nirantk/geneticsQA-train huggingface dataset:
Question: How is bladder wall thickness measured?

Context:
Modifications of the bladder wall (organ damage) in patients with bladder outlet obstruction: ultrasound parameters.
Early identification of bladder changes by noninvasive transabdominal ultrasound
Measurement of the bladder wall thickness (BWT) or detrusor wall thickness (DWT) by US is reliable,
Also conventional US detects established signs of bladder damage: diverticulosis, trabecolations in the bladder wall (pseudo-diverticula),
non-invasive US of the bladder wall
BladderScan BVM 9500 device (Diagnostic Ultrasound, Bothell, WA) was used to measure bladder wall thickness
ultrasonography-estimated bladder weight and bladder wall thickness 
To identify measurements of ultrasonography (US)-derived bladder wall thickness (BWT) 
transabdominal US measurements of BWT and
Transvaginal ultrasound measurement of bladder wall thickness: 
ultrasound (US) techniques to measure bladder wall thickness (BWT).
Women underwent US measurement of BWT
Transabdominal and transperineal US for measuring BWT
ultrasound bladder and detrusor wall thickness
Ultrasonic measurements of urinary bladders are suitable to quantify bladder wall hypertrophy
ultrasonic bladder wall measurements t
Preliminary data on the automatic measurement of bladder wall thickness were reported, suggesting a good repeatability and agreement with conventional ultrasound imaging
 conventional ultrasound bladder wall thickness (BWT) measurements 
Ultrasonographic measurement of bladder wall thickness 
All children underwent ultrasonography to measure bladder wall thickness
Ultrasonographic assessment of bladder wall thickness is a sensitive screening tool 
ultrasound for bladder wall thickness (BWT)
transabdominal ultrasonography for bladder volume and detrusor muscle thickness
Transabdominal ultrasonography with a high-frequency probe was performed to obtain the anterior, posterior, and lateral bladder wall thicknesses.
ultrasonographic estimate of bladder wall thickness. 
ultrasonographic estimate of bladder wall thickness. 
there are marked differences in sonographic findings in male and female neonates in regard to renal pelvic dilatation, renal size and bladder wall thickness
BWT was measured by suprapubic ultrasonography.
transvaginal ultrasound measurement of bladder wall thickness
The measurement of a mean bladder wall thickness greater than 5 mm with transvaginal ultrasound 

Answer: Ultrasound
Exact answer: Ultrasound
Question: What roles do zinc-dependent endopeptidases play in physiological and pathological processes through ECM cleavage?

Context:
matrix metalloproteinase (MMP)-9
matrix metalloproteinase-3 (MMP-3) gene 
matrix metalloproteinases (MMPs)
Matrix metalloproteinase-9 (MMP-9) is a secreted glycoprotein with a major role in shaping the extracellular matrix and a detailed understanding of the secretory mechanism could help identify methods to correct diseases resulting from dysregulation of secretion.
Gelatinase B/matrix metalloproteinase-9 (MMP-9) (EC 3.4.24.35) cleaves many substrates and is produced by most cell types as a zymogen
Extracellular matrix metalloproteinases (MMPs) are a family of zinc-dependent neutral endopeptidases involved in physiological and pathological processes, through the cleavage of extracellular matrix.
Extracellular matrix metalloproteinases (MMPs) are a family of endopeptydases which recquire a zinc ion at their active site, for proteolityc activity.
matrix metalloproteinase (MMP)-9
matrix metalloproteinase-3 (MMP-3) gene 
matrix metalloproteinases (MMPs)
Matrix metalloproteinase-9 (MMP-9) is a secreted glycoprotein with a major role in shaping the extracellular matrix and a detailed understanding of the secretory mechanism could help identify methods to correct diseases resulting from dysregulation of secretion.
Gelatinase B/matrix metalloproteinase-9 (MMP-9) (EC 3.4.24.35) cleaves many substrates and is produced by most cell types as a zymogen
Extracellular matrix metalloproteinases (MMPs) are a family of zinc-dependent neutral endopeptidases involved in physiological and pathological processes, through the cleavage of extracellular matrix.
Extracellular matrix metalloproteinases (MMPs) are a family of endopeptydases which recquire a zinc ion at their active site, for proteolityc activity.

Answer: Zinc-dependent endopeptidases, specifically extracellular matrix metalloproteinases (MMPs), are involved in physiological and pathological processes through the cleavage of the extracellular matrix. These enzymes play a crucial role in remodeling the ECM and regulating various cellular functions.
Question: Does smoking increase risk for glioblastoma?

