nirantk/geneticsQA-train huggingface dataset:
Question: Are DNA helicases involved in progeroid syndromes?

Context:
Among these syndromes, relevant advances have recently been made in Werner syndrome, one of several progeroid syndromes characterized by defective DNA helicases,
Progeroid syndromes (PSs) constitute a group of disorders characterized by clinical features mimicking physiological aging at an early age.
However, all the characterized PSs enter in the field of rare monogenic disorders and several causative genes have been identified. These can be separated in subcategories corresponding to (i) genes encoding DNA repair factors, in particular, DNA helicases, and (ii) genes affecting the structure or post-translational maturation of lamin A, a major nuclear component.
None of the known progerias represents true precocious ageing. Some of them, including Werner (WS), Bloom (BS), and Rothmund-Thomson syndromes (RTS) as well as combined xeroderma pigmentosa-Cockayne syndrome (XP-CS) are characterised by features resembling precocious ageing and the increased risk of malignant disease. Such phenotypes result from the mutations of the genes encoding proteins involved in the maintenance of genomic integrity, in most cases DNA helicases.
Single-gene mutations can produce human progeroid syndromes--phenotypes that mimic usual or "normative" aging.
The prototypic example of the former is the Werner syndrome, a condition caused by mutations of the RecQ family of DNA helicases.
Progeria and progeroid syndromes are characterized by the earlier onset of complex senescent phenotypes. WRN was originally identified as a gene responsible for Werner syndrome (WS; "Progeria of Adults"). The WRN gene product has RecQ-type helicase domains in the central region of the protein.

Answer: Yes, mutations in genes coding for DNA helicases were found to induce progeroid syndromes, such as Werner syndrome (WS) or Bloom syndrome (BS).
Exact answer: yes
Question: Is physical performance influenced by thyroid hormone metabolism?

Context:
Longitudinal analysis showed that in Eut men higher baseline FT4 was significantly (p = 0.02) predictive of a lower SPPB score at the 3-year follow-up
Even a modest thyroid hormone excess is associated with a reduced physical function in elderly men.
Oral L-thyroxine treatment was started and at a 1-month follow-up examination, mental status and physical performance were improved
In a population of independently living elderly men, higher FT4 and rT3 concentrations are associated with a lower physical function
She had generalised weakness of muscles, cold intolerance and a reduced physical performance.
Replacement therapy by oral administration of L-thyroxin resulted in a gradual improvement of the patient's state
multivariate analysis revealed that total T3 was an independent predictor of VO2max
changes in thyroid hormone were closely correlated to myocardial functional status in patients with heart failure.
THR among patients with SCH is beneficial not only by improvement in lipid profile, as well as by improvement in cognitive and functional status,
CONCLUSIONS: Even a modest thyroid hormone excess is associated with a reduced physical function in elderly men.
Subclinical hyperthyroidism (SH) may be responsible for many cardiovascular changes, including an impaired exercise performance.
BACKGROUND: Physiological changes in thyroid hormone concentrations might be related to changes in the overall physical function in the elderly.

Answer: Yes.
Exact answer: yes
Question: List packages for transcription factor binding sites' (TFBS) analysis available in R/Bioconductor

Context:
Clustered occurrence of multiple TFs at genomic sites may arise from chromatin accessibility and local cooperation between TFs, or binding sites may simply appear clustered if the profiles are generated from diverse cell populations. Overlaps in TF binding profiles may also result from measurements taken at closely related time intervals. It is thus of great interest to distinguish TFs that directly regulate gene expression from those that are indirectly associated with gene expression. Graphical models, in particular Bayesian networks, provide a powerful mathematical framework to infer different types of dependencies. However, existing methods do not perform well when the features (here: TF binding profiles) are highly correlated, when their association with the biological outcome is weak, and when the sample size is small. Here, we develop a novel computational method, the Neighbourhood Consistent PC (NCPC) algorithms, which deal with these scenarios much more effectively than existing methods do. We further present a novel graphical representation, the Direct Dependence Graph (DDGraph), to better display the complex interactions among variables. NCPC and DDGraph can also be applied to other problems involving highly correlated biological features. Both methods are implemented in the R package ddgraph, available as part of Bioconductor
Here, we present MMDiff, a robust, broadly applicable method for detecting differences between sequence count data sets. Based on quantifying shape changes in signal profiles, it overcomes challenges imposed by the highly structured nature of the data and the paucity of replicates
Supervised detection of conserved motifs in DNA sequences with cosmo
We here introduce an algorithm, called cosmo, that allows this search to be supervised by specifying a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may be formulated, for example, on the basis of prior knowledge about the structure of the transcription factor in question. The algorithm is based on the same two-component multinomial mixture model used by MEME, with stronger reliance, however, on the likelihood principle instead of more ad-hoc criteria like the E-value
dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis.
TFBS: Computational framework for transcription factor binding site analysis.

