instruction stringlengths 225 2.35k | input stringlengths 89 1.5k | response stringclasses 698 values |
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<Instruct>: Given the context 'Because B. burgdorferi cells do not contain detectable levels of intracellular Fe, it seems unlikely that DNA is a major target for damage via the Fenton reaction in this bacterium (Posey and Gherardini, 2000).', 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>: [b. burgdorferi]
<Options>: A: borreliales bacterium
B: borreliella americana (borrelia americana) (aka borreliella americana)
C: borrelia
D: borrelia burgdorferi group (aka borreliella)
E: lyme disease spirochete (aka borreliella burgdorferi)
F: None of the above. | [E] |
<Instruct>: Given the context 'When B. burgdorferi cells were exposed to high concentrations of ROS (e.g. H2O2), there was no effect on the spontaneous mutation rate (Fig. 2A) or the number of DNA lesions (AP sites or 8-oxoguanine) (Fig.', 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>: [b. burgdorferi]
<Options>: A: borrelia americana (aka borreliella americana)
B: borrelia burgdorferi (aka borreliella burgdorferi)
C: borrelia genomosp. 1 (aka borreliella genomosp. 1)
D: borreliella burgdorferi b31 (borrelia burgdorferi str. b31) (aka borreliella burgdorferi b31)
E: borreliales bacterium
F: None of the above. | [B] |
<Instruct>: Given the context 'It should be noted that in these experiments, a wild-type strain of B. burgdorferi was used and presumably all of the endogenous oxidative stress enzymes were expressed.', 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>: [b. burgdorferi]
<Options>: A: borrelomyces (aka mycoplasma)
B: borreliella americana (borrelia americana) (aka borreliella americana)
C: borreliella genomospecies 1 (aka borreliella genomosp. 1)
D: borreliales bacterium
E: borrelia burgdorferi (aka borreliella burgdorferi)
F: None of the above. | [E] |
<Instruct>: Given the context 'However, we do not believe this to be the case as the concentration of oxidants used in these experiments were significantly higher than concentrations known to cause DNA damage in E. coli and other pathogenic bacteria.
', 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>: [e. coli]
<Options>: A: escherichia sp.
B: enterobacteriaceae bacterium
C: prokaryotes (aka bacteria)
D: escherichia/shigella coli (aka escherichia coli)
E: enterobacteriales (aka enterobacterales)
F: None of the above. | [D] |
<Instruct>: Given the context 'However, we do not believe this to be the case as the concentration of oxidants used in these experiments were significantly higher than concentrations known to cause DNA damage in E. coli and other pathogenic bacteria.
', 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>: [e. coli]
<Options>: A: enterobacteriaceae bacterium
B: escherichia sp.
C: enterobacteriales (aka enterobacterales)
D: prokaryotes (aka bacteria)
E: None of the above. | [E] |
<Instruct>: Given the context 'The lack of detectable DNA damage in B. burgdorferi cells under the conditions tested could be the result of very efficient DNA repair systems.', 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>: [b. burgdorferi]
<Options>: A: borrelia burgdorferi (aka borreliella burgdorferi)
B: borreliales bacterium
C: borreliella genomospecies 1 (aka borreliella genomosp. 1)
D: borrelia
E: borreliella americana (borrelia americana) (aka borreliella americana)
F: None of the above. | [A] |
<Instruct>: Given the context 'Bacteria, such as E. coli, harbour genes encoding repair enzymes (i.e. MutM, MutY, Ung, AlkA, MutS, MutL, ExoIII, EndoVIII, PolI, RecJ).', 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>: [e. coli]
<Options>: A: enterobacteriaceae bacterium
B: e. coli (aka escherichia coli)
C: prokaryotes (aka bacteria)
D: escherichia
E: escherichia coli k12 (aka escherichia coli k-12)
F: None of the above. | [B] |
<Instruct>: Given the context 'Interestingly, the B. burgdorferi genome does not contain genes encoding homologues of MutM, MutY or EndoVIII, suggesting that it would be difficult for the cells to efficiently repair 8-oxoguanine sites using this pathway.', 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>: [b. burgdorferi]
<Options>: A: borreliella americana (borrelia americana) (aka borreliella americana)
B: borrelia garinii (aka borreliella garinii)
C: borreliales bacterium
D: borrelomyces (aka mycoplasma)
E: borrelia burgdorferi (aka borreliella burgdorferi)
F: None of the above. | [E] |
<Instruct>: Given the context 'B. burgdorferi does harbour the genes encoding the enzymes Ung (monofunctional gylcosylase, BB0053), MutS (BB0797, BB0098), MutL (BB0211), ExoIII (BB0114), PolI (BB0548), LigI (BB0552) and RecJ (BB0254) (Fraser et al., 1997) which are involved in excision and repair, via S-BER or L-BER, of deaminated, alkylated, methylated or mismatched bases.', 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>: [b. burgdorferi]
<Options>: A: borrelomyces (aka mycoplasma)
B: borreliella burgdorferi (lyme disease spirochete) (aka borreliella burgdorferi)
C: borreliales bacterium
D: borrelia garinii (aka borreliella garinii)
E: borrelia genomosp. 1 (aka borreliella genomosp. 1)
F: None of the above. | [B] |
<Instruct>: Given the context 'Clearly, these repair systems in B. burgdorferi do not seem as robust at defending against oxidation of DNA as those described in E. coli.', 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>: [b. burgdorferi; e. coli]
<Options>: A: borrelia burgdorferi sensu lato (aka borreliella)
B: lyme disease spirochete (aka borreliella burgdorferi)
C: enterobacterales (enterobacteriaceae and related endosymbionts) (aka enterobacterales)
D: borrelia genomosp. 1 (aka borreliella genomosp. 1)
E: escherichia
F: borrelia americana (aka borreliella americana)
G: escherichia sp.
H: borrelia fainii (aka candidatus borrelia fainii)
I: escherichia coli k12 (aka escherichia coli k-12)
J: e. coli (aka escherichia coli)
K: None of the above. | [B; J] |
<Instruct>: Given the context 'Clearly, these repair systems in B. burgdorferi do not seem as robust at defending against oxidation of DNA as those described in E. coli.', 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>: [b. burgdorferi; e. coli]
<Options>: A: borrelia garinii (aka borreliella garinii)
B: enterobacteriales (aka enterobacterales)
C: escherichia phage
D: borrelia fainii (aka candidatus borrelia fainii)
E: escherichia
F: borrelia burgdorferi sensu lato (aka borreliella)
G: borreliella burgdorferi (lyme disease spirochete) (aka borreliella burgdorferi)
H: escherichia coli (escherichia/shigella coli) (aka escherichia coli)
I: escherichia coli k12 (aka escherichia coli k-12)
J: borreliales bacterium
K: None of the above. | [G; H] |
<Instruct>: Given the context 'The lack of key repair enzymes in this system may indicate that B. burgdorferi DNA is not subjected to the same challenge from ROS as is E. coli.
