anand-s/m_qalm huggingface dataset:
Question: Which are the main transcriptional activators of circadian oscillations?
Answer: Mammalian CLOCK and BMAL1 are two members of bHLH-PAS-containing family of transcription factors that represent the positive elements of circadian autoregulatory feedback loop. Nuclear/cytoplasm distribution of CLOCK was found to be under circadian regulation.  Two basic helix-loop-helix (bHLH) PAS (for Period-Arnt-Sim) domain-containing transcriptional activators, CLOCK and BMAL1, are known to regulate gene expression by interacting with a promoter element termed the E-box (CACGTG).
Question: Which are the main transcriptional activators of circadian oscillations?
Answer: Mammalian CLOCK and BMAL1 are two members of bHLH-PAS-containing family of transcription factors that represent the positive elements of circadian autoregulatory feedback loop.  We have examined abundance, posttranslational modifications, cellular localization of endogenous and ectopically expressed CLOCK and BMAL1 proteins. Formation of CLOCK/BMAL1 complex following ectopic coexpression of both proteins is followed by their codependent phosphorylation, which is tightly coupled to CLOCK nuclear translocation and degradation
Question: Which pipelines are used for analyzing data from ChIP-nexus experiments?
Answer: PeakXus and Q-nexus enable comprehensive transcription factor binding site discovery from ChIP-nexus experiments.
Question: Which are the synonyms of prostate-specific antigen?
Answer: Prostate-specific antigen (PSA) is a 33 kDa single chain glycoprotein belonging to the kallikrein family of serine proteases which is produced by epithelial cells of both normal and malignant prostate tissue. PSA is an important marker for the diagnosis of prostate cancer. PSA is also known as human kallikrein-related peptidase 3 (hK3).
Question: Which are the synonyms of prostate-specific antigen?
Answer: Human kallikrein-related peptidase 3 (hK3), also known as prostate-specific antigen (PSA), is a 33 kDa single chain glycoprotein belonging to the kallikrein family of serine proteases. (PMID: 19079621)
Question: Which genes belong to the AUX/IAA family of transcription repressors in plants?
Answer: The Aux/IAA proteins are auxin-sensitive repressors that mediate diverse physiological and developmental processes in plants [1, 2]. There are 29 Aux/IAA genes in Arabidopsis that exhibit unique but partially overlapping patterns of expression Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors
Question: Which genes belong to the AUX/IAA family of transcription repressors in plants?
Answer: The Aux/IAA proteins are auxin-sensitive repressors that mediate diverse physiological and developmental processes in plants [1, 2]. There are 29 Aux/IAA genes in Arabidopsis that exhibit unique but partially overlapping patterns of expression
Question: Which genes belong to the AUX/IAA family of transcription repressors in plants?
Answer: The Aux/IAA proteins are auxin-sensitive repressors that mediate diverse physiological and developmental processes in plants [1, 2]. Several DREB/CBF TFs directly promote transcription of the IAA5 and IAA19 genes in response to abiotic stress.  Auxin enhances the binding of Aux/IAA proteins to the receptor TIR1, which is an F-box protein that is part of the E3 ubiquitin ligase complex SCF(TIR1).
Question: Which genes belong to the AUX/IAA family of transcription repressors in plants?
Answer: Auxin is sensed by SCFTIR1-IAA6 and SCFTIR1-IAA19 co-receptor complexes, which leads to IAA6/IAA19 ubiquitylation in vitro and IAA6/IAA19 degradation in vivo. EgrIAA4 protein is localized in the nucleus and functions as an auxin-responsive repressor. Evidence also exists for SCF(TIR1)-mediated ubiquitination of the Aux/IAA proteins SHY2/IAA3 and BDL/IAA12
Question: Which genes belong to the AUX/IAA family of transcription repressors in plants?