Context:
Glioma risk has consistently been inversely associated with allergy history but not with smoking history despite putative biologic plausibility.
No relation was observed between glioma risk and smoking (odds ratio = 0.92, 95% confidence interval: 0.77, 1.10; P = 0.37), and there were no interactions for glioma risk of smoking history with any of the risk alleles. 
Non-smokers with G/A and A/A genotype showed increased glioma risk compared with G/G genotype (adjusted OR = 1.72, 95%CI: 1.29-2.30, p = 0.0002 and adjusted OR = 1.81, 95%CI: 1.10-2.99, p = 0.020, respectively). This association was not found in ever- or current-smokers. 
There was no significant association between glioma and alcohol consumption, smoking and mobile phone use. 
RESULTS: We found no associations between the GSTM3, GSTP1, NQO1, CYP1A1, GSTM1, or GSTT1 polymorphisms and adult brain tumor risk with the possible exception of a weak association between the G-C (Val-Ala) GSTP1 105/114 haplotype and glioma [odds ratio (OR), 0.73; 95% confidence interval (95% CI), 0.54, 0.99], nor was there an interaction between the effects of the GSTM3 or GSTP1 polymorphisms and cigarette smoking.
We did not find any evidence for an association with life-style characteristics such as cigarette smoking, alcohol consumption, use of drugs of any kind, or dietary intake of cured or smoked meat or fish.
No relation was observed between glioma risk and smoking (odds ratio = 0
Glioma risk has consistently been inversely associated with allergy history but not with smoking history despite putative biologic plausibility
Compared with nonsmokers, duration of cigarette smoking, number of cigarettes smoked per day and pack-years of smoking were associated with increased glioma risk, although the increases in risk were relatively modest
Among ever smokers, women who reported having quit smoking had a 51% increase in risk of glioma compared with never smokers (HR = 1.51, 95% CI = 0.97-2.34), while current smokers did not appear to have an increase in risk

Answer: No. Smoking does not increase risk for glioblastoma.
Exact answer: no
Question: Can tetracycline affect tooth formation?

Context:
he results of that study, reported earlier (Rebich et al., 1983), indicated that over one-fifth of the American Indian children had discoloration of the dentition due to ingestion of tetracycline during the years of tooth formatio
ale Wistar rats prelabeled with tetracycline to mark surfaces of bone and tooth formation-mineralization were placed into orbit for 18.5 days aboard the Soviet COSMOS-1129 Biosatellit
It was concluded that the increased tetracycline incorporation reflected a higher rate of mineralization associated with faster tooth formation in the unimpeded toot
n this investigation an attempt has been made to determine the relationship between the staining of permanent teeth by tetracycline administered during the period of tooth formation with the dosage of the drug and the duration of therap
 definite relationship between total dosage and staining and duration of administration and staining was established; the condition occurred with greater frequency (in more than one-third of the children) when the total dosage exceeded 3 g. or the duration of treatment was longer than 10 days
This case report suggests the possibility that discoloration from tetracycline may not be limited to tooth development in the child, but may also affect the adult dentition

Answer: Tetracycline is incorporated in the teeth during their formation and leads to their permanent staining. A definite relationship between total dosage and staining and duration of administration and staining was established; the condition occurred with greater frequency (in more than one-third of the children) when the total dosage exceeded 3 g. or the duration of treatment was longer than 10 days.
Exact answer: yes
Question: Is myasthenia gravis associated with osteoporosis?

