anand-s/m_qalm huggingface dataset:
Question: Which antibiotics target peptidoglycan biosynthesis?
Answer: Under some conditions, both ramoplanin and vancomycin probes produce helicoid staining patterns along the cylindrical walls of B. subtilis cells. This work has implications for the design of ramoplanin derivatives and may influence how other proposed substrate binding antibiotics are studied. This was confirmed by in vitro studies involving a wall-membrane particulate fraction from Gaffkya homari in which peptidoglycan synthesis from UDP-MurNAc-tetrapeptide was inhibited by ramoplanin but not by vancomycin. New results support a two-state model for septal and peripheral PG synthesis at mid-cell, involvement of essential cell division proteins in PG remodeling, and mid-cell localization of proteins that organize PG biosynthesis and that form the protein translocation apparatus.
Antibiotics which inhibit bacterial peptidoglycan biosynthesis are the most widely used in current clinical practice. Cells treated with ampicillin, D-cycloserine, or fosfomycin had only one chloroplast after cell division, suggesting that the cells divided without chloroplast division. The antibiotics bacitracin and vancomycin showed no obvious effect. Colchicine inhibits Closterium cell elongation after division.  Surprisingly, also cinnamycin of Streptomyces cinnamoneus cinnamoneus), previously known to bind specifically to phosphatidylethanolamin of biological membranes, provoked strong cell wall biosynthetic stress. Other substances include fluorescent derivatives of two PG-binding antibiotics, vancomycin and ramoplanin. The muraymycins constitute a new antibiotic family whose core structure contains a glycosylated uronic acid derivative joined by an aminopropane group to a hexahydro-2-imino-4-pyrimidylglycyl residue (epicapreomycidine) containing dipeptide that is further extended by a urea-valine moiety. The muraymycins inhibited peptidoglycan biosynthesis. Ramoplanin is a cyclicdepsipeptide antibiotic that inhibits peptidoglycan biosynthesis. The lantibiotic mersacidin inhibits peptidoglycan biosynthesis at the level of transglycosylation. Ramoplanin, a new lipoglycopeptide antibiotic, inhibits cell wall peptidoglycan biosynthesis in gram-positive bacteria.
Question: List bacterial species identified in the iceman tissues.
Answer: Spirochete Treponema denticola
Clostridium perfringens
Clostridium ghonii
Clostridium sordellii
Eubacterium tenue
Bacteroides sp
Vibrio
Sphingomonas
Afipia
Curtobacterium
Microbacterium
Agromyces
Question: Which characteristics are used in the SLEDAI index for SLE patients?
Answer: The SLEDAi is a "weighted" index of 9 organ systems for disease activity in SLE which includes: 8 for central nervous system and vascular, 4 for renal and musculoskeletal, 2 for serosal, dermal, immunologic, and 1 for constitutional and hematologic.
Twenty-four variables were identified as important factors in a disease activity index. This generated a "weighted" index of 9 organ systems for disease activity in SLE, the SLEDAI 8 for central nervous system and vascular, 4 for renal and musculoskeletal, 2 for serosal, dermal, immunologic, and 1 for constitutional and hematologic.
Question: Which algorithms have been developed for analysing CRISPR/Cas9 knockout screens data?
Answer: HiTSelect and MAGeCK (Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout)
Question: Which cellular processes are regulated by Nanog?
Answer: The pluripotency sustaining factor Nanog, controls a cascade of pathways that are intricately connected to govern pluripotency, self-renewal, genome surveillance and cell fate determination. Elevated expression of Nanog has also been reported to result in clonal expansion of murine ESCs, but it also plays a role in tumor development. A positive regulator of cell proliferation, it is essential for G1 to S transition in human embryonic stem cells while it regulates primordial germ cell migration.
Question: Which are the known inhibitors of the TPL2/MAP3K8 protein?