Answer: The Aux/IAA proteins are auxin-sensitive repressors that mediate diverse physiological and developmental processes in plants [1, 2]. Auxin dose-response assays revealed that IAA9 downregulated lines were hypersensitive to auxin, although the only early auxin-responsive gene that was found to be upregulated in the antisense lines was IAA3. We report here that the downregulation of IAA9, a tomato (Solanum lycopersicum) gene from a distinct subfamily of Aux/IAA genes, results in a pleiotropic phenotype, consistent with its ubiquitous expression pattern. While no mutation in any member of subfamily IV has been reported to date, the phenotypes associated with the downregulation of IAA9 reveal distinct and novel roles for members of the Aux/IAA gene family. Aux/IAA proteins are short-lived nuclear proteins that repress expression of primary/early auxin response genes in protoplast transfection assays. Here, we systematically dissect auxin sensing by SCFTIR1-IAA6 and SCFTIR1-IAA19 co-receptor complexes, and assess IAA6/IAA19 ubiquitylation in vitro and IAA6/IAA19 degradation in vivo. Binding of Aux/IAA proteins leads to degradation via the 26S proteasome, but evidence for SCF(TIR1)-mediated poly-ubiquitination of Aux/IAA proteins is lacking.
Question: Which genes belong to the AUX/IAA family of transcription repressors in plants?
Answer: The Aux/IAA proteins are auxin-sensitive repressors that mediate diverse physiological and developmental processes in plants [1, 2]. The tomato Aux/IAA transcription factor IAA9 is involved in fruit development and leaf morphogenesis. There are 29 Aux/IAA genes in Arabidopsis that exhibit unique but partially overlapping patterns of expression. Several DREB/CBF TFs directly promote transcription of the IAA5 and IAA19 genes in response to abiotic stress. Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors. While no mutation in any member of subfamily IV has been reported to date, the phenotypes associated with the downregulation of IAA9 reveal distinct and novel roles for members of the Aux/IAA gene family. Nce for SCF-mediated ubiquitination of the Aux/IAA proteins SHY2/IAA3 and BDL/IAA12. Aux/IAA proteins are short-lived nuclear proteins that repress expression of primary/early auxin response genes in protoplast transfection assays. We showed that EgrIAA4 protein is localized in the nucleus and functions as an auxin-responsive repressor. Here, we systematically dissect auxin sensing by SCFTIR1-IAA6 and SCFTIR1-IAA19 co-receptor complexes, and assess IAA6/IAA19 ubiquitylation in vitro and IAA6/IAA19 degradation in vivo.
Question: Which genes belong to the AUX/IAA family of transcription repressors in plants?
Answer: Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors. The Aux/IAA proteins are auxin-sensitive repressors that mediate diverse physiological and developmental processes in plants [1, 2]. There are 29 Aux/IAA genes in Arabidopsis that exhibit unique but partially overlapping patterns of expression. The tomato Aux/IAA transcription factor IAA9 is involved in fruit development and leaf morphogenesis. Several DREB/CBF TFs directly promote transcription of the IAA5 and IAA19 genes in response to abiotic stress. Here, we systematically dissect auxin sensing by SCFTIR1-IAA6 and SCFTIR1-IAA19 co-receptor complexes, and assess IAA6/IAA19 ubiquitylation in vitro and IAA6/IAA19 degradation in vivo. We showed that EgrIAA4 protein is localized in the nucleus and functions as an auxin-responsive repressor. Auxin dose-response assays revealed that IAA9 downregulated lines were hypersensitive to auxin, although the only early auxin-responsive gene that was found to be upregulated in the antisense lines was IAA3. While no mutation in any member of subfamily IV has been reported to date, the phenotypes associated with the downregulation of IAA9 reveal distinct and novel roles for members of the Aux/IAA gene family.
Question: Which mutated genes are associated with isolated ectopia lentis?
Answer: Isolated ectopia lentis (EL) is caused by mutation in genes:
1) ADAMTSL4 and 
2) Fibrillin-1 (FBN1).
