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bioasq_trainv0_factoidyesno_pcnt20_n1609_test100

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type stringclasses 2 values	question stringlengths 13 210	answer stringlengths 5 521	golden_answers sequencelengths 1 22	ideal_answer stringlengths 3 22.1k	documents sequencelengths 1 133	snippets listlengths 0 125	asq_challenge int64 5 13	folder_name stringclasses 6 values	concepts sequencelengths 0 97 ⌀	triples listlengths 0 4.35k ⌀	id stringlengths 24 24	data_source stringclasses 2 values
factoid	What disease can be treated with Glofitamab?	['DLBCL']	[ "DLBCL", "Diffuse Large B-cell Lymphoma", "Diffuse Large B Cell Lymphoma", "DLBCL lymphoma", "Large B-cell lymphoma" ]	['Glofitamab is being tested for treatment of DLBCL after CAR T-Cell Therapy']	[ "http://www.ncbi.nlm.nih.gov/pubmed/35626120", "http://www.ncbi.nlm.nih.gov/pubmed/34941996", "http://www.ncbi.nlm.nih.gov/pubmed/36198538" ]	[ { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35626120", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 78, "text": "Glofitamab Treatment in Relapsed or Refractory DLBCL after CAR T-Cell Therapy." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35626120", "endSection": "abstract", "offsetInBeginSection": 361, "offsetInEndSection": 624, "text": "In this study, we evaluated the safety and efficacy of a monotherapy with the bispecific CD20xCD3 antibody glofitamab in patients who progressed after CAR T treatment. We report nine consecutive patients with progressive DLBCL after preceding CAR T-cell therapy. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35626120", "endSection": "abstract", "offsetInBeginSection": 1106, "offsetInEndSection": 1284, "text": "Our data suggest that glofitamab treatment is well tolerated and effective in patients with DLBCL relapsing after CAR T-cell therapy and can enhance residual CAR T-cell activity." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/36198538", "endSection": "abstract", "offsetInBeginSection": 674, "offsetInEndSection": 976, "text": "Bispecific antibodies such as epcoritamab, mosunetuzumab, and glofitamab, anti-CD19 antibody drug tafasitamab combined with lenalidomide, CD19 antibody drug conjugate loncastuximab tesirine, oral selective inhibitor of nuclear export selinexor, and several new agents have been investigated for DLBCL. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/34941996", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 200, "text": "Glofitamab, a novel CD20xCD3, T-cell-engaging bispecific antibody, exhibited single-agent activity in Study NP30179, a first-in-human, phase 1 trial in relapsed/refractory B-cell non-Hodgkin lymphoma." } ]	12	BioASQ-training12b	null	null	63eeeb70f36125a426000005	bioasq_factoid
yesno	Does metformin interfere thyroxine absorption?	['No']	[ "No" ]	['There are not reported data indicating that metformin interferes with thyroxine absorption']	[ "http://www.ncbi.nlm.nih.gov/pubmed/23554450", "http://www.ncbi.nlm.nih.gov/pubmed/23264396", "http://www.ncbi.nlm.nih.gov/pubmed/23244059", "http://www.ncbi.nlm.nih.gov/pubmed/23154888", "http://www.ncbi.nlm.nih.gov/pubmed/23072197", "http://www.ncbi.nlm.nih.gov/pubmed/21748540", "http://www.ncbi.nlm.nih.gov/pubmed/21633823", "http://www.ncbi.nlm.nih.gov/pubmed/21435090", "http://www.ncbi.nlm.nih.gov/pubmed/21468525", "http://www.ncbi.nlm.nih.gov/pubmed/21041167" ]	[]	5	BioASQ-training5b	[ "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?field=uid&exact=Find+Exact+Term&term=D008687", "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?field=uid&exact=Find+Exact+Term&term=D013974", "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?field=uid&exact=Find+Exact+Term&term=D000042" ]	null	51406e6223fec90375000009	bioasq_yesno
yesno	Is there a relation between ANP and transcapillary albumin escape?	['yes']	[ "yes" ]	A possible role of ANP gene in conferring protection from nephropathy and microvascular damage in type 1 diabetes is present. ANP infusion in healthy subjects caused a shift of plasma water and electrolytes from the circulation, with albumin escape as a secondary phenomenon	[ "http://www.ncbi.nlm.nih.gov/pubmed/10405209", "http://www.ncbi.nlm.nih.gov/pubmed/7579054", "http://www.ncbi.nlm.nih.gov/pubmed/8432776", "http://www.ncbi.nlm.nih.gov/pubmed/9815090", "http://www.ncbi.nlm.nih.gov/pubmed/9338510", "http://www.ncbi.nlm.nih.gov/pubmed/8065837", "http://www.ncbi.nlm.nih.gov/pubmed/9702472", "http://www.ncbi.nlm.nih.gov/pubmed/2956451", "http://www.ncbi.nlm.nih.gov/pubmed/2148091", "http://www.ncbi.nlm.nih.gov/pubmed/2173580", "http://www.ncbi.nlm.nih.gov/pubmed/23927843", "http://www.ncbi.nlm.nih.gov/pubmed/10092997", "http://www.ncbi.nlm.nih.gov/pubmed/1837999", "http://www.ncbi.nlm.nih.gov/pubmed/1320716", "http://www.ncbi.nlm.nih.gov/pubmed/2142858", "http://www.ncbi.nlm.nih.gov/pubmed/15481764", "http://www.ncbi.nlm.nih.gov/pubmed/12087555", "http://www.ncbi.nlm.nih.gov/pubmed/2958207", "http://www.ncbi.nlm.nih.gov/pubmed/8853382", "http://www.ncbi.nlm.nih.gov/pubmed/2526450", "http://www.ncbi.nlm.nih.gov/pubmed/2148510", "http://www.ncbi.nlm.nih.gov/pubmed/2952859", "http://www.ncbi.nlm.nih.gov/pubmed/2210073", "http://www.ncbi.nlm.nih.gov/pubmed/17070433" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/10405209", "endSection": "abstract", "offsetInBeginSection": 2008, "offsetInEndSection": 2257, "text": "Thus, in a large ethnically homogeneous cohort of diabetic subjects, our data show: (1) a significant association of C708/T polymorphism with microalbuminuria in long-term diabetes and with both lower plasma ANP levels and widespread albumin leakage" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/10405209", "endSection": "abstract", "offsetInBeginSection": 2376, "offsetInEndSection": 2511, "text": "hese results suggest a possible role of PND gene in conferring protection from nephropathy and microvascular damage in type 1 diabetes." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/7579054", "endSection": "abstract", "offsetInBeginSection": 1247, "offsetInEndSection": 1462, "text": "Moreover, the increased susceptibility of the glomerular capillaries in diabetics to ANP seems to be part of a more generalized capillary abnormality, because ANP also increases the transcapillary escape of albumin." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/8432776", "endSection": "abstract", "offsetInBeginSection": 1263, "offsetInEndSection": 1433, "text": "In summary, low dose ANP infusion in healthy subjects caused a shift of plasma water and electrolytes from the circulation, with albumin escape as a secondary phenomenon." } ]	5	BioASQ-training5b	[ "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D009320", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D000418", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D017461", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D012709", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D013668" ]	[]	5321b8a39b2d7acc7e000009	bioasq_yesno
yesno	Has dupilumab been FDA approved for atopic dermatitis?	['yes']	[ "yes" ]	['Yes, dupilumab has been approved by FDA for atopic dermatitis.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/31603635", "http://www.ncbi.nlm.nih.gov/pubmed/32344789", "http://www.ncbi.nlm.nih.gov/pubmed/32439390", "http://www.ncbi.nlm.nih.gov/pubmed/31364023", "http://www.ncbi.nlm.nih.gov/pubmed/30785362" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/31364023", "endSection": "abstract", "offsetInBeginSection": 315, "offsetInEndSection": 575, "text": "Recent advances and understanding of the pathogenesis of AD have resulted in new therapies that target specific pathways with increased efficacy and the potential for less systemic side effects. New FDA-approved therapies for AD are crisaborole and dupilumab. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/30785362", "endSection": "abstract", "offsetInBeginSection": 225, "offsetInEndSection": 510, "text": "In March of 2017, the United States Food and Drug Administration (FDA) approved dupilumab for the treatment of moderate-to-severe atopic dermatitis in adults that is uncontrolled with topical medications, becoming the first biologic agent approved to treat this chronic skin condition." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/32439390", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 83, "text": "Dupilumab is the first US FDA approved biologic for treatment of atopic dermatitis." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/32344789", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 99, "text": "Dupilumab is the first biological treatment approved for moderate-to-severe atopic dermatitis (AD)." } ]	11	BioASQ-training11b	null	null	606b718994d57fd87900006b	bioasq_yesno
yesno	Does Rad9 interact with Aft1 in S.cerevisiae?	['yes']	[ "yes" ]	['Yes. Rad9 functions together with Aft1 on DNA damage-prone chromatin to facilitate genome surveillance, thereby ensuring rapid and effective response to possible DNA damage events.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/25300486" ]	[ { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25300486", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 142, "text": "Rad9 interacts with Aft1 to facilitate genome surveillance in fragile genomic sites under non-DNA damage-inducing conditions in S. cerevisiae." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25300486", "endSection": "abstract", "offsetInBeginSection": 186, "offsetInEndSection": 1376, "text": "Here we show that Rad9 checkpoint protein, known to mediate the damage signal from upstream to downstream essential kinases, interacts with Aft1 transcription factor in the budding yeast. Aft1 regulates iron homeostasis and is also involved in genome integrity having additional iron-independent functions. Using genome-wide expression and chromatin immunoprecipitation approaches, we found Rad9 to be recruited to 16% of the yeast genes, often related to cellular growth and metabolism, while affecting the transcription of ∼2% of the coding genome in the absence of exogenously induced DNA damage. Importantly, Rad9 is recruited to fragile genomic regions (transcriptionally active, GC rich, centromeres, meiotic recombination hotspots and retrotransposons) non-randomly and in an Aft1-dependent manner. Further analyses revealed substantial genome-wide parallels between Rad9 binding patterns to the genome and major activating histone marks, such as H3K36me, H3K79me and H3K4me. Thus, our findings suggest that Rad9 functions together with Aft1 on DNA damage-prone chromatin to facilitate genome surveillance, thereby ensuring rapid and effective response to possible DNA damage events." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25300486", "endSection": "abstract", "offsetInBeginSection": 186, "offsetInEndSection": 372, "text": "Here we show that Rad9 checkpoint protein, known to mediate the damage signal from upstream to downstream essential kinases, interacts with Aft1 transcription factor in the budding yeast" }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25300486", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 141, "text": "Rad9 interacts with Aft1 to facilitate genome surveillance in fragile genomic sites under non-DNA damage-inducing conditions in S. cerevisiae" }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25300486", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 142, "text": "Rad9 interacts with Aft1 to facilitate genome surveillance in fragile genomic sites under non-DNA damage-inducing conditions in S. cerevisiae." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25300486", "endSection": "abstract", "offsetInBeginSection": 186, "offsetInEndSection": 786, "text": "Here we show that Rad9 checkpoint protein, known to mediate the damage signal from upstream to downstream essential kinases, interacts with Aft1 transcription factor in the budding yeast. Aft1 regulates iron homeostasis and is also involved in genome integrity having additional iron-independent functions. Using genome-wide expression and chromatin immunoprecipitation approaches, we found Rad9 to be recruited to 16% of the yeast genes, often related to cellular growth and metabolism, while affecting the transcription of ?2% of the coding genome in the absence of exogenously induced DNA damage. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25300486", "endSection": "abstract", "offsetInBeginSection": 786, "offsetInEndSection": 1376, "text": "Importantly, Rad9 is recruited to fragile genomic regions (transcriptionally active, GC rich, centromeres, meiotic recombination hotspots and retrotransposons) non-randomly and in an Aft1-dependent manner. Further analyses revealed substantial genome-wide parallels between Rad9 binding patterns to the genome and major activating histone marks, such as H3K36me, H3K79me and H3K4me. Thus, our findings suggest that Rad9 functions together with Aft1 on DNA damage-prone chromatin to facilitate genome surveillance, thereby ensuring rapid and effective response to possible DNA damage events." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25300486", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 142, "text": "Rad9 interacts with Aft1 to facilitate genome surveillance in fragile genomic sites under non-DNA damage-inducing conditions in S. cerevisiae." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25300486", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 142, "text": "Rad9 interacts with Aft1 to facilitate genome surveillance in fragile genomic sites under non-DNA damage-inducing conditions in S. cerevisiae." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25300486", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 142, "text": "Rad9 interacts with Aft1 to facilitate genome surveillance in fragile genomic sites under non-DNA damage-inducing conditions in S. cerevisiae." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25300486", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 142, "text": "Rad9 interacts with Aft1 to facilitate genome surveillance in fragile genomic sites under non-DNA damage-inducing conditions in S. cerevisiae." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25300486", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 142, "text": "Rad9 interacts with Aft1 to facilitate genome surveillance in fragile genomic sites under non-DNA damage-inducing conditions in S. cerevisiae." } ]	5	BioASQ-training5b	[ "http://www.uniprot.org/uniprot/RAD9_SCHPO", "http://www.uniprot.org/uniprot/RAD9B_BOVIN", "http://www.uniprot.org/uniprot/RAD9B_RAT", "http://www.uniprot.org/uniprot/RAD9B_MOUSE", "http://www.uniprot.org/uniprot/RAD9A_HUMAN", "http://www.uniprot.org/uniprot/RAD9A_MOUSE", "http://www.uniprot.org/uniprot/RAD9B_HUMAN", "http://www.uniprot.org/uniprot/RHNO1_MOUSE", "http://www.uniprot.org/uniprot/RHNO1_HUMAN", "http://www.nlm.nih.gov/cgi/mesh/2016/MB_cgi?field=uid&exact=Find+Exact+Term&term=D012441", "http://www.biosemantics.org/jochem#4263227", "http://www.nlm.nih.gov/cgi/mesh/2016/MB_cgi?field=uid&exact=Find+Exact+Term&term=D029701", "http://www.uniprot.org/uniprot/RAD9_SCHOT", "http://www.uniprot.org/uniprot/RAD9_YEAST", "http://www.uniprot.org/uniprot/NPBL_COPC7" ]	[]	56b9c937ac7ad10019000001	bioasq_yesno
factoid	What is the effect of carbamazepine on CYP3A4?	['Induces', 'inducer', 'induction']	[ "Induces", "inducer", "induction" ]	['Carbamazepine is an inducer of CYP3A4.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/31650711" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/31650711", "endSection": "abstract", "offsetInBeginSection": 274, "offsetInEndSection": 379, "text": "Carbamazepine, a UGT and cytochrome P450 3A4 inducer, is a first-line treatment for trigeminal neuralgia." } ]	11	BioASQ-training11b	null	null	606ab57394d57fd87900004f	bioasq_factoid
factoid	Do archaeal genomes contain one or multiple origins of replication?	['mostly multiple']	[ "mostly multiple", "multiple", "mostly", "primarily multiple", "largely multiple" ]	Some archaea replicate from single origins but most archaea and all eukaryotes replicate using multiple origins.	[ "http://www.ncbi.nlm.nih.gov/pubmed/15197606", "http://www.ncbi.nlm.nih.gov/pubmed/12646230", "http://www.ncbi.nlm.nih.gov/pubmed/12237132", "http://www.ncbi.nlm.nih.gov/pubmed/24185008", "http://www.ncbi.nlm.nih.gov/pubmed/23375370", "http://www.ncbi.nlm.nih.gov/pubmed/22978470", "http://www.ncbi.nlm.nih.gov/pubmed/22942672", "http://www.ncbi.nlm.nih.gov/pubmed/22812406", "http://www.ncbi.nlm.nih.gov/pubmed/20978102", "http://www.ncbi.nlm.nih.gov/pubmed/20667100", "http://www.ncbi.nlm.nih.gov/pubmed/18922777", "http://www.ncbi.nlm.nih.gov/pubmed/17511521", "http://www.ncbi.nlm.nih.gov/pubmed/17392430", "http://www.ncbi.nlm.nih.gov/pubmed/16249118", "http://www.ncbi.nlm.nih.gov/pubmed/15876567", "http://www.ncbi.nlm.nih.gov/pubmed/11521661" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/15197606", "endSection": "abstract", "offsetInBeginSection": 1056, "offsetInEndSection": 1407, "text": "Therefore, these lines of evidence strongly suggest that the identified region is a replication origin, which is designated as oriC1. The analysis of the y component of the Z curve, i.e., MK disparity curve, suggests the presence of another replication origin corresponding to one of the peaks in the MK disparity curve at around 1,388 kb of the genom" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/12237132", "endSection": "abstract", "offsetInBeginSection": 927, "offsetInEndSection": 1039, "text": "Our results strongly suggest that the single replication origin of M. mazei is situated at the intergenic region" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/24185008", "endSection": "abstract", "offsetInBeginSection": 294, "offsetInEndSection": 424, "text": "Bacteria and some archaea replicate from single origins, whereas most archaea and all eukaryotes replicate using multiple origins." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/23375370", "endSection": "abstract", "offsetInBeginSection": 17, "offsetInEndSection": 95, "text": "multiple DNA replication origins are a hallmark of Eukaryotes and some Archaea" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/22978470", "endSection": "abstract", "offsetInBeginSection": 403, "offsetInEndSection": 509, "text": "Multiple orc/cdc6-associated replication origins were predicted in all of the analyzed haloarchaeal genome" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/22942672", "endSection": "abstract", "offsetInBeginSection": 717, "offsetInEndSection": 822, "text": "different replication origins in some archaeal genomes leave quite different patterns of strand asymmetry" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/22812406", "endSection": "abstract", "offsetInBeginSection": 218, "offsetInEndSection": 301, "text": "the single chromosome of Pyrobaculum calidifontis contains four replication origins" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/20978102", "endSection": "abstract", "offsetInBeginSection": 469, "offsetInEndSection": 569, "text": "six archaeal genomes from the genus Sulfolobus containing three origins of replication were selected" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/20667100", "endSection": "abstract", "offsetInBeginSection": 641, "offsetInEndSection": 835, "text": "The strong replication-biased structuring of the Sulfolobus chromosome implies that the multiple replication origins serve purposes other than simply shortening the time required for replication" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/18922777", "endSection": "abstract", "offsetInBeginSection": 237, "offsetInEndSection": 295, "text": "The 3 DNA replication origins of Sulfolobus acidocaldarius" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/17511521", "endSection": "abstract", "offsetInBeginSection": 459, "offsetInEndSection": 665, "text": "We have used a combination of genetic, biochemical, and bioinformatic approaches to map DNA replication origins in H. volcanii. Five autonomously replicating sequences were found adjacent to cdc6/orc1 genes" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/17392430", "endSection": "abstract", "offsetInBeginSection": 325, "offsetInEndSection": 427, "text": "the multiple replication origin paradigm has also been demonstrated within the archaeal domain of life" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/16249118", "endSection": "abstract", "offsetInBeginSection": 17, "offsetInEndSection": 132, "text": "multiple chromosome replication origins in Sulfolobus species has added yet another eukaryotic trait to the archaea" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/15876567", "endSection": "abstract", "offsetInBeginSection": 197, "offsetInEndSection": 434, "text": "We employed Z-curve analysis to identify one replication origin in the Methanocaldococcus jannaschii genome, two replication origins in the Halobacterium species NRC-1 genome and one replication origin in the Methanosarcina mazei genome." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/11521661", "endSection": "abstract", "offsetInBeginSection": 104, "offsetInEndSection": 245, "text": "Archaea seem to replicate using a single origin (as do eubacteria) even though archaeal replication factors are more like those of eukaryotes" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/12646230", "endSection": "abstract", "offsetInBeginSection": 739, "offsetInEndSection": 877, "text": "Based on the above analysis, a model of replication of Halobacterium NRC-1 with two replication origins and two termini has been proposed." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/12646230", "endSection": "abstract", "offsetInBeginSection": 1132, "offsetInEndSection": 1285, "text": "In addition, the potential multiple replication origins of the archaeon Sulfolobus solfataricus are suggested by the analysis based on the Z curve method" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/22978470", "endSection": "abstract", "offsetInBeginSection": 12, "offsetInEndSection": 140, "text": "While multiple replication origins have been observed in archaea, considerably less is known about their evolutionary processes." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/22978470", "endSection": "abstract", "offsetInBeginSection": 1608, "offsetInEndSection": 1680, "text": "multiple orc/cdc6-associated replication origins in haloarchaeal genomes" } ]	5	BioASQ-training5b	[ "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D018741", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D020745" ]	[]	52fe58f82059c6d71c00007a	bioasq_factoid