Answer: [1,7]naphthyridine-3-carbonitriles and quinoline-3-carbonitriles were the first Tumor Progression Loci-2 (Tpl2) kinase inhibitors. 4-alkylamino-[1,7]naphthyridine-3-carbonitriles are also known to inhibit Tpl2 function as well as quinoline-3-carbonitrile derivatives, thieno[3,2-d]pyrimidines and 2,4-disubstituted thieno[2,3-c]pyridines, indazoles, 4-Alkylamino-[1,7]naphthyridine-3-carbonitriles and generally molecules belonging to the wide categories of quinoline-3-carbonitriles, indazoles and thieno-pyrimidines.
Honokiol
Thieno[3,2-d]pyrimidines and thieno[2,3-c]pyridine
Quinoline-3-carbonitrile derivatives (8-halo-4-(3-chloro-4-fluoro-phenylamino)-6-[(1H-[1,2,3]triazol-4-ylmethyl)-amino]-quinoline-3-carbonitriles; 8-bromo-4-(3-chloro-4-fluorophenylamino)-6-[(1-methyl-1H-imidazol-4-yl)methylamino]quinoline-3-carbonitrile; 4-alkylamino-[1,7]naphthyridine-3-carbonitrile; 1,7-naphthyridine-3-carbonitriles)
Indazoles
Luteolin
1,7-naphtyridine-3-carbonitrile
Question: Which classes of endogenous retroelements are known to date?
Answer: Endogenous retroelements fall into two distinct classes: retrotransposons containing LTRs (Long Terminal Repeats), and retrostransposons lacking LTRs.
Question: Which R packages have been developed for studying TADs?
Answer: TADCompare is an R Package for differential and temporal analysis of Topologically Associated Domains. SpectralTAD is an R package for defining a hierarchy of topologically associated domains using spectral clustering.
TADCompare is a method for differential analysis of boundaries of interacting domains between two or more Hi-C datasets. SpectralTAD is a method for defining a hierarchy of topologically associated domains using spectral clustering.
Question: Which are the clinical characteristics of TSC?
Answer: Tuberous sclerosis or tuberous sclerosis complex (TSC) is a rare multi-system genetic disease that causes benign tumors to grow in the brain and on other vital organs such as the kidneys, heart, eyes, lungs, and skin. A combination of symptoms may include seizures, intellectual disability, developmental delay, behavioral problems, skin abnormalities, lung and kidney disease. TSC is caused by a mutation of either of two genes, TSC1 and TSC2, which code for the proteins hamartin and tuberin respectively. These proteins act as tumor growth suppressors, agents that regulate cell proliferation and differentiation.
Question: Which molecules are targeted by defactinib?
Answer: PURPOSE: VS-6063 (also known as defactinib or PF-04554878) is a second-generation inhibitor of focal adhesion kinase and proline-rich tyrosine kinase-2.
Question: List the diseases for which there are point-of-care breath tests
Answer: Point of care breath tests are available for lung cancer, pulmonary embolism, respiratory distress syndrome, methanol intoxication, kidney diseases, liver diseases, Helicobacter pylori infection, asthma, sepsis, heart failure, diabetes and tuberculosis.
Question: List 3 indications for rituximab.
Answer: Rituximab  is used to treat rheumatoid arthritis as well as poly- and dermatomyositis, chronic lymphocytic leukemia, juvenile idiopathic arthritis, and Pemphigus foliaceus (PF).
Question: Name triad of Wernicke encephalopathy.
Answer: Wernicke's encephalopathy is a triad of ophthalmoplegia, ataxia and confusion seen in alcoholics with dietary vitamin B1 (thiamine) deficiency.
Question: List diseases that are caused by the Meningococcus B?
Answer: The prevention of paediatric bacterial meningitis and septicaemia has recently entered a new era with the availability of two vaccines against capsular group B meningococcus
Both bacterial meningitis and septicemia can be caused by Meningococcus B
the prevention of paediatric bacterial meningitis and septicaemia has entered a new era with the availability of two vaccines against capsular group b meningoco
Question: List targeted genome editing methodologies
Answer: Genome editors such as CRISPR/Cas9 and TALENs are at the forefront of research into methodologies for targeted modification of the mammalian genome.
