), thyroglobulin (669 kDa), apoferritin (443 kDa), alcohol dehydrogenase (150 kDa), and bovine serum albumin (66 kDa).', select the correct biomedical concept for each m... | <Mentions>: [bovine]
<Options>: A: bos bubalis (aka bubalus bubalis)
B: bovidae
C: cattle (aka bos)
D: domestic cattle (aka bos taurus)
E: bos taurus x bos indicus (aka bos indicus x bos taurus)
F: None of the above. | [D] |
<Instruct>: Given the context 'Yeast were lysed as described for polyribosome analysis, with an additional clarification by passage through a 0.2 µm syringe-tip filter (Acrodisc) and run over the column at a rate of 0.5 ml/min in polyribosome lysis buffer following treatment with the indicated reagents.', select the co... | <Mentions>: [yeast]
<Options>: A: saccharomycodes
B: saccharomyces cerevisiae x saccharomyces mikatae
C: saccharomyces albicans (aka candida albicans)
D: saccharomyces sp.
E: saccharomyces cerevisiae (desm.) meyen ex e.c. hansen, 1883 (aka saccharomyces cerevisiae)
F: None of the above. | [E] |
<Instruct>: Given the context 'α-FLAG affinity chromatography
For most experiments, one liter yeast cultures were grown to early log-phase and harvested by centrifugation.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each mention, s... | <Mentions>: [yeast]
<Options>: A: saccharomyces cf. cerevisiae
B: candida/saccharomycetales (aka candida/saccharomycales clade)
C: mycoderma cerevisiae (aka saccharomyces cerevisiae)
D: saccharomyces hansenii (aka debaryomyces hansenii)
E: saccharomyces cerevisiae x saccharomyces mikatae
F: None of the above. | [C] |
<Instruct>: Given the context 'FLAG–Scp160p fusion protein was detected by incubation of the filter with mouse M2 anti-FLAG monoclonal antibody (10 µg/ml final concentration), followed by HRP-conjugated sheep anti-mouse secondary antibody (Amersham), diluted 1:5000 as per the manufacturer’s instructions, and ECL reagen... | <Mentions>: [mouse; sheep]
<Options>: A: mouse (aka mus <genus>)
B: house mouse (aka mus musculus)
C: cow (aka bos taurus) (aka bos taurus)
D: ovis sp.
E: domestic sheep (aka ovis aries)
F: mus musculoides (mus musculoides enclavae) (aka mus musculoides)
G: cattle (aka bos)
H: mus molossinus (aka mus musculus molossinu... | [B; E] |
<Instruct>: Given the context 'FLAG–Scp160p fusion protein was detected by incubation of the filter with mouse M2 anti-FLAG monoclonal antibody (10 µg/ml final concentration), followed by HRP-conjugated sheep anti-mouse secondary antibody (Amersham), diluted 1:5000 as per the manufacturer’s instructions, and ECL reagen... | <Mentions>: [mouse; sheep]
<Options>: A: mus (aka mus <subgenus>) (aka mus <subgenus>)
B: mus cricetus (aka cricetus cricetus)
C: eastern european house mouse (aka mus musculus musculus)
D: ovis aries vignei (aka ovis vignei)
E: ovis
F: wild sheep (aka ovis aries)
G: suidae (pigs (aka suidae))
H: mice (aka mus sp.) (ak... | [J; F] |
<Instruct>: Given the context 'By performing a standard analysis using bovine serum albumin, the stain was able to detect ~15 ng total protein per lane.
', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each mention, separated by semic... | <Mentions>: [bovine]
<Options>: A: boveria
B: cattle (aka bos)
C: bos taurus (bos primigenius taurus) (aka bos taurus)
D: bos taurus x bos indicus (aka bos indicus x bos taurus)
E: bos bubalis bubalis (aka bubalus bubalis bubalis)
F: None of the above. | [C] |
<Instruct>: Given the context 'RESULTS
Expression of tagged Scp160p in yeast
An N-terminal FLAG-tagged form of Scp160p was created to facilitate detection of the protein in cells and extracts (Fig. 1A).', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected o... | <Mentions>: [yeast]
<Options>: A: saccharomycodes
B: saccharomyces albicans (aka candida albicans)
C: baker's yeast (aka saccharomyces cerevisiae)
D: saccharomycetes (hemiascomycetes) (aka saccharomycetes)
E: saccharomyceta
F: None of the above. | [C] |
<Instruct>: Given the context 'RESULTS
Expression of tagged Scp160p in yeast
An N-terminal FLAG-tagged form of Scp160p was created to facilitate detection of the protein in cells and extracts (Fig. 1A).', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected o... | <Mentions>: [yeast]
<Options>: A: saccharomyceta
B: saccharomyces albicans (aka candida albicans)
C: saccharomycetes (hemiascomycetes) (aka saccharomycetes)
D: saccharomycodes
E: None of the above. | [E] |
<Instruct>: Given the context 'To probe functionality of this fusion protein, we used two-step gene replacement (18) to substitute the modified allele into the SCP160 locus of haploid yeast, and then tested the morphological phenotype of the resultant cells.', select the correct biomedical concept for each mention usin... | <Mentions>: [yeast]
<Options>: A: saccharomyces cf. cerevisiae/paradoxus (saccharomyces cerevisiae or paradoxus) (aka saccharomyces cf. cerevisiae/paradoxus)
B: mycoderma cerevisiae (aka saccharomyces cerevisiae)
C: true yeasts (aka saccharomycotina)
D: saccharomyces lactis (aka kluyveromyces lactis)
E: saccharomyces c... | [B] |
<Instruct>: Given the context 'In all cases, yeast expressing tagged Scp160p in place of the native protein appeared indistinguishable from the corresponding wild-type strains (data not shown).', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, o... | <Mentions>: [yeast]
<Options>: A: candida/saccharomycetales (aka candida/saccharomycales clade)
B: saccharomycodes
C: saccharomyces albicans (aka candida albicans)
D: saccharomyceta
E: saccharomyces cerevisiae (saccharomyces cerevisiae (desm.) meyen ex e.c. hansen, 1883) (aka saccharomyces cerevisiae)
F: None of the ab... | [E] |
<Instruct>: Given the context 'As a negative control, we also deleted almost the entire SCP160 coding region from the genomes of these yeast strains (Fig. 1A), and confirmed the expected mutant phenotype (data not shown).
', select the correct biomedical concept for each mention using the provided options. Answer by l... | <Mentions>: [yeast]
<Options>: A: saccharomyceta
B: saccharomyces lactis (aka kluyveromyces lactis)
C: brewer's yeast (aka saccharomyces cerevisiae)
D: saccharomyces cf. cerevisiae/paradoxus (saccharomyces cerevisiae or paradoxus) (aka saccharomyces cf. cerevisiae/paradoxus)
E: saccharomyces sp.