factoid	What disease can be treated with Trofinetide?	['Rett syndrome']	[ "Rett syndrome", "Rett's syndrome", "Rett disorder", "Rett's disorder", "MECP2-related disorder", "MECP2 syndrome" ]	['Trofinetide is approved for Rett syndrome.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/28964591", "http://www.ncbi.nlm.nih.gov/pubmed/37714122", "http://www.ncbi.nlm.nih.gov/pubmed/38017349", "http://www.ncbi.nlm.nih.gov/pubmed/37568516", "http://www.ncbi.nlm.nih.gov/pubmed/37291210", "http://www.ncbi.nlm.nih.gov/pubmed/35622206", "http://www.ncbi.nlm.nih.gov/pubmed/38035006", "http://www.ncbi.nlm.nih.gov/pubmed/37635789", "http://www.ncbi.nlm.nih.gov/pubmed/35149233", "http://www.ncbi.nlm.nih.gov/pubmed/30918097", "http://www.ncbi.nlm.nih.gov/pubmed/37191913" ]	[ { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37291210", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 75, "text": "Trofinetide for the treatment of Rett syndrome: a randomized phase 3 study." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37291210", "endSection": "abstract", "offsetInBeginSection": 1209, "offsetInEndSection": 1414, "text": "Significant improvement for trofinetide compared with placebo was observed for the coprimary efficacy endpoints, suggesting that trofinetide provides benefit in treating the core symptoms of Rett syndrome." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37191913", "endSection": "abstract", "offsetInBeginSection": 317, "offsetInEndSection": 459, "text": "Trofinetide was approved in March 2023 in the USA for the treatment of Rett syndrome in adult and pediatric patients 2 years of age and older." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37635789", "endSection": "abstract", "offsetInBeginSection": 964, "offsetInEndSection": 1188, "text": "In LAVENDER, the FDA-approved drug trofinetide significantly improved the RSBQ total score over placebo in girls and women with RTT and change from baseline for all RSBQ subscores were directionally in favor of trofinetide. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37568516", "endSection": "abstract", "offsetInBeginSection": 276, "offsetInEndSection": 369, "text": " Recently, Trofinetide was approved by the USFDA on 10 March 2023 as the first RTT treatment." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37568516", "endSection": "abstract", "offsetInBeginSection": 1678, "offsetInEndSection": 1873, "text": "Trofinetide is one of the important milestones for RTT therapy and is the beginning of a new era for the therapy of RTT, FXS, autism spectrum disorder (ASD), brain injury, stroke, and other NDDs." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/38035006", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 55, "text": "Trofinetide-a new chapter in rett syndrome's treatment." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/38035006", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 480, "text": "Trofinetide is the first drug approved by the FDA to treat Rett Syndrome in children aged 2 years or above. The drug significantly improved Rett syndrome behavioral scores Rett syndrome behavioral questionnaire in clinical studies. Although further research is needed to assess potential adverse events, Trofinetide's notable efficacy signifies a significant advancement in Rett syndrome treatment, offering a new therapeutic avenue with the potential to ameliorate the condition." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/38035006", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 231, "text": "Trofinetide is the first drug approved by the FDA to treat Rett Syndrome in children aged 2 years or above. The drug significantly improved Rett syndrome behavioral scores Rett syndrome behavioral questionnaire in clinical studies." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/38035006", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 107, "text": "Trofinetide is the first drug approved by the FDA to treat Rett Syndrome in children aged 2 years or above." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/38035006", "endSection": "abstract", "offsetInBeginSection": 108, "offsetInEndSection": 480, "text": "The drug significantly improved Rett syndrome behavioral scores Rett syndrome behavioral questionnaire in clinical studies. Although further research is needed to assess potential adverse events, Trofinetide's notable efficacy signifies a significant advancement in Rett syndrome treatment, offering a new therapeutic avenue with the potential to ameliorate the condition." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/38035006", "endSection": "abstract", "offsetInBeginSection": 232, "offsetInEndSection": 480, "text": "Although further research is needed to assess potential adverse events, Trofinetide's notable efficacy signifies a significant advancement in Rett syndrome treatment, offering a new therapeutic avenue with the potential to ameliorate the condition." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28964591", "endSection": "abstract", "offsetInBeginSection": 1237, "offsetInEndSection": 1586, "text": "SION: Trofinetide was well tolerated in adolescent and adult females with Rett syndrome. Although this study had a relatively short duration in a small number of subjects with an advanced stage of disease, consistent efficacy trends at the higher dose were observed in several outcome measures that assess important dimensions of Rett syndrome. Thes" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35622206", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 246, "text": "BACKGROUND AND OBJECTIVE: Trofinetide, a synthetic analog of tripeptide glycine-proline-glutamate, is an investigational agent for the treatment of Rett syndrome, a neurodevelopmental disorder with affected individuals requiring lifelong support." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/38017349", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 111, "text": "BACKGROUND AND OBJECTIVE: Trofinetide is the first drug to be approved for the treatment of Rett syndrome, a ne" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37568516", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 369, "text": "Rett syndrome (RTT) is a rare disability causing female-oriented pediatric neurodevelopmental unmet medical need. RTT was recognized in 1966. However, over the past 56 years, the United States Food and Drug Administration (USFDA) has authorized no effective treatment for RTT. Recently, Trofinetide was approved by the USFDA on 10 March 2023 as the first RTT treatment." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35622206", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 220, "text": "BACKGROUND AND OBJECTIVE: Trofinetide, a synthetic analog of tripeptide glycine-proline-glutamate, is an investigational agent for the treatment of Rett syndrome, a neurodevelopmental disorder with affected individuals r" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/30918097", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 269, "text": "OBJECTIVE: To determine safety, tolerability, and pharmacokinetics of trofinetide and evaluate its efficacy in female children/adolescents with Rett syndrome (RTT), a debilitating neurodevelopmental condition for which no pharmacotherapies directed at core features are" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28964591", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 274, "text": "BACKGROUND: This study aimed to determine the safety and tolerability of trofinetide and to evaluate efficacy measures in adolescent and adult females with Rett syndrome, a serious and debilitating neurodevelopmental condition for which no therapies are available for its co" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37714122", "endSection": "abstract", "offsetInBeginSection": 997, "offsetInEndSection": 1230, "text": "There are drugs in the research phase such as oxytocin, vasopressin and even some developed for specific entities related to autism such as arbaclofen in Fragile X and Trofinetide that has just been approved for use in Rett syndrome." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37191913", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 460, "text": "Trofinetide (DAYBUE™), an oral, small molecule, synthetic analog of glycine-proline-glutamate [GPE; the N-terminal tripeptide derivative of insulin like growth factor-1 (IGF-1)], is being developed by Neuren Pharmaceuticals and Acadia Pharmaceuticals for the treatment of rare childhood neurodevelopmental disorders. Trofinetide was approved in March 2023 in the USA for the treatment of Rett syndrome in adult and pediatric patients 2 years of age and older. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35149233", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 844, "text": "INTRODUCTION: Rett syndrome (RTT) is a debilitating neurodevelopmental disorder with no approved treatments. Trofinetide is a synthetic analog of glycine-proline-glutamate, the N-terminal tripeptide of insulin-like growth factor 1. In a phase 2, placebo-controlled trial in 82 females with RTT aged 5-15 years, a significant (p ≤ 0.042) improvement over placebo was observed with the highest trofinetide dose (200 mg/kg twice daily [BID]) on three measures: Rett Syndrome Behaviour Questionnaire (RSBQ), Clinical Global Impression-Improvement (CGI-I), and RTT-Clinician Domain Specific Concerns-Visual Analog Scale (RTT-DSC-VAS). Trofinetide was well tolerated at all doses (50, 100, and 200 mg/kg BID). A phase 3 trial utilizing disease-specific and novel scales was designed to investigate the efficacy and safety of trofinetide in girls and " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/38017349", "endSection": "abstract", "offsetInBeginSection": 22, "offsetInEndSection": 172, "text": "VE: Trofinetide is the first drug to be approved for the treatment of Rett syndrome, a neurodevelopmental disorder. The purpose of the study is to ful" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37714122", "endSection": "abstract", "offsetInBeginSection": 1165, "offsetInEndSection": 1230, "text": "Trofinetide that has just been approved for use in Rett syndrome." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35622206", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 245, "text": "BACKGROUND AND OBJECTIVE: Trofinetide, a synthetic analog of tripeptide glycine-proline-glutamate, is an investigational agent for the treatment of Rett syndrome, a neurodevelopmental disorder with affected individuals requiring lifelong support" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/38017349", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 136, "text": "BACKGROUND AND OBJECTIVE: Trofinetide is the first drug to be approved for the treatment of Rett syndrome, a neurodevelopmental disorder" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/30918097", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 279, "text": "OBJECTIVE: To determine safety, tolerability, and pharmacokinetics of trofinetide and evaluate its efficacy in female children/adolescents with Rett syndrome (RTT), a debilitating neurodevelopmental condition for which no pharmacotherapies directed at core features are available" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28964591", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 285, "text": "BACKGROUND: This study aimed to determine the safety and tolerability of trofinetide and to evaluate efficacy measures in adolescent and adult females with Rett syndrome, a serious and debilitating neurodevelopmental condition for which no therapies are available for its core features" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37191913", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 582, "text": "Trofinetide (DAYBUE™), an oral, small molecule, synthetic analog of glycine-proline-glutamate [GPE; the N-terminal tripeptide derivative of insulin like growth factor-1 (IGF-1)], is being developed by Neuren Pharmaceuticals and Acadia Pharmaceuticals for the treatment of rare childhood neurodevelopmental disorders. Trofinetide was approved in March 2023 in the USA for the treatment of Rett syndrome in adult and pediatric patients 2 years of age and older. This article summarizes the milestones in the development of trofinetide leading to this first approval for Rett syndrome." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37191913", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 459, "text": "Trofinetide (DAYBUE™), an oral, small molecule, synthetic analog of glycine-proline-glutamate [GPE; the N-terminal tripeptide derivative of insulin like growth factor-1 (IGF-1)], is being developed by Neuren Pharmaceuticals and Acadia Pharmaceuticals for the treatment of rare childhood neurodevelopmental disorders. Trofinetide was approved in March 2023 in the USA for the treatment of Rett syndrome in adult and pediatric patients 2 years of age and older." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37191913", "endSection": "abstract", "offsetInBeginSection": 317, "offsetInEndSection": 582, "text": "Trofinetide was approved in March 2023 in the USA for the treatment of Rett syndrome in adult and pediatric patients 2 years of age and older. This article summarizes the milestones in the development of trofinetide leading to this first approval for Rett syndrome." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/38017349", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 249, "text": "BACKGROUND AND OBJECTIVE: Trofinetide is the first drug to be approved for the treatment of Rett syndrome, a neurodevelopmental disorder. The purpose of the study is to fully characterize the metabolic and excretion profiles of trofinetide in humans" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37291210", "endSection": "abstract", "offsetInBeginSection": 62, "offsetInEndSection": 271, "text": "Trofinetide is a synthetic analog of glycine-proline-glutamate, the N-terminal tripeptide of the insulin-like growth factor 1 protein, and has demonstrated clinical benefit in phase 2 studies in Rett syndrome." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28964591", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 111, "text": "A Double-Blind, Randomized, Placebo-Controlled Clinical Study of Trofinetide in the Treatment of Rett Syndrome." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/37291210", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 271, "text": "Rett syndrome is a rare, genetic neurodevelopmental disorder. Trofinetide is a synthetic analog of glycine-proline-glutamate, the N-terminal tripeptide of the insulin-like growth factor 1 protein, and has demonstrated clinical benefit in phase 2 studies in Rett syndrome." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/30918097", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 93, "text": "Double-blind, randomized, placebo-controlled study of trofinetide in pediatric Rett syndrome." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35149233", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 217, "text": "INTRODUCTION: Rett syndrome (RTT) is a debilitating neurodevelopmental disorder with no approved treatments. Trofinetide is a synthetic analog of glycine-proline-glutamate, the N-terminal tripeptide of insulin-like gr" } ]	13	BioASQ-training13b	null	null	65d134bd1930410b13000037	bioasq_factoid
factoid	Which species of bacteria did the mitochondria originate from?	[['Biologists agree that the ancestor of mitochondria was an alpha-proteobacterium.']]	[ "alpha-proteobacterium", "α-proteobacterium", "alpha proteobacteria", "alpha proteobacterium", "alphaproteobacteria", "alphaproteobacterium", "alpha proteobacterium ancestor", "ancestor of mitochondria" ]	['Biologists agree that the ancestor of mitochondria was an alpha-proteobacterium. Although the Alphaproteobacteria are thought to be the closest relatives of the mitochondrial progenitor, there is dispute as to what its particular sister group is. Accumulating evolutionary data point to a monophyletic origin of mitochondria from the order Rickettsiales. Phylogenetic analyses indicate that R. prowazekii is more closely related to mitochondria than is any other microbe studied so far.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/21300273", "http://www.ncbi.nlm.nih.gov/pubmed/21217797", "http://www.ncbi.nlm.nih.gov/pubmed/17251118", "http://www.ncbi.nlm.nih.gov/pubmed/16822756", "http://www.ncbi.nlm.nih.gov/pubmed/12594925", "http://www.ncbi.nlm.nih.gov/pubmed/11508688", "http://www.ncbi.nlm.nih.gov/pubmed/10376009", "http://www.ncbi.nlm.nih.gov/pubmed/9823893", "http://www.ncbi.nlm.nih.gov/pubmed/9711305", "http://www.ncbi.nlm.nih.gov/pubmed/16157484", "http://www.ncbi.nlm.nih.gov/pubmed/16381962" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/21300273", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 412, "text": "Recently, α-proteobacteria have been shown to possess virus-like gene transfer agents that facilitate high frequency gene transfer in natural environments between distantly related lineages. This system could have driven the genomic integration of the mitochondrial progenitor and its proto-eukaryote host and contributed to the evolutionary mosaic of genes seen in modern-day prokaryotic and eukaryotic genomes." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/21217797", "endSection": "abstract", "offsetInBeginSection": 80, "offsetInEndSection": 245, "text": "Although the Alphaproteobacteria are thought to be the closest relatives of the mitochondrial progenitor, there is dispute as to what its particular sister group is." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/21217797", "endSection": "abstract", "offsetInBeginSection": 1172, "offsetInEndSection": 1440, "text": "More detailed phylogenetic analyses with additional Alphaproteobacteria and including genes from the mitochondria of Reclinomonas americana found matches of mitochondrial genes to those of members of the Rickettsiaceae, Anaplasmataceae, and Rhodospirillaceae families." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/17251118", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 80, "text": "Biologists agree that the ancestor of mitochondria was an alpha-proteobacterium." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/16822756", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 80, "text": "Mitochondria originated by permanent enslavement of purple non-sulphur bacteria." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/12594925", "endSection": "abstract", "offsetInBeginSection": 192, "offsetInEndSection": 339, "text": "Phylogenetic analyses based on genes located in the mitochondrial genome indicate that these genes originated from within the alpha-proteobacteria." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/12594925", "endSection": "abstract", "offsetInBeginSection": 1133, "offsetInEndSection": 1393, "text": "The strong relationship with alpha-proteobacterial genes observed for some mitochondrial genes, combined with the lack of such a relationship for others, indicates that the modern mitochondrial proteome is the product of both reductive and expansive processes." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/11508688", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 107, "text": "Accumulating evolutionary data point to a monophyletic origin of mitochondria from the order Rickettsiales." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/10376009", "endSection": "abstract", "offsetInBeginSection": 338, "offsetInEndSection": 511, "text": "Evolutionary analyses of proteins encoded in the genome contain the strongest phylogenetic evidence to date for the view that mitochondria descend from alpha-proteobacteria." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/9823893", "endSection": "abstract", "offsetInBeginSection": 218, "offsetInEndSection": 551, "text": "The functional profiles of these genes show similarities to those of mitochondrial genes: no genes required for anaerobic glycolysis are found in either R. prowazekii or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and the respiratory-chain complex is found in R. prowazekii." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/9823893", "endSection": "abstract", "offsetInBeginSection": 1119, "offsetInEndSection": 1250, "text": "Phylogenetic analyses indicate that R. prowazekii is more closely related to mitochondria than is any other microbe studied so far." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/9711305", "endSection": "abstract", "offsetInBeginSection": 175, "offsetInEndSection": 464, "text": "The phylogenetic analysis supports the hypothesis that mitochondria are derived from the alpha-proteobacteria and more specifically from within the Rickettsiaceae. We have estimated that the common ancestor of mitochondria and Rickettsiaceae dates back to more than 1500 million years ago." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/16381962", "endSection": "abstract", "offsetInBeginSection": 434, "offsetInEndSection": 665, "text": "GOBASE also includes a fully reannotated genome sequence of Rickettsia prowazekii, one of the closest bacterial relatives of mitochondria, and will shortly expand to contain more data from bacteria from which organelles originated." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/9823893", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 76, "text": "The genome sequence of Rickettsia prowazekii and the origin of mitochondria." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/9823893", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 76, "text": "The genome sequence of Rickettsia prowazekii and the origin of mitochondria." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/9823893", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 76, "text": "The genome sequence of Rickettsia prowazekii and the origin of mitochondria." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/9823893", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 76, "text": "The genome sequence of Rickettsia prowazekii and the origin of mitochondria." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/9823893", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 76, "text": "The genome sequence of Rickettsia prowazekii and the origin of mitochondria." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/16157484", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 128, "text": "Although mitochondria derive from alpha-proteobacteria, many proteins acting in this organelle did not originate from bacteria." } ]	5	BioASQ-training5b	[ "http://www.nlm.nih.gov/cgi/mesh/2016/MB_cgi?field=uid&exact=Find+Exact+Term&term=D001419", "http://amigo.geneontology.org/amigo/term/GO:0005739", "http://www.nlm.nih.gov/cgi/mesh/2016/MB_cgi?field=uid&exact=Find+Exact+Term&term=D008928" ]	[]	56c58f1b5795f9a73e000001	bioasq_factoid