Genome editors such as CRISPR/Cas9 and TALENs are at the forefront of research into methodologies for targeted modification of the mammalian genome. Targeted genome editing (TALEN) was recently introduced as a method to manipulate eukaryotic genomes in a targeted manner with high efficiency and specificity.
Genome editors such as CRISPR/Cas9 and TALENs are at the forefront of research into methodologies for targeted modification of the mammalian genome. The choice of genome editing tool should be determined by the desired genome editing outcome. Such a rational approach is likely to benefit research outputs for groups working in fields as diverse as modification of cell lines, to animal models for disease studies, or gene therapy strategies.
Question: What type of cancers and inherited diseases have been associated to mutations in the Notch pathway?
Answer: So far, mutations in Notch and other components of its signaling pathway have been implicated in an array of human diseases (T-cell leukemia and other cancers,  Multiple Sclerosis,  CADASIL,  Alagille Syndrome,  Spondylocostal Dysostosis), but more pathologies are likely to be associated with Notch in the future due to its network complexity.
Question: List diseases associated with the  Dopamine Receptor D4 (DRD4).
Answer: The 5-repeat allele of a common length polymorphism in the gene that encodes the dopamine D4 receptor (DRD4) is robustly associated with the risk of attention deficit hyperactivity disorder (ADHD).
Question: Which diseases are associated with Alu element insertion?
Answer: Diseases associated with Alu element insertion are the following: myotonic dystrophy type 2, Friedreich ataxia, spinocerebellar ataxia type 10, autosomal dominant optic atrophy, Menkes disease, hyper-IgM with immunodeficiency syndrome (HIGM), and anterior pituitary aplasia.
Question: Which drugs are included in GI cocktail?
Answer: "GI cocktail" is a mixture of liquid antacid, viscous lidocaine, and an anticholinergic.
Question: Which cancers compose Carney's triad?
Answer: Carney's triad is a rare pathogenic entity which consists of 3 rare soft tissue tumors: gastric leiomyosarcoma, pulmonary chondroma and extraadrenal paraganglioma. It is usually diagnosed in young women. The presence of three tumors at the same time is not required for its diagnosis (incomplete Carney's Triad).
Question: List the classical triad of symptoms of the Melkersson–Rosenthal syndrome.
Answer: The Melkersson-Rosenthal syndrome consists of the classical triad of symptoms:
1) orofacial oedema 
2) fissured tongue (lingua plicata) and
3) facial paralysis.
Question: Name five programs for transcript quantification from RNASeq experiments
Answer: Popular programs for transcript quantification from RNASeq experiments include: Cufflinks, RSEM, Flux Capacitor, Mitie, Miso, Tigar, Montebello, Drut, Traph, Pome, IsoformEx, Neuma,
Question: List the major families of Histones.
Answer: Five histone families (H1, H2A, H2B, H3, and H4).
Question: Variants in which genes cause nonsyndromic retinal degeneration?
Answer: Variants in DYNC2H1, IFT81, USH2A and ABHD12 can cause nonsyndromic retinal degeneration.
Question: Which acetylcholinesterase inhibitors are used for treatment of myasthenia gravis?
Answer: Pyridostigmine and neostygmine are acetylcholinesterase inhibitors that are used as first-line therapy for symptomatic treatment of myasthenia gravis. Pyridostigmine is the most widely used acetylcholinesterase inhibitor. Extended release pyridotsygmine and novel acetylcholinesterase inhibitors inhibitors with oral antisense oligonucleotides are being studied.
Question: List fluorescent reporter proteins.
Answer: Fluorescent and luminescent reporter genes have become popular tools for the real-time monitoring of gene expression in living cells:
green fluorescent protein
Timer
red fluorescent protein
yellow fluorescent protein
beta-phycoerythrin
coral fluorescent reporter protein
enhanced green fluorescent reporter protein
mCherry
Question: In which nuclear compartments is heterochromatin located?