Question: Which genes are thought to be involved in medulloblastoma development?
Answer: Medulloblastomas are the most frequent malignant brain tumors affecting children. Disease development has been suggested to be associated with a significant number of genes, such as PTCH1, SUFU, PTEN, CREBBP, PTEN, MYT1L, NFIA, NFIB, TEAD1, TGIF2, IGF2, PCDH10, BMI1, MYC, OTX2, RASSF1A, HIC1, and CASP8.
Question: Which genetic defects are observed in Prader-Willi syndrome?
Answer: The predominant genetic defects in Prader-Willi syndrome are 15q11-13 deletions of paternal origin and maternal chromosome 15 uniparental disomy, or rare imprinting mutations, combined with monoallelic expression of the paternal alleles.
Question: Which myosin isozymes are located within the pericuticular necklace of the hair cell?
Answer: The hair cell is located in the inner ear, a tissue that is particularly reliant on actin-rich structures and unconventional myosin isozymes. Within the pericuticular necklace, a domain of the hair cell, certain unconventional myosin isozymes are located, namely myosins-Ibeta, myosin-VI, and myosin-VIIa.
Question: What micro-RNAs are useful in the diagnosis and prognosis of Heart Failure?
Answer: In particular, miR-214, miR-423-5p, appear to be promising for the diagnosis, prognosis and management of HF patients.
Question: Which methods are used for genome segmentation of gene expression data?
Answer: Most of the used methods are variations of Markov Models such as Markov Chain Monte Carlo (MCMC) or Combinatorial methods.
Question: Which methods are used for genome segmentation of gene expression data?
Answer: We use piecewise constant intensity models with varying number of pieces, and show how a reversible jump Markov Chain Monte Carlo (RJMCMC) method can be used to obtain a posteriori distribution on the intensity of the patterns along the genome.
Question: Which methods are used for genome segmentation of gene expression data?
Answer: We use piecewise constant intensity models with varying number of pieces, and show how a reversible jump Markov Chain Monte Carlo (RJMCMC) method can be used to obtain a posteriori distribution on the intensity of the patterns along the genome. We introduce Markov models for segmentation of symbolic sequences, extending a segmentation procedure based on the Jensen-Shannon divergence that has been introduced earlier. Our method is based on a combinatorial genome segmentation solely using information on combinations of epigenetic marks.
Question: Which methods are used for genome segmentation of gene expression data?
Answer: . We introduce Markov models for segmentation of symbolic sequences, extending a segmentation procedure based on the Jensen-Shannon divergence that has been introduced earlier.. Our method is based on a combinatorial genome segmentation solely using information on combinations of epigenetic marks.. We use piecewise constant intensity models with varying number of pieces, and show how a reversible jump Markov Chain Monte Carlo (RJMCMC) method can be used to obtain a posteriori distribution on the intensity of the patterns along the genome.
Question: Which methods are used for genome segmentation of gene expression data?
Answer: reversible jump markov chain monte carlo (rjmcmc) method
Question: Which methods are used for genome segmentation of gene expression data?
Answer: We use piecewise constant intensity models with varying number of pieces, and show how a reversible jump Markov Chain Monte Carlo (RJMCMC) method can be used to obtain a posteriori distribution on the intensity of the patterns along the genome. We introduce Markov models for segmentation of symbolic sequences, extending a segmentation procedure based on the Jensen-Shannon divergence that has been introduced earlier.
Question: Which major signaling pathways are regulated by RIP1?
Answer: necroptosis
apoptosis  
pro-survival/inflammation NF-κB activation
Question: With which complexes is the protein SUS1 associated?
Answer: Sus1/ENY2 is a component of the SAGA and TREX-2 complexes
Question: Data from which major epigenome projects are contained in the DeepBlue epigenomic data server?
