nirantk/geneticsQA-train huggingface dataset:
Question: What kind of chromatography is HILIC?

Context:
hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC LC-MS/MS) method
Hydrophilic-interaction liquid chromatography (HILIC) is a widely used technique for small polar molecule analysis 
hydrophilic-interaction LC (HILIC)
A hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC LC-MS/MS) method 
Hydrophilic Interaction Chromatography (HILIC) 
n this study a hydrophilic interaction chromatographic (HILIC) method 

Answer: Hydrophilic Interaction Chromatography (HILIC)
Exact answer: Hydrophilic Interaction Chromatography
Question: Describe what is the advantage of using a stain free protein gel in a Western Blot experiment?

Context:
V3 stain-free workflow for a practical, convenient, and reliable total protein loading control in western blotting.
The V3 stain-free workflow makes the western blot process faster, transparent, more quantitative and reliable.
Direct Blue 71 (DB71) staining-a novel, sensitive, dye-binding staining method compatible with immunodetection-may offer advantages over these traditional loading control methods.
Direct Blue 71 staining as a destaining-free alternative loading control method for Western blotting.
Stain-Free technology as a normalization tool in Western blot analysis.
Stain-Free technology appears to be more reliable, more robust, and more sensitive
tain-Free technology offers the additional advantages of providing checkpoints throughout the Western blotting process by allowing rapid visualization of gel separation and protein transfer.

Answer: Stain-Free technology can be used as a normalization tool in Western blot analysis.
Question: In which isochores are Alu elements enriched?

Context:
 the vast majority of Alu sequences were shown to have the highest density in GC-rich isochores
Alu sequences being unstable in the GC-poor isochores but stable in the compositionally matching GC-rich isochores,
Alu retrotransposons do not show a homogeneous distribution over the human genome but have a higher density in GC-rich (H) than in AT-rich (L) isochores
This result, together with the known higher selective disadvantage of recombination products in H isochores, points to Alu-Alu recombination as the main agent provoking the density shift of Alus toward the GC-rich parts of the genome
whereas GC-rich Alus are mostly present in GC-rich isochores
the present results on Alu and LINE stability/exclusion predict significant losses of Alu DNA from the GC-poor isochores during evolution, a phenomenon apparently due to negative selection against sequences that differ from the isochore composition
The frequency of Alu sequences also increases with increasing GC, but attains a maximum in H2 isochores, in agreement with previous experimental data
The CpG levels of both Alus and CpG islands increase with their GC levels
characterized as a GC-rich isochore enriched for CpG islands, genes, and Alu-like repeats
Microsatellites and SINES (Alu, B1, B2) are found at roughly equal frequencies in introns from all isochore classes
The results indicate that the short repeats of the B1 family of mouse and of the Alu I family of man are most frequent in the heavy components, whereas the long repeats of the BamHI family of mouse and of the Kpn I family of man are mainly present in the two light components.

Answer: Alu elements are enriched in high GC% isochores due to reduced Alu loss by recombination in these regions. The frequency of Alu sequences increases with increasing GC, but attains a maximum in H2 isochores.
Exact answer: H2, H3
Question: Is Alu hypomethylation associated with breast cancer?

Context:
Alu and LINE-1 hypomethylation is associated with HER2 enriched subtype of breast cancer
In IBC, Alu hypomethylation correlated with negative estrogen receptor (ER) status
In survival analyses, low Alu methylation status tended to be associated with poor disease-free survival of the patients.
Alu hypomethylation is probably a late event during breast cancer progression
prominent hypomethylation of Alu and LINE-1 in HER2 enriched subtype may be related to chromosomal instability of this specific subtype.
DNA methylation for three repetitive elements (LINE1, Sat2 and Alu) were analyzed in invasive ductal carcinoma of the breast, paired adjacent normal tissue and WBC from 40 breast cancer patients
DNA methylation for the three repetitive elements was lower in tumor compared to adjacent tissue and WBC DNA.

Answer: Yes, Alu elements were found to be hypomethylated in breast cancer, especially in the HER2-enriched subtype. Furthermore, Alu hypomethylation was identified as a late event during breast cancer progression, and in invasive breast cancer, tended to be associated with negative estrogen receptor status and poor disease-free survival of the patients.
Alu and LINE-1 hypomethylation is associated with HER2 enriched subtype of breast cancer  
Exact answer: yes
Question: Are there telemedicine applications for chronic pain management?