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
Question: Which are the types of viral meningitis?
Answer: Aseptic meningitis is the most common type of meningitis and is characterized by meningeal inflammation that is not linked to identifiable bacterial pathogens in cerebrospinal fluid (CSF). It can be originated from infection from:
1) Varicella-zoster virus (VZV)
2) Herpes simplex types I and II (HSV-1, HSV-2)
3) Epstein-Barr virus (EBV) 
4) Cytomegalovirus (CMV) 
5) Enteroviruses (EV) 
6) Parechoviruses (HPeV) 
7) Human rhinoviruses (HRVs) 
8) Echovirus types 6, 9, 11
9) West Nile Virus (WNV)
Question: What are the effects of ILK ablation?
Answer: Depending on the tissue or cell where ILK is ablated we see different effects:
Ablation of ILK in heart results in dilated cardiomyopathy and spontaneous heart failure
Ablation of ILK in fibroblasts leads to impaired healing due to a severe reduction in the number of myofibroblasts
Ablation of ILK in osteoclasts inhibits bone resorption
Ablation of ILK in liver results in enhanced and prolonged cell proliferation and hepatomegaly after phenobarbital administration and in abnormal histology
Ablation of ILK in podocytes caused an aberrant distribution of nephrin and alpha-actinin-4
Question: Which histone modifications are correlated with transcription elongation?
Answer: This is accompanied by reductions in the level of H3K36 trimethylation, a posttranslational histone modification associated with efficient transcriptional elongation, and the number of full-length transcripts from these genes. The 3' ZNF exons contain H3K36me3, a mark of transcriptional elongation.
Question: Which are the most common methods for circular RNA detection from RNASeq?
Answer: The main algorithms are circRNA_finder, find_circ, CIRCexplorer, CIRI, and MapSplice.
Here, we use common RNAseq datasets to scrutinize and compare the output from five different algorithms; circRNA_finder, find_circ, CIRCexplorer, CIRI, and MapSplice and evaluate the levels of bona fide and false positive circRNAs based on RNase R resistance. 
Here, we use common RNAseq datasets to scrutinize and compare the output from five different algorithms; circRNA_finder, find_circ, CIRCexplorer, CIRI, and MapSplice and evaluate the levels of bona fide and false positive circRNAs based on RNase R resistance.
CircRNAs are novel members of the non-coding RNA family. Several pipelines have been developed to specifically identify these non-linear reads and consequently predict the landscape of circRNAs based on deep sequencing datasets. Here, we use common RNAseq datasets to scrutinize and compare the output from five different algorithms; circRNA_finder, find_circ, CIRCexplorer, CIRI, and MapSplice and evaluate the levels of bona fide and false positive circRNAs based on RNase R resistance.
, use common rnaseq datasets to scrutinize and compare the output from five different algorithms; circrna_finder , find_circ , circexplorer , ciri , and mapsplice and evaluate the levels of bona fide and false positive circrnas based on rnase r resistance. . 
here, we use common rnaseq datasets to scrutinize and compare the output from five different algorithms; circrna.finder, find.circ, circexplorer, ciri, and mapsplice and evaluate the levels of bona fide and false positive circrnas based on rnase r resistance.
Question: Which microRNAs are involved in exercise adaptation?
Answer: miR-1, miR-133, miR-208a, miR-206, miR-494, miR-146a, miR-222, miR-21, miR-221, miR-20a, miR-133a, miR-133b, miR-23, miR-107 and miR-181 are involved in exercise adaptation
Question: Name three binding partners of cofilin 2.
Answer: Cofilin 2 can bind miR-201a, the protein 14-3-3, and ATP/ADP-Pi-actin filaments.
Question: Where can we find the protein lacritin?
Answer: The protein lacritin can be found in lacrimal and salivary glands as well as in tear fluid and in the thyroid.