Answer: The DeepBlue Epigenomic Data Server contains data from four major epigenome projects, namely ENCODE, ROADMAP, BLUEPRINT and DEEP.
Question: List side effects of radiation therapy?
Answer: radiation-induced tumors
radiation necrosis
microangiopathy
progressive leukencephalopathy
pneumonitis
disturbance of the blood-brain barrier
radionecrosis of brain tissue
radiogenic liver damage
mucositis
colitis
osteitis
osteoradionecrosis
myositis
Radiation-induced fibrosis
Acute skin reactions
Question: List the two most important hematological features of the Evans syndrome
Answer: Evans syndrome is a rare autoimmune disorder, which is characterized by immune thrombocytopenia and autoimmune hemolytic anemia.
Question: Which conditions are manifested by TRIM8 mutations?
Answer: TRIM8 mutations are associated with epilepsy, epileptic encephalopathy, developmental delay and intellectual disability.
Question: Which conditions are manifested by TRIM8 mutations?
Answer: Mutations in the TRIM8 gene, which encodes the triggering receptor encoded in myeloid cells 8 (TRIM8) are associated with epilepsy, epileptic encephalopathy, developmental delay and intellectual disability.
Question: Which conditions are manifested by TRIM8 mutations?
Answer: Focal segmental glomerulosclerosis, severe developmental delay, intellectual disability and epilepsy.
Question: Which conditions are manifested by TRIM8 mutations?
Answer: Mutations in TRIM8 gene have been described in patients with severe developmental delay, epileptic encephalopathy, developmental delay and intellectual disability.
Question: Which genes are responsible for the high-altitude adaptation of Tibetans?
Answer: Recent studies have identified genes involved in high-altitude adaptation in Tibetans. Genetic variants/haplotypes within regions containing three of these genes (EPAS1, EGLN1, and PPARA) are associated with relatively decreased hemoglobin levels observed in Tibetans at high altitude, providing corroborative evidence for genetic adaptation to this extreme environment.  A gene (HMOX2) involved in heme catabolism, harbors potentially adaptive variants in Tibetans.
Question: Which genes are responsible for the high-altitude adaptation of Tibetans?
Answer: Recent studies have identified genes involved in high-altitude adaptation in Tibetans. Three of these genes, EPAS1, EGLN1 and PPARA, regulate or are regulated by hypoxia inducible factor, a principal controller of erythropoiesis and other organismal functions. Two functional loci in the promoter of EPAS1 gene involved in high-altitude adaptation of Tibetans.
Question: Which genes are responsible for the high-altitude adaptation of Tibetans?
Answer: EGLN1 (or HIFPH2, MIM 606425) and EPAS1 (or HIF2A, MIM 603349), both related to hypoxia-inducible factor, were found most differentiated in the two regions, respectively. Genetic variants/haplotypes within regions containing three of these genes (EPAS1, EGLN1, and PPARA) are associated with relatively decreased hemoglobin levels observed in Tibetans at high altitude, providing corroborative evidence for genetic adaptation to this extreme environment. Three of these genes, EPAS1, EGLN1 and PPARA, regulate or are regulated by hypoxia inducible factor, a principal controller of erythropoiesis and other organismal functions.
Question: Which genes are responsible for the high-altitude adaptation of Tibetans?
Answer: Genetic variants/haplotypes within regions containing three of these genes (EPAS1, EGLN1, and PPARA) are associated with relatively decreased hemoglobin levels observed in Tibetans at high altitude, providing corroborative evidence for genetic adaptation to this extreme environment.
Question: Which are the most under-represented oligonucleotides in higher eukaryote genomes?
Answer: The oligonucleotides containing the CG and TA dinucleotide are generally under-represented in higher eukaryote genomes
Question: Which are the most under-represented oligonucleotides in higher eukaryote genomes?