', 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>: [b. burgdorferi; e. coli]
<Options>: A: borrelia fainii (aka candidatus borrelia fainii)
B: escherichia
C: enterobacteriaceae bacterium
D: borrelomyces (aka mycoplasma)
E: lyme disease spirochete (aka borreliella burgdorferi)
F: borreliella genomospecies 1 (aka borreliella genomosp. 1)
G: escherichia sp.
H: borreliales bacterium
I: enterobacteria (aka enterobacteriaceae)
J: escherichia/shigella coli (aka escherichia coli)
K: None of the above. | [E; J] |
<Instruct>: Given the context 'The lack of key repair enzymes in this system may indicate that B. burgdorferi DNA is not subjected to the same challenge from ROS as is E. coli.
', 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>: [b. burgdorferi; e. coli]
<Options>: A: borrelia fainii (aka candidatus borrelia fainii)
B: escherichia sp.
C: enterobacteriaceae bacterium
D: borrelomyces (aka mycoplasma)
E: borreliella genomospecies 1 (aka borreliella genomosp. 1)
F: escherichia
G: borreliales bacterium
H: enterobacteria (aka enterobacteriaceae)
I: lyme disease spirochete (aka borreliella burgdorferi)
J: None of the above. | [I; J] |
<Instruct>: Given the context 'The lack of key repair enzymes in this system may indicate that B. burgdorferi DNA is not subjected to the same challenge from ROS as is E. coli.
', 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>: [b. burgdorferi; e. coli]
<Options>: A: borrelia americana (aka borreliella americana)
B: borreliella (borrelia burgdorferi sensu lato) (aka borreliella)
C: escherichia coli (strain b) (aka escherichia coli b)
D: enterobacteriales (aka enterobacterales)
E: lyme disease spirochete (aka borreliella burgdorferi)
F: candidatus borrelia africana (borrelia africana) (aka candidatus borrelia africana)
G: e. coli (aka escherichia coli)
H: borrelia fainii (aka candidatus borrelia fainii)
I: enterobacteria (aka enterobacteriaceae)
J: prokaryotes (aka bacteria)
K: None of the above. | [E; G] |
<Instruct>: Given the context 'In contrast to most bacteria, B. burgdorferi membranes contained significant levels of unsaturated fatty acids, such as linoleic acid and linolenic acid, which were derived from the growth media (Table 1).', 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>: [b. burgdorferi]
<Options>: A: borreliella genomospecies 1 (aka borreliella genomosp. 1)
B: borreliella (borrelia burgdorferi sensu lato) (aka borreliella)
C: borrelia burgdorferi b31 (aka borreliella burgdorferi b31)
D: borreliella burgdorferi (lyme disease spirochete) (aka borreliella burgdorferi)
E: borrelia
F: None of the above. | [D] |
<Instruct>: Given the context 'Thus, it seemed possible that lipids and/or proteins rather than DNA are the primary targets of ROS in B. burgdorferi.', 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>: [b. burgdorferi]
<Options>: A: lyme disease spirochete (aka borreliella burgdorferi)
B: borreliella (borrelia burgdorferi sensu lato) (aka borreliella)
C: borrelomyces (aka mycoplasma)
D: borreliales bacterium
E: borrelia fainii (aka candidatus borrelia fainii)
F: None of the above. | [A] |
<Instruct>: Given the context 'As B. burgdorferi may be exposed to potentially harmful oxygen species at different stages of the infective cycle, the ability to protect its membrane lipids from ROS should be required for survival in the different host environments.', 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>: [b. burgdorferi]
<Options>: A: borrelia americana (aka borreliella americana)
B: borreliella burgdorferi (lyme disease spirochete) (aka borreliella burgdorferi)
C: borrelia garinii (aka borreliella garinii)
D: borrelia africana (aka candidatus borrelia africana)
E: borreliella genomospecies 1 (aka borreliella genomosp. 1)
F: None of the above. | [B] |
<Instruct>: Given the context 'In H. pylori, lipid hydroperoxide levels in ahpC mutants are approximately three times higher than in wild-type cells, suggesting a role for AhpC in reducing organic peroxides (Wang et al., 2006a,b).', 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>: [h. pylori]
<Options>: A: helicobacter
B: helicobacter cholecystus
C: campylobacter pylori (aka helicobacter pylori)
D: helicobacter pylori (strain ss1) (aka helicobacter pylori ss1)
E: helicobacter bovis (aka candidatus helicobacter bovis)
F: None of the above. | [C] |
<Instruct>: Given the context 'In exponentially growing E. coli, Imlay and Fridovich (1991) have shown that both O2- and H2O2 are generated by the autoxidation of components of the respiratory chain during oxygen metabolism.', 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>: [e. coli]
<Options>: A: bacterium coli (aka escherichia coli)
B: 'escherichia faecalis' (aka escherichia faecalis)
C: escherichia coli k12 (aka escherichia coli k-12)
D: unspecified coliform bacterium
E: enterobacterales (enterobacteriaceae and related endosymbionts) (aka enterobacterales)
F: None of the above. | [A] |
<Instruct>: Given the context 'In contrast, B. burgdorferi is very metabolically limited and has no enzymes for the TCA cycle or respiration.', 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>: [b. burgdorferi]
<Options>: A: borrelia
B: borrelia africana (aka candidatus borrelia africana)
C: borrelia fainii (aka candidatus borrelia fainii)
D: borrelia burgdorferi b31 (aka borreliella burgdorferi b31)
E: borrelia burgdorferi (aka borreliella burgdorferi)
F: None of the above. | [E] |
<Instruct>: Given the context 'In addition, the current practice of growing B. burgdorferi under atmospheric oxygen could itself be unintentionally compromising cell integrity during in vitro manipulations.