Answer: Neighbourhood Consistent PC (NCPC) algorithms, MMDiff and cosmo.
Exact answer: Neighbourhood Consistent PC (NCPC) algorithms
MMDiff
cosmo
dPattern
TFBS
Question: List angiocrine factors

Context:
Ccl4 and neurotensin (Nts) (angiocrine factors)
vascular endothelial growth factor (VEGF)-A was identified as the most abundantly expressed factor, 
angiocrine factors tissue inhibitor of metalloproteinases-1 (Timp-1) and thrombospondin 3 (THBS3) 
We found that Slit2, which is negatively regulated by endothelial EphA2 receptor, is one such tumor suppressive angiocrine factor. 
angiocrine factors, including hepatocyte growth factor (HGF) and Wnt2.

Answer: Angiocrine factors are: Ccl4, neurotensin, vascular endothelial growth factor, metalloproteinases-1, thrombospondin 3, Slit2, hepatocyte growth factor, Wnt2. 
Exact answer: Ccl4, neurotensin, vascular endothelial growth factor, metalloproteinases-1, thrombospondin 3, Slit2, hepatocyte growth factor, Wnt2
Question: In which nuclear compartments is heterochromatin located?

Context:
This compartment localizes into three main regions: the peripheral heterochromatin, perinucleolar heterochromatin, and pericentromeric heterochromatin
By separating cells according to transgene expression we show here that silencing appears to be associated with histone H3 lysine 9 trimethylation (H3K9me3), DNA methylation and the localization of the silenced gene to a specific nuclear compartment enriched in these modifications
The cell nucleus is divided into chromosome territories and the extrachromosomal domain. The latter includes several structural and functional compartments involved in RNA processing and transport.
We also describe a new apocentric nuclear compartment with a unique set of histone modifications that occurs as a zone of chromatin surrounding centromeric heterochromatin in differentiated lymphocytes. 
Little is known about the mechanisms of gene targeting within the nucleus and its effect on gene expression, but most studies have concluded that genes located near the nuclear periphery are silenced by heterochromatin
After TSA and NaBt treatment, the HP1 proteins were repositioned more internally in the nucleus, being closely associated with interchromatin compartments, while centromeric heterochromatin was relocated closer to the nuclear periphery
Taking into account the different heterochromatic and euchromatic compartments of the genome, our data suggest that the relative abundance of Ty3/gypsy LTRrs along each chromosome arm is determined mainly by the different proportions of heterochromatin, particularly pericentric heterochromatin, relative to total arm length

Answer: This compartment localizes into three main regions: the peripheral heterochromatin, perinucleolar heterochromatin, and pericentromeric heterochromatin. Silencing appears to be associated with histone H3 lysine 9 trimethylation (H3K9me3), DNA methylation and the localization of the silenced gene to a specific nuclear compartment enriched in these modification
Exact answer: peripheral heterochromatin, perinucleolar heterochromatin, pericentromeric heterochromatin
Question: Describe Wellens' Syndrome.