Context:
An integrated cognitive-behavioral and physical therapy group protocol has been developed and then implemented at remote sites using videoconferencing technology to provide pain management for veterans. 
Tele-pain management: use of videoconferencing technology in the delivery of an integrated cognitive-behavioral and physical therapy group intervention.
It is feasible to provide treatment to women veterans living in rural areas by utilizing video-teleconferencing technology between larger VA medical centers and facilities at CBOCs in more rural settings
The results suggest that a smartphone-delivered intervention with diaries and personalized feedback can reduce catastrophizing and prevent increases in functional impairment and symptom levels in women with chronic widespread pain following inpatient rehabilitation.
 Of the studies available, there are very few randomized trials of telehealth pain care and only one general overview of e-health and chronic pain, which dedicates just a few paragraphs to telehealth.
therapy adaptation and the resultant specification for the SMART2 project-a technology-based self-management system for assisting long-term health conditions, including chronic pain
Results showed the use of videoconferencing for this group of patients is useable and satisfactory for both patients and staff, that the patients save time and money, and that for a system where videoconferencing equipment is already in use, it is also cost effective. Staff were able to identify new patient problems. 
This pilot study indicates that telemedicine follow-up consultations for chronic pain patients are feasible and cost-saving. Patients and anesthesiologists were highly satisfied with telemedicine consultation.

Answer: Yes, telemedicine is  feasible and cost-effective for education and therapy of patients with chronic pain.
Yes, there are.
Exact answer: yes
Question: What is the function of TALENs?

Context:
Transcription activator-like effector nucleases (TALENs) are programmable nucleases that join FokI endonuclease with the modular DNA-binding domain of TALEs

Answer:  These chimeric enzymes can be used to introduce a double strand break at a specific genomic site which then can become the substrate for error-prone non-homologous end joining (NHEJ), generating mutations at the site of cleavage. Artificial transcription activator-like effector nucleases (TALENs) provide a powerful new approach for targeted zebrafish genome editing and functional genomic applications. Transcription Activator-Like Effector Nucleases (TALENs) consist of a nuclease domain fused to a DNA binding domain which is engineered to bind to any genomic sequence. Transcription activator-like effector nucleases (TALENs) are programmable nucleases that join FokI endonuclease with the modular DNA-binding domain of TALEs.
Transcription Activator-Like Effector Nucleases (TALENs) consist of a nuclease domain fused to a DNA binding domain which is engineered to bind to any genomic sequence. These chimeric enzymes can be used to introduce a double strand break at a specific genomic site which then can become the substrate for error-prone non-homologous end joining (NHEJ), generating mutations at the site of cleavage. TALENs provide a powerful new approach for targeted genome editing and functional genomic applications.
Question: Is rivaroxaban metabolized in kidneys?

Context:
The novel oral anticoagulants (i.e., dabigatran, apixaban, rivaroxaban) all undergo renal metabolism to varying degrees, and hence dosing, efficacy, and safety require special consideration in CKD patients.
The new oral anticoagulants have relatively little data in patients with severe renal impairment, and all have an element of renal excretion.
Now new anticoagulant drugs(dabigatran and rivaroxaban) can become available. Therefore, we have to learn how to use those drugs. They have to carefully be used because they discharge from kidney and old aged patients have potential renal dysfunction. 
In the everyday practice it will be necessary to be very cautious in patients with impaired renal function, as all these drugs are eliminated by kidneys.
Dabigatran etexilate and rivaroxaban carry the highest risk due to a high degree of renal excretion, whereas the risk for apixaban, edoxaban and betrixaban seems lower.
However, all these agents undergo renal clearance to varying degrees, and hence dosing, efficacy, and safety require special consideration in patients with CKD. 
Rivaroxaban being excreted via kidney and liver, some precautions should apply in case of liver insufficiency. 
Rivaroxaban elimination is mainly renal, but also through faecal matter and by hepatic metabolism. 

Answer: rivaroxaban undergoes renal metabolism
Exact answer: yes
Question: Can the Micro-C XL method achieve mononucleosome resolution?

