nirantk/geneticsQA-train huggingface dataset:
Question: For the treatment of which conditions can atypical neuroleptic drugs be used?

Context:
Further clinical implications are described (capability of learning the therapeutic strategies, deliverability in broader clinical settings, acceptability by patients, combination with atypical neuroleptic drugs,and treatment of choice in risk populations).
Intervention strategies are a multimodal psychological programme for the intervention in early prodromal stages and a combination of psychotherapy with atypical neuroleptic drugs in the late prodromal stages. 
Atypical neuroleptic drugs have enriched our treatment programs, especially in childhood and adolescent schizophrenia. Reviewed here is the use of atypical neuroleptics in children and adolescents with a schizophrenic disorder. 
o prove whether weight gain is a relevant side effect of atypical neuroleptics, the charts of all patients admitted with DSM-III-R diagnoses of schizophrenia, schizoaffective disorder, or delusional disorder in the years 1991 to 1995 were evaluated.
The handwriting of 18 schizophrenic patients before and during treatment with typical (haloperidol, haloperidol decanoate) and atypical (clozapine, risperidone) neuroleptic drugs was examined.
Atypical and typical neuroleptics, when administered chronically, can bring about profound but contrasting changes in schizophrenic symptoms and motor activation and dramatically modulate brain neurochemistry
Recent studies suggest that clozapine is more effective than typical neuroleptics for patients with treatment-resistant schizophrenia.
Acute and late onset movement disorders frequently complicate the treatment of psychosis with typical neuroleptic drugs like haloperidol, but not with atypical neuroleptic drugs like clozapine. 
Only the group of boys presented other comorbidities such as negativism and conduct disorders; approximately 25% of them required treatment with atypical neuroleptic drugs.
Atypical neuroleptic drugs are the preferred treatment for symptoms such as delusions, hallucinations, agitation and aggressive behaviour.
Monotherapeutic treatment with new atypical neuroleptic drugs had a more positive effect on the mental health related quality of life (MCS) in comparison to treatment with polypharmacological treatment but not with oral conventional antipsychotics. 

Answer: Atypical neuroloeptic drugs are antipsychotics used in patients with schizophrenia, schizoaffective disorder, delusional disorder, psychotic disorders, psychotic relapse in neuroleptic malignant syndrome and attention deficit hyperactivity disorder when presenting with negativism and conduct disorder.
Exact answer: schizophrenia
schizophrenia psychosis
schizoaffective disorder
delusional disorder
psychotic relapse in neuroleptic malignant syndrome
attention deficit hyperactivity disorder (ADHD) with negativism or conduct disorders
psychotic disorders
Question: Galassi classification is used for which disorder?

Context:
 All these patients were divided into three subgroups according to Galassi classification. 
We are led to conclude that Fenestration is suitable for cysts of types I and II (Galassi classification), cysto-peritoneal shunting is better for cysts of type III.
According to Galassi classification they were subdivided into 3 groups.
According to Galassi classification they were subdivided in three groups.
On follow-up CT scan and MRI, cysts of types I and II (Galassi classification) exhibited a steady tendency to reduction or obliteration.
All cysts were type II according to Galassi classification.
Chronic subdural hemorrhage into a giant arachnoidal cyst (Galassi classification type III).
The authors present CT and MRI of a patient with an extremely large arachnoidal cyst (Galassi classification type III). 
The authors present CT and MRI of a patient with an extremely large arachnoidal cyst (Galassi classification type III).
Unusual volume reduction of Galassi grade III arachnoid cyst following head trauma.
The authors present CT and MRI of a patient with an extremely large arachnoidal cyst (Galassi classification type III).

Answer: Galassi classification system is used to classify arachnoid cysts.
Exact answer: arachnoid cyst
Question: What systems have been developed for the numbering of antibody residues?

