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RAG Datasets 12

What is the function of the AIRE gene at the embryonic stage?

Aire regulates the expression of differentiation-associated genes and self-renewal of embryonic stem cells. Aire and Deaf1 help regulate the ectopic expression of diverse tissue-specific antigens to establish self-immune tolerance. Knockdown of Aire in mouse ESCs resulted in significantly decreased clone-forming efficiency as well as attenuated cell cycle, suggesting Aire plays a role in ESC self-renewal. Aire promotes the expression of the pluripotent factor Lin28 and the self-renewal of ES cells.

[19008896, 21952165, 22540148, 20226168, 19302042]

What is the principle of the PAR-CLIP methodology?

In particular, PAR-CLIP utilizes a photoactivatable nucleoside for more efficient crosslinking. A recent method, PAR-CLIP, uses photoreactive nucleosides to crosslink RBPs to target RNAs in cells prior to immunoprecipitation. One characteristic feature of cDNA libraries prepared by PAR-CliP is that the precise position of crosslinking can be identified by mutations residing in the sequenced cDNA.

[21559008, 23706177, 22213601, 24297251, 22152485, 22844102, 21851591, 21816340, 20371350, 21572407, 22885304, 20644507, 23368412, 22926237]

Which drugs are utilized to treat amiodarone-induced thyroitoxicosis?

Amiodarone-induced thyrotoxicosis treatment includes anti-thyroid drugs and steroid therapy Radio Iodine Treatment (RIT) may be a safe and useful method of AIT therapy in patients with low RAIU, in whom other treatment methods are contraindicated. Lithium is a useful and safe medication for treatment of iodine-induced thyrotoxicosis caused by amiodarone. Thyrodectomy may be necessary in presence of unresponsiveness to standard medical treatments

[2781955, 12727944, 21135419, 9217642, 11901034, 16910349, 7946779, 16544025, 19675515]

How is spastic diplegia diagnosed?

Diagnosis of spastic diplegia is mainly carried out with through clinical gait analysis (CGA), with variations such as 1-minute walk, LSU, and 10-meter walk tests, or Gross Motor Function Measure-88 (GMFM-88). Other methods used for evaluation of patients include brain magnetic resonance imaging (MRI) and motor function, presence of epileptic episodes, and IQ or developmental quotient.

[24901761, 21310339, 25276040, 24239880, 17826455, 20829081, 10427678, 1743414, 23085499, 25700542, 24409030, 24182356, 16344032, 2816867, 15157997, 23121133, 2600179, 7270517, 12549749, 17509240]

Which is the genetic defect causing Neurofibromatosis type 1?

Neurofibromatosis type 1 (NF1) is due to all types of mutations in the neurofibromin (NF1) gene.

[14722917, 2129297, 16323217, 21567923, 16835897]

Which is the human selenoprotein that contains several Se-Cys residues?

Selenoprotein P, that contains 10 selenocysteines.

[19345254, 11122377, 10692426, 7637580, 20417644, 15104205, 9288402, 17000762, 15777501]

Which package is available for analysing genomic interactions in R/Bioconductor?

r3Cseq is an R/Bioconductor package designed to perform 3C-seq data analysis in a number of different experimental designs. The package reads a common aligned read input format, provides data normalization, allows the visualization of candidate interaction regions and detects statistically significant chromatin interactions, thus greatly facilitating hypothesis generation and the interpretation of experimental results.

[23671339]

How many clinical trials for off-label drugs in neonates are cited in the literature.

There are no reports on clinical trials of off-label drugs in neonates. An analysis of Pediatric Investigation Plans submitted between 2007 and 2010 shows that neonates were included in the study of 4 products, but it is unknown if the trial drugs are off-label and if the trials are being conducted at all.

[20821198]

Are stress granules involved in the pathogenesis of Amyotrophic Lateral Sclerosis?