F: None of the above. | [C] |
<Instruct>: Given the context 'Scp160p associates with polyribosomes
To test the hypothesis that Scp160p associates with polyribosomes we used sucrose gradient ultracentrifugation to size-fractionate subcellular components of lysates prepared from yeast expressing the N-terminal FLAG-tagged Scp160p protein.', select th... | <Mentions>: [yeast]
<Options>: A: saccharomyces cf. cerevisiae/paradoxus (saccharomyces cerevisiae or paradoxus) (aka saccharomyces cf. cerevisiae/paradoxus)
B: baker's yeast (aka saccharomyces cerevisiae)
C: saccharomyceta
D: saccharomyces sp.
E: saccharomyces albicans (aka candida albicans)
F: None of the above. | [B] |
<Instruct>: Given the context 'A convenient internal control for these gradients was provided by an unknown endogenous yeast cross-reacting protein at ~100 kDa, that exemplified the migration pattern of a free protein, appearing only in the upper fractions of the gradient (Fig.', select the correct biomedical concept f... | <Mentions>: [yeast]
<Options>: A: budding yeasts & others (aka saccharomycotina)
B: saccharomycetes (hemiascomycetes) (aka saccharomycetes)
C: saccharomyces hansenii (aka debaryomyces hansenii)
D: baker's yeast (aka saccharomyces cerevisiae)
E: candida/saccharomycetales (aka candida/saccharomycales clade)
F: None of th... | [D] |
<Instruct>: Given the context 'To determine whether the migration pattern of Scp160p in these sucrose gradients truly reflected association with yeast polyribosomes, lysates were pre-treated with either 30 mM EDTA or 50 U/ml', select the correct biomedical concept for each mention using the provided options. Answer by ... | <Mentions>: [yeast]
<Options>: A: saccharomyces cf. cerevisiae/paradoxus (saccharomyces cerevisiae or paradoxus) (aka saccharomyces cf. cerevisiae/paradoxus)
B: saccharomyces lactis (aka kluyveromyces lactis)
C: saccharomyces sp.
D: saccharomyceta
E: saccharomyces cerevisiae (saccharomyces cerevisiae (desm.) meyen ex e... | [E] |
<Instruct>: Given the context 'The fact that RNase treatment and high salt both generated Scp160p species of similar apparent molecular weight suggests that these high salt concentrations resulted in the disassociation of RNA, and perhaps other components, from Scp160p.
Pab1p and Bfr1p are present in EDTA-resistant Sc... | <Mentions>: [yeast]
<Options>: A: budding yeasts & others (aka saccharomycotina)
B: saccharomyces cf. cerevisiae/paradoxus (saccharomyces cerevisiae or paradoxus) (aka saccharomyces cf. cerevisiae/paradoxus)
C: saccharomyces lactis (aka kluyveromyces lactis)
D: brewer's yeast (aka saccharomyces cerevisiae)
E: saccharom... | [D] |
<Instruct>: Given the context 'In addition, we performed mock purifications using lysates from yeast expressing the wild-type allele of SCP160 without the FLAG epitope (Fig. 5F), or with an unrelated FLAG-tagged protein, human galactose 1-phosphate uridylyltransferase (GALT) (Fig.', select the correct biomedical concep... | <Mentions>: [yeast; human]
<Options>: A: saccharomycotina (budding yeasts & others) (aka saccharomycotina)
B: homo sapiens (human) (aka homo sapiens)
C: mammals (aka mammalia)
D: this
E: candida/saccharomycetales (aka candida/saccharomycales clade)
F: homo (humans) (aka homo)
G: saccharomycetes (hemiascomycetes) (aka s... | [I; B] |
<Instruct>: Given the context 'In addition, we performed mock purifications using lysates from yeast expressing the wild-type allele of SCP160 without the FLAG epitope (Fig. 5F), or with an unrelated FLAG-tagged protein, human galactose 1-phosphate uridylyltransferase (GALT) (Fig.', select the correct biomedical concep... | <Mentions>: [yeast; human]
<Options>: A: saccharomyces cf. cerevisiae
B: suborder
C: candida/saccharomycetales (aka candida/saccharomycales clade)
D: primate (aka primates)
E: this
F: species
G: human (aka homo sapiens)
H: saccharomyces albicans (aka candida albicans)
I: saccharomyces cerevisiae (saccharomyces cerevisi... | [I; G] |
<Instruct>: Given the context 'Monomeric Scp160p migrates as a ~450 kDa protein under native conditions
As a first step to characterize the post RNase/NaCl 450 kDa Scp160p species we compared it with Scp160p over-expressed and purified from an exogenous host, the yeast Pichia pastoris.', select the correct biomedical c... | <Mentions>: [yeast; pichia pastoris]
<Options>: A: pichia anomala (aka wickerhamomyces anomalus)
B: zygosaccharomyces pastoris (aka komagataella pastoris)
C: saccharomyceta
D: saccharomyces pasteurianus (aka saccharomyces pastorianus)
E: saccharomyces albicans (aka candida albicans)
F: brewer's yeast (aka saccharomyces... | [F; B] |
<Instruct>: Given the context 'Monomeric Scp160p migrates as a ~450 kDa protein under native conditions
As a first step to characterize the post RNase/NaCl 450 kDa Scp160p species we compared it with Scp160p over-expressed and purified from an exogenous host, the yeast Pichia pastoris.', select the correct biomedical c... | <Mentions>: [yeast; pichia pastoris]
<Options>: A: pichia pastoris dsmz 70382 (aka komagataella pastoris dsmz 70382)
B: mycoderma cerevisiae (aka saccharomyces cerevisiae)
C: saccharomyces cerevisiae or paradoxus (aka saccharomyces cf. cerevisiae/paradoxus)
D: saccharomyces cerevisiae x saccharomyces mikatae
E: sacchar... | [B; I] |
<Instruct>: Given the context 'To test this hypothesis, yeast expressing FLAG–Scp160p were transfected with a centromeric plasmid, YCplac22–HA–Scp160p, encoding a distinct, HA-tagged allele of the protein.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selecte... | <Mentions>: [yeast]
<Options>: A: saccharomyces cerevisiae (saccharomyces cerevisiae (desm.) meyen ex e.c. hansen, 1883) (aka saccharomyces cerevisiae)
B: saccharomyces cerevisiae x saccharomyces mikatae
C: saccharomyces cerevisiae or paradoxus (aka saccharomyces cf. cerevisiae/paradoxus)
D: saccharomyceta
E: saccharom... | [A] |
<Instruct>: Given the context 'As seen in Figure 7C, when yeast co-expressing the two alleles were lysed and the FLAG-tagged protein was isolated as described above, no HA–Scp160p co-purified with the FLAG–Scp160p.', select the correct biomedical concept for each mention using the provided options. Answer by listing th... | <Mentions>: [yeast]
<Options>: A: saccharomyces cerevisiae or paradoxus (aka saccharomyces cf. cerevisiae/paradoxus)
B: saccharomyces sp.