Context:
NTRODUCTION: Wellens Syndrome (WS) is a condition characterized by typical changes in ECG, which are biphasic T-wave inversions (less common) or symmetric and deeply inverted T waves (including 75%) in lead V2-V3 chest derivations. 
BACKGROUND: Reperfusion after coronary occlusion (myocardial infarction, MI), as in Wellens' syndrome, is often represented on ECG as T-wave inversion in the leads overlying the affected myocardial wall(s). 
Her presentation was concerning for acute coronary syndrome, Wellens syndrome in particular, given the elevated troponin levels, lack of ST segment changes, and characteristic T-wave findings. 
Omnious T-wave inversions: Wellens' syndrome revisited.
Wellens' syndrome is characterized by T-wave changes in electrocardiogram (EKG) during pain-free period in a patient with intermittent angina chest pain. 
We describe a case of a 42-year-old man, with a previous episode of angina and a normal ECG and serum cardiac markers, and a two months later finding of biphasic T wave in leads V2-V3 and deeply inverted T wave in V4-V5 at a asymptomatic occupational evaluation. This is a typical ECG pattern of Wellens' syndrome.
Whereas the Wellens' syndrome is characterized by symmetrically inverted T-waves with preserved R waves in the precordial leads suggestive of impending myocardial infarction due to a critical proximal left anterior descending stenosis, the pseudo-Wellens' syndrome caused by coronary artery spasm has also rarely been reported in literature.
The Wellens electrocardiogram (ECG) pattern of dynamic T-wave inversion in the anterior leads is observed in clinical conditions characterized by reversible left ventricular (LV) dysfunction (stunned myocardium), either ischemic or nonischemic
Wellens Syndrome (WS) is a condition characterized by typical changes in ECG, which are biphasic T-wave inversions (less common) or symmetric and deeply inverted T waves (including 75%) in lead V2-V3 chest derivations.
The initial electrocardiogram (ECG) showed biphasic T-waves in V2-V4, which was recognized as Wellens' syndrome, or acute coronary T-wave syndrome.

Answer: Wellens Syndrome (WS) is a condition characterized by typical changes in ECG, which are biphasic T-wave inversions (less common) or symmetric and deeply inverted T waves (including 75%) in lead V2-V3 chest derivations.
Question: Why does cranberry juice help combat urinary tract infections?

Context:
 Cranberry products affect the surface properties, such as fimbriae and lipopolysaccharides, and adhesion of fimbriated and nonfimbriated E. coli. 
 Cranberry juice has been shown to be effective in preventing adhesion of bacteria such as Escherichia coli to the bladder epithelium.
Inhibition of adherence to an extent of about 70% with multi-drug resistant E. coli strains was observed on uroepithelial cell. The anti-adherence bioactivity of the proanthocyanidin was detected at concentrations of 10-50 µg/ml with significant bacteriuria. 
Still with regard to antibiotic treatment in women, a recently published study investigated also the potential cranberry juice interaction with beta-lactam antibiotics supporting the hypothesis that cranberry juice in usual quantities as prophylaxis for UTI is not likely to alter the pharmacokinetics of these oral antibiotics.
In vitro studies have shown that binding of the P fimbriae of Escherichia coli to the uroepithelial tissue can be inhibited in the presence of proanthocyanidins, the active ingredient of cranberries.
NDM at concentrations between 0.2/mL and 1mg/mL significantly (P<.05) decreased secretion of extracellular FTF, as well as down-regulated ftf expression in a dose-dependent manner. NDM also markedly reduced the luciferase activity under the ftf promoter.
Cranberry juice has long been recognized in folk medicine as a therapeutic agent, mainly in urinary tract infections. Its proposed mechanism of action is antiadhesion of bacteria. 
The AFM adhesion force measurements were consistent with the results of a hemagglutination assay, confirming that oral consumption of CJC could act against adhesion of uropathogenic E. coli.
These data suggest that daily consumption of concentrated cranberry juice can significantly prevent the recurrence of symptomatic UTIs in children.

Answer: Cranberry products affect the surface properties, such as fimbriae and lipopolysaccharides, and adhesion of fimbriated and nonfimbriated E. coli.
Question: What is known about the effect of acupuncture in smoking cessation ?