factoid	What is the enzymatic activity of PARL?	['PARL are serine proteases']	[ "PARL", "Presenilin-associated rhomboid-like protein", "Presenilin-associated rhomboid-like", "PARL serine protease" ]	['the mitochondrial protease presenilin-associated rhomboid-like (PARL). Rhomboids are a recently discovered family of widely distributed intramembrane serine proteases.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/17938163", "http://www.ncbi.nlm.nih.gov/pubmed/21415861", "http://www.ncbi.nlm.nih.gov/pubmed/21355049", "http://www.ncbi.nlm.nih.gov/pubmed/19859837" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/21355049", "endSection": "abstract", "offsetInBeginSection": 743, "offsetInEndSection": 970, "text": "Here we demonstrate that the mitochondrial protease presenilin-associated rhomboid-like (PARL) can affect the proteolytic processing of PINK1 and that normal PINK1 localization and stability requires PARL's catalytic activity. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/21415861", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 210, "text": "The mitochondrial rhomboid protease Parl governs apoptosis, morphology, metabolism and might be implicated in Parkinson's disease, but the structural basis of its activity and complex regulation remain unknown." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/19859837", "endSection": "abstract", "offsetInBeginSection": 43, "offsetInEndSection": 248, "text": ". In this study, we evaluated the mRNA levels of presenilins-associated rhomboid-like protein (PARL) and mitochondrial content and enzyme activity from skeletal muscle isolated from insulin-resistant rats." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/17938163", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 97, "text": "Rhomboids are a recently discovered family of widely distributed intramembrane serine proteases. " } ]	6	BioASQ-training6b	null	null	58dfe6b56fddd3e83e000004	bioasq_factoid
factoid	ZF2001 is used for which disease?	['COVID-19']	[ "COVID-19", "Coronavirus Disease 2019", "SARS-CoV-2 infection", "2019-nCoV", "Novel Coronavirus", "Wuhan Coronavirus", "COVID", "Coronavirus" ]	['ZF2001 is used for COVID-19.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/35617368", "http://www.ncbi.nlm.nih.gov/pubmed/35568034", "http://www.ncbi.nlm.nih.gov/pubmed/35634276", "http://www.ncbi.nlm.nih.gov/pubmed/35596222" ]	[ { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35617368", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 217, "text": "Safety and immunogenicity of heterologous boost immunization with an adenovirus type-5-vectored and protein-subunit-based COVID-19 vaccine (Convidecia/ZF2001): A randomized, observer-blinded, placebo-controlled trial." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35617368", "endSection": "abstract", "offsetInBeginSection": 134, "offsetInEndSection": 420, "text": "We assessed the safety and immunogenicity of heterologous immunization with a recombinant adenovirus type-5-vectored Coronavirus Disease 2019 (COVID-19) vaccine (Convidecia, hereafter referred to as CV) and a protein-subunit-based COVID-19 vaccine (ZF2001, hereafter referred to as ZF)." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35617368", "endSection": "abstract", "offsetInBeginSection": 3124, "offsetInEndSection": 3314, "text": "CONCLUSIONS: Heterologous boosting with ZF2001 following primary vaccination with Convidecia is more immunogenic than a single dose of Convidecia and is not associated with safety concerns. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35634276", "endSection": "abstract", "offsetInBeginSection": 1434, "offsetInEndSection": 1539, "text": "Conclusion: SARS-CoV-2 vaccines (CoronaVac, BBIBP-CorV, and ZF2001) are safe in thyroid cancer patients. " }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35596222", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 93, "text": "Effective protection of ZF2001 against the SARS-CoV-2 Delta variant in lethal K18-hACE2 mice." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35596222", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 260, "text": "To investigate the protective efficacy and mechanism of ZF2001 (a protein subunit vaccine with conditional approval in China) to SARS-CoV-2 Delta variant-induced severe pneumonia, the lethal challenge model of K18-hACE2 transgenic mice was used in this study. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35568034", "endSection": "abstract", "offsetInBeginSection": 97, "offsetInEndSection": 233, "text": "Previously, we developed the protein subunit vaccine ZF2001 based on the dimeric receptor-binding domain (RBD) of prototype SARS-CoV-2. " } ]	12	BioASQ-training12b	null	null	63f03c47f36125a42600001e	bioasq_factoid
factoid	Which plant does oleuropein originate from?	['Olive tree']	[ "Olive tree", "Olea europaea", "European olive", "Olive", "Olive plant" ]	['Oleuropein originates from olive trees, and is specifically found in olive leaf extracts.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/29099642" ]	[ { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/29099642", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 88, "text": "Oleuropein Is Responsible for the Major Anti-Inflammatory Effects of Olive Leaf Extract." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/29099642", "endSection": "abstract", "offsetInBeginSection": 745, "offsetInEndSection": 854, "text": "Oleuropein is the only OLE component that has shown anti-inflammatory effects at a concentration of 20 μg/mL." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/29099642", "endSection": "abstract", "offsetInBeginSection": 1015, "offsetInEndSection": 1242, "text": "Downregulation of TNFα secretion in PMNCs culture in response to OLE treatment indicates that this polyphenol-rich extract has an anti-inflammatory effect, and oleuropein is the major OLE component responsible for this effect. " } ]	11	BioASQ-training11b	null	null	5c890ad575a4a5d21900000d	bioasq_factoid
factoid	In which breast cancer patients can palbociclib be used?	[['hormone receptor-positive, human epidermal growth factor receptor 2-negative']]	[ "hormone receptor-positive, human epidermal growth factor receptor 2-negative", "HR-positive, HER2-negative", "hormone receptor-positive, HER2-negative", "HR+/HER2-", "estrogen receptor-positive, human epidermal growth factor receptor 2-negative", "ER-positive, HER2-negative" ]	['Palbociclib is useful for women with hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancer.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/26236140", "http://www.ncbi.nlm.nih.gov/pubmed/25524798", "http://www.ncbi.nlm.nih.gov/pubmed/25792301" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/26236140", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 184, "text": "Women with hormone receptor-positive, human epidermal growth factor receptor 2- negative breast cancer-the most common subtype-have new options as palbociclib and similar drugs debut. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25524798", "endSection": "abstract", "offsetInBeginSection": 441, "offsetInEndSection": 637, "text": "We aimed to assess the safety and efficacy of palbociclib in combination with letrozole as first-line treatment of patients with advanced, oestrogen receptor-positive, HER2-negative breast cancer." } ]	5	BioASQ-training5b	[ "http://www.nlm.nih.gov/cgi/mesh/2016/MB_cgi?field=uid&exact=Find+Exact+Term&term=D001943", "http://www.disease-ontology.org/api/metadata/DOID:1612" ]	[]	56d06e043975bb303a000011	bioasq_factoid
factoid	With which cancers has the loss of SMARCB1 been associated?	['chordomas', 'childhood chordomas', 'infantile chordomas', 'CCs']	[ "chordomas", "childhood chordomas", "infantile chordomas", "CCs", "chordoma" ]	['Genotyping cancer-associated genes in chordoma identifies mutations in oncogenes and areas of chromosomal loss involving CDKN2A, PTEN, and SMARCB1 Loss of SMARCB1/INI1 expression is considered to be a hallmark for childhood chordomas (CCs)', 'We therefore sought to identify novel mutations to better understand chordoma biology and to potentially identify therapeutic targets Genotyping cancer-associated genes in chordoma identifies mutations in oncogenes and areas of chromosomal loss involving CDKN2A, PTEN, and SMARCB1', 'The diagnosis is all the more challenging that other poorly differentiated cancers lose SMARCB1 expression, such as epithelioid sarcomas (ES), renal medullary carcinomas (RMC) or undifferentiated chordomas (UC) Loss of SMARCB1/INI1 expression is considered to be a hallmark for childhood chordomas (CCs)', 'Loss of SMARCB1/INI1 expression is considered to be a hallmark for childhood chordomas (CCs).', 'Genotyping cancer-associated genes in chordoma identifies mutations in oncogenes and areas of chromosomal loss involving CDKN2A, PTEN, and SMARCB1. Loss of SMARCB1/INI1 expression is considered to be a hallmark for childhood chordomas . The diagnosis is all the more challenging that other poorly differentiated cancers lose SMARCB1 expression, such as epithelioid sarcomas . ']	[ "http://www.ncbi.nlm.nih.gov/pubmed/28825187", "http://www.ncbi.nlm.nih.gov/pubmed/28427232", "http://www.ncbi.nlm.nih.gov/pubmed/27635948", "http://www.ncbi.nlm.nih.gov/pubmed/24983247", "http://www.ncbi.nlm.nih.gov/pubmed/28812319" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/24983247", "endSection": "abstract", "offsetInBeginSection": 71, "offsetInEndSection": 204, "text": "We therefore sought to identify novel mutations to better understand chordoma biology and to potentially identify therapeutic targets" }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/24983247", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 146, "text": "Genotyping cancer-associated genes in chordoma identifies mutations in oncogenes and areas of chromosomal loss involving CDKN2A, PTEN, and SMARCB1" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/24983247", "endSection": "abstract", "offsetInBeginSection": 1520, "offsetInEndSection": 1884, "text": "When this data is paired with the studies showing 18 of 21 chordoma samples displaying copy loss at the locus for CDKN2A, 17 of 21 chordoma samples displaying copy loss at PTEN, and 3 of 4 chordoma samples displaying deletion at the SMARCB1 locus, we can infer that a loss of heterozygosity at these three loci may play a significant role in chordoma pathogenesis." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/27635948", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 46, "text": "SMARCB1/INI1 Involvement in Pediatric Chordoma" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/27635948", "endSection": "abstract", "offsetInBeginSection": 1011, "offsetInEndSection": 1170, "text": "All 8 cases were positive for brachyury, whereas there was no nuclear SMARCB1/INI1 expression in 4 of the 8 cases, including the poorly differentiated chordoma" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/27635948", "endSection": "abstract", "offsetInBeginSection": 536, "offsetInEndSection": 722, "text": " In this study, we considered immunohistochemistry and SMARCB1/INI1 mutational status to examine SMARCB1 status in a series of pediatric chordomas (7 classic and 1 poorly differentiated)" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/27635948", "endSection": "abstract", "offsetInBeginSection": 1643, "offsetInEndSection": 1703, "text": "pathogenic involvement of SMARCB1/INI1 in childhood chordoma" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28427232", "endSection": "abstract", "offsetInBeginSection": 170, "offsetInEndSection": 380, "text": "The diagnosis is all the more challenging that other poorly differentiated cancers lose SMARCB1 expression, such as epithelioid sarcomas (ES), renal medullary carcinomas (RMC) or undifferentiated chordomas (UC)" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28825187", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 92, "text": "Loss of SMARCB1/INI1 expression is considered to be a hallmark for childhood chordomas (CCs)" }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28812319", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 89, "text": "Poorly differentiated chordoma with loss of SMARCB1/INI1 expression in pediatric patients" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28812319", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 346, "text": "Identification of loss of SMARCB1/INI1 expression in poorly differentiated (PD) chordoma in pediatric patients suggests that PD chordoma is an entity molecularly distinct from conventional chordoma or atypical teratoid/rhabdoid tumor, which is also characterized by loss of SMARCB1/INI1 expression by inactivating mutation of the SMARCB1/INI gene" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28812319", "endSection": "abstract", "offsetInBeginSection": 348, "offsetInEndSection": 452, "text": "So far, around 20 cases of pediatric PD chordoma with loss of SMARCB1/INI1 expression have been reported" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28812319", "endSection": "abstract", "offsetInBeginSection": 454, "offsetInEndSection": 596, "text": "Here, we report two cases of pediatric PD chordoma with loss of SMARCB1/INI1 expression, which is very rare among the pediatric chordoma types" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28812319", "endSection": "abstract", "offsetInBeginSection": 1128, "offsetInEndSection": 1336, "text": "Based on the clival location and histologic findings along with the loss of SMARCB1/INI1 expression and positivity for nuclear brachyury staining, the final pathologic diagnosis for both cases was PD chordoma" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28825187", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 93, "text": "Loss of SMARCB1/INI1 expression is considered to be a hallmark for childhood chordomas (CCs)." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28427232", "endSection": "abstract", "offsetInBeginSection": 170, "offsetInEndSection": 381, "text": "The diagnosis is all the more challenging that other poorly differentiated cancers lose SMARCB1 expression, such as epithelioid sarcomas (ES), renal medullary carcinomas (RMC) or undifferentiated chordomas (UC)." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/28825187", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 801, "text": "loss of smarcb1 ini1 expression is considered to be a hallmark for childhood chordomas ccs although mutation loss of 22q has strongly established the loss of smarcb1 ini1 in cancers the cause in ccs remains elusive recent studies suggest role of mirnas in regulation of smarcb1 ini1 expressions we examined 5 reported target predicted mirnas to smarcb1 ini1 in smarcb1 ini1 immunonegative and immunopositive cases and found upregulation of mir 671 5p and mir 193a 5p in smarcb1 ini1 immunonegative cases notably these two mirnas were significantly predicted to target tgf β signaling suggestive of dysregulation of developmental and osteoblast regulation pathway in ccs overall we suggest mir 671 5p and mir 193a 5p mediated epigenetic mode of smarcb1 ini1 loss and downregulated tgf β pathway in ccs." }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/27635948", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 93, "text": "smarcb1 ini1 involvement in pediatric chordoma a mutational and immunohistochemical analysis" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/27635948", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 1725, "text": "chordomas arise in the skull base and spine and usually occur in adults and are rare in the pediatric population cases of chordoma in pediatric age are often poorly differentiated showing cytologic atypia increased cellularity and mitosis and their aggressive behavior is associated with a high incidence of metastatic spread and a short patient survival recent studies have described loss of smarcb1 ini1 protein in poorly differentiated chordomas associated not with point mutations but with smarcb1 ini1 gene deletions instead in this study we considered immunohistochemistry and smarcb1 ini1 mutational status to examine smarcb1 status in a series of pediatric chordomas 7 classic and 1 poorly differentiated we performed immunohistochemical tests for ini1 brachyury s100 and cytokeratins and conducted a genetic analysis on the smarcb1 coding sequence nm 003073 using the sanger method and multiplex ligation dependent probe amplification to detect abnormal copy numbers of the gene locus all 8 cases were positive for brachyury whereas there was no nuclear smarcb1 ini1 expression in 4 of the 8 cases including the poorly differentiated chordoma genetic analysis identified a missense mutation in 2 cases and a nonsense mutation associated with loss of smarcb1 ini1 protein and features of poorly differentiated tumor in 1 these mutations were novel variants occurring in heterozygosity and they were judged to be pathogenic by 3 different bioinformatic tools in 7 of 8 cases we performed multiplex ligation dependent probe amplification and 3 cases showed deletions at the smarcb1 locus our results confirm the pathogenic involvement of smarcb1 ini1 in childhood chordoma we also describe 3 novel pathogenic mutations." } ]	11	BioASQ-training11b	null	null	5a86f074faa1ab7d2e00003a	bioasq_factoid
factoid	What is the tradename of apixaban?	['Eliquis']	[ "Eliquis", "Apixaban", "Bristol-Myers Squibb", "Eliquis (apixaban)" ]	['The tradename of apixaban is Eliquis.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/23677804" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/23677804", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 164, "text": "The direct factor Xa inhibitor apixaban (Eliquis(®)) has predictable pharmacodynamics and pharmacokinetics and does not require routine anticoagulation monitoring. " } ]	11	BioASQ-training11b	null	null	5c920fc3ecadf2e73f000011	bioasq_factoid
factoid	Which receptor tyrosine kinase is commonly mutated or amplified in pediatric glioma cases?	['PDGFRA', 'Platelet derived growth factor-alpha', 'Platelet derived growth factor-alpha (PDGFRA)']	[ "PDGFRA", "Platelet derived growth factor-alpha", "Platelet derived growth factor-alpha (PDGFRA)", "Platelet-derived growth factor receptor alpha", "PDGF receptor alpha", "PDGF receptor alpha chain", "PDGF alpha receptor" ]	['Pediatric high-grade glioma (pHGG), including both diffuse midline glioma (DMG) and non-midline tumors, continues to be one of the deadliest oncologic diagnoses. Targeted therapy options aimed at key oncogenic receptor tyrosine kinase (RTK) drivers using small-molecule RTK inhibitors have been extensively studied, but the absence of proper in vivo modeling that recapitulates pHGG biology has historically been a research challenge. Over 20% of pHGG have been found in sequencing studies to have alterations in platelet derived growth factor-alpha (PDGFRA), making growth factor modeling and inhibition via targeted tyrosine kinases a promising research direction.', 'Receptor tyrosine kinase (RTK) alterations are commonly found in pediatric high-grade glioma (pHGG), including diffuse midline glioma (DMG) and non-midline tumors. Sequencing studies have revealed that over 20% of pHGG cases have alterations in platelet derived growth factor-alpha (PDGFRA). This has made growth factor modeling and inhibition via targeted tyrosine kinases a significant area of interest in pHGG research. The challenge in this field has been the lack of proper in vivo modeling that accurately represents pHGG biology.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/26727948", "http://www.ncbi.nlm.nih.gov/pubmed/27582545", "http://www.ncbi.nlm.nih.gov/pubmed/35978801", "http://www.ncbi.nlm.nih.gov/pubmed/23970477", "http://www.ncbi.nlm.nih.gov/pubmed/26744350", "http://www.ncbi.nlm.nih.gov/pubmed/20479398", "http://www.ncbi.nlm.nih.gov/pubmed/23438035" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35978801", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 160, "text": "Pediatric high-grade glioma (pHGG), including both diffuse midline glioma (DMG) and non-midline tumors, continues to be one of the deadliest oncologic diagnoses" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35978801", "endSection": "abstract", "offsetInBeginSection": 201, "offsetInEndSection": 473, "text": " Targeted therapy options aimed at key oncogenic receptor tyrosine kinase (RTK) drivers using small-molecule RTK inhibitors has been extensively studied, but the absence of proper in vivo modeling that recapitulate pHGG biology has historically been a research challenge. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/35978801", "endSection": "abstract", "offsetInBeginSection": 710, "offsetInEndSection": 934, "text": "Over 20% of pHGG have been found in sequencing studies to have alterations in platelet derived growth factor-alpha (PDGFRA), making growth factor modeling and inhibition via targeted tyrosine kinases a rich vein of interest." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/23438035", "endSection": "abstract", "offsetInBeginSection": 693, "offsetInEndSection": 773, "text": "PDGFRA amplification was frequent in pediatric (29.3%) and adult (20.9%) tumors." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/23970477", "endSection": "abstract", "offsetInBeginSection": 244, "offsetInEndSection": 450, "text": "Genome-wide analyses of copy number imbalances previously showed that platelet-derived growth factor receptor α (PDGFRA) is the most frequent target of focal amplification in pediatric HGGs, including DIPGs" } ]	13	BioASQ-training13b	null	null	6630390b187cba990d000035	bioasq_factoid
yesno	Are PDXK mutations linked to polyneuropathy?	['yes']	[ "yes" ]	['Yes, PDXK mutations are linked to polyneuropathy.', 'Yes, PDXK mutations are associated with autosomal recessive polyneuropathy.', "Yes. PDXK mutations cause polyneuropathy responsive to pyridoxal 5'-phosphate supplementation.", 'Yes, PDXK mutations are associated with delayed polyneuropathy.', 'Yes, point mutations in PDXK gene may be associated with peripheral neuropathy.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/31187503", "http://www.ncbi.nlm.nih.gov/pubmed/32522499" ]	[ { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/31187503", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 89, "text": "PDXK mutations cause polyneuropathy responsive to pyridoxal 5'-phosphate supplementation." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/31187503", "endSection": "abstract", "offsetInBeginSection": 11, "offsetInEndSection": 1971, "text": "To identify disease-causing variants in autosomal recessive axonal polyneuropathy with optic atrophy and provide targeted replacement therapy.METHODS: We performed genome-wide sequencing, homozygosity mapping, and segregation analysis for novel disease-causing gene discovery. We used circular dichroism to show secondary structure changes and isothermal titration calorimetry to investigate the impact of variants on adenosine triphosphate (ATP) binding. Pathogenicity was further supported by enzymatic assays and mass spectroscopy on recombinant protein, patient-derived fibroblasts, plasma, and erythrocytes. Response to supplementation was measured with clinical validated rating scales, electrophysiology, and biochemical quantification.RESULTS: We identified biallelic mutations in PDXK in 5 individuals from 2 unrelated families with primary axonal polyneuropathy and optic atrophy. The natural history of this disorder suggests that untreated, affected individuals become wheelchair-bound and blind. We identified conformational rearrangement in the mutant enzyme around the ATP-binding pocket. Low PDXK ATP binding resulted in decreased erythrocyte PDXK activity and low pyridoxal 5'-phosphate (PLP) concentrations. We rescued the clinical and biochemical profile with PLP supplementation in 1 family, improvement in power, pain, and fatigue contributing to patients regaining their ability to walk independently during the first year of PLP normalization.INTERPRETATION: We show that mutations in PDXK cause autosomal recessive axonal peripheral polyneuropathy leading to disease via reduced PDXK enzymatic activity and low PLP. We show that the biochemical profile can be rescued with PLP supplementation associated with clinical improvement. As B6 is a cofactor in diverse essential biological pathways, our findings may have direct implications for neuropathies of unknown etiology characterized by reduced PLP levels. ANN NEUROL 2019;86:225-240." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/31187503", "endSection": "abstract", "offsetInBeginSection": 1483, "offsetInEndSection": 1656, "text": "RETATION: We show that mutations in PDXK cause autosomal recessive axonal peripheral polyneuropathy leading to disease via reduced PDXK enzymatic activity and low PLP. We sh" }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/31187503", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 88, "text": "PDXK mutations cause polyneuropathy responsive to pyridoxal 5'-phosphate supplementation" }, { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/32522499", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 106, "text": "Hereditary polyneuropathy with optic atrophy due to PDXK variant leading to impaired Vitamin B6 metabolism" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/31187503", "endSection": "abstract", "offsetInBeginSection": 1477, "offsetInEndSection": 1650, "text": "INTERPRETATION: We show that mutations in PDXK cause autosomal recessive axonal peripheral polyneuropathy leading to disease via reduced PDXK enzymatic activity and low PLP." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/31187503", "endSection": "abstract", "offsetInBeginSection": 754, "offsetInEndSection": 901, "text": "RESULTS: We identified biallelic mutations in PDXK in 5 individuals from 2 unrelated families with primary axonal polyneuropathy and optic atrophy." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/31187503", "endSection": "abstract", "offsetInBeginSection": 1496, "offsetInEndSection": 1653, "text": "show that mutations in PDXK cause autosomal recessive axonal peripheral polyneuropathy leading to disease via reduced PDXK enzymatic activity and low PLP. We" } ]	11	BioASQ-training11b	null	null	6031002d1cb411341a000129	bioasq_yesno
factoid	Which is the literature-based database of phenotypes?	['PheneBank']	[ "PheneBank", "PhenomeBank", "Phene Bank" ]	['PheneBank is a Web-portal for retrieving human phenotype-disease associations that have been text-mined from the whole of Medline. This approach exploits state-of-the-art machine learning for concept identification by utilising an expert annotated rare disease corpus from the PMC Text Mining subset. Evaluation of the system for entities is conducted on a gold-standard corpus of rare disease sentences and for associations against the Monarch initiative data.', 'PheneBank is a Web-portal for retrieving human phenotype-disease associations that have been text-mined from the whole of Medline.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/34788791" ]	[ { "beginSection": "title", "document": "http://www.ncbi.nlm.nih.gov/pubmed/34788791", "endSection": "title", "offsetInBeginSection": 0, "offsetInEndSection": 53, "text": "PheneBank: a literature-based database of phenotypes." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/34788791", "endSection": "abstract", "offsetInBeginSection": 312, "offsetInEndSection": 772, "text": "PheneBank is a Web-portal for retrieving human phenotype-disease associations that have been text-mined from the whole of Medline. Our approach exploits state-of-the-art machine learning for concept identification by utilising an expert annotated rare disease corpus from the PMC Text Mining subset. Evaluation of the system for entities is conducted on a gold-standard corpus of rare disease sentences and for associations against the Monarch initiative data." } ]	11	BioASQ-training11b	null	null	621e63a43a8413c653000051	bioasq_factoid
factoid	What is the mode of inheritance of Acromicric dysplasia?	['autosomal dominant']	[ "autosomal dominant", "AD", "autosomal dominant inheritance", "dominant inheritance", "dominant trait" ]	Acromicric dysplasia has an autosomal dominant mode of inheritance	[ "http://www.ncbi.nlm.nih.gov/pubmed/22791552", "http://www.ncbi.nlm.nih.gov/pubmed/19396027", "http://www.ncbi.nlm.nih.gov/pubmed/11694546" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/22791552", "endSection": "abstract", "offsetInBeginSection": 696, "offsetInEndSection": 840, "text": "AD has an autosomal dominant mode of inheritance, distinct facial and skeleton features (a hoarse voice and internal notch of the femoral head)." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/19396027", "endSection": "abstract", "offsetInBeginSection": 616, "offsetInEndSection": 830, "text": "Finally, WMS is transmitted either by an autosomal dominant or an autosomal recessive (AR) mode of inheritance, GD by an autosomal recessive mode of inheritance and AD by an autosomal dominant mode of inheritance. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/11694546", "endSection": "abstract", "offsetInBeginSection": 1332, "offsetInEndSection": 1507, "text": "The condition appeared to be sporadic in 16 cases but the observation of vertical transmission in three families was consistent with an autosomal dominant mode of inheritance." } ]	5	BioASQ-training5b	[ "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D040582", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D001848" ]	[]	53318685d6d3ac6a3400003d	bioasq_factoid
yesno	Is phosphoenolpyruvate carboxykinase 1 (PCK1) the rate-limiting enzyme in gluconeogenesis?	['yes']	[ "yes" ]	['Yes, Pck1 is a rate-limiting gluconeogenic enzyme, where its deficiency or mutation contributes to serious clinical situations as neonatal hypoglycemia and liver failure.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/31883179", "http://www.ncbi.nlm.nih.gov/pubmed/31911238", "http://www.ncbi.nlm.nih.gov/pubmed/32004540", "http://www.ncbi.nlm.nih.gov/pubmed/32001301", "http://www.ncbi.nlm.nih.gov/pubmed/32058049" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/31911238", "endSection": "abstract", "offsetInBeginSection": 12, "offsetInEndSection": 107, "text": "Phosphoenolpyruvate carboxykinase (PEPCK) is a metabolic enzyme in the gluconeogenesis pathway," }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/32001301", "endSection": "abstract", "offsetInBeginSection": 972, "offsetInEndSection": 1112, "text": "PEPCK, a key enzyme involved in gluconeogenesis associated with a decrease in the expression of master genes involved in the VLDL synthesis " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/32004540", "endSection": "abstract", "offsetInBeginSection": 590, "offsetInEndSection": 905, "text": "Transcriptome analysis of rate-limiting enzymes involved in hepatic gluconeogenesis revealed that moxifloxacin and gatifloxacin at a concentration of 1000 μM did not affect the expression of key gluconeogenic enzymes such as phosphoenolpyruvate carboxykinase, glucose 6-phosphatase, and fructose 1,6-bisphosphatase." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/31883179", "endSection": "abstract", "offsetInBeginSection": 115, "offsetInEndSection": 280, "text": "Pck1 is a rate-limiting gluconeogenic enzyme, where its deficiency or mutation contributes to serious clinical situations as neonatal hypoglycemia and liver failure." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/32058049", "endSection": "abstract", "offsetInBeginSection": 498, "offsetInEndSection": 572, "text": "the gluconeogenesis key enzymes PEPCK (phosphoenolpyruvate carboxykinase) " } ]	11	BioASQ-training11b	null	null	6033f5541cb411341a00014c	bioasq_yesno
factoid	What bacteria is associated with Gastric cancer and peptic ulcers?	['helicobacter pylori']	[ "Helicobacter pylori", "H. pylori", "Campylobacter pylori", "Campylobacter mustelae", "Helicobacter heilmannii" ]	['Helicobacter pylori (H. pylori), a gram-negative microaerophilic bacterial pathogen that colonizes the stomachs of more than half of all humans, is linked to chronic gastritis, peptic ulcers and gastric cancer.', 'Peptic ulcer and gastric cancer are caused by the same bacteria, Helicobacter pylori.']	[ "http://www.ncbi.nlm.nih.gov/pubmed/7886456", "http://www.ncbi.nlm.nih.gov/pubmed/29764950", "http://www.ncbi.nlm.nih.gov/pubmed/29432909", "http://www.ncbi.nlm.nih.gov/pubmed/15610081", "http://www.ncbi.nlm.nih.gov/pubmed/25539656", "http://www.ncbi.nlm.nih.gov/pubmed/16583309", "http://www.ncbi.nlm.nih.gov/pubmed/29446491", "http://www.ncbi.nlm.nih.gov/pubmed/8341988" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/29432909", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 229, "text": "Helicobacter Pylori (H. pylori) is a gram-negative bacteria infecting numerous people all over the world. It has been established that H. pylori play an important role in pathogenesis of gastritis, peptic ulcer and gastric cancer" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/29446491", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 210, "text": "Helicobacter pylori (H. pylori), a gram-negative microaerophilic bacterial pathogen that colonizes the stomachs of more than half of all humans, is linked to chronic gastritis, peptic ulcers and gastric cancer." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/29764950", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 65, "text": "Strains of Helicobacter pylori that cause ulcer or gastric cancer" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/25539656", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 120, "text": "BACKGROUND Helicobacter pylori chronic infection is associated with chronic gastritis, peptic ulcer, and gastric cancer." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/15610081", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 135, "text": "Helicobacter pylori has been linked to chronic gastritis, peptic ulcers, gastric cancer and mucosa-associated lymphoid tissue lymphoma." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/7886456", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 110, "text": "The human pathogen Helicobacter pylori is associated with gastritis, peptic ulcer disease, and gastric cancer." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/8341988", "endSection": "abstract", "offsetInBeginSection": 415, "offsetInEndSection": 572, "text": "The pathogenesis of peptic ulcer and gastric cancer is closely associated with H. pylori gastritis and its subsequent atrophic sequelae (atrophic gastritis)." } ]	11	BioASQ-training11b	null	null	5e3c6c9eb5b409ea53000022	bioasq_factoid