', 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>: [b. burgdorferi]
<Options>: A: borreliales bacterium
B: borreliella burgdorferi (lyme disease spirochete) (aka borreliella burgdorferi)
C: borrelia africana (aka candidatus borrelia africana)
D: borrelia
E: borrelia americana (aka borreliella americana)
F: None of the above. | [B] |
<Instruct>: Given the context 'Analyses of the B. burgdorferi genome indicates that only a few genes encoding putative oxidative stress/intracellular redox proteins (SodA, NapA, BosR, CoADR, Trx and TrxR)', 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>: [b. burgdorferi]
<Options>: A: candidatus borrelia africana (borrelia africana) (aka candidatus borrelia africana)
B: borrelia americana (aka borreliella americana)
C: borrelia garinii (aka borreliella garinii)
D: lyme disease spirochete (aka borreliella burgdorferi)
E: borrelia genomosp. 1 (aka borreliella genomosp. 1)
F: None of the above. | [D] |
<Instruct>: Given the context 'Analyses of the B. burgdorferi genome indicates that only a few genes encoding putative oxidative stress/intracellular redox proteins (SodA, NapA, BosR, CoADR, Trx and TrxR)', 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>: [b. burgdorferi]
<Options>: A: candidatus borrelia africana (borrelia africana) (aka candidatus borrelia africana)
B: borrelia genomosp. 1 (aka borreliella genomosp. 1)
C: borrelia garinii (aka borreliella garinii)
D: borrelia americana (aka borreliella americana)
E: None of the above. | [E] |
<Instruct>: Given the context 'Despite this apparent ‘deficiency’ in the number of ROS-protective enzymes, B. burgdorferi cells appear to be able to cope with physiologically relevant levels of ROS.', 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>: [b. burgdorferi]
<Options>: A: borreliales bacterium
B: borrelia garinii (aka borreliella garinii)
C: borrelomyces (aka mycoplasma)
D: borreliella genomospecies 1 (aka borreliella genomosp. 1)
E: borreliella burgdorferi (lyme disease spirochete) (aka borreliella burgdorferi)
F: None of the above. | [E] |
<Instruct>: Given the context 'There are several factors that would contribute to this phenomenon: (i) as B. burgdorferi does not harbour the genes encoding respiratory enzymes nor metabolize oxygen, it seems unlikely that significant levels of ROS are generated via the incomplete reduction of O2 during cellular metabolism.', 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>: [b. burgdorferi]
<Options>: A: borreliales bacterium
B: borrelia fainii (aka candidatus borrelia fainii)
C: lyme disease borrelia (aka borreliella)
D: borrelomyces (aka mycoplasma)
E: borrelia burgdorferi (aka borreliella burgdorferi)
F: None of the above. | [E] |
<Instruct>: Given the context 'This would suggest that potential ROS challenges to B. burgdorferi would come almost completely from extracellular sources with little contribution from intracellularly generated ROS; (ii) owing to a lack of understanding of the physiological conditions in vector and host tissues infected with B. burgdorferi, it is difficult to assess the levels and/or sites of the potential ROS challenge during the infective cycle and (iii) most importantly, analyses of the potential targets for ROS in B. burgdorferi strongly suggested that the major targets of oxidative damage are different and perhaps less extensive in this bacterium than in other bacterial pathogens (e.g. E. coli).', 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>: [b. burgdorferi; e. coli]
<Options>: A: borrelia burgdorferi (aka borreliella burgdorferi)
B: escherichia coli (escherichia/shigella coli) (aka escherichia coli)
C: escherichia coli b (escherichia coli (strain b)) (aka escherichia coli b)
D: borreliella (borrelia burgdorferi sensu lato) (aka borreliella)
E: borreliales bacterium
F: unspecified coliform bacterium
G: escherichia coli k12 (aka escherichia coli k-12)
H: enterobacterales (enterobacteriaceae and related endosymbionts) (aka enterobacterales)
I: borrelia burgdorferi b31 (aka borreliella burgdorferi b31)
J: borrelia garinii (aka borreliella garinii)
K: None of the above. | [A; B] |
<Instruct>: Given the context 'This would suggest that potential ROS challenges to B. burgdorferi would come almost completely from extracellular sources with little contribution from intracellularly generated ROS; (ii) owing to a lack of understanding of the physiological conditions in vector and host tissues infected with B. burgdorferi, it is difficult to assess the levels and/or sites of the potential ROS challenge during the infective cycle and (iii) most importantly, analyses of the potential targets for ROS in B. burgdorferi strongly suggested that the major targets of oxidative damage are different and perhaps less extensive in this bacterium than in other bacterial pathogens (e.g. E. coli).', 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>: [b. burgdorferi; e. coli]
<Options>: A: bacterium coli (aka escherichia coli)
B: escherichia sp.
C: enterobacterales (enterobacteriaceae and related endosymbionts) (aka enterobacterales)
D: borrelia fainii (aka candidatus borrelia fainii)
E: borreliella americana (borrelia americana) (aka borreliella americana)
F: borrelia africana (aka candidatus borrelia africana)
G: borrelia burgdorferi (aka borreliella burgdorferi)
H: borreliella burgdorferi b31 (borrelia burgdorferi str. b31) (aka borreliella burgdorferi b31)
I: escherichia coli k12 (aka escherichia coli k-12)
J: prokaryotes (aka bacteria)
K: None of the above. | [G; A] |
<Instruct>: Given the context 'Taken together, this suggests that B. burgdorferi would be innately more resistant to ROS and require a less extensive repertoire of enzymes to protect the cells from oxidative damage.
', 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>: [b. burgdorferi]
<Options>: A: borreliales bacterium
B: borrelomyces (aka mycoplasma)
C: borrelia garinii (aka borreliella garinii)
D: borrelia fainii (aka candidatus borrelia fainii)
E: lyme disease spirochete (aka borreliella burgdorferi)
F: None of the above. | [E] |
<Instruct>: Given the context 'Experimental procedures
Strains, growth conditions and reagents
Borrelia burgdorferi strain B31A3 and strain B314 (Sadziene et al., 1993) were grown in modified BSK-II (Barbour, 1984) medium at 34°C under an atmosphere of 0–20% O2 with 5% CO2 and the balance N2.', 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>: [borrelia burgdorferi]
<Options>: A: borreliella burgdorferi (lyme disease spirochete) (aka borreliella burgdorferi)
B: borrelia
C: borreliales bacterium
D: borrelia burgdorferi sensu lato (aka borreliella)
E: candidatus borrelia africana (borrelia africana) (aka candidatus borrelia africana)
F: None of the above. | [A] |
<Instruct>: Given the context 'E. coli strain Top10, strain TA4315 (ahpCF) (Storz et al., 1989) and CM1319 (mutM) (Bridges et al., 1996) were grown in Luria–Bertani (LB) at 37°C with shaking.