C: saccharomyces hansenii (aka debaryomyces hansenii)
D: mycoderma cerevisiae (aka saccharomyces cerevisiae)
E: saccharomyceta
F: None of the above. | [D] |
<Instruct>: Given the context 'The data presented here demonstrate two main points regarding the biochemical associations and function of Scp160p in yeast.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each mention, separated by semi... | <Mentions>: [yeast]
<Options>: A: saccharomyces cerevisiae (saccharomyces cerevisiae (desm.) meyen ex e.c. hansen, 1883) (aka saccharomyces cerevisiae)
B: saccharomyces hansenii (aka debaryomyces hansenii)
C: saccharomyceta
D: saccharomyces cerevisiae x saccharomyces mikatae
E: saccharomyces cf. cerevisiae
F: None of t... | [A] |
<Instruct>: Given the context 'Furthermore, by utilizing yeast co-expressing two distinct epitope-tagged versions of Scp160p, we have ruled out the possibility of self-association of Scp160p.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one... | <Mentions>: [yeast]
<Options>: A: saccharomyces albicans (aka candida albicans)
B: saccharomyces cerevisiae (saccharomyces cerevisiae (desm.) meyen ex e.c. hansen, 1883) (aka saccharomyces cerevisiae)
C: saccharomycodes
D: saccharomyceta
E: saccharomyces cerevisiae x saccharomyces mikatae
F: None of the above. | [B] |
<Instruct>: Given the context 'In conclusion we have shown convincing evidence that Scp160p exists in yeast cytoplasmic extracts primarily associated with polyribosomes.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each mention, sep... | <Mentions>: [yeast]
<Options>: A: saccharomyces sp.
B: saccharomyces cerevisiae or paradoxus (aka saccharomyces cf. cerevisiae/paradoxus)
C: candida/saccharomycetales (aka candida/saccharomycales clade)
D: mycoderma cerevisiae (aka saccharomyces cerevisiae)
E: saccharomyces cerevisiae x saccharomyces mikatae
F: None of... | [D] |
<Instruct>: Given the context 'In conclusion we have shown convincing evidence that Scp160p exists in yeast cytoplasmic extracts primarily associated with polyribosomes.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each mention, sep... | <Mentions>: [yeast]
<Options>: A: candida/saccharomycetales (aka candida/saccharomycales clade)
B: saccharomyces sp.
C: saccharomyces cerevisiae or paradoxus (aka saccharomyces cf. cerevisiae/paradoxus)
D: saccharomyces cerevisiae x saccharomyces mikatae
E: None of the above. | [E] |
<Instruct>: Given the context 'The presence of Pab1p suggests that Scp160p associates with polyribosomes as a component of an mRNP, demonstrating Scp160p to be the first S.cerevisiae multiple-KH domain protein characterized to function in this way.
', select the correct biomedical concept for each mention using the p... | <Mentions>: [s.cerevisiae]
<Options>: A: baker's yeast (aka saccharomyces cerevisiae)
B: saccharomyceta
C: saccharomyces globosus (aka saccharomyces uvarum)
D: saccharomyces paradoxus
E: saccharomyces cerevisiae x saccharomyces paradoxus
F: None of the above. | [A] |
<Instruct>: Given the context 'Discovery of genes implicated in whirling disease infection and resistance in rainbow trout using genome-wide expression profiling
Abstract
Background
Whirling disease, caused by the pathogen Myxobolus cerebralis, afflicts several salmonid species.', select the correct biomedical concept ... | <Mentions>: [rainbow trout; myxobolus cerebralis]
<Options>: A: river trout (aka salmo trutta fario)
B: salmons and trouts (aka salmoniformes)
C: salmo mykiss (aka oncorhynchus mykiss)
D: myxobolus cerebralis
E: myxobolus neurophilus (myxosoma neurophila) (aka myxobolus neurophilus)
F: sea trout (aka salmo trutta trutt... | [C; D] |
<Instruct>: Given the context 'Discovery of genes implicated in whirling disease infection and resistance in rainbow trout using genome-wide expression profiling
Abstract
Background
Whirling disease, caused by the pathogen Myxobolus cerebralis, afflicts several salmonid species.', select the correct biomedical concept ... | <Mentions>: [rainbow trout; myxobolus cerebralis]
<Options>: A: myxobolus oralis
B: myxobolus neurophilus (myxosoma neurophila) (aka myxobolus neurophilus)
C: myxobolus cerebralis
D: trouts, salmons & chars (aka salmoninae)
E: streptocephalus simplex
F: salmons and trouts (aka salmoniformes)
G: sea trout (aka salmo tru... | [J; C] |
<Instruct>: Given the context 'Rainbow trout are particularly susceptible and may suffer high mortality rates.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each mention, separated by semicolon. | <Mentions>: [rainbow trout]
<Options>: A: japanese salmon (aka oncorhynchus masou)
B: salmo keta (aka oncorhynchus keta)
C: oncorhynchus mykiss (oncorhynchus nerka mykiss) (aka oncorhynchus mykiss)
D: salmo trutta trutta (sea trout) (aka salmo trutta trutta)
E: trouts, salmons & chars (aka salmoninae)
F: None of the ab... | [C] |
<Instruct>: Given the context 'In this study, genome-wide expression profiling using cDNA microarrays was conducted for resistant Hofer and susceptible Trout Lodge rainbow trout strains following pathogen exposure with the primary objective of identifying specific genes implicated in whirling disease resistance.