Answer: TpA is the most underepresented dinucleotide followed closely by CpG. For trinucleotides, GCA/TGC tends to be under-represented in phage, human viral, and eukaryotic sequences, and CTA/TAG is strongly under-represented in many prokaryotic, eukaryotic, and viral sequences. For higher lengts alternating Purine/Pyrimidine tracts are underepresented up to 60%.
Question: Which are the most under-represented oligonucleotides in higher eukaryote genomes?
Answer: Oligonucleotides containing CG and TA dinucleoides
Question: What eye disease(s) are associated with ocular toxoplasmosis?
Answer: Retinochoroiditis is the most frequent manifestation of congenital toxoplasmosis Infectious uveitis accounted for 37% of posterior uveitis cases of which toxoplasmosis was the most common cause. Toxoplasmosis was the most common cause of posterior uveitis (60%)
Question: What eye disease(s) are associated with ocular toxoplasmosis?
Answer: A large percentage of posterior and infectious uveitis is associate with toxoplasmosis. Retinochoroiditis is associated with congenital toxoplasmosis.
Question: What eye disease(s) are associated with ocular toxoplasmosis?
Answer: the most frequent manifestation of congenital toxoplasmosis is retinochoroiditis.
Question: What eye disease(s) are associated with ocular toxoplasmosis?
Answer: Retinochoroiditis is the most frequent manifestation of congenital toxoplasmosis
Question: What eye disease(s) are associated with ocular toxoplasmosis?
Answer: yes, ocular toxoplasmosis is associated with retinochoroiditis.
Question: What eye disease(s) are associated with ocular toxoplasmosis?
Answer: Toxoplasmosis was the most common cause of posterior uveitis (60%) Retinochoroiditis is the most frequent manifestation of congenital toxoplasmosis Infectious uveitis accounted for 37% of posterior uveitis cases of which toxoplasmosis was the most common cause.
Question: What eye disease(s) are associated with ocular toxoplasmosis?
Answer: The eye disease(s) associated with ocular toxoplasmosis are:1) ocular syphthalmia, 2) retinochoroiditis, 3) juvenile idiopathic arthritis and4) chorioretinitis.
Question: What eye disease(s) are associated with ocular toxoplasmosis?
Answer: Toxoplasmosis was the most common cause of posterior uveitis (60%) for infectious uveritis, herpetic iridocyclitis, ocular toxoplasmosa, and bacterial endophthalmitis increased in patients with congenital tasma.
Question: What eye disease(s) are associated with ocular toxoplasmosis?
Answer: Diseases associated with ocular toxoplasmosis are ocular syphilis, retinochoroiditis, juvenile idiopathic arthritis and chorioretinitis.
Question: What eye disease(s) are associated with ocular toxoplasmosis?
Answer: Diseases associated with ocular toxoplasmosis are:1) ocular syphilis, 2) retinochoroiditis, 3) juvenile idiopathic arthritis and4) chorioretinitis.
Question: What eye disease(s) are associated with ocular toxoplasmosis?
Answer: Ocular toxoplasmosis (OTS) is a rare but life threatening complication of ocular syphilis, which is followed by retinochoroiditis, juvenile idiopathic arthritis and chorioretinitis.
Question: Which are currently available software tools for detecting rare codon clusters in coding sequences?
Answer: Rare codon clusters (RCCs) correspond to regions along mRNA sequences where among the possible choices of synonymous codons those  with lower usage are observed. Due to the fact that relative codon frequencies have been shown to correlate with their cognate tRNA frequencies, RCCs indicate possible translational attenuation sites. A few tools specific for this task have been described in the literature, namely: LaTcOm, %MinMax, PAUSE, Sherlocc, Sliding Window (RiboTempo)
Question: Name 4 circular RNA molecules associated with carcinogenesis.
Answer: circ-ABCB10 knockdown suppressed the proliferation and increased apoptosis of breast cancer cells.
Hsa_circ_0058246 was elevated in tumor specimens of patients with poor clinical outcomes.