Context:
IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) of any species which belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT consists of five databases, ten on-line tools and more than 8,000 HTML pages of Web resources. IMGT provides a common access to standardized data from genome, genetics, proteome and three-dimensional structures. 
amino acid positions according to the IMGT unique numbering (NUMEROTATION) that are used in IMGT/3Dstructure-DB cards, results of contact analysis and renumbered flat files.
Standardized sequence and structure analysis of antibody using IMGT(®) databases and tools allows one to bridge, for the first time, the gap between antibody sequences and three-dimensional (3D) structures. This is achieved through the IMGT Scientific chart rules, based on the IMGT-ONTOLOGY concepts of classification (IMGT gene and allele nomenclature), description (IMGT standardized labels), and numerotation (IMGT unique numbering and IMGT Colliers de Perles). 
Kabat Database was initially started in 1970 to determine the combining site of antibodies based on the available amino acid sequences at that time.
comparative analysis of the main-chain conformation of the L1, L2, L3, H1 and H2 hypervariable regions in 17 immunoglobulin structures that have been accurately determined at high resolution is described. This involves 79 hypervariable regions in all. We also analysed a part of the H3 region in 12 of the 15 VH domains considered here. On the basis of the residues at key sites the 79 hypervariable regions can be assigned to one of 18 different canonical structures. We show that 71 of these hypervariable regions have a conformation that is very close to what can be defined as a "standard" conformation of each canonical structure. These standard conformations are described in detail. The other eight hypervariable regions have small deviations from the standard conformations that, in six cases, involve only the rotation of a single peptide group
the basis of comparative studies of known antibody structures and sequences it has been argued that there is a small repertoire of main-chain conformations for at least five of the six hypervariable regions of antibodies, and that the particular conformation adopted is determined by a few key conserved residues.

Answer: The most prevalent antibody numbering systems are the Kabat system, the Chothia system as well as the IMGT numbering system.
Question: Is zyxin a focal adhesion protein?

Context:
 zyxin from FAs
zyxin relocation from focal adhesions 
. Here we systematically examined the expression, localization, and function of zyxin, a focal adhesion protein
focal adhesion protein zyxin
Focal adhesions formed in the absence of α-actinins are delayed in their maturation, exhibit altered morphology, have decreased amounts of Zyxin and VASP, and reduced adhesiveness to extracellular matrix
one focal adhesion protein (zyxin)
Zyxin is a focal adhesion protein that has been implicated in the modulation of cell adhesion and motility
 focal adhesion proteins (vinculin, talin, zyxin, FAK, and paxilin)
Such paxillin-positive complexes mature into focal adhesions by tyrosine phosphorylation and recruitment of zyxin. 
Zyxin concentrates at focal adhesions 
zyxin, a focal adhesion protein,
Focal adhesion proteins Zyxin and Vinculin are co-distributed at tubulobulbar complexes.
 Here we explore the prediction that zyxin, a focal adhesion protein known to be present at podosomes, also is present at apical TBCs
the association of zyxin with focal adhesions is force-dependent, smaller zyxin-positive adhesion as well as its higher turnover rate suggests that the traction force in focal adhesion on 350 nm topography is decreased.
. Zyxin is a focal adhesion protein that responds to external mechanical forces;
Vinculin and zyxin in focal adhesions but not integrins are seen to bridge ligand gaps. 
The focal adhesion protein zyxin
. To explore how this response is regulated by focal adhesion-associated proteins the expression levels of paxillin, focal adhesion kinase (FAK), and zyxin were knocked down using gene silencing techniques
 Zyxin is an adaptor protein at focal adhesion plaque
ocked localization of zyxin at focal adhesion sites

Answer: Yes, zyxin is a focal adhesion protein.
Exact answer: yes
Question: Which R package is used for the detection of chromosomal abnormalities from microarray data?

Context:
CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data
CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.
It is implemented as an R package that analyzes Affymetrix *.CEL files and comes with flexible plotting functions, easing visualization of chromosomal abnormalities.CAFE is available from https://bitbucket.org/cob87icW6z/cafe/ as both source and compiled packages for Linux and Windows.
SUMMARY: The current methods available to detect chromosomal abnormalities from DNA microarray expression data are cumbersome and inflexible. CAFE has been developed to alleviate these issues. It is implemented as an R package that analyzes Affymetrix *.CEL files and comes with flexible plotting functions, easing visualization of chromosomal abnormalities.AVAILABILITY AND IMPLEMENTATION: CAFE is available from https://bitbucket.org/cob87icW6z/cafe/ as both source and compiled packages for Linux and Windows.
SUMMARY: The current methods available to detect chromosomal abnormalities from DNA microarray expression data are cumbersome and inflexible. CAFE has been developed to alleviate these issues.
CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.

Answer: CAFE is an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.
Exact answer: CAFE
Question: Where is the TAZ (G4.5) is located in humans?