', se... | <Mentions>: [rainbow trout]
<Options>: A: salmo mykiss (aka oncorhynchus mykiss)
B: trouts, salmons & chars (aka salmoninae)
C: salmo trutta trutta (sea trout) (aka salmo trutta trutta)
D: salmons and trouts (aka salmoniformes)
E: salmo gilae (aka oncorhynchus gilae)
F: None of the above. | [A] |
<Instruct>: Given the context 'Results
Several genes were significantly up-regulated in skin following pathogen exposure for both the resistant and susceptible rainbow trout strains.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each... | <Mentions>: [rainbow trout]
<Options>: A: salmo gilae gilae (aka oncorhynchus gilae gilae)
B: trouts, salmons & chars (aka salmoninae)
C: japanese salmon (aka oncorhynchus masou)
D: rainbow trout (aka oncorhynchus mykiss)
E: salmons and trouts (aka salmoniformes)
F: None of the above. | [D] |
<Instruct>: Given the context 'Conclusion
The present study has provided an initial view into the genetic basis underlying immune response and resistance of rainbow trout to the whirling disease parasite.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected... | <Mentions>: [rainbow trout]
<Options>: A: salmon trout (aka oncorhynchus masou)
B: black sea salmon (aka salmo labrax)
C: salmo gilae gilae (aka oncorhynchus gilae gilae)
D: oncorhynchus mykiss (oncorhynchus nerka mykiss) (aka oncorhynchus mykiss)
E: oncorhynchus gilae (salmo gilae) (aka oncorhynchus gilae)
F: None of ... | [D] |
<Instruct>: Given the context 'Background
Whirling disease was first described among farmed rainbow trout (Oncorhynchus mykiss), a native North American salmonid species, introduced to Germany as a food fish in the late 1800s', select the correct biomedical concept for each mention using the provided options. Answer by... | <Mentions>: [rainbow trout; oncorhynchus mykiss]
<Options>: A: oncorhynchus gilae gilae (salmo gilae gilae) (aka oncorhynchus gilae gilae)
B: golden trout (aka oncorhynchus mykiss aguabonita)
C: rainbow trout (aka oncorhynchus mykiss)
D: oncorhynchus keta (chum salmon) (aka oncorhynchus keta)
E: brook trout (aka salvel... | [C; C] |
<Instruct>: Given the context 'Background
Whirling disease was first described among farmed rainbow trout (Oncorhynchus mykiss), a native North American salmonid species, introduced to Germany as a food fish in the late 1800s', select the correct biomedical concept for each mention using the provided options. Answer by... | <Mentions>: [rainbow trout; oncorhynchus mykiss]
<Options>: A: oncorhynchus keta (chum salmon) (aka oncorhynchus keta)
B: oncorhynchus mykiss (oncorhynchus nerka mykiss) (aka oncorhynchus mykiss)
C: sea trout (aka salmo trutta trutta)
D: river trout (aka salmo trutta fario)
E: salmo gilae (aka oncorhynchus gilae)
F: ja... | [B; B] |
<Instruct>: Given the context 'Whirling disease is associated with systemic infections by the myxozoan Myxobolus cerebralis, a parasite with presumed origins among salmonid fish in Eurasia [2,3].', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options,... | <Mentions>: [myxobolus cerebralis]
<Options>: A: myxobolus fundamentalis
B: myxobolus oralis
C: myxobolus cerebralis
D: myxobolus neurophilus (myxosoma neurophila) (aka myxobolus neurophilus)
E: myxobolus neurofontinalis
F: None of the above. | [C] |
<Instruct>: Given the context 'Rainbow trout are highly susceptible to whirling disease and the introduction of the parasite to the U.S.A. in the 1950s had immediate economic impacts on salmonid hatcheries in both eastern and western states [2].', select the correct biomedical concept for each mention using the provide... | <Mentions>: [rainbow trout]
<Options>: A: japanese salmon (aka oncorhynchus masou)
B: sea trout (aka salmo trutta trutta)
C: salmo mykiss (aka oncorhynchus mykiss)
D: brook trout (aka salvelinus fontinalis)
E: trouts, salmons & chars (aka salmoninae)
F: None of the above. | [C] |
<Instruct>: Given the context 'The disease has more recently been recognized as the principal cause of major population declines among wild rainbow trout populations in the intermountain region of the U.S.A with serious negative impacts on sportfishing and allied industries [5-7].', select the correct biomedical concep... | <Mentions>: [rainbow trout]
<Options>: A: black sea salmon (aka salmo labrax)
B: oncorhynchus gilae (salmo gilae) (aka oncorhynchus gilae)
C: salmo keta (aka oncorhynchus keta)
D: river trout (aka salmo trutta)
E: salmo mykiss (aka oncorhynchus mykiss)
F: None of the above. | [E] |
<Instruct>: Given the context 'Additionally, concerns continue over the potential negative ecologic impacts of whirling disease on wild salmonid populations, particularly threatened or endangered salmonids such as bull trout (Salvelinus confluentus), cutthroat trout (Oncorhynchus clarki), and steelhead (Oncorhynchus my... | <Mentions>: [bull trout; salvelinus confluentus; cutthroat trout; oncorhynchus clarki]
<Options>: A: salvelinus albus (white char) (aka salvelinus albus)
B: river trout (aka salmo trutta)
C: salvelinus malma x salvelinus leucomaenis
D: cutthroat trout (aka oncorhynchus clarkii)
E: yellowfin cutthroat trout (aka oncorhy... | [J; J; D; D] |
<Instruct>: Given the context 'Additionally, concerns continue over the potential negative ecologic impacts of whirling disease on wild salmonid populations, particularly threatened or endangered salmonids such as bull trout (Salvelinus confluentus), cutthroat trout (Oncorhynchus clarki), and steelhead (Oncorhynchus my... | <Mentions>: [bull trout; salvelinus confluentus; cutthroat trout; oncorhynchus clarki]
<Options>: A: salvelinus malma x salvelinus leucomaenis
B: cutthroat trout (aka oncorhynchus clarkii)
C: oncorhynchus clarki utah (aka oncorhynchus clarkii utah)
D: rio grande cutthroat trout (aka oncorhynchus clarkii virginalis)
E: ... | [R; R; B; B] |
<Instruct>: Given the context 'Additionally, concerns continue over the potential negative ecologic impacts of whirling disease on wild salmonid populations, particularly threatened or endangered salmonids such as bull trout (Salvelinus confluentus), cutthroat trout (Oncorhynchus clarki), and steelhead (Oncorhynchus my... | <Mentions>: [bull trout; salvelinus confluentus; cutthroat trout; oncorhynchus clarki]