Circ-FBXW7 expression positively associated with glioblastoma patient overall survival.
ciRS-7 promotes the development of cancer by acting as sponge of miR-7.
Question: List potential reasons regarding why potentially important genes are ignored
Answer: Differences in attention can be explained, to a large extent, exclusively from a small set of identifiable chemical, physical, and biological properties of genes. Together with knowledge about homologous genes from model organisms, these features accurately predict the number of publications on individual human genes, the year of their first report, the levels of funding awarded by the National Institutes of Health (NIH), and the development of drugs against disease-associated genes.
Question: Please list the syndromes that are part of Castleman's disease AKA TAFRO
Answer: The syndromes that are part of Castleman's disease AKA TAFRO are:1) organomegaly, 2) anasarca, 3) myelofibrosis, 4) thrombocytopenia and 5) reticulin fibrosis.
Question: Please list the syndromes that are part of Castleman's disease AKA TAFRO
Answer: TAFRO (or Castleman-Kojima) syndrome has been gradually recognized in recent years. It is a systemic inflammatory disease characterized by thrombocytopenia (T), anasarca (A), myelofibrosis/fever (F), renal dysfunction/reticulin fibrosis (R), and organomegaly (O).
Question: Please list the syndromes that are part of Castleman's disease AKA TAFRO
Answer: TAFRO syndrome is defined as CD with thrombocytopenia, anasarca, fever, reticulin fibrosis, and organomegaly.
Question: Please list the syndromes that are part of Castleman's disease AKA TAFRO
Answer: The syndromes that are part of Castleman's disease AKA TAFRO are organomegaly, anasarca, myelofibrosis, thrombocytopenia, reticulin fibrosis and renal dysfunction.
Question: Please list the syndromes that are part of Castleman's disease AKA TAFRO
Answer: The syndromes that are part of Castleman's disease AKA TAFRO are organomegaly, anasarca, myelofibrosis, thrombocytopenia and reticulin fibrosis. There is also renal dysfunction.
Question: Please list the syndromes that are part of Castleman's disease AKA TAFRO
Answer: TAFRO syndrome (thrombocytopenia, anasarca, myelofibrosis, renal dysfunction, and organomegaly).
Question: Please list the syndromes that are part of Castleman's disease AKA TAFRO
Answer: TAFRO syndrome (thrombocytopenia, anasarca, myelofibrosis, renal dysfunction, and organomegaly) is an atypical manifestation of multicentric Castleman's disease.
Question: Which are the musculoskeletal manifestations of Marfan syndrome?
Answer: Musculoskeletal manifestations of Marfan syndrome include scoliosis, dural ectasia, pectus excavatum and carinatum, arachnodactyly, otto pelvis (protrusio acetabuli), dolichostenomelia and ligamentous laxity.
Question: Which are the subtypes of Pfeiffer syndrome?
Answer: Pfeiffer syndrome is divided into three clinical subtypes.
Question: Which are the subtypes of Pfeiffer syndrome?
Answer: Pfeiffer syndrome is divided into three clinical subtypes. Type 1 "classic" Pfeiffer syndrome involves individuals with mild manifestations including brachycephaly, midface hypoplasia and finger and toe abnormalities; it is associated with normal intelligence and generally good outcome. Type 2 consists of cloverleaf skull, extreme proptosis, finger and toe abnormalities, elbow ankylosis or synostosis, developmental delay and neurological complications. Type 3 is similar to type 2 but without a cloverleaf skull.
Question: Which treatment methods were compared in the EXCEL Trial?
Answer: EXCEL trial compared Everolimus Eluting Stent vs. Coronary Artery Bypass Surgery for Effectiveness of Left Main Revascularization.
Question: List Pentalogy of Fallot.
Answer: Pentalogy of Fallot consists of a pulmonic stenosis, a ventricular septal defect, an overriding aorta, a right ventricular hypertrophy and a patent foramen ovale.