', 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>: [e. coli]
<Options>: A: bacillus coli (aka escherichia coli)
B: prokaryotes (aka bacteria)
C: escherichia faecalis ('escherichia faecalis') (aka escherichia faecalis)
D: escherichia
E: enterobacteriaceae bacterium
F: None of the above. | [A] |
<Instruct>: Given the context 'Per cent survivability assays
Borrelia burgdorferi strain B31A3 was grown to a cell density of 5 × 107 cells ml−1 in BSK II under microaerobic (3% O2) conditions, the culture split and the cells treated with varying concentrations of oxidants (0–50 mM t-butyl hydroperoxide or H2O2) at 34°C for 4 h. After the incubation, cells were diluted in fresh BSK II, plated on BSK plates and incubated 7–14 days at 34°C.', 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>: [borrelia burgdorferi]
<Options>: A: candidatus borrelia africana (borrelia africana) (aka candidatus borrelia africana)
B: borrelia fainii (aka candidatus borrelia fainii)
C: borrelia burgdorferi b31 (aka borreliella burgdorferi b31)
D: borreliella burgdorferi (lyme disease spirochete) (aka borreliella burgdorferi)
E: borrelia
F: None of the above. | [D] |
<Instruct>: Given the context 'Per cent survivability assays
Borrelia burgdorferi strain B31A3 was grown to a cell density of 5 × 107 cells ml−1 in BSK II under microaerobic (3% O2) conditions, the culture split and the cells treated with varying concentrations of oxidants (0–50 mM t-butyl hydroperoxide or H2O2) at 34°C for 4 h. After the incubation, cells were diluted in fresh BSK II, plated on BSK plates and incubated 7–14 days at 34°C.', 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>: [borrelia burgdorferi]
<Options>: A: candidatus borrelia africana (borrelia africana) (aka candidatus borrelia africana)
B: borrelia
C: borrelia burgdorferi b31 (aka borreliella burgdorferi b31)
D: borrelia fainii (aka candidatus borrelia fainii)
E: None of the above. | [E] |
<Instruct>: Given the context 'Determination of the spontaneous mutation rate
To determine spontaneous resistance to coumermycin A1, B. burgdorferi B31A3 cells were grown under microaerobic conditions to a cell density of 5 × 107 cells ml−1 and treated with 5 mM H2O2 for 1 h at 34°C.', 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>: [b. burgdorferi]
<Options>: A: borrelia genomosp. 1 (aka borreliella genomosp. 1)
B: borreliella burgdorferi b31 (borrelia burgdorferi str. b31) (aka borreliella burgdorferi b31)
C: borrelia fainii (aka candidatus borrelia fainii)
D: borrelomyces (aka mycoplasma)
E: lyme disease spirochete (aka borreliella burgdorferi)
F: None of the above. | [E] |
<Instruct>: Given the context 'Measurement of DNA base lesions
Borrelia burgdorferi B31A3 cells were grown in BSK-II under microaerobic conditions to a cell density of 5 × 107 cells ml−1, treated with various oxidants (1 or 10 mM t-butyl hydroperoxide, 1 or 10 mM H2O2, 10 mM paraquat or lipoxidase) for 4 h and total DNA was isolated using Wizard Genomic DNA Purification Kit (Promega Corp., Madison, WI).', 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>: [borrelia burgdorferi]
<Options>: A: borrelia burgdorferi (aka borreliella burgdorferi)
B: borrelia
C: borreliales bacterium
D: borrelia burgdorferi sensu lato (aka borreliella)
E: borrelia genomosp. 1 (aka borreliella genomosp. 1)
F: None of the above. | [A] |
<Instruct>: Given the context 'As a control, E. coli TA4315 cells were grown in minimal media to OD600 of 0.4, treated with 0 or 100 µM H2O2 for 30 min and DNA isolated.', 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>: [e. coli]
<Options>: A: unspecified coliform bacterium
B: escherichia phage
C: e. coli (aka escherichia coli)
D: escherichia coli b (escherichia coli (strain b)) (aka escherichia coli b)
E: escherichia
F: None of the above. | [C] |
<Instruct>: Given the context 'B. burgdorferi strain B314 cells were grown under microaerobic conditions and DNA isolated.', 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>: [b. burgdorferi]
<Options>: A: borreliella americana (borrelia americana) (aka borreliella americana)
B: borrelomyces (aka mycoplasma)
C: borreliales bacterium
D: borrelia garinii (aka borreliella garinii)
E: borrelia burgdorferi (aka borreliella burgdorferi)
F: None of the above. | [E] |
<Instruct>: Given the context 'To determine the amount of 8-oxoguanine in B. burgdorferi DNA, cells were grown and treated as described above and DNA isolated.', 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>: [b. burgdorferi]
<Options>: A: borrelia burgdorferi (aka borreliella burgdorferi)
B: borreliella americana (borrelia americana) (aka borreliella americana)
C: borrelia fainii (aka candidatus borrelia fainii)
D: borrelia
E: borreliales bacterium
F: None of the above. | [A] |
<Instruct>: Given the context 'As a control, E. coli CM1319 (mutM) cells were grown in LB to OD600 of 0.4, treated with 0 or 100 µM H2O2 for 1 h and DNA isolated.', 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>: [e. coli]
<Options>: A: bacterium coli (aka escherichia coli)
B: escherichia faecalis ('escherichia faecalis') (aka escherichia faecalis)
C: enterobacteriaceae bacterium
D: escherichia phage
E: unspecified coliform bacterium
F: None of the above. | [A] |
<Instruct>: Given the context 'Lipid analyses
To determine fatty acid content in B. burgdorferi total membranes, B. burgdorferi strain B31A3 was grown under anaerobic conditions to a cell density of 5 × 107 cells ml−1, harvested by centrifugation (5000 g, 15 min, 4°C) and washed two times with HN (20 mM NaCl, 50 mM Hepes, pH 7.6) buffer.', 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>: [b. burgdorferi]
<Options>: A: borreliella americana (borrelia americana) (aka borreliella americana)
B: borrelia garinii (aka borreliella garinii)
C: borreliales bacterium
D: borreliella burgdorferi (lyme disease spirochete) (aka borreliella burgdorferi)
E: borrelia genomosp. 1 (aka borreliella genomosp. 1)
F: None of the above. | [D] |
<Instruct>: Given the context 'To determine the effects of oxidants on fatty acid composition, a 1.5 l culture of B. burgdorferi strain B31A3 was grown under microaerobic conditions to a cell density of 5 × 107 cells ml−1.', 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>: [b. burgdorferi]
<Options>: A: borreliella genomospecies 1 (aka borreliella genomosp. 1)
B: borreliella americana (borrelia americana) (aka borreliella americana)
C: borrelomyces (aka mycoplasma)
D: borrelia africana (aka candidatus borrelia africana)
E: borrelia burgdorferi (aka borreliella burgdorferi)
F: None of the above. | [E] |
<Instruct>: Given the context 'Measurement of MDA
Borrelia burgdorferi strain B31A3 was grown aerobically, microaerobically and anaerobically as described above to a cell density of 5 × 107 cells ml−1.', 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>: [borrelia burgdorferi]
<Options>: A: lyme disease spirochete (aka borreliella burgdorferi)
B: borrelia africana (aka candidatus borrelia africana)
C: borrelia
D: borrelia genomosp. 1 (aka borreliella genomosp. 1)
E: borreliales bacterium
F: None of the above. | [A] |
<Instruct>: Given the context 'As a negative control, E. coli Top10 cells were grown to OD600 of 0.4, treated with 0 or 5 mM AAPH for 30 min and MDA measured as above.', 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>: [e. coli]
<Options>: A: escherichia coli (escherichia/shigella coli) (aka escherichia coli)
B: enterobacteria (aka enterobacteriaceae)
C: escherichia
D: prokaryotes (aka bacteria)
E: unspecified coliform bacterium
F: None of the above. | [A] |
<Instruct>: Given the context 'As a negative control, E. coli Top10 cells were grown to OD600 of 0.4, treated with 0 or 5 mM AAPH for 30 min and MDA measured as above.', 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>: [e. coli]
<Options>: A: prokaryotes (aka bacteria)
B: enterobacteria (aka enterobacteriaceae)
C: escherichia
D: unspecified coliform bacterium
E: None of the above. | [E] |
<Instruct>: Given the context 'As a positive control, mouse myeloma SP2/O cells were cultured with HYQ-CCM1 (HyClone) medium at 37°C in a humidified 5% CO2 atmosphere, treated with 1 mM AAPH at 37°C for 4 h (Chotimarkorn et al., 2005) and MDA measured as above.