<Options>: A: rio grande cutthroat trout (aka oncorhynchus clarkii virginalis)
B: salvelinus profundus (salmo salvelinus profundus) (aka salvelinus profundus)
C: salvelinus namaycush (salmo namaycush) (aka salvelinus namaycush)
D: ap... | [H; H; N; N] |
<Instruct>: Given the context 'Additionally, concerns continue over the potential negative ecologic impacts of whirling disease on wild salmonid populations, particularly threatened or endangered salmonids such as bull trout (Salvelinus confluentus), cutthroat trout (Oncorhynchus clarki), and steelhead (Oncorhynchus my... | <Mentions>: [bull trout; salvelinus confluentus; cutthroat trout; oncorhynchus clarki]
<Options>: A: rainbow trout (aka oncorhynchus mykiss)
B: salmo gilae gilae (aka oncorhynchus gilae gilae)
C: lake ohrid brown trout (aka salmo letnica)
D: salvia concolor
E: oncorhynchus clarki pleuriticus (aka oncorhynchus clarkii p... | [G; G; H; H] |
<Instruct>: Given the context 'Additionally, concerns continue over the potential negative ecologic impacts of whirling disease on wild salmonid populations, particularly threatened or endangered salmonids such as bull trout (Salvelinus confluentus), cutthroat trout (Oncorhynchus clarki), and steelhead (Oncorhynchus my... | <Mentions>: [bull trout; salvelinus confluentus; cutthroat trout; oncorhynchus clarki]
<Options>: A: oncorhynchus clarki utah (aka oncorhynchus clarkii utah)
B: oncorhynchus clarki seleniris (aka oncorhynchus clarkii seleniris)
C: salvelinus malma malma x salvelinus leucomaenis
D: lake ohrid brown trout (aka salmo letn... | [K; K; O; O] |
<Instruct>: Given the context 'Additionally, concerns continue over the potential negative ecologic impacts of whirling disease on wild salmonid populations, particularly threatened or endangered salmonids such as bull trout (Salvelinus confluentus), cutthroat trout (Oncorhynchus clarki), and steelhead (Oncorhynchus my... | <Mentions>: [steelhead; oncorhynchus mykiss]
<Options>: A: salmo gilae gilae (aka oncorhynchus gilae gilae)
B: salmon trout (aka oncorhynchus masou)
C: salmo tshawytscha (aka oncorhynchus tshawytscha)
D: oncorhynchus gilae (salmo gilae) (aka oncorhynchus gilae)
E: salmoneus
F: atlantic salmon (aka salmo salar)
G: salmo... | [G; G] |
<Instruct>: Given the context 'Additionally, concerns continue over the potential negative ecologic impacts of whirling disease on wild salmonid populations, particularly threatened or endangered salmonids such as bull trout (Salvelinus confluentus), cutthroat trout (Oncorhynchus clarki), and steelhead (Oncorhynchus my... | <Mentions>: [steelhead; oncorhynchus mykiss]
<Options>: A: salmo gilae (aka oncorhynchus gilae)
B: salmo mykiss (aka oncorhynchus mykiss)
C: salmo salar (atlantic salmon) (aka salmo salar)
D: sebastes marinus norvegicus (aka sebastes norvegicus)
E: oncorhynchus ishikawae (aka oncorhynchus masou ishikawae)
F: chum salmo... | [B; B] |
<Instruct>: Given the context '[8,9].
Myxobolus cerebralis has a complex life cycle that includes two alternate hosts, a salmonid fish and an oligochaete worm, Tubifex tubifex [10,11].', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for ea... | <Mentions>: [myxobolus cerebralis; tubifex tubifex]
<Options>: A: streptocephalus simplex
B: sludge worm (aka tubifex tubifex)
C: myxobolus cerebralis
D: henneguya cerebralis
E: morococcus cerebrosus
F: tubifex benedii (aka tubificoides benedii)
G: myxobolus lentisuturalis
H: tubifex sp. hrv-2001
I: tubifex sp. aeb-200... | [C; B] |
<Instruct>: Given the context '[8,9].
Myxobolus cerebralis has a complex life cycle that includes two alternate hosts, a salmonid fish and an oligochaete worm, Tubifex tubifex [10,11].', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for ea... | <Mentions>: [myxobolus cerebralis; tubifex tubifex]
<Options>: A: coniophora cerebella
B: tubifex sp. mes-2003
C: eunice tubifex
D: tubifex cf. tubifex mk-2019
E: lumbricus tubifex (aka tubifex tubifex)
F: myxobolus neurobius
G: myxobolus cerebralis
H: tylodelphys cerebralis
I: tubifex benedii (aka tubificoides benedii... | [G; E] |
<Instruct>: Given the context '[8,9].
Myxobolus cerebralis has a complex life cycle that includes two alternate hosts, a salmonid fish and an oligochaete worm, Tubifex tubifex [10,11].', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for ea... | <Mentions>: [myxobolus cerebralis; tubifex tubifex]
<Options>: A: streptocephalus simplex
B: tubifex benedii (aka tubificoides benedii)
C: coniophora cerebella
D: eunice tubifex
E: tubifex sp. mes-2003
F: tylodelphys cerebralis
G: myxobolus neurobius
H: tubifex cf. tubifex mk-2019
I: myxobolus cerebralis
J: None of the... | [I; J] |
<Instruct>: Given the context 'Infection in the salmonid host begins when microscopic waterborne actinospore stages of M. cerebralis are released from the worm and contact the skin of the fish host.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected optio... | <Mentions>: [m. cerebralis]
<Options>: A: striatula
B: mesopeplum
C: neurocallis
D: glomus cerebriforme
E: falco tinnunculus interstinctus (falco interstinctus) (aka falco tinnunculus interstinctus)
F: None of the above. | [F] |
<Instruct>: Given the context 'Actinospores, also referred to as triactinomyxons for M. cerebralis, attach preferentially to fins and the buccal cavity where they release one or more of three coiled polar filaments which penetrate and then anchor them to the epidermis[12].', select the correct biomedical concept for ea... | <Mentions>: [m. cerebralis]
<Options>: A: mesopeplum
B: paraglomus
C: paracephaleus
D: somniosus
E: neurocallis
F: None of the above. | [F] |
<Instruct>: Given the context 'Death of infected fish or ingestion by fish or avian predators releases myxospores from the fish tissues and they may be ingested by the second host, the benthic dwelling oligochaete T. tubifex [19].', select the correct biomedical concept for each mention using the provided options. Answ... | <Mentions>: [t. tubifex]
<Options>: A: leucotrichia tubifex
B: tubifex sp.