Context:
We present Micro-C XL, an improved method for analysis of chromosome folding at mononucleosome resolution
We present Micro-C XL, an improved method for analysis of chromosome folding at mononucleosome resolution.
Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome.
Micro-C XL provides a single assay to interrogate chromosome folding at length scales from the nucleosome to the full genome.

Answer: Yes. Micro-C XL is an improved method for analysis of chromosome folding at mononucleosome resolution.
Exact answer: yes
Question: What is the role of SERCA in diabetic cardiomyopathy?

Context:
Compared with control group, [Ca(2+)](i) and the expression of CaSR, RyR and SERCA/PLN were decreased, while PKC-α and PLN were significantly increased in a time-dependent manner in diabetic group
Diabetic rats showed impaired cardiac structure and function compared with control rats. The expression of PKC, PLB increased significantly, while the PPI-1, SERCA-2 and RyR expression decreased. Treatment with breviscapine could reverse the cardiac dysfunction and structure changes in diabetic cardiomyopathy rats, and decrease the expression of PKC and PLB, as well as increase the expression of PPI-1, SERCA-2 and RyR.
Diabetic Ren-2 rats developed impairment of both active and passive phases of diastole, accompanied by reductions in SERCA-2a ATPase and phospholamban along with activation of the fetal gene program.
The levels of SERCA and GLUT4, but not PLB, were significantly reduced in diabetic hearts compared with controls.
CONCLUSIONS: CASQ2, FKBP12.6 and SERCA2a were down-regulated in diabetic cardiomyopathy.
Reduced sarcoplasmic calcium ATPase (SERCA2a) expression has been shown to play a significant role in the cardiac dysfunction in diabetic cardiomyopathy.
Depressed sarcoplasmic reticulum (SR) Ca(2+)-ATPase (SERCA2a) and Ca(2+)-release channels (ryanodine receptor RyR2) are involved in diabetic cardiomyopathy, however, the implication of intracellular calcium handling proteins in SR is undefined.
The depressed sarcoplasmic reticulum (SR) Ca2+-ATPase (SERCA2a) and Ca2+-release channels (ryanodine receptor RyR2) are involved in the diabetic cardiomyopathy.
Slowed relaxation in diabetic cardiomyopathy (CM) is partially related to diminished expression of the sarcoplasmic reticulum (SR) Ca2+-ATPase SERCA2a.

Answer: Diabetic cardiomyopathy is accompanied by reduced SERCA levels and activity in later stages. The up-regulation of SERCA2a in the early phase of type 2 diabetes is an important physiological adaptation of the heart.
Question: Which is the major phytoalexin in alfalfa (Medicago sativa L.)?

Context:
Medicarpin, the major phytoalexin in alfalfa, is synthesized via the isoflavonoid branch of phenylpropanoid metabolism.
Medicarpin, the major phytoalexin in alfalfa, is synthesized by way of the isoflavonoid branch of phenylpropanoid metabolism.
The major phytoalexin in alfalfa is the isoflavonoid (-)-medicarpin (or 6aR, 11aR)-medicarpin.
The isoflavonoid conjugates medicarpin-3-O-glucoside-6-O-malonate (MGM), afrormosin-7-O-glucoside (AG), and afrormosin-7-O-glucoside-6-O-malonate (AGM) were isolated and characterized from cell suspension cultures of alfalfa (Medicago sativa L.), where they were the major constitutive secondary metabolites.
Alfalfa (Medicago sativa L.) cell suspension cultures accumulated high concentrations of the pterocarpan phytoalexin medicarpin, reaching a maximum within 24 hours after exposure to an elicitor preparation from cell walls of the phytopathogenic fungus Colletotrichum lindemuthianum.
The isoflavonoid conjugates medicarpin-3-O-glucoside-6''-O-malonate (MGM), afrormosin-7-O-glucoside (AG), and afrormosin-7-O-glucoside-6''-O-malonate (AGM) were isolated and characterized from cell suspension cultures of alfalfa (Medicago sativa L.), where they were the major constitutive secondary metabolites
The major phytoalexin in alfalfa is the isoflavonoid (-)-medicarpin (or 6aR, 11aR)-medicarpin
Medicarpin, the major phytoalexin in alfalfa, is synthesized via the isoflavonoid branch of phenylpropanoid metabolism
Medicarpin, the major phytoalexin in alfalfa, is synthesized by way of the isoflavonoid branch of phenylpropanoid metabolism

Answer: The major phytoalexin in alfalfa (Medicago sativa L.) is the isoflavonoid (-)-medicarpin (or 6aR, 11aR)-medicarpin. Medicarpin is synthesized via the isoflavonoid branch of phenylpropanoid metabolism.
Exact answer: medicarpin
Question: List common symptoms of patients with the DOORS syndrome.