', 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>: [mouse]
<Options>: A: mus molossinus (aka mus musculus molossinus)
B: mus musculus (house mouse) (aka mus musculus)
C: mice (aka mus <genus>) (aka mus <genus>)
D: mus musculus domesticus (western european house mouse) (aka mus musculus domesticus)
E: eastern european house mouse (aka mus musculus musculus)
F: None of the above. | [B] |
<Instruct>: Given the context 'Identification of lipid damage using Diphenyl-1-pyrenylphosphine fluorescent stain
Borrelia burgdorferi strain B31A3 cells were grown microaerobically as described above until a cell density of 5 × 107 cells ml−1 was obtained.', 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>: [borrelia burgdorferi]
<Options>: A: borrelia americana (aka borreliella americana)
B: borrelia burgdorferi (aka borreliella burgdorferi)
C: borreliella burgdorferi b31 (borrelia burgdorferi str. b31) (aka borreliella burgdorferi b31)
D: borreliella genomosp. 1 (borreliella genomospecies 1) (aka borreliella genomosp. 1)
E: candidatus borrelia africana (borrelia africana) (aka candidatus borrelia africana)
F: None of the above. | [B] |
<Instruct>: Given the context 'Briefly, after cells were stained with the Red Fluorescent dye, 2 ml of rabbit serum was added to stop the reaction and the mixture incubated for 1 min at RT.', 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>: [rabbit]
<Options>: A: cattle (aka bos)
B: lepus europaeus europaeus
C: swamp rabbit (aka sylvilagus aquaticus)
D: leporidae (rabbits and hares) (aka leporidae)
E: japanese white rabbit (aka oryctolagus cuniculus)
F: None of the above. | [E] |
<Instruct>: Given the context 'As a positive control, mouse myeloma SP2/O cells were cultured with HYQ-CCM1 (HyClone) medium at 37°C in a humidified 5% CO2 atmosphere, treated with 1 mM AAPH at 37°C for 4 h (Chotimarkorn et al., 2005) and stained as described above.', 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>: [mouse]
<Options>: A: mouse (aka mus <genus>)
B: mus <subgenus> (mus (aka mus <subgenus>))
C: mus molossinus (aka mus musculus molossinus)
D: mus musculoides (mus musculoides enclavae) (aka mus musculoides)
E: house mouse (aka mus musculus)
F: None of the above. | [E] |
<Instruct>: Given the context 'As a negative control, E. coli Top10 cells were grown to OD600 of 0.4, treated with 0 or 5 mM AAPH for 30 min and stained as described above.
', 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>: [e. coli]
<Options>: A: unspecified coliform bacterium
B: escherichia phage
C: 'escherichia faecalis' (aka escherichia faecalis)
D: enterococcus coli (aka escherichia coli)
E: escherichia coli k12 (aka escherichia coli k-12)
F: None of the above. | [D] |
<Instruct>: Given the context 'Electron microscopy
Borrelia burgdorferi cells were grown under microaerobic or anaerobic conditions to a cell density of 5 × 107 cells ml−1.', 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>: [borrelia burgdorferi]
<Options>: A: borrelia fainii (aka candidatus borrelia fainii)
B: borrelia africana (aka candidatus borrelia africana)
C: lyme disease spirochete (aka borreliella burgdorferi)
D: borreliales bacterium
E: borrelia burgdorferi b31 (aka borreliella burgdorferi b31)
F: None of the above. | [C] |
<Instruct>: Given the context 'In the initial analysis of the autoantibody profile in 39 Chinese BD patients, autoantibodies to cellular proteins were uncovered in 23% as determined by immunoblotting.', 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>: [patients]
<Options>: A: this
B: other (aka unidentified)
C: cancer
D: homo (humans) (aka homo)
E: homo sapiens (human) (aka homo sapiens)
F: None of the above. | [E] |
<Instruct>: Given the context 'Serum from a BD patient was used as a probe to immunoscreen a λZAP expression cDNA library.', 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>: [patient]
<Options>: A: mouse (aka mus musculus)
B: aides
C: homo sapiens (human) (aka homo sapiens)
D: goes
E: this
F: None of the above. | [C] |
<Instruct>: Given the context 'Reactivity was also examined with normal control sera and disease control sera from patients with lupus and Sjögren's syndrome.', 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>: [patients]
<Options>: A: subsection
B: homo sapiens (human) (aka homo sapiens)
C: suborder
D: other (aka unidentified)
E: theraps
F: None of the above. | [B] |
<Instruct>: Given the context 'Six independent candidate clones were isolated from the cDNA library screen and were identified as overlapping partial human kinectin cDNAs.', 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>: [human]
<Options>: A: human (aka homo sapiens)
B: birds (aka aves)
C: genus
D: eutherian mammals (aka eutheria)
E: homo (humans) (aka homo)
F: None of the above. | [A] |
<Instruct>: Given the context 'Six independent candidate clones were isolated from the cDNA library screen and were identified as overlapping partial human kinectin cDNAs.', 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>: [human]
<Options>: A: eutherian mammals (aka eutheria)
B: genus
C: homo (humans) (aka homo)
D: birds (aka aves)
E: None of the above. | [E] |
<Instruct>: Given the context 'The finding that kinectin was an autoantigen was verified in 9 out of 39 (23%) BD patient sera by immunoprecipitation of the in vitro translation products.', 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>: [patient]
<Options>: A: this
B: theraps
C: homo sapiens (human) (aka homo sapiens)
D: goes
E: other (aka unidentified)
F: None of the above. | [C] |
<Instruct>: Given the context 'Nevertheless, since the 1960s, there have been reports of autoantibodies against certain unknown components of human oral mucosa in sera of patients with BD.', 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>: [human; patients]
<Options>: A: human (aka homo sapiens)
B: animals (aka metazoa)
C: mus <genus> (mice (aka mus <genus>))
D: species
E: primate (aka primates)
F: probles
G: cancer
H: cellular organisms (biota) (aka cellular organisms)
I: kingdom
J: None of the above. | [A; A] |
<Instruct>: Given the context 'Nevertheless, since the 1960s, there have been reports of autoantibodies against certain unknown components of human oral mucosa in sera of patients with BD.', 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>: [human; patients]
<Options>: A: kingdom
B: species
C: macrobiotus sapiens
D: mus <genus> (mice (aka mus <genus>))
E: eutherian mammals (aka eutheria)
F: probles
G: human (aka homo sapiens)
H: humans (aka homo)
I: cancer
J: None of the above. | [G; G] |
<Instruct>: Given the context 'Since then, sporadic reports on findings of autoantibodies in this disease have been described, such as antibodies to retinal antigen(s), heat shock protein (HSP) of some strains of Streptococcus sanguis cross-reactive with human HSP polypeptide', 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>: [streptococcus sanguis; human]
<Options>: A: streptococcus suis
B: genus
C: species
D: this
E: streptococcus sanguinis
F: animals (aka metazoa)
G: human (aka homo sapiens)
H: streptococcus mutans
I: streptococcus infantis
J: streptococcus caprinus (aka streptococcus gallolyticus)