Context:
Tafazzin (EC 2.3.1.23) is a Phospholipid Transacylase involved in Cardiolipin remodeling on mitochondrial membrane and coded by TAZ gene (Cytogenetic Location: Xq28) in human.
Barth syndrome is an X-linked cardiomyopathy with neutropenia and 3-methylglutaconic aciduria. Recently, mutations in the G4.5 gene, located in Xq28, have been described in four probands with Barth syndrome. 
The disorder is caused by mutations in the tafazzin (TAZ/G4.5) gene located on Xq28.
Disabling mutations or deletions of the tafazzin (TAZ) gene, located at Xq28, cause the disorder by reducing remodeling of cardiolipin, a principal phospholipid of the inner mitochondrial membrane
The tafazzin gene (TAZ) is located at Xq28 and encodes a protein involved in the transacylation of cardiolipin, an essential mitochondrial phospholipid
The disorder is caused by mutations in the tafazzin (TAZ/G4.5) gene located on Xq28
The disorder is caused by mutations in the tafazzin (TAZ/G4.5) gene located on Xq28.
Recently, mutations in the G4.5 gene, located in Xq28, have been described in four probands with Barth syndrome.

Answer: TAZ gene (G4.5) is located on Xq28 in humans.
Exact answer: Xq28
Question: Is the protein lefty an inhibitor of nodal?

Context:
The expression of lefty, an inhibitor of nodal is often reduced in tumor cells.
 Nodal, and an inhibitor, Lefty.
as well as the expression of Lefty, an inhibitor of nodal signaling,
he Nodal inhibitor lefty
The morphogen Nodal was proposed to form a long-range signaling gradient via a reaction-diffusion system, on the basis of differential diffusion rates of Nodal and its antagonist Lefty.

Answer: Yes, lefty is an inhibitor of nodal.
Exact answer: yes
Question: List types of avoided words in bacterial genomes

Context:
Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes.
Short palindromic sequences (4, 5 and 6 bp palindromes) are avoided at a statistically significant level in the genomes of several bacteria, including the completely sequenced Haemophilus influenzae and Synechocystis sp. genomes and in the complete genome of the archaeon Methanococcus jannaschii.
Palindromes corresponding to sites for restriction enzymes from other species are also avoided, albeit less significantly, suggesting that in the course of evolution bacterial DNA has been exposed to a wide spectrum of restriction enzymes, probably as the result of lateral transfer mediated by mobile genetic elements, such as plasmids and prophages
Palindromic words appear to accumulate in DNA once it becomes isolated from restriction-modification systems, as demonstrated by the case of organellar genomes
In certain cases, a comparison of avoided palindromic words in taxonomically related bacteria shows a pattern of relatedness of their R-M systems.
Recognition sites for type II restriction and modification enzymes in genomes of several bacteria are recognized as semi-palindromic motifs and are avoided at a significant degree.
On the basis of the set of most avoided words, and in accordance to the IUPAC coding standards, suggestions are made regarding potential recognition sequences. In certain cases, a comparison of avoided palindromic words in taxonomically related bacteria shows a pattern of relatedness of their R-M systems.

Answer: Short palindromic sequences (4, 5 and 6 bp palindromes) are avoided at a statistically significant level in the genomes of several bacteria, including the completely sequenced Haemophilus influenzae and Synechocystis sp. genomes and in the complete genome of the archaeon Methanococcus jannaschii. Palindromes corresponding to sites for restriction enzymes from other species are also avoided, albeit less significantly, suggesting that in the course of evolution bacterial DNA has been exposed to a wide spectrum of restriction enzymes, probably as the result of lateral transfer mediated by mobile genetic elements, such as plasmids and prophages. Palindromic words appear to accumulate in DNA once it becomes isolated from restriction-modification systems, as demonstrated by the case of organellar genomes.
Exact answer: Short palindromic sequences (4, 5 and 6 bp palindromes)
Palindromes corresponding to sites for restriction enzymes from other species
Question: Are deletions of chromosomal regulatory boundaries associated with congenital disease?

Context:
Deletions of chromosomal regulatory boundaries are associated with congenital disease.
Our results suggest that enhancer adoption caused by deletions of regulatory boundaries may contribute to a substantial minority of copy-number variation phenotypes and should thus be taken into account in their medical interpretation
Deletions of chromosomal regulatory boundaries are associated with congenital disease
Deletions of chromosomal regulatory boundaries are associated with congenital disease.

Answer: Yes. Enhancer adoption caused by deletions of regulatory boundaries may contribute to a substantial minority of copy-number variation phenotypes and should thus be taken into account in their medical interpretation.
Exact answer: yes
Question: Is there an association between serum interleukin-6 concentrations and outcomes of stroke patients?