Context:
We performed PVP in 4 patients with generalized MG associated with recent steroid-induced symptomatic VFs. 
In this case report, we used tacrolimus to successfully treat a 13-year-old boy with ocular MG who had suffered from severe steroid complications, including a failure of thrive and osteoporosis.
 INTRODUCTION: Myasthenia gravis (MG) is a neuromuscular disease which has been associated with an increased falls risk and glucocorticoid-induced osteoporosis, recognized determinants of increased fracture risk. 
RESULTS: Compared to the control cohort, there was no statistically significant increased risk observed in patients with MG for any fracture (adjusted hazard ratio [AHR] 1.11; 95 % confidence interval [CI], 0.84-1.47) or osteoporotic fractures (AHR 0.98 [95 % CI 0.67-1.41]). Further, use of oral glucocorticoids up to a cumulative dose exceeding 5 g prednisolone equivalents did not increase risk of osteoporotic fracture (AHR 0.99 [95 % CI, 0.31-3.14]) compared with MG patients without glucocorticoid exposure.
The RANKL/OPG ratio and indices of bone metabolisms are also not affected by THX, although THX increases the levels of IL-7 and RANKL.
Both disorders had been controlled for around 15 years by oral prednisolone and a cholinesterase inhibitor following surgical removal of invasive thymoma and radiotherapy, but muscular weakness due to myalgia and an increase in serum levels of myogenic enzymes, mainly ascribable to the recurrence of PM, reappeared immediately after cessation of these drugs, which was done because the patient had multiple bone fractures and severe osteoporosis due to the long-term corticosteroid therapy. 
We measured bone density in 36 patients (26 females and 10 males) who had undergone long-term prednisolone administration, and found a decrease in bone density in 31% of female patients and osteoporosis in only 11.5% (three cases).
In conclusion, prednisolone-treated patients with myasthenia gravis have an acceptable risk of bone loss if prophylactic medication is administered.
INTRODUCTION: Myasthenia gravis (MG) is a neuromuscular disease which has been associated with an increased falls risk and glucocorticoid-induced osteoporosis, recognized determinants of increased fracture risk.
Alendronate should be used with caution in patients with myasthenia gravis who have corticosteroid-induced osteoporosis
In this paper we present two cases of young women who developed severe PAO with vertebral fractures: a 42-year-old woman with a family history of osteoporosis, and a 21-year-old woman affected with myasthenia gravis
Myasthenia gravis (MG) is a neuromuscular disease which has been associated with an increased falls risk and glucocorticoid-induced osteoporosis, recognized determinants of increased fracture risk

Answer: Myasthenia gravis (MG) is a neuromuscular disease which has been associated with an increased risk of glucocorticoid-induced osteoporosis. Thymectomy can also increase risk for osteoporosis. Appropriate osteoporosis preventive measures can reduce osteoporosis risk in MG patients.
Exact answer: yes
Question: Magnetic beads has been used in numerous applications. List some coatings used.

Context:
aptamer-based magnetic separation system 
enzymes coated to magnetic beads
 Aptamers are short, single-stranded (ss) oligonucleotidesable to recognize target molecules with high affinity. 
 Recent developments involve immobilization of tagged enzymes onto magnetic nanoparticles. 
Using magnetic beads to immobilize DNAs containing various types of structures, we evaluated the in vitro binding activities of two well-characterized DNA repair proteins, Escherichia coli MutS and human p53.
An affinity capture involved enzymatic assay for thrombin by using peptide aptamers as affinity ligands on magnetic beads
During phage selection the biotinylated antigens are bound to streptavidin coupled magnetic beads, 
 aptamer-functionalized magnetic beads 
native antibody immobilized to magnetic beads
Plasma membrane isolation using immobilized concanavalin A magnetic beads.
streptavidin magnetic beads
 Digoxin was coated onto the surface of streptavidin magnetic beads. 
covalent immobilization of the antigen onto carboxylic-modified magnetic beads (HOOC-MBs) activated with N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide (EDC) and N-hydroxysulfosuccinimide (sulfo-NHS), and further incubation in a mixture solution containing variable concentrations of the antigen and a fixed concentration of an HRP-labeled detection antibody. 
Aptamers against HNE were immobilized on magnetic beads
The high specificity was obtained by using the magnetic beads and aptamers,
Multiple targets (maltase, invertase, lipase) were immobilized on the magnetic beads by covalent linkage using 1-(3-dimethyl-aminopropyl)-3-ethyl-carbodiimide (EDC) and N-hydroxysuccinimide (NHS) as reaction reagents, respectively.
TiO2 -coated magnetic beads
antibody-targeted magnetic beads
A special SELEX library was constructed with the aim to immobilize this library on magnetic beads
streptavidin-coupled magnetic beads
aptamers loaded on the magnetic beads 
His-affinity magnetic beads
treptavidin-coated magnetic beads
, synthesized DNA is bound to magnetic beads
streptavidin-modified magnetic microbeads 
oligo(dT) magnetic beads

Answer: aptamers
enzymes
streptavidin
concanavalin A
carboxylic-modified 
TiO2
antibodies
SELEX library
synthesized DNA
C18
C8
oligo(dT)
Exact answer: aptamers
enzymes
streptavidin
concanavalin A
carboxylic-modified
TiO2
antibodies
SELEX library
synthesized DNA
C18
C8
oligo(dT)
Question: Can telomere length shortening be reversed by telomerase?