C: tubbreva
D: tubicinella
E: sludge worm (aka tubifex tubifex)
F: None of the above. | [E] |
<Instruct>: Given the context 'Susceptibility to whirling disease in U.S. rainbow trout strains is pervasive with only two of the tested native strains displaying any degree of resistance, which may be inconsistent and relatively moderate [21,22].', select the correct biomedical concept for each mention using the provi... | <Mentions>: [rainbow trout]
<Options>: A: river trout (aka salmo trutta fario)
B: salmon trout (aka oncorhynchus masou)
C: brook trout (aka salvelinus fontinalis)
D: salmo mykiss (aka oncorhynchus mykiss)
E: salmo gilae (aka oncorhynchus gilae)
F: None of the above. | [D] |
<Instruct>: Given the context 'Hatchery rainbow trout in Germany (Hofer strain), however, have acquired a degree of resistance to whirling disease that is consistently much higher than any domestic rainbow strains and comparable to that of brown trout (Salmon trutta), which are native to Europe and typically asymptomat... | <Mentions>: [rainbow trout; brown trout; salmon trutta]
<Options>: A: rainbow trout (aka oncorhynchus mykiss)
B: western australian salmon (aka arripis truttaceus)
C: salmo trutta trutta (sea trout) (aka salmo trutta trutta)
D: trouts, salmons & chars (aka salmoninae)
E: lake ohrid brown trout (aka salmo letnica)
F: sa... | [A; L; L] |
<Instruct>: Given the context 'Hatchery rainbow trout in Germany (Hofer strain), however, have acquired a degree of resistance to whirling disease that is consistently much higher than any domestic rainbow strains and comparable to that of brown trout (Salmon trutta), which are native to Europe and typically asymptomat... | <Mentions>: [rainbow trout; brown trout; salmon trutta]
<Options>: A: river trout (aka salmo trutta fario)
B: salmo gilae (aka oncorhynchus gilae)
C: black sea salmon (aka salmo labrax)
D: salmo trutta trutta (sea trout) (aka salmo trutta trutta)
E: trouts, salmons & chars (aka salmoninae)
F: salmonids (aka salmonidae)... | [K; M; M] |
<Instruct>: Given the context 'Hatchery rainbow trout in Germany (Hofer strain), however, have acquired a degree of resistance to whirling disease that is consistently much higher than any domestic rainbow strains and comparable to that of brown trout (Salmon trutta), which are native to Europe and typically asymptomat... | <Mentions>: [rainbow trout; brown trout; salmon trutta]
<Options>: A: salmonids (aka salmonidae)
B: salmo gilae (aka oncorhynchus gilae)
C: brook trout (aka salvelinus fontinalis)
D: trouts, salmons & chars (aka salmoninae)
E: salmo trutta fario (river trout) (aka salmo trutta fario)
F: river trout (aka salmo trutta fa... | [H; M; M] |
<Instruct>: Given the context 'Hatchery rainbow trout in Germany (Hofer strain), however, have acquired a degree of resistance to whirling disease that is consistently much higher than any domestic rainbow strains and comparable to that of brown trout (Salmon trutta), which are native to Europe and typically asymptomat... | <Mentions>: [rainbow trout; brown trout; salmon trutta]
<Options>: A: salmo trutta (river trout) (aka salmo trutta)
B: rv-brown trout
C: australian salmon (aka arripis trutta)
D: rainbow trout (aka oncorhynchus mykiss)
E: abant trout (aka salmo abanticus)
F: salmo abanticus (salmo trutta abanticus) (aka salmo abanticus... | [D; A; A] |
<Instruct>: Given the context 'Laboratory tests comparing rainbow trout strains under the same environmental conditions and pathogen exposure indicate that the Hofer strain's ability to combat M. cerebralis infection has a genetic basis.', select the correct biomedical concept for each mention using the provided option... | <Mentions>: [rainbow trout; m. cerebralis]
<Options>: A: neuroctenus
B: paracephaleus
C: mesopsocus
D: salmo keta (aka oncorhynchus keta)
E: japanese salmon (aka oncorhynchus masou)
F: oncorhynchus mykiss (oncorhynchus nerka mykiss) (aka oncorhynchus mykiss)
G: neurocallis
H: falco tinnunculus interstinctus (falco inte... | [F; K] |
<Instruct>: Given the context 'Laboratory tests comparing rainbow trout strains under the same environmental conditions and pathogen exposure indicate that the Hofer strain's ability to combat M. cerebralis infection has a genetic basis.', select the correct biomedical concept for each mention using the provided option... | <Mentions>: [rainbow trout; m. cerebralis]
<Options>: A: river trout (aka salmo trutta fario)
B: oncorhynchus mykiss (oncorhynchus nerka mykiss) (aka oncorhynchus mykiss)
C: trouts, salmons & chars (aka salmoninae)
D: salmon trout (aka oncorhynchus masou)
E: encephalartos
F: cerebratulus
G: cranistus
H: somniosus
I: cr... | [B; K] |
<Instruct>: Given the context 'Recently, controlled crosses of the Hofer strain and a susceptible strain (Colorado River rainbow trout [CRR]) demonstrated that resistance to whirling disease was inherited by progeny [24] and heritability estimates are currently underway.
', select the correct biomedical concept for eac... | <Mentions>: [rainbow trout]
<Options>: A: salmons and trouts (aka salmoniformes)
B: trouts, salmons & chars (aka salmoninae)
C: japanese salmon (aka oncorhynchus masou)
D: river trout (aka salmo trutta fario)
E: salmo mykiss (aka oncorhynchus mykiss)
F: None of the above. | [E] |
<Instruct>: Given the context 'The discovery of the resistant Hofer strain allowed us to conduct an intraspecific comparison of susceptible and resistant rainbow trout in order to gain insight into the genetic basis underlying whirling disease susceptibility for this species.', select the correct biomedical concept for... | <Mentions>: [rainbow trout]
<Options>: A: sea trout (aka salmo trutta trutta)
B: river trout (aka salmo trutta)
C: golden trout (aka oncorhynchus mykiss aguabonita)
D: rainbow trout (aka oncorhynchus mykiss)
E: river trout (aka salmo trutta fario)
F: None of the above. | [D] |
<Instruct>: Given the context 'In this study, microarray analysis was used to examine expression changes in a resistant and susceptible strain of rainbow trout following exposure to M. cerebralis, the pathogen causing whirling disease.', select the correct biomedical concept for each mention using the provided options.... | <Mentions>: [rainbow trout; m. cerebralis]
<Options>: A: salmo trutta (river trout) (aka salmo trutta)
B: encephalus
C: neurocallis
D: black sea salmon (aka salmo labrax)
E: salmo keta (aka oncorhynchus keta)
F: cerebratulus
G: striatula
H: salmo trutta trutta (sea trout) (aka salmo trutta trutta)
I: paregle
J: oncorhy... | [J; K] |
<Instruct>: Given the context 'In this study, microarray analysis was used to examine expression changes in a resistant and susceptible strain of rainbow trout following exposure to M. cerebralis, the pathogen causing whirling disease.', select the correct biomedical concept for each mention using the provided options.... | <Mentions>: [rainbow trout; m. cerebralis]
<Options>: A: glomus cerebriforme
B: river trout (aka salmo trutta fario)
C: cranistus
D: trouts, salmons & chars (aka salmoninae)
E: encephalus
F: rainbow trout (aka oncorhynchus mykiss)
G: mesopsocus
H: salmo gilae (aka oncorhynchus gilae)
I: striatula
J: salmo gilae gilae (... | [F; K] |
<Instruct>: Given the context 'We have also found a gene which is significantly up-regulated in the resistant but remains unchanged in the susceptible rainbow trout strain following pathogen exposure that is a likely candidate gene for involvement in conferring whirling disease resistance.