Context:
 In addition, IL-6 concentrations affect clinical outcomes in ischemic stroke.
After appropriate adjustment, the odds ratios for the association of markers and poor outcome (comparing the upper and the lower third) were interleukin-6, 3.1 (95% CI: 1.9-5.0); C-reactive protein, 1.9 (95% CI: 1.2-3.1); fibrinogen, 1.5 (95% CI: 1.0-2.36); white cell count, 2.1 (95% CI: 1.3-3.4); and glucose 1.3 (95% CI: 0.8-2.1). The results for interleukin-6 were similar to other studies. 
-6 and IL-10 levels were higher in patients with poor outcome. On logistic regression analysis, higher values of IL-6 were significantly associated with clinical outcome at 1 month (odds ratio [OR], 1.25; 95% confidence interval [CI], 1.02-1.54). 
In hemorrhagic stroke, high levels of IL-6 in the early phase indicated a poor neurological outcome.
Initially elevated levels of hs-IL-6 at presentation further correlated with unfavorable clinical outcomes (by NIHSS and mRs) at both time points. Analysis of variance in the different quartiles identified an hs-IL-6 gradient-dependent correlation at both time points, such that the higher the initial hs-IL-6 concentration, the higher the elevation in inflammatory biomarkers and the poorer the neurological state at both time points (p<0.001 for NIHSS and p=0.001 for mRs, for trend across quartiles). CONCLUSIONS: This study demonstrates the potential of employing hs-IL-6 as an early stage biomarker for the prognosis of acute ischemic stroke. 
Another negative correlation was found between IL-6 and CNS scores (r = -0.451, p = 0.000).
In addition, increased levels of IL-6 and reduced levels of protein C and protein S may play a role in acute ischemic stroke severity.
Variables that are predictors of adverse stroke outcome include erythrocyte sedimentation rate, and levels of C-reactive protein (CRP), interleukin-6, tumour necrosis factor-alpha and intercellular adhesion molecule-1. 

Answer: Yes. Greater serum interleukin-6 concentrations are associated with worse outcomes in ischemic and hemmorhagic stroke patients
Exact answer: yes
Question: Which packages are used for performing overlap analysis of genomic regions in R/bioconductor?

Context:
At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

Answer: IRanges, GenomicRanges, and GenomicFeatures provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.
At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.
Exact answer: IRanges, GenomicRanges, GenomicFeatures
Question: What is the phenotype of people carrying mutations in the gene PRDM12?

Context:
The evolutionarily conserved transcription factor PRDM12 controls sensory neuron development and pain perception.
Here we show that PRDM12 is a key regulator of sensory neuronal specification in Xenopus. Modeling of human PRDM12 mutations that cause hereditary sensory and autonomic neuropathy (HSAN) revealed remarkable conservation of the mutated residues in evolution.
Transcriptional regulator PRDM12 is essential for human pain perception.
 New therapeutic options have recently been derived from studies of individuals with congenital insensitivity to pain (CIP). Here we identified 10 different homozygous mutations in PRDM12 (encoding PRDI-BF1 and RIZ homology domain-containing protein 12) in subjects with CIP from 11 families. Prdm proteins are a family of epigenetic regulators that control neural specification and neurogenesis. 
 However, the study of genetic disorders rendering individuals completely unable to feel pain offers hope. All causes of congenital painlessness affect nociceptors, evolutionarily conserved specialist neurons able to sense all type of tissue damage. The discovery of new genes essential for sensing pain (SCN11A, PRDM12, and CLTCL1) has provided unexpected insights into the biological mechanisms that drive distinct stages of nociception.

Answer: New therapeutic options have recently been derived from studies of individuals with congenital insensitivity to pain (CIP). Here we identified 10 different homozygous mutations in PRDM12 (encoding PRDI-BF1 and RIZ homology domain-containing protein 12) in subjects with CIP from 11 families.
Exact answer: congenital insensitivity to pain, CIP
Question: Is insulin-like growth factor-I (IGF-I) able to affect tendon protein synthesis in classic Ehlers-Danlos syndrome patients?

Context:
Tendon protein synthesis rate in classic Ehlers-Danlos patients can be stimulated with insulin-like growth factor-I
IGF-I injections significantly increased FSR values in cEDS patients but not in controls
In conclusion, baseline protein synthesis rates in connective tissue appeared normal in cEDS patients, and the patients responded with an increased tendon protein synthesis rate to IGF-I injections
In conclusion, baseline protein synthesis rates in connective tissue appeared normal in cEDS patients, and the patients responded with an increased tendon protein synthesis rate to IGF-I injections
IGF-I injections significantly increased FSR values in cEDS patients but not in controls (delta values: cEDS 0

Answer: Tendon protein synthesis rate in classic Ehlers-Danlos patients can be stimulated with insulin-like growth factor-I  
In an experimental setting, baseline protein synthesis rates in connective tissue appeared normal in classic Ehlers-Danlos syndrome patients, and the patients responded with an increased tendon protein synthesis rate to IGF-I injections.
Exact answer: yes