Context:
Ear acupressure (EAP) and ear acupuncture have been used for smoking cessation, and some positive results have been reported
Auricular (ear) acupressure has been purported to be beneficial in achieving smoking cessation in some studies, while in others has been deemed insignificant
Acupuncture combined with auricular point sticking and pressing has reliable therapeutic effect for smoking cessation
Acupuncture has been promoted as a treatment modality for smoking cessation. However, its efficacy still remains controversial
Our results showed that auricular acupuncture did not have a better efficacy in smoking cessation compared to sham acupuncture. Combined acupuncture with behavior counseling or with nicotine replacement therapy should be used in further smoking cessation trials to enhance the success rate of smoking cessation.
Combining ten studies showed auricular acupuncture at 'correct' points to be more effective than control interventions, odds ratio 2.24 (95% CI 1.61, 3.10),
Auricular acupuncture appears to be effective for smoking cessation, but the effect may not depend on point location.
The combination of auricular acupressure and Internet-assisted smoking cessation program was more efficacious than auricular acupressure alone in terms of quit rate.
auricular acupuncture in smoking cessation has some effect.
With a one-year success rate of 41.1% ear acupuncture is a competitive alternative to orthodox medicine withdrawal methods. Acupuncture treatment can be applied and adapted individually, furthermore it is economical and without side effects.
Auriculotherapy is an useful aid for giving up smoking. It is easy and painless, has no secondary effects and it is economic.
the combined acupuncture-education group showing the greatest effect from treatment.
Acupuncture and education, alone and in combination, significantly reduce smoking; however, combined they show a significantly greater effect, as seen in subjects with a greater pack-year history.
A double blind, randomized, placebo-controlled clinical study was conducted to evaluate the efficacy of laser acupuncture treatment in adolescent smokers. 
Thus, there was no significant difference in the rates of smoking cessation in the treatment and control groups.
This simple ear electroacupuncture treatment was significantly more effective in helping volunteers to quit smoking than placebo treatment.

Answer: Ear acupressure (EAP) and ear acupuncture have been used for smoking cessation, and some positive results have been reported.
Auricular (ear) acupressure has been purported to be beneficial in achieving smoking cessation in some studies, while in others has been deemed insignificant.
The combined acupuncture-education group showing the greatest effect from treatment.
Question: What is the role of trifluridine in the novel nucleoside antitumor agent TAS-102?

Context:
PURPOSE: Trifluridine (TFT) is an antitumor component of a novel nucleoside antitumor agent, TAS-102, which consists of TFT and tipiracil hydrochloride (thymidine phosphorylase inhibitor).
TAS-102, a combination of trifluorothymidine and the thymidine phosphorylase inhibitor TPI in a 1:0.5 ratio, is a novel oral formulation, which is active in 5FU-resistant models, both in vitro and in xenograft models.
TAS-102 is a novel oral nucleoside antitumor agent consisting of trifluridine and tipiracil hydrochloride at a molar ratio of 1:0.5. 
PURPOSE: TAS-102 is an orally administered anticancer agent composed of α,α,α-trifluorothymidine (FTD) and thymidine phosphorylase inhibitor (TPI). 
Novel DNA synthesis inhibitors for the treatment of gastrointestinal malignancies include a combination of the antimetabolite TAS-102, which consists of trifluorothymidine with a thymidine phosphorylase inhibitor, and a novel micellar formulation of cisplatin NC-6004 that uses a nanotechnology-based drug delivery system. 
Repeated oral dosing of TAS-102 confers high trifluridine incorporation into DNA and sustained antitumor activity in mouse models.
TAS-102 is a novel oral nucleoside antitumor agent containing trifluridine (FTD) and tipiracil hydrochloride (TPI).

Answer: Trifluridine (TFT) is an antitumor component of TAS-102, which is a novel nucleoside antitumor agent. It is combined with tipiracil hydrochloride (thymidine phosphorylase inhibitor) in TAS-102.
Question: What role does Synapsin III play in presynaptic terminals?