K: None of the above. | [E; G] |
<Instruct>: Given the context 'Since then, sporadic reports on findings of autoantibodies in this disease have been described, such as antibodies to retinal antigen(s), heat shock protein (HSP) of some strains of Streptococcus sanguis cross-reactive with human HSP polypeptide', 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>: [streptococcus sanguis; human]
<Options>: A: homo sapiens (human) (aka homo sapiens)
B: streptococcus sanguinis
C: macrobiotus sapiens
D: streptococcus ovis
E: animals (aka metazoa)
F: primate (aka primates)
G: streptococcus infantis
H: placental mammals (aka eutheria)
I: streptococcus equinus (streptococcus bovis) (aka streptococcus equinus)
J: streptococcus dentalis
K: None of the above. | [B; A] |
<Instruct>: Given the context 'Materials and methods
Patients and sera
The currently used empirical criteria for the diagnosis of BD in this study were the criteria proposed by the International Study Group for BD (abbreviated as 'International Criteria')', 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>: [patients]
<Options>: A: suborder
B: subsection
C: homo sapiens (human) (aka homo sapiens)
D: aides
E: homo (humans) (aka homo)
F: None of the above. | [C] |
<Instruct>: Given the context 'Materials and methods
Patients and sera
The currently used empirical criteria for the diagnosis of BD in this study were the criteria proposed by the International Study Group for BD (abbreviated as 'International Criteria')', 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>: [patients]
<Options>: A: subsection
B: homo (humans) (aka homo)
C: suborder
D: aides
E: None of the above. | [E] |
<Instruct>: Given the context 'The study subjects of 39 Chinese BD patients comprised 17 males and 22 females, mean age 37 ± 11.3 years old, who were divided into two subgroups: 25 typical BD patients (Group I, satisfying the International Criteria) and 14 clinically diagnosed BD patients who had recurrent oral ulcers and one of the symptoms of genital ulcers, eye symptoms or skin lesions as defined by the International Criteria, as well as additional symptom(s) closely related to BD as listed in the International Criteria, that is, gastrointestinal ulcerations, deep vein thrombosis or arthralgia/arthritis without evidence that the latter symptoms might be related to any other disease (Group II, defined as 'probable BD' in this study).', 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>: [patients]
<Options>: A: theraps
B: circe
C: homo sapiens (human) (aka homo sapiens)
D: other (aka unidentified)
E: this
F: None of the above. | [C] |
<Instruct>: Given the context 'Disease controls included 10 patients with SLE and 10 with SjS, all satisfying corresponding international classification criteria.', 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>: [patients]
<Options>: A: mouse (aka mus musculus)
B: cancer
C: homo sapiens (human) (aka homo sapiens)
D: theraps
E: probles
F: None of the above. | [C] |
<Instruct>: Given the context 'All BD patients and disease controls involved in the study were patients treated at the Rheumatology Department of Ren Ji Hospital, Shanghai, China, where their clinical data and serum samples were collected.', 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>: [patients]
<Options>: A: this
B: homo sapiens (human) (aka homo sapiens)
C: other (aka unidentified)
D: theraps
E: subsection
F: None of the above. | [B] |
<Instruct>: Given the context 'This study was approved by the institution review board of Ren Ji Hospital which is affiliated with Shanghai Second Medical University, and each patient involved gave informed consent.', 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>: [patient]
<Options>: A: subsection
B: isolate
C: homo sapiens (human) (aka homo sapiens)
D: data
E: species
F: None of the above. | [C] |
<Instruct>: Given the context 'Cell lines and cell extracts
HeLa (ATCC CCL 2.2) and T24 (human transitional cell bladder carcinoma) were obtained from the American Type Culture Collection (Rockville, MD, USA).', 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>: [human]
<Options>: A: mammals (aka mammalia)
B: suborder
C: this
D: avian (aka aves)
E: homo sapiens (human) (aka homo sapiens)
F: None of the above. | [E] |
<Instruct>: Given the context 'A bovine aortic endothelial cell line was kindly provided by Dr Eugene G Levin from the Scripps Research Institute (La Jolla, CA, USA).', 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>: [bovine]
<Options>: A: cow (aka bos taurus) (aka bos taurus)
B: boveria
C: bos taurus indicus (aka bos indicus)
D: bos bubalis (aka bubalus bubalis)
E: bos (cattle) (aka bos)
F: None of the above. | [A] |
<Instruct>: Given the context 'Cells were cultured in DMEM containing 10% calf serum, harvested and extracted in Buffer A (150 mM NaCl, 10 mM Tris-HCl, pH7.2, 0.5% Nonidet P-40) with protease inhibitor (Complete™; Boehringer Mannheim, Indianapolis, IN, USA).', 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>: [calf]
<Options>: A: boveria
B: bovine (aka bos taurus)
C: horses (aka equidae)
D: veturius
E: bovidae
F: None of the above. | [B] |
<Instruct>: Given the context 'Western blot
Whole cell lysates from bovine aortic endothelial cell, HeLa and T24 cells were resolved individually by discontinuous 7.5% gel SDS-PAGE according to Laemmli's method', 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>: [bovine]
<Options>: A: bos bubalis bubalis (aka bubalus bubalis bubalis)
B: cow (aka bos taurus) (aka bos taurus)
C: bovidae
D: bos (cattle) (aka bos)
E: bovinae
F: None of the above. | [B] |
<Instruct>: Given the context 'Nitrocellulose strips were blocked with 3% nonfat milk in PBS containing 0.05% Tween-20 (PBS-T) and then incubated with BD patient sera and normal control sera (1:100 dilution) at room temperature for 1 h. Filters were washed extensively with PBS-T to remove any unbound antibodies.', 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>: [patient]
<Options>: A: human (aka homo sapiens)
B: data
C: cancer
D: aides
E: circe
F: None of the above. | [A] |
<Instruct>: Given the context 'Bound antibodies were detected with polyvalent, peroxidase-conjugated goat anti-human Ig and visualized by incubating the nitrocellulose strips in chemiluminescent reagents (NEN Life Science Products Inc., Boston, MA, USA) and exposing to Kodak XAR-5 films.
', 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>: [goat; human]
<Options>: A: donkey (aka equus asinus)
B: domestic goat (aka capra hircus)
C: cellular organisms (biota) (aka cellular organisms)
D: capra aegagrus (capra hircus aegagrus) (aka capra aegagrus)
E: genus
F: capra hircus cretica (capra aegagrus cretica) (aka capra hircus cretica)
G: capra
H: human (aka homo sapiens)
I: mammals (aka mammalia)
J: avian (aka aves)
K: None of the above. | [B; H] |
<Instruct>: Given the context 'Bound antibodies were detected with polyvalent, peroxidase-conjugated goat anti-human Ig and visualized by incubating the nitrocellulose strips in chemiluminescent reagents (NEN Life Science Products Inc., Boston, MA, USA) and exposing to Kodak XAR-5 films.