factoid	What is the reason for the narcolepsy cases developed after H1N1 influenza vaccination?	['The proposed mechanism for postvaccination narcolepsy is one in which an environmental trigger causes or enhances an antibody-mediated autoimmune response in patients with a preexisting genetic susceptibility.']	[ "postvaccination narcolepsy", "vaccination-induced narcolepsy", "narcolepsy following vaccination", "narcolepsy due to vaccination", "autoimmune narcolepsy", "antibody-mediated narcolepsy", "genetic susceptibility narcolepsy", "post-vaccination narcolepsy" ]	The proposed mechanism for postvaccination narcolepsy is one in which an environmental trigger causes or enhances an antibody-mediated autoimmune response in patients with a preexisting genetic susceptibility.	[ "http://www.ncbi.nlm.nih.gov/pubmed/24048081", "http://www.ncbi.nlm.nih.gov/pubmed/23884811", "http://www.ncbi.nlm.nih.gov/pubmed/23486871", "http://www.ncbi.nlm.nih.gov/pubmed/22530521", "http://www.ncbi.nlm.nih.gov/pubmed/22213222", "http://www.ncbi.nlm.nih.gov/pubmed/21963829", "http://www.ncbi.nlm.nih.gov/pubmed/21866560", "http://www.ncbi.nlm.nih.gov/pubmed/21676420" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/24048081", "endSection": "abstract", "offsetInBeginSection": 747, "offsetInEndSection": 957, "text": "The proposed mechanism for postvaccination narcolepsy is one in which an environmental trigger causes or enhances an antibody-mediated autoimmune response in patients with a preexisting genetic susceptibility. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/21963829", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 224, "text": "The loss of hypothalamic hypocretin/orexin (hcrt) producing neurons causes narcolepsy with cataplexy. An autoimmune basis for the disease has long been suspected and recent results have greatly strengthened this hypothesis. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/21963829", "endSection": "abstract", "offsetInBeginSection": 663, "offsetInEndSection": 776, "text": "pointing towards processes such as molecular mimicry or bystander activation as crucial for disease development. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/21676420", "endSection": "abstract", "offsetInBeginSection": 581, "offsetInEndSection": 840, "text": "Although no formal link can be established, the unusual characteristics of the reported cases and the striking temporal relationship suggests that narcolepsy may be the result of an autoimmune reaction triggered by H1N1 vaccination in susceptible individuals." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/23486871", "endSection": "abstract", "offsetInBeginSection": 1141, "offsetInEndSection": 1251, "text": "Pandemrix vaccination is a precipitating factor for narcolepsy, especially in combination with HLA-DQB1*0602. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/22213222", "endSection": "abstract", "offsetInBeginSection": 363, "offsetInEndSection": 524, "text": "Recently identified autoantibodies to Tribbles homologue 2 in some patients, as well as cases associated with H1N1 vaccination, support an autoimmune mechanism. " }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/21866560", "endSection": "abstract", "offsetInBeginSection": 1367, "offsetInEndSection": 1701, "text": "n China, narcolepsy onset is highly correlated with seasonal and annual patterns of upper airway infections, including H1N1 influenza. In 2010, the peak seasonal onset of narcolepsy was phase delayed by 6 months relative to winter H1N1 infections, and the correlation was independent of H1N1 vaccination in the majority of the sample." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/23884811", "endSection": "abstract", "offsetInBeginSection": 2016, "offsetInEndSection": 2141, "text": "H1N1 vaccination was strongly associated with an increased risk of narcolepsy-cataplexy in both children and adults in France" } ]	5	BioASQ-training5b	[ "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D009290", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D053118", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D014612", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D014611", "http://www.disease-ontology.org/api/metadata/DOID:8986" ]	[]	530cf54dab4de4de0c000009	bioasq_factoid
factoid	What is the prognostic role of thyroid hormone in patients with heart failure?	['There is a relationship between altered thyroid profile and mortality in patients with heart failure']	[ "thyroid profile", "thyroid function tests", "thyroid hormone levels", "altered thyroid profile", "thyroid panel", "thyroid tests", "thyroid assessment", "thyroid evaluation" ]	Altered thyroid profile, particularly sick euthyroid syndrome, is an independent predictor of mortality in patients with chronic heart failure, adding prognostic information to conventional clinical and functional cardiac parameters.	[ "http://www.ncbi.nlm.nih.gov/pubmed/20978564", "http://www.ncbi.nlm.nih.gov/pubmed/22870736", "http://www.ncbi.nlm.nih.gov/pubmed/19181292", "http://www.ncbi.nlm.nih.gov/pubmed/19006851", "http://www.ncbi.nlm.nih.gov/pubmed/15694896", "http://www.ncbi.nlm.nih.gov/pubmed/15642542", "http://www.ncbi.nlm.nih.gov/pubmed/12963854", "http://www.ncbi.nlm.nih.gov/pubmed/2358611", "http://www.ncbi.nlm.nih.gov/pubmed/17315395", "http://www.ncbi.nlm.nih.gov/pubmed/23555069", "http://www.ncbi.nlm.nih.gov/pubmed/19110971", "http://www.ncbi.nlm.nih.gov/pubmed/18221125", "http://www.ncbi.nlm.nih.gov/pubmed/16499159", "http://www.ncbi.nlm.nih.gov/pubmed/8333797", "http://www.ncbi.nlm.nih.gov/pubmed/23369135", "http://www.ncbi.nlm.nih.gov/pubmed/19917524", "http://www.ncbi.nlm.nih.gov/pubmed/23435988", "http://www.ncbi.nlm.nih.gov/pubmed/8960429", "http://www.ncbi.nlm.nih.gov/pubmed/2189307", "http://www.ncbi.nlm.nih.gov/pubmed/17893267", "http://www.ncbi.nlm.nih.gov/pubmed/17966446", "http://www.ncbi.nlm.nih.gov/pubmed/9489964", "http://www.ncbi.nlm.nih.gov/pubmed/15259379", "http://www.ncbi.nlm.nih.gov/pubmed/12165115", "http://www.ncbi.nlm.nih.gov/pubmed/17923583", "http://www.ncbi.nlm.nih.gov/pubmed/20024637" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/20978564", "endSection": "abstract", "offsetInBeginSection": 1115, "offsetInEndSection": 1429, "text": " Cumulative survival was significantly lower among patients with free triiodothyronine < 2.12 pg/mL and among patients with brain natriuretic peptide > 686 pg/mL. In multivariate analysis, the significant independent predictors of major cardiac events were age, free triiodothyronine, and brain natriuretic peptide" }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/22870736", "endSection": "abstract", "offsetInBeginSection": 1261, "offsetInEndSection": 1430, "text": "The T3 was more meaningful than the BNP in the prognosis of CHF. The BNP and T3 combination detection was more valuable in determining the severity of CHF and prognosis." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/19181292", "endSection": "abstract", "offsetInBeginSection": 1611, "offsetInEndSection": 1679, "text": "fT3 and BNP hold an independent and additive prognostic value in HF." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/19006851", "endSection": "abstract", "offsetInBeginSection": 808, "offsetInEndSection": 1177, "text": "Univariate regression analysis showed that TSH (p<0.0001), fT3 (p<0.0001), fT4 (p=0.016) and fT3/fT4 (p<0.0001) were associated with heart failure progression but multivariate analysis showed that only TSH considered as a continuous variable (p = 0.001) as well as subclinical hypothyroidism (TSH > 5.5 mUI/l; p=0.014) remained significantly associated with the events." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/15694896", "endSection": "abstract", "offsetInBeginSection": 1816, "offsetInEndSection": 2003, "text": "Low T(3) levels are an independent predictor of mortality in patients with chronic heart failure, adding prognostic information to conventional clinical and functional cardiac parameters." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/15642542", "endSection": "abstract", "offsetInBeginSection": 1010, "offsetInEndSection": 1181, "text": "Sixteen patients (14%) died during the follow-up period; their fT3/fT4 ratio was significantly lower than the patients who survived (1.31+/-0.37 vs. 2.01+/-0.72, p<0.001)." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/12963854", "endSection": "abstract", "offsetInBeginSection": 1549, "offsetInEndSection": 1717, "text": "The authors conclude that among elderly patients with heart failure, lower triiodothyronine concentrations are more prevalent and are associated with a worse prognosis." }, { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/2358611", "endSection": "abstract", "offsetInBeginSection": 976, "offsetInEndSection": 1190, "text": "A low free T3 index/reverse T3 ratio is associated with poor ventricular function and nutritional status and is the strongest predictor yet identified for short-term outcome in patients with advanced heart failure." } ]	5	BioASQ-training5b	[ "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D005067", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D006333", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D013963", "http://www.disease-ontology.org/api/metadata/DOID:6000", "http://www.disease-ontology.org/api/metadata/DOID:9651", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D054143", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D006321", "http://www.nlm.nih.gov/cgi/mesh/2014/MB_cgi?field=uid&exact=Find+Exact+Term&term=D011379" ]	[]	531b2fc3b166e2b80600003c	bioasq_factoid
factoid	Which de novo mutation in FGFR cause achondroplasia?	['G380R']	[ "G380R", "Gly380Arg", "Glycine to Arginine at position 380", "G380R mutation", "G380R variant" ]	['Recurrent missense mutations in a CpG doublet of the transmembrane domain of the FGFR3 protein (glycine substituted with arginine at residue 380, G380R).']	[ "http://www.ncbi.nlm.nih.gov/pubmed/8078586" ]	[ { "beginSection": "abstract", "document": "http://www.ncbi.nlm.nih.gov/pubmed/8078586", "endSection": "abstract", "offsetInBeginSection": 0, "offsetInEndSection": 1476, "text": "Achondroplasia, the most common cause of chondrodysplasia in man (1 in 15,000 live births), is a condition of unknown origin characterized by short-limbed dwarfism and macrocephaly. More than 90% of cases are sporadic and there is an increased paternal age at the time of conception of affected individuals, suggesting that de novo mutations are of paternal origin. Affected individuals are fertile and achondroplasia is transmitted as a fully penetrant autosomal dominant trait, accounting for rare familial forms of the disease (10%). In contrast, homozygous achondroplasia is usually lethal in the neonatal period and affects 25% of the offspring of matings between heterozygous achondroplasia parents. The gene responsible for achondroplasia has been mapped to chromosome 4p16.3 (refs 7, 8); the genetic interval encompassing the disease gene contains a member of the fibroblast-growth-factor receptor (FGFR3) family which is expressed in articular chondrocytes. Here we report the finding of recurrent missense mutations in a CpG doublet of the transmembrane domain of the FGFR3 protein (glycine substituted with arginine at residue 380, G380R) in 17 sporadic cases and 6 unrelated familial forms of achondroplasia. We show that the mutant genotype segregates with the disease in these families. Thus it appears that recurrent mutations of a single amino acid in the transmembrane domain of the FGFR3 protein account for all cases (23/23) of achondroplasia in our series." } ]	11	BioASQ-training11b	null	null	5e2e11a1fbd6abf43b000021	bioasq_factoid

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