Question: Which diseases are associated with the Yaa gene?
Answer: The Y-linked autoimmune accelerating gene mutation (yaa), first discovered in the BXSB mouse strain, is known to accelerate spontaneous autoantibody production and subsequent development of lupus disease. It has also been shown to be associated with various autoimmune conditions such as lupus-like syndrome, collagen induced arthrits and glomerulonephritis.
Diseases associated with the Yaa gene include aids, systemic lupus erythematosus, maids, rheumatoid arthritis, arthritis, l upus nephritis, murine acquired immunodeficiency syndrome, and lupUS-like nephitis.
The Yaa gene-mediated acceleration of murine lupus: Yaa- T cells from non-autoimmune mice collaborate with Yaa+ B cells to produce Lupus autoantibodies in vivo.
The Y-linked autoimmune accelerating gene mutation (yaa), first discovered in the BXSB mouse strain, is known to accelerate spontaneous autoantibody production and subsequent development of lupus disease.
Diseases associated with the Yaa gene include aids, systemic lupus erythematosus,maids, rheumatoid arthritis, arthritis, l upus nephritis, murine acquired immunodeficiency syndrome, lUPus-like nephitis and other inflammatory bowel diseases.
Diseases associated with the Yaa gene include aids, systemic lupus erythematosus,maids, rheumatoid arthritis, l upus nephritis, murine acquired immunodeficiency syndrome, lUPus and lupUS-like nephitis.
F1 mice, a model in which the lupus-like autoimmune syndrome observed in male mice is associated with the presence of an as yet unidentified Y chromosome-linked autoimmune acceleration gene, Yaa.
 Yaa is a Y-chromosome-linked gene that accelerates autoimmune diseases in some autoimmune-prone strains of mice The role of the Yaa gene in lupus syndrome The Y chromosome-linked "autoimmune accelerating" yaa gene suppresses collagen-induced arthritis
Yaa is a Y-chromosome-linked gene that accelerates autoimmune diseases in some autoimmune-prone strains of mice . BXSB mice spontaneously develop a lupus-like syndrome that is accelerated by the Yaa gene . Yaa mice bearing the NZB chromosome 13 locus displayed increased serum gp70 production, but not glomerulonephritis .
Diseases associated with the Yaa gene include aids, systemic lupus erythematosus, maids, rheumatoid arthritis, arthritis, l upus nephritis, murine acquired immunodeficiency syndrome, and lUPus-like nephitis.
Diseases associated with the Yaa gene include aids, systemic lupus erythematosus,maids, rheumatoid arthritis, l upus nephritis and murine acquired immunodeficiency syndrome.
Question: Which proteins constitute the methyl-directed mismatch repair system (MMR) in bacteria?
Answer: The mismatch repair system (MMR) recognizes and corrects mismatched or unpaired bases caused mainly by DNA polymerase, and contributes to the fidelity of DNA replication in living cells. In bacteria, the methyldirected mismatch repair (MMR) is comprised of MutS and MutL proteins, encoded by the mutS/L operon.
Question: Which pathological conditions are caused by mutations in the CYLD gene?
Answer: Since loss of CYLD expression can be observed in different types of human cancer, it is now well established that CYLD acts as a tumor suppressor gene. Pathogenic mutations in CYLD can be identified in patients affected with Brooke-Spiegler syndrome, (Familial) Cylindromatosis or multiple familial trichoepithelioma. CYLD expression has also been reported to be  dramatically downregulated in basal cell carcinoma (BCC), the most common cancer in humans.
Question: Which gene mutations are responsible for isolated Non-compaction cardiomyopathy?
Answer: The gene mutations that have been shown to be the causes of isolated non-compaction cardiomyopathy are alpha-tropomyosin, alpha-tropomyosin, troponin T and desmoplakin
cardiac β-myosin heavy chain gene (MYH7)
c.349G>A (p.D117N) in the ZASP gene
mutation in the isoform-1 specific region of the DSP C-terminus
pE96K mutation in the cardiac troponin T gene (TNNT2)
Question: Which bacteria cause diphtheria?