Stress granules are cytoplasmic inclusions that repress translation of a subset of RNAs in times of cellular stress, and several proteins implicated in neurodegeneration (i.e. Ataxin-2 and SMN) interact with stress granules. Mutant FUS proteins that cause amyotrophic lateral sclerosis incorporate into stress granules. ALS-linked mutations in profilin 1 alter stress granule dynamics, providing further evidence for the potential role of stress granules in ALS pathogenesis. ALS mutations in FUS NLS can impair FUS nuclear localization, induce cytoplasmic inclusions and stress granules, and potentially perturb RNA metabolism.

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Does TGF-beta play a role in cardiac regeneration after myocardial infarction?

TGFβ signaling orchestrates the beneficial interplay between scar-based repair and cardiomyocyte-based regeneration to achieve complete heart regeneration.

[18985280, 17322368, 19966054, 15883211, 23293297, 10198196, 16842199, 12374778, 22513374]

Is there a genetic component for happiness?

Results of studies on genetic factors indicated an average effectiveness of genetic about 35 -50 percent on happiness. The MAOA gene predicts happiness in women. The heritability of happiness was estimated at 22% for males and 41% in females.

[20440640, 19728071, 26060713, 20981772, 20397744, 23769682, 24690898, 22885141, 19569406]

What enzyme is inhibied by Opicapone?

Opicapone is a novel catechol-O-methyltransferase (COMT) inhibitor to be used as adjunctive therapy in levodopa-treated patients with Parkinson's disease

[24925090, 23248072, 24148813, 23336248, 24271646]

What kind of affinity purification would you use in order to isolate soluble lysosomal proteins?

The rationale for purification of the soluble lysosomal proteins resides in their characteristic sugar, the mannose-6-phosphate (M6P), which allows an easy purification by affinity chromatography on immobilized M6P receptors.

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Which are the genes thought to be regulated by EWS/FLI?

The EWS/FLI translocation product is the causative oncogene in Ewing sarcoma and acts as an aberrant transcription factor. EWS/FLI dysregulates gene expression during tumorigenesis by abnormally activating or repressing genes. The expression levels of a significant number of genes are affected in Ewing sarcoma, some of which are known to be directly or indirectly regulated by EWS/FLI. Such genes are BCL11B, NRoB1, GSTM4, NKX2.2 and p53.

[23527175, 16697960, 17114343, 18927503, 15492248, 19920188, 19718047]

Do archaeal genomes contain one or multiple origins of replication?

Some archaea replicate from single origins but most archaea and all eukaryotes replicate using multiple origins.

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Which pathological conditions are caused by mutations in the CYLD gene?

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.

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Which is the genetic basis of Spinal Muscular Atrophy (SMA)?

The molecular genetic basis of spinal muscular atrophy (SMA), an autosomal recessive neuromuscular disorder, is the loss of function of the survival motor neuron gene (SMN1). Mutations of the SMN1 gene are responsible for SMA. A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy. A critical question is why only the homozygous loss of SMN1, and not SMN2, results in spinal muscular atrophy (SMA). H4F5 is also highly deleted in type I SMA chromosomes, and thus is a candidate phenotypic modifier for SMA. The molecular genetic basis of spinal muscular atrophy (SMA), an autosomal recessive neuromuscular disorder, is the loss of function of the survival motor neuron gene (SMN1).

[22323744, 19062530, 22628388, 9073029, 20225030, 12220455, 12115944, 17076267, 9731538, 19646678, 11442327, 10339583]

Which are the common symptoms of Cushing's syndrome?

Cushing syndrome is the constellation of signs and symptoms caused by protracted exposure to glucocorticoids. Presenting features commonly include weight gain, growth retardation, hirsutism, obesity, striae, acne and hypertension.

[17322955, 24062268]

Which is the third subunit of the TSC1-TSC2 complex upstream of mTORC1?

TBC1D7 was identified as a stably associated and ubiquitous third core subunit of the TSC1-TSC2 complex. It was demonstrated that TSC1-TSC2-TBC1D7 (TSC-TBC) is the functional complex that senses specific cellular growth conditions and possesses Rheb-GAP activity to negatively regulate mTORC1 activity. In agreement with this, TBC1D7 knockdown was shown to result in increased mTORC1 signaling, delayed induction of