Context:
Telomere length is regulated around an equilibrium set point. Telomeres shorten during replication and are lengthened by telomerase. Disruption of the length equilibrium leads to disease; thus, it is important to understand the mechanisms that regulate length at the molecular level. 
High telomerase activity is detected in nearly all human cancers but most human cells are devoid of telomerase activity. There is well-documented evidence that reactivation of telomerase occurs during cellular transformation. In humans, tumors can rely in reactivation of telomerase or originate in a telomerase positive stem/progenitor cell, or rely in alternative lengthening of telomeres, a telomerase-independent telomere-length maintenance mechanism.
 Together, these observations may provoke a re-evaluation of telomere and telomerase based therapies, both in telomerase inhibition for cancer therapy and telomerase activation for tissue regeneration and anti-ageing strategies.
Telomeres progressively shorten throughout life. A hallmark of advanced malignancies is the ability for continuous cell divisions that almost universally correlates with the stabilization of telomere length by the reactivation of telomerase.
Telomerase-mediated telomere elongation provides cell populations with the ability to proliferate indefinitely. Telomerase is capable of recognizing and extending the shortest telomeres in cells;
Telomerase gene therapy rescues telomere length, bone marrow aplasia, and survival in mice with aplastic anemia.

Answer: Yes, telomerase gene therapy rescues telomere length, bone marrow aplasia, and survival in mice with aplastic anemia.
Exact answer: yes
Question: Which R package is used for visualization of linear and circular karyotypes?

Context:
chromDraw: an R package for visualization of linear and circular karyotypes.
The chromDraw graphical tool was developed as a user-friendly graphical tool for visualizing both linear and circular karyotypes based on the same input data matrix. The output graphics, saved in two different formats (EPS and SVG), can be easily imported to and modified in presentation and image-editing computer programs. The tool is freely distributed under GNU General Public License (GPL) and can be installed from Bioconductor or from the chromDraw home page.
The chromDraw graphical tool was developed as a user-friendly graphical tool for visualizing both linear and circular karyotypes based on the same input data matrix.
chromDraw: an R package for visualization of linear and circular karyotypes.
The chromDraw graphical tool was developed as a user-friendly graphical tool for visualizing both linear and circular karyotypes based on the same input data matrix.

Answer: The chromDraw graphical tool was developed as a user-friendly graphical tool for visualizing both linear and circular karyotypes based on the same input data matrix. The output graphics, saved in two different formats (EPS and SVG), can be easily imported to and modified in presentation and image-editing computer programs. The tool is freely distributed under GNU General Public License (GPL) and can be installed from Bioconductor or from the chromDraw home page.
The chromDraw graphical tool was developed as a user-friendly graphical tool for visualizing both linear and circular karyotypes based on the same input data matrix. The tool is freely distributed under GNU General Public License (GPL) and can be installed from Bioconductor or from the chromDraw home page.
Exact answer: chromDraw
Question: Which medication should be administered when managing patients with suspected acute opioid overdose?

Context:
Opioid overdose has a high mortality, but is often reversible with appropriate overdose management and naloxone (opioid antagonist). 
Training clinicians how to manage an opioid overdose and administer naloxone was effective.
For patients who have ingested dextromethorphan and are sedated or comatose, naloxone, in the usual doses for treatment of opioid overdose, can be considered for prehospital administration, particularly if the patient has respiratory depression
Naloxone hydrochloride, an injectable opioid antagonist which reverses the respiratory depression, sedation and hypotension associated with opioids, has long been used to treat opioid overdose. 
Experts have suggested that, as part of a comprehensive overdose prevention strategy, naloxone should be provided to heroin users for peer administration after an overdose. 
Patients who received naloxone for known or presumed opioid overdose were formally evaluated one hour later for multiple potential predictor variables. 
Patients with presumed opioid overdose can be safely discharged one hour after naloxone administration
To determine whether naloxone administered i.v. to out-of-hospital patients with suspected opioid overdose would have a more rapid therapeutic onset than naloxone given subcutaneously (s.q.).
Subjects received either naloxone 0.4 mg i.v. (n = 74) or naloxone 0.8 mg s.q. (n = 122), for respiratory depression of <10 breaths/min. 
There was no clinical difference in the time interval to respiratory rate > or =10 breaths/min between naloxone 0.8 mg s.q. and naloxone 0.4 mg i.v. for the out-of-hospital management of patients with suspected opioid overdose. 
To illustrate this problem, we report the case of a patient inappropriately treated with naloxone and the results of a retrospective review of the medical records of 15 consecutive patients with cancer treated with naloxone in the emergency department over a 5-month period. 
Management of opioid overdose, whether illicit or iatrogenic, requires the prompt and skillful use of opioid overdose, whether illicit or iatrogenic, requires the prompt and skillful use of opioid antagonists. 
 The proportion of clinicians willing to use naloxone in an opioid overdose rose from 77% to 99% after training. Barriers to implementing training were clinician time and confidence, service resources, client willingness and naloxone formulation.
Opioid overdose is rarely the primary cause of altered mental status in cancer patients receiving opioid therapy. The inappropriate administration of naloxone to reverse an abnormal mental status can cause severe withdrawal symptoms and pain. 