', 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>: [goat; human]
<Options>: A: primate (aka primates)
B: donkey (aka equus asinus)
C: capreolus
D: macrobiotus sapiens
E: goats (aka capra hircus)
F: probles
G: capraita
H: human (aka homo sapiens)
I: kingdom
J: capra hircus aegagrus (aka capra aegagrus)
K: None of the above. | [E; H] |
<Instruct>: Given the context 'Screening of phage cDNA expression library with antibody probes
Serum from a BD patient showing the highest antibody titer in immunoblotting was selected as a probe and used at a dilution of 1:300 for initial immunoscreening of approximately 106 recombinants from a T24 cDNA expression library.', 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>: [patient]
<Options>: A: goes
B: other (aka unidentified)
C: kingdom
D: homo sapiens (human) (aka homo sapiens)
E: genus
F: None of the above. | [D] |
<Instruct>: Given the context 'In brief, 1 μg of the pBK-CMV plasmid identified in the screening outlined above was added as template in a 50-μl reaction for the coupled in vitro transcription and translation reaction with a rabbit reticulocyte lysate system (Promega, Madison, WI, USA) in the presence of 35S-methionine (Trans-35S label; ICN Biochemicals, Costa Mesa, CA, USA) and RNasin® Ribonuclease Inhibitor (Stratagene) as recommended by the manufacturer (Promega).', 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>: [rabbit]
<Options>: A: european hare (aka lepus europaeus)
B: cattle (aka bos)
C: marsh rabbit (aka sylvilagus palustris)
D: lepus cuniculus (aka oryctolagus cuniculus)
E: leporidae (rabbits and hares) (aka leporidae)
F: None of the above. | [D] |
<Instruct>: Given the context 'Results and discussion
Autoantibody detection in sera from BD patients
Initial examination of a group of 39 BD patients using indirect immunofluorescence (IIF) on a HEp-2 cell substrate did not yield any characteristic nuclear or cytoplasmic staining patterns.', 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>: [patients]
<Options>: A: circe
B: homo sapiens (human) (aka homo sapiens)
C: subsection
D: mus musculus (house mouse) (aka mus musculus)
E: homo (humans) (aka homo)
F: None of the above. | [B] |
<Instruct>: Given the context 'In this study, the use of bovine aortic endothelial cells as substrate for IIF did not provide any additional data.', 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>: [bovine]
<Options>: A: bos taurus x bos indicus (aka bos indicus x bos taurus)
B: bos indicus (bos primigenius indicus) (aka bos indicus)
C: bovine (aka bos taurus)
D: bos bubalis bubalis (aka bubalus bubalis bubalis)
E: bos bubalis (aka bubalus bubalis)
F: None of the above. | [C] |
<Instruct>: Given the context 'However, Western blot analysis of the BD sera began to show some interesting autoreactivity using cell lysates from both HeLa and bovine aortic endothelial cells.', 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>: [bovine]
<Options>: A: bovinae
B: boveria
C: bos primigenius taurus (aka bos taurus)
D: bos (cattle) (aka bos)
E: bos taurus x bos indicus (aka bos indicus x bos taurus)
F: None of the above. | [C] |
<Instruct>: Given the context 'Since the 49 kDa and 120 kDa bands were observed in cell extracts from bovine as well as human cell lines, these autoantigens might be evolutionarily conserved.
', 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>: [bovine; human]
<Options>: A: homo sapiens (human) (aka homo sapiens)
B: bos indicus (bos primigenius indicus) (aka bos indicus)
C: bovidae
D: bos bubalis (aka bubalus bubalis)
E: bos bovis (aka bos taurus)
F: cattle (aka bos)
G: animals (aka metazoa)
H: kingdom
I: mammals (aka mammalia)
J: genus
K: None of the above. | [E; A] |
<Instruct>: Given the context 'Since the 49 kDa and 120 kDa bands were observed in cell extracts from bovine as well as human cell lines, these autoantigens might be evolutionarily conserved.
', 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>: [bovine; human]
<Options>: A: bos indicus (bos primigenius indicus) (aka bos indicus)
B: animals (aka metazoa)
C: bos bubalis (aka bubalus bubalis)
D: cattle (aka bos)
E: kingdom
F: bovidae
G: genus
H: mammals (aka mammalia)
I: bos bovis (aka bos taurus)
J: None of the above. | [I; J] |
<Instruct>: Given the context 'Since the 49 kDa and 120 kDa bands were observed in cell extracts from bovine as well as human cell lines, these autoantigens might be evolutionarily conserved.
', 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>: [bovine; human]
<Options>: A: eutherian mammals (aka eutheria)
B: domestic cow (aka bos taurus)
C: avian (aka aves)
D: bos taurus indicus (aka bos indicus)
E: boveria
F: homo sapiens (human) (aka homo sapiens)
G: bos taurus x bos indicus (aka bos indicus x bos taurus)
H: probles
I: humans (aka homo)
J: bos sp.
K: None of the above. | [B; F] |
<Instruct>: Given the context 'I definitive BD patients with the strongest reactivity to 49 kDa and 120 kDa antigens (Fig. 1, lane 2) was selected as antibody probe for expression library screening.