Context:
Deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures (DOORS) syndrome is a rare autosomal recessive disorder of unknown cause. 
Through a search of available case studies and communication with collaborators, we identified families that included at least one individual with at least three of the five main features of the DOORS syndrome: deafness, onychodystrophy, osteodystrophy, intellectual disability, and seizures. 

Answer: DOORS syndrome is a constellation of deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures. It is a rare autosomal recessive disorder of unknown cause.
Exact answer: deafness, onychodystrophy, osteodystrophy, mental retardation, seizures
Question: Which SLC family is FLVCR1 a member of?

Context:
Feline leukemia virus subgroup C receptor (FLVCR1), a member of the SLC49 family of four paralogous genes, is a cell surface heme exporter, essential for erythropoiesis and systemic iron homeostasis.
Feline leukemia virus subgroup C receptor (FLVCR1), a member of the SLC49 family of four paralogous genes, is a cell surface heme exporter, essential for erythropoiesis and systemic iron homeostasis.
Feline leukemia virus subgroup C receptor (FLVCR1), a member of the SLC49 family of four paralogous genes, is a cell surface heme exporter, essential for erythropoiesis and systemic iron homeostasis. Disruption of FLVCR1 function blocks development of erythroid progenitors, likely due to heme toxicity.
 Heme is critical for a variety of cellular processes, but excess intracellular heme may result in oxidative stress and membrane injury. Feline leukemia virus subgroup C receptor (FLVCR1), a member of the SLC49 family of four paralogous genes, is a cell surface heme exporter, essential for erythropoiesis and systemic iron homeostasis.
Heme is critical for a variety of cellular processes, but excess intracellular heme may result in oxidative stress and membrane injury. Feline leukemia virus subgroup C receptor (FLVCR1), a member of the SLC49 family of four paralogous genes, is a cell surface heme exporter, essential for erythropoiesis and systemic iron homeostasis.

Answer: Feline leukemia virus subgroup C receptor (FLVCR1) is a member of the SLC49 family.
Exact answer: SLC49
Question: Does NADPH oxidase 5 require any subunit for function?

Context:
Nox5 forms a functional oligomer mediated by self-association of its dehydrogenase domain.
 While Nox1-4 require regulatory subunits, including p22phox, Nox5 activity does not depend on any subunits. 
 Thus, Nox5 forms a catalytically active oligomer in the membrane that is mediated by its dehydrogenase domain. 
Coexpression of specific Nox catalytic subunits (Nox1, Nox2, Nox3, Nox4, or Nox5) along with their corresponding regulatory subunits (NOXO1/NOXA1 for Nox1; p47phox/p67phox/Rac for Nox2; NOXO1 for Nox3; no subunits for Nox4 or Nox5) resulted in marked production of reactive oxygen. 

Answer: No, NADPH oxidase 5 (NOX5) does not require any subunits for function.
Exact answer: no
Question: Are there any functional differences between Mfd and its human Cocaine syndrome protein B (CSB) homolog?

Context:
In humans, the TCR coupling factor, CSB, plays a critical role in restoring transcription following both UV-induced and oxidative DNA damage. It also contributes indirectly to the global repair of some forms of oxidative DNA damage. The Escherichia coli homolog, Mfd, is similarly required for TCR of UV-induced lesions.
Mfd may be functionally distinct from its human CSB homolog in that it does not detectably contribute to the recovery of gene expression or global repair following oxidative damage.
CSB has an ATPase activity that is stimulated strongly by DNA; however, it neither acts as a helicase nor does it dissociate stalled RNA polymerase II, suggesting a coupling mechanism in humans different from that in prokaryotes. 
In addition, these findings imply that Mfd may be functionally distinct from its human CSB homolog in that it does not detectably contribute to the recovery of gene expression or global repair following oxidative damage.
In addition, these findings imply that Mfd may be functionally distinct from its human CSB homolog in that it does not detectably contribute to the recovery of gene expression or global repair following oxidative damage.
In contrast, no difference was detected in the rate of transcription recovery in mfd, uvrA, fpg, nth, or polB dinB umuDC mutants relative to wild-type cells following oxidative damage