Context:
Synapsin is an evolutionarily conserved presynaptic phosphoprotein.
Synapsins as a family of presynaptic terminal phosphoprotein participates in neuronal development
Synapsin III (SynIII) is a phosphoprotein
The neuronal phosphoprotein synapsin III
Synapsin II is a member of the neuronal phosphoprotein family.
phosphoprotein synapsin
Synapsin is an evolutionarily conserved presynaptic phosphoprotein.
Synapsins as a family of presynaptic terminal phosphoprotein participates in neuronal development
Synapsin III (SynIII) is a phosphoprotein
The neuronal phosphoprotein synapsin III
Synapsin II is a member of the neuronal phosphoprotein family.
phosphoprotein synapsin

Answer: Synapsin III (SynIII) is a phosphoprotein that plays a role in presynaptic terminals.
Question: Which genes does thyroid hormone receptor beta1 regulate in the liver?

Context:
our data suggests that TRbeta1-mediated down regulation of hepatic LDLr gene may play a critical role in iodine excess-induced hypercholesterolemic effects.
These data suggest that ChREBP mRNA expression is positively regulated by TR-beta1 and TH at the transcriptional level in mammals. This novel observation indicates that TH fine-tunes hepatic lipogenesis via regulating SREBP-1c and ChREBP gene expression reciprocally.
In contrast treatment with L-T3 produced an increase in S14 and ME but no change in TR beta-/- mice. From these results, it can be concluded that regulation of HR and EE are independent of TR beta. With the exception of serum cholesterol concentration and liver ME mRNA accumulation, all other markers of TH action examined during TH deprivation exhibited the expected responses in the absence of TR beta.
However, the T3-activated expression of the GH gene in GH3-PV and ME gene in SK-Hep-1-PV was repressed by approximately 30% and 90%, respectively, indicating the lack of correlation of PV/TRpbeta1 protein ratio with the dominant negative potency of mutant PV.
Transient cotransfection of P450R promoter/chloramphenicol acetyl transferase (CAT) constructs and the thyroid hormone receptor beta1 (TR beta1) expression plasmid into rat hepatoma H4IIE cells resulted in a 2.4-fold induction of promoter activity that was both T3 and TR beta1 dependent.
At the molecular level, we detected a dose-dependent attenuation of hepatic low density lipoprotein receptor (LDLr) and thyroid hormone receptor beta1 (TRbeta1) expression in parallel to the change of serum cholesterol.

Answer: LDL receptor"//
"ChREBP"//
"ME", "malic enzyme"//
"cytochrome P450 oxidoreductase"//
Exact answer: LDL receptor, ChREBP, Carbohydrate response element binding protein, ME, malic enzyme, cytochrome P450 oxidoreductase
Question: What are some treatment options for stress urinary incontinence (SUI) that persist after 12 months?

Context:
The initial treatment for SUI that persists after 12 months consists of conservative measures such as pelvic floor muscle exercises and behavioral therapy. Properly selected and informed patients can also be treated efficiently with minimally invasive procedures such as the implantation of a male suburethral sling, although the experience with such devices is not extensive. However, the implantation of artificial urinary sphincter is the gold standard therapy.
treatments such as periurethral injection of bulking agents, artificial urinary sphincter (AUS) implantation, and sub-urethral sling positioning. The artificial urethral sphincter has represented, until today, the gold standard but, in the recent years, sling systems have been investigated as minimally invasive alternative options.
Today, three different sling procedures are commonly performed: bone-anchored, readjustable, and trans-obturator slings systems.
The bone anchored suburethral synthetic sling is a simple and attractive procedure that can produce immediate good results with low morbidity, especially when strictly selected patients are treated. 
BAUS implantation is a safe, effective, minimally invasive option for iatrogenic male incontinence due to ISD. It compares favourably with AUS.

Answer: Some treatment options for stress urinary incontinence (SUI) that persist after 12 months include conservative measures such as pelvic floor muscle exercises and behavioral therapy, as well as minimally invasive procedures like the implantation of a male suburethral sling. The gold standard therapy is the implantation of an artificial urinary sphincter.