', select the correct biomed... | <Mentions>: [rainbow trout]
<Options>: A: oncorhynchus mykiss (oncorhynchus nerka mykiss) (aka oncorhynchus mykiss)
B: river trout (aka salmo trutta fario)
C: brook trout (aka salvelinus fontinalis)
D: salmo keta (aka oncorhynchus keta)
E: japanese salmon (aka oncorhynchus masou)
F: None of the above. | [A] |
<Instruct>: Given the context 'Results and Discussion
Quantitative PCR conducted on caudal fin tissues at two hours post exposure to M. cerebralis demonstrated each fish strain had similar initial pathogen loads, although there was substantial variation between individual fish within each strain.', select the correct b... | <Mentions>: [m. cerebralis]
<Options>: A: neuroctenus
B: cranistus
C: falco interstinctus (aka falco tinnunculus interstinctus)
D: paracephaleus
E: cerebratulus
F: None of the above. | [F] |
<Instruct>: Given the context 'These mean values and standard deviations are similar to those obtained in additional studies of susceptible rainbow trout when examined at early time points post TAM exposure (unpublished data).
', select the correct biomedical concept for each mention using the provided options. Answer ... | <Mentions>: [rainbow trout]
<Options>: A: salmo trutta trutta (sea trout) (aka salmo trutta trutta)
B: black sea salmon (aka salmo labrax)
C: oncorhynchus gilae (salmo gilae) (aka oncorhynchus gilae)
D: trouts, salmons & chars (aka salmoninae)
E: rainbow trout (aka oncorhynchus mykiss)
F: None of the above. | [E] |
<Instruct>: Given the context 'In order to study genes involved in whirling disease response, resistant and susceptible rainbow trout strains were exposed to M. cerebralis and RNA from skin tissue was converted to cDNA and hybridized onto microarrays.', select the correct biomedical concept for each mention using the p... | <Mentions>: [rainbow trout; m. cerebralis]
<Options>: A: paraglomus
B: river trout (aka salmo trutta fario)
C: cranidium
D: encephalus
E: salmons and trouts (aka salmoniformes)
F: salmo gilae gilae (aka oncorhynchus gilae gilae)
G: mesopsocus
H: distremocephalus
I: oncorhynchus mykiss (oncorhynchus nerka mykiss) (aka o... | [I; K] |
<Instruct>: Given the context 'In order to study genes involved in whirling disease response, resistant and susceptible rainbow trout strains were exposed to M. cerebralis and RNA from skin tissue was converted to cDNA and hybridized onto microarrays.', select the correct biomedical concept for each mention using the p... | <Mentions>: [rainbow trout; m. cerebralis]
<Options>: A: falco tinnunculus interstinctus (falco interstinctus) (aka falco tinnunculus interstinctus)
B: striatula
C: oncorhynchus gilae (salmo gilae) (aka oncorhynchus gilae)
D: salmo keta (aka oncorhynchus keta)
E: oncorhynchus mykiss (oncorhynchus nerka mykiss) (aka onc... | [E; K] |
<Instruct>: Given the context 'In order to study genes involved in whirling disease response, resistant and susceptible rainbow trout strains were exposed to M. cerebralis and RNA from skin tissue was converted to cDNA and hybridized onto microarrays.', select the correct biomedical concept for each mention using the p... | <Mentions>: [rainbow trout; m. cerebralis]
<Options>: A: brook trout (aka salvelinus fontinalis)
B: salmo keta (aka oncorhynchus keta)
C: somniosus
D: striatula
E: oncorhynchus gilae (salmo gilae) (aka oncorhynchus gilae)
F: encephalus
G: cranistus
H: salmon trout (aka oncorhynchus masou)
I: falco tinnunculus interstin... | [J; J] |
<Instruct>: Given the context 'A combined total of 17 genes or features (14 annotated genes, 3 unknown features) were differentially expressed in one or both strains following pathogen exposure and are involved with rainbow trout infection response to whirling disease exposure.', select the correct biomedical concept f... | <Mentions>: [rainbow trout]
<Options>: A: salmo gilae gilae (aka oncorhynchus gilae gilae)
B: trouts, salmons & chars (aka salmoninae)
C: river trout (aka salmo trutta)
D: salmo trutta trutta (sea trout) (aka salmo trutta trutta)
E: salmo mykiss (aka oncorhynchus mykiss)
F: None of the above. | [E] |
<Instruct>: Given the context 'It is our hope that future genome sequencing will enable the construction of more comprehensive microarray platforms for economically important aquaculture species, such as Atlantic salmon and rainbow trout.
', select the correct biomedical concept for each mention using the provided opti... | <Mentions>: [atlantic salmon; rainbow trout]
<Options>: A: salmonid fish
B: salmo salar (atlantic salmon) (aka salmo salar)
C: salmo gilae (aka oncorhynchus gilae)
D: rainbow trout (aka oncorhynchus mykiss)
E: trouts, salmons & chars (aka salmoninae)
F: river trout (aka salmo trutta fario)
G: black sea salmon (aka salm... | [B; D] |
<Instruct>: Given the context 'It is our hope that future genome sequencing will enable the construction of more comprehensive microarray platforms for economically important aquaculture species, such as Atlantic salmon and rainbow trout.
', select the correct biomedical concept for each mention using the provided opti... | <Mentions>: [atlantic salmon; rainbow trout]
<Options>: A: salmo mykiss (aka oncorhynchus mykiss)
B: japanese salmon (aka oncorhynchus masou)
C: salmoneus
D: atlantic salmon (aka salmo salar)
E: golden trout (aka oncorhynchus mykiss aguabonita)
F: trouts, salmons & chars (aka salmoninae)
G: salmonid fish
H: salmons and... | [D; A] |
<Instruct>: Given the context 'Additionally, the comparison of two rainbow trout strains (i.e., resistant versus susceptible) added another layer of complexity to the analysis.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each menti... | <Mentions>: [rainbow trout]
<Options>: A: brook trout (aka salvelinus fontinalis)
B: river trout (aka salmo trutta)
C: trouts, salmons & chars (aka salmoninae)
D: salmon trout (aka oncorhynchus masou)
E: rainbow trout (aka oncorhynchus mykiss)
F: None of the above. | [E] |
<Instruct>: Given the context 'Viral Hemorrhagic Septicemia Virus (VHSV) induced protein and neighbor of COX-4 are the only annotated genes without known molecular functions.
', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each mentio... | <Mentions>: [viral hemorrhagic septicemia virus; vhsv]
<Options>: A: vibrio phage vhml (vibrio harveyi bacteriophage vhml) (aka vibrio phage vhml)
B: epizootic hemorrhagic disease virus ehd (aka epizootic hemorrhagic disease virus)
C: viral hemorrhagic septicemia virus 07-71 (viral hemorrhagic septicemia virus (strain ... | [G; G] |
<Instruct>: Given the context 'Viral Hemorrhagic Septicemia Virus (VHSV) induced protein and neighbor of COX-4 are the only annotated genes without known molecular functions.
', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each mentio... | <Mentions>: [viral hemorrhagic septicemia virus; vhsv]
<Options>: A: haemorrhagic kidney syndrome virus
B: vector vhb
C: infectious hemorrhagic syndrome virus
D: vhmlvirus (vhml-like phages) (aka vhmlvirus)
E: hemorrhagic septicemia virus (aka viral hemorrhagic septicemia virus)
F: vhulanivirus
G: viral hemorrhagic sep... | [E; E] |
<Instruct>: Given the context 'Viral Hemorrhagic Septicemia Virus (VHSV) induced protein and neighbor of COX-4 are the only annotated genes without known molecular functions.
', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected options, one for each mentio... | <Mentions>: [viral hemorrhagic septicemia virus; vhsv]
<Options>: A: vhmlvirus (vhml-like phages) (aka vhmlvirus)
B: vhulanivirus
C: viral hemorrhagic septicemia virus (strain makah) (aka viral hemorrhagic septicemia virus strain makah)
D: harvey murine sarcoma virus
E: vector vhb
F: shfv (aka simian hemorrhagic fever ... | [I; I] |
<Instruct>: Given the context 'The interferon system is one of the first lines of host defense against invading pathogens for vertebrates (for review see [26]), including teleost fish (for review see [27]).', select the correct biomedical concept for each mention using the provided options. Answer by listing the select... | <Mentions>: [teleost fish]
<Options>: A: fishes (aka actinopterygii)
B: teleostei (teleost fishes) (aka teleostei)
C: salmons and trouts (aka salmoniformes)
D: vertebrata <vertebrates> (vertebrates) (aka vertebrata <vertebrates>)
E: teleost fish (teleostean fish) (aka teleost fish)
F: None of the above. | [E] |
<Instruct>: Given the context 'Other economically important salmonid pathogens, such as infectious pancreatic necrosis virus and infectious salmon anaemia virus have been found to activate both type I and type II interferon (IFN) responses in the Atlantic salmon host following infection [28].', select the correct biome... | <Mentions>: [infectious pancreatic necrosis virus; infectious salmon anaemia virus; atlantic salmon]
<Options>: A: infectious pancreatic necrosis virus - he
B: aquareovirus a (aka aquareovirus salmonis)
C: infectious pancreatic necrosis virus (ipnv (aka infectious pancreatic necrosis virus))
D: sockeye salmon (aka onco... | [C; J; N] |
<Instruct>: Given the context 'Other economically important salmonid pathogens, such as infectious pancreatic necrosis virus and infectious salmon anaemia virus have been found to activate both type I and type II interferon (IFN) responses in the Atlantic salmon host following infection [28].', select the correct biome... | <Mentions>: [infectious pancreatic necrosis virus; infectious salmon anaemia virus; atlantic salmon]
<Options>: A: infectious salmonid anemia virus (aka infectious salmon anemia virus)
B: black sea salmon (aka salmo labrax)
C: infectious pancreatic necrosis virus (strain n1) (aka infectious pancreatic necrosis virus - ... | [G; M; N] |
<Instruct>: Given the context 'Other economically important salmonid pathogens, such as infectious pancreatic necrosis virus and infectious salmon anaemia virus have been found to activate both type I and type II interferon (IFN) responses in the Atlantic salmon host following infection [28].', select the correct biome... | <Mentions>: [infectious pancreatic necrosis virus; infectious salmon anaemia virus; atlantic salmon]
<Options>: A: infectious pancreatic necrosis virus serotype a5 (infectious pancreatic necrosis virus (serotype a5)) (aka infectious pancreatic necrosis virus serotype a5)
B: salmonidae (salmonids) (aka salmonidae)
C: ip... | [C; J; M] |
<Instruct>: Given the context 'Other economically important salmonid pathogens, such as infectious pancreatic necrosis virus and infectious salmon anaemia virus have been found to activate both type I and type II interferon (IFN) responses in the Atlantic salmon host following infection [28].', select the correct biome... | <Mentions>: [infectious pancreatic necrosis virus; infectious salmon anaemia virus; atlantic salmon]
<Options>: A: atlantic salmon (aka salmo salar)
B: infectious pancreatic necrosis virus serotype a5 (infectious pancreatic necrosis virus (serotype a5)) (aka infectious pancreatic necrosis virus serotype a5)
C: salmonid... | [O; E; A] |
<Instruct>: Given the context 'The PPAR-α-interacting complex protein 285 is a transcriptional co-activator with helicase activity [48] and has sequence similarity to a rainbow trout VHSV-induced protein.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected... | <Mentions>: [rainbow trout; vhsv]
<Options>: A: viral haemorrhagic septicaemia virus vhsv (aka viral hemorrhagic septicemia virus)
B: sea trout (aka salmo trutta trutta)
C: golden trout (aka oncorhynchus mykiss aguabonita)
D: vibrio phage vb_vhas-vhb1
E: harvey murine sarcoma virus
F: salmo mykiss (aka oncorhynchus myk... | [F; A] |
<Instruct>: Given the context 'The PPAR-α-interacting complex protein 285 is a transcriptional co-activator with helicase activity [48] and has sequence similarity to a rainbow trout VHSV-induced protein.', select the correct biomedical concept for each mention using the provided options. Answer by listing the selected... | <Mentions>: [rainbow trout; vhsv]
<Options>: A: vhulanivirus
B: his1v (aka his 1 virus)
C: oncorhynchus mykiss (oncorhynchus nerka mykiss) (aka oncorhynchus mykiss)
D: viral hemorrhagic septicemia virus (vhsv (aka viral hemorrhagic septicemia virus))
E: salmons and trouts (aka salmoniformes)
F: japanese salmon (aka onc... | [C; D] |
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