Answer: Both Cockayne syndrome protein B (CSB) and Mfd are involved in transcription-coupled repair. CSB is the human TCR coupling factor and Mfd is the bacterial TCR coupling factor. However, unlike Mfd, CSB does not act as a helicase nor does it dissociate stalled RNA polymerase II, suggesting a coupling mechanism in humans different from that in prokaryotes. Moreover, Mfd may be functionally distinct from its human CSB homolog in that it does not detectably contribute to the recovery of gene expression or global repair following oxidative damage.
Exact answer: yes
Question: Is Wnt16b secreted in response to chemotherapy?

Context:
 In this study, we found WNT16B could be expressed and secreted into the microenvironment by human ovarian fibroblasts after DNA damage-associated treatment, including chemotherapy drugs and radiation.
In a recent article in Nature Medicine, Sun et al. show that increased expression of Wnt family member wingless-type MMTV integration site family member 16B (WNT16B) by the tumor microenvironment in response to cytotoxic damage and signals through the canonical Wnt pathway to promote tumor growth and chemotherapy resistance. 
Using a genome-wide analysis of transcriptional responses to genotoxic stress induced by cancer therapeutics, we identified a spectrum of secreted proteins derived from the tumor microenvironment that includes the Wnt family member wingless-type MMTV integration site family member 16B (WNT16B).

Answer: Yes, WNT16B is secreted into the microenvironment by human ovarian fibroblasts after DNA damage-associated treatment, including chemotherapy drugs and radiation.
Exact answer: yes
Question: Which proteins compose the error prevention GO (8-oxo-G) system in Pseudomonas putida?

Context:
the GO repair enzymes MutY, MutM, and MutT are involved in the prevention of base substitution mutations in carbon-starved P. putida.
Our results demonstrated that the GO repair enzymes MutY, MutM, and MutT are involved in the prevention of base substitution mutations in carbon-starved P. putida.

Answer: In P. putida (Pseudomonas putida) the error prevention GO (8-oxo-G) system is composed of MutY, MutM, and MutT enzymes.
Exact answer: MutY, MutM, MutT
Question: What is the role of photodynamic therapy for meningioma treatment?

Context:
CONCLUSIONS: Efficacy of 5-ALA PDT could be increased by adjunction of ciprofloxacin in conventional clinical dosing and by prolongation of ALA incubation time. 
CONCLUSION: Gefitinib can inhibit ABCG2-mediated PpIX efflux from malignant brain tumor cells to increase the intracellular PpIX and thereby enhance the PDT effect.
CONCLUSION: ALA-PDT was more effective in killing U-105MG glioma cells than CH-157MN meningioma cells.
These data indicate unique features of AlPc which suggests its application as a potent, non-toxic photosensitizer in the photodynamic therapy of human meningiomas.
Photodynamic therapy is being investigated as an adjuvant treatment for intracranial neoplasms. 
It was found that PDT using haematoporphyrin derivative as a photosensitizing drug showed dose-dependent activity against a variety of histological subtypes of meningioma. 
Photodynamic therapy is a promising treatment for human brain tumors because of the selective retention of certain compounds by tumor cells. 
Susceptibility to 5-aminolevulinic acid based photodynamic therapy in WHO I meningioma cells corresponds to ferrochelatase activity.
We conclude that differences in intracellular PpIX concentrations between HBL-52 and BEN-MEN-1 benign meningioma cells were mainly due to differences in FECH activity and that these differences correspond to their susceptibility to 5-ALA-induced PDT.
Photodynamic therapy (PDT) has been employed in the management of recurrent cerebral gliomas but its activity against meningiomas has not been specifically studied.
Enhancing the effect of 5-aminolevulinic acid based photodynamic therapy in human meningioma cells.
An in vitro study of the effect of photodynamic therapy on human meningiomas.
Photodynamic therapy (PDT) has been employed in the management of recurrent cerebral gliomas but its activity against meningiomas has not been specifically studied. 

Answer: Photodynamic therapy was shown to have activity againt meningioma treatment. Gefitinib and ciprofloxacin enhance efficacy of photodynamic therapy.