Answer: Naloxone is opioid anagonist that should be administered for all patients with suspected acute opioid overdose. Intravenous naltrexone hydrochloride is usually administered, however, other formulations, including enteral methylnaltrexone, nebulized naloxone and subcutaneous naloxone, are under investigation and can be used under certain circumstances.
Exact answer: naloxone
Question: Are there any HCV replication inhibitors available?

Context:
We report here the discovery of the first small-molecule HCV infectivity inhibitor, GS-563253, also called HCV infectivity inhibitor 1 (HCV II-1). 
Resistance to mericitabine (prodrug of HCV NS5B polymerase inhibitor PSI-6130) is rare and conferred by the NS5B S282T mutation.
We tested the ability of NA808 to inhibit SPT's enzymatic activity in FLR3-1 replicon cells
The SPT inhibitor NA808 prevents replication of HCV genotypes 1a, 1b, 2a, 3a, and 4a in cultured hepatocytes and in mice with humanized livers.
Vaniprevir (phase III clinical trials) and MK-5172 (phase II clinical trials) are two potent antiviral compounds that target NS3/4A protease
treatment for hepatitis C virus (HCV) infection has been significantly improved with the approval of the first two HCV NS3/4A protease inhibitors, telaprevir (Incivek) and boceprevir (Victrelis). 
Combination therapy with telaprevir and BMS-788329 (NS5A inhibitor) reduced serum HCV RNA to undetectable levels. The presence of an NS3-V36A telaprevir resistance mutation resulted in poor response to telaprevir monotherapy but showed significant HCV reduction when telaprevir was combined with BMS-788329. However, a BMS-788329-resistant strain emerged at low frequency. Infection with a BMS-788329-resistant NS5A-L31V mutation rapidly resulted in gain of an additional NS5A-Y93A mutation that conferred telaprevir resistance during combination therapy
HCV NS5A replication complex inhibitors, exemplified by Daclatasvir (BMS-790052), represent a new class of DAA
ACH-806 (or GS-9132) is a novel, small-molecule inhibitor specific for hepatitis C virus (HCV). 
Telaprevir and boceprevir are the first two protease inhibitor (PI) DAAs to be approved for combination therapy with pegylated interferon (PEG-IFN) and ribavirin (RBV). 
symmetrical bidentate structure of the NS5A inhibitor BMS-790052, a series of new monodentate molecules were designed
In vitro, boceprevir is more active than telaprevir against the HCV G3 NS3/4A enzyme in cell-based and biochemical assays and against G3 isolates in replicon assays
Alisporivir is the most advanced host-targeting antiviral in clinical development. Alisporivir blocks HCV replication by neutralizing the peptidyl-prolyl isomerase activity of the abundant host cytosolic protein, cyclophilin A
Interestingly, the NS5A inhibitor daclatasvir (BMS-790052) caused a decrease in serum HCV RNA levels by about two orders of magnitude within 6 h of administration

Answer: Chronic hepatitis C virus (HCV) infection is a worldwide health problem causing serious complications, such as liver cirrhosis and hepatoma. Small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) have been reported to suppress gene expression significantly. HCV seems a suitable candidate for targets of siRNAs, as HCV is a positive single-strand RNA virus and replicates in the cytoplasm.  Based on results, nowadays there are few HCV replication inhibitors such as GS-563253, PSI-6130, NA-808, BMS-790052, GS-9132 and BMS-788329.
Exact answer: yes