Answer: Diphtheria is caused by the bacteria:
1) Corynebacterium ulcerans and 
2) Corynebacterium diphtheriae.
Question: Which mutations of alpha-myosin heavy chain gene are implicated in hypertrophic cardiomyopathy?
Answer: The following mutations of alpha-myosin heavy chain gene are implicated in hypertrophic cardiomyopathy: R403Q; Q1065H and Arg-249-->Gln
Question: Before 2019, what neurologic diseases are associated with the tau protein?
Answer: Tau proteins are involved in the pathogenesis of multiple sclerosis and amyotrophic lateral sclerosis.
Both Alzheimer's Disease and Multiple Sclerosis are associated with tau protein
Question: Which are the enzymes involved in the control of tubulin acetylation?
Answer: Acetyltransferase MEC-17, and deacetylases SIRT2 (Sirtuin 2), HDAC6 (histone deacetylase 6) and dTip60 are known to control the levels of tubulin acetylation.
Question: List two common features of Tay syndrome.
Answer: Tay syndrome is a rare autosomal recessive genetic disorder characterized by congenital ichthyosis and trichothiodystrophy (abnormal brittle hair). Other less common features of this syndrome are photosensitivity, low birth weight, short stature, mental retardation, delayed neuromuscular development and other CNS anomalies, dysplasia of nails, hypoplasia of subcutaneous fatty tissue, prematurely aged facial appearance, hypogonadism, cataracts, osteosclerosis, dysphonia, and increased susceptibility to infections.
Question: List available circular RNA prediction tools.
Answer: circRNA_finder, find_circ, CIRCexplorer, CIRI, and MapSplice.
Question: List the different subtypes of thyroid cancer.
Answer: The different histologic subtypes of thyroid cancer include papillary, follicular, anaplastic, medullary, and Hürthle cell carcinomas.
Question: Which histone modification discriminates between active and poised enhancers?
Answer: Monomethylation of histone H3 on Lys 4 (H3K4me1) and acetylation of histone H3 on Lys 27 (H3K27ac) are histone modifications that are highly enriched over the body of actively transcribed genes and on enhancers.
Question: List the types of the Cardiorenal syndrome (CRS) according to the five-part classification system.
Answer: Cardiorenal syndromes (CRS) have been recently classified into five distinct entities, each with different major pathophysiologic mechanisms. 
CRS type 1: acute worsening of heart function (AHF-ACS) leading to kidney injury and/or dysfunction. 
CRS type 2: chronic abnormalities in heart function (CHF-CHD) leading to kidney injury or dysfunction. 
CRS type 3: acute worsening of kidney function (AKI) leading to heart injury and/or dysfunction. 
CRS type 4: chronic kidney disease (CKD) leading to heart injury, disease and/or dysfunction. 
CRS type 5: systemic conditions leading to simultaneous injury and/or dysfunction of heart and kidney.
Question: Which are the key players on radial glial specification to ependymal cells?
Answer: Mcidas and GemC1/Lynkeas specify embryonic radial glial cells. Both proteins were initially described as cell cycle regulators revealing sequence similarity to Geminin. They are expressed in radial glial cells committed to the ependymal cell lineage during embryogenesis, while overexpression and knock down experiments showed that are sufficient and necessary for ependymal cell generation.
Question: What are the 3 types of ultraviolet (UV) solar radiation?
Answer: Solar ultraviolet (UV) radiation, an ubiquitous environmental carcinogen, is classified depending on the wavelength, into three regions; short-wave UVC (200-280 nm), mid-wave UVB (280-320 nm), and long-wave UVA (320- 400 nm)
short-wave UVC (200-280 nm), medium-wave UVB (280-320 nm), and long-wave UVA (320-400 nm).
short-wave UVC (200-280 nm), medium-wave UVB (280-320 nm), and long-wave UVA (320-400 nm).