', 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>: [patients]
<Options>: A: theraps
B: this
C: subsection
D: human (aka homo sapiens)
E: aides
F: None of the above. | [D] |
<Instruct>: Given the context 'Their identities were established as overlapping partial cDNAs of human kinectin, ranging from 1.9 kb to 3 kb (Fig. 2a).', 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>: [human]
<Options>: A: human (aka homo sapiens)
B: kingdom
C: eutherian mammals (aka eutheria)
D: cellular organisms (biota) (aka cellular organisms)
E: genus
F: None of the above. | [A] |
<Instruct>: Given the context 'The full-length human kinectin (GenBank accession number NM_182926[27]) has 4,816 bases containing an open reading frame coding 1,357 amino acid residues with molecular mass 156 kDa.', 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>: [human]
<Options>: A: humans (aka homo)
B: animals (aka metazoa)
C: primate (aka primates)
D: cellular organisms (biota) (aka cellular organisms)
E: homo sapiens (human) (aka homo sapiens)
F: None of the above. | [E] |
<Instruct>: Given the context 'Kinectin was initially identified in chick embryo brain microsome as an integral membrane protein anchored in endoplasmic reticulum and involved in kinesin-driven vesicle motility along microtubules [28,29].', 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>: [chick]
<Options>: A: gallus gallus gallus (gallus gallus philippensis) (aka gallus gallus gallus)
B: fopius
C: gallorhynchus
D: gallio
E: gallus gallus (gallus gallus domesticus) (aka gallus gallus)
F: None of the above. | [E] |
<Instruct>: Given the context 'Yeast two-hybrid screen studies from several laboratories have revealed the interaction of the Rho family of GTPase with kinectin, and have shown the functional links among RhoG, kinectin and kinesin, with kinectin as a key effector of RhoG microtubule-dependent cellular activity [32].', 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>: [yeast]
<Options>: A: saccharomycodes
B: candida/saccharomycetales (aka candida/saccharomycales clade)
C: saccharomyces cf. cerevisiae/paradoxus (saccharomyces cerevisiae or paradoxus) (aka saccharomyces cf. cerevisiae/paradoxus)
D: saccharomyces cerevisiae x saccharomyces mikatae
E: saccharomyces cerevisiae (desm.) meyen ex e.c. hansen, 1883 (aka saccharomyces cerevisiae)
F: None of the above. | [E] |
<Instruct>: Given the context 'Out of 39 BD patient sera, nine (23%) recognized the BD44 translation product (Fig. 3), whereas sera from 20 normal controls, 10 SLE and 10 SjS patients did not show reactivity.', 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>: [patient; patients]
<Options>: A: mus musculus (house mouse) (aka mus musculus)
B: kingdom
C: aides
D: theraps
E: probles
F: humans (aka homo)
G: homo sapiens (human) (aka homo sapiens)
H: None of the above. | [G; G] |
<Instruct>: Given the context 'Out of 39 BD patient sera, nine (23%) recognized the BD44 translation product (Fig. 3), whereas sera from 20 normal controls, 10 SLE and 10 SjS patients did not show reactivity.', 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>: [patient; patients]
<Options>: A: homo sapiens (human) (aka homo sapiens)
B: mouse (aka mus musculus)
C: kingdom
D: humans (aka homo)
E: cancer
F: proxys
G: subsection
H: probles
I: None of the above. | [A; A] |
<Instruct>: Given the context 'Among the nine anti-kinectin positive patients, six (6/25, 24%) were from Group I (definitive BD) including the BD patient whose serum was used in the immunoscreening of expression cDNA library, and three (3/14, 21.4%) patients were from the Group II (probable BD) in this study.', 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>: [patients; patient]
<Options>: A: mus <genus> (mice (aka mus <genus>))
B: probles
C: genus
D: theraps
E: aides
F: data
G: human (aka homo sapiens)
H: mouse (aka mus musculus)
I: None of the above. | [G; G] |
<Instruct>: Given the context 'Among the nine anti-kinectin positive patients, six (6/25, 24%) were from Group I (definitive BD) including the BD patient whose serum was used in the immunoscreening of expression cDNA library, and three (3/14, 21.4%) patients were from the Group II (probable BD) in this study.', 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>: [patients; patient]
<Options>: A: theraps
B: circe
C: suborder
D: cancer
E: species
F: mouse (aka mus musculus)
G: human (aka homo sapiens)
H: proxys
I: aides
J: None of the above. | [G; G] |
<Instruct>: Given the context 'The combined data substantiated the finding that kinectin is an autoantigen that can be recognized by sera from 23% of Chinese BD patients in this study with at least one immunoreactive region or autoepitope residing within the BD44 encoded polypeptide.
', 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>: [patients]
<Options>: A: goes
B: other (aka unidentified)
C: circe
D: human (aka homo sapiens)
E: genus
F: None of the above. | [D] |
<Instruct>: Given the context 'As discussed above, differential diagnosis of BD might be confusing in clinical practice since no specific laboratory test is available, and some patients may have symptoms and signs strongly suggestive of BD but do not fully satisfy the International Criteria, as in the Group II (probable BD) patients in our study group.', 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>: [patients]
<Options>: A: mus <genus> (mice (aka mus <genus>))
B: homo sapiens (human) (aka homo sapiens)
C: circe
D: homo (humans) (aka homo)
E: subsection
F: None of the above. | [B] |
<Instruct>: Given the context 'A number of investigators have pointed out that a comprehensive analysis of the clinical data for a given patient is very important for correct clinical diagnosis of BD, and that classification/diagnosis criteria, including the International Criteria, should be followed but should not be exclusive.', 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>: [patient]
<Options>: A: human (aka homo sapiens)
B: aides
C: proxys
D: other (aka unidentified)
E: suborder
F: None of the above. | [A] |
<Instruct>: Given the context 'The observation that three out of 14 patients in the probable BD group also had antibody to kinectin and the similar percentage of positive reactors between this group and Group I (21.4% versus 24%) supports this notion.', 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>: [patients]
<Options>: A: theraps
B: species
C: cancer
D: goes
E: human (aka homo sapiens)
F: None of the above. | [E] |
<Instruct>: Given the context 'The further use of non-clinical parameters such as immunological biomarkers as adjuncts to identify BD patients could be of help in the classification of this disease entity
While our work was ongoing, anti-kinectin antibodies were reported in sera from patients with hepatocellular carcinoma (HCC)', 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>: [patients]
<Options>: A: suborder
B: theraps
C: subsection
D: other (aka unidentified)
E: homo sapiens (human) (aka homo sapiens)
F: None of the above. | [E] |
<Instruct>: Given the context 'The further use of non-clinical parameters such as immunological biomarkers as adjuncts to identify BD patients could be of help in the classification of this disease entity
While our work was ongoing, anti-kinectin antibodies were reported in sera from patients with hepatocellular carcinoma (HCC)', 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>: [patients]
<Options>: A: subsection
B: suborder
C: theraps
D: other (aka unidentified)
E: None of the above. | [E] |
<Instruct>: Given the context 'The first HCC report [35] identified kinectin as a tumor-associated antigen from the screening of an autologous cDNA library constructed from the cancer of a 30-year-old patient from Guangxi, China.', 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>: [patient]
<Options>: A: mouse (aka mus musculus)
B: homo sapiens (human) (aka homo sapiens)
C: goes
D: humans (aka homo)
E: probles
F: None of the above. | [B] |
<Instruct>: Given the context 'This report stated that four out of five HCC patients tested were positive for anti-kinectin antibody', 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>: [patients]
<Options>: A: homo (humans) (aka homo)
B: human (aka homo sapiens)
C: mus <genus> (mice (aka mus <genus>))
D: circe
E: goes
F: None of the above. | [B] |
<Instruct>: Given the context 'In 2004, another laboratory also reported the cloning of kinectin as a tumor-associated antigen from a (presumably) different 30-year-old Chinese HCC patient [36].', 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>: [patient]
<Options>: A: kingdom
B: human (aka homo sapiens)
C: proxys
D: circe
E: species
F: None of the above. | [B] |
<Instruct>: Given the context 'In contrast, anti-kinectin antibodies were not detected in other studies of HCC patients associated with our laboratory [39,40].', 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>: [patients]
<Options>: A: homo sapiens (human) (aka homo sapiens)
B: circe
C: goes
D: probles
E: genus
F: None of the above. | [A] |
<Instruct>: Given the context 'The initial report by Hirano et al. identified kinectin by screening an aplastic anemia patient for candidate antigens using a Clontech human fetal liver cDNA expression library and it was concluded that seven out of 18 aplastic anemia patients were positive for anti-kinectin while none of the normal or disease controls had this antibody', 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>: [patient; human; patients]
<Options>: A: primate (aka primates)
B: subsection
C: biota (aka cellular organisms)
D: probles
E: goes
F: cancer
G: genus
H: aides
I: humans (aka homo)
J: other (aka unidentified)
K: homo sapiens (human) (aka homo sapiens)
L: kingdom
M: this
N: None of the above. | [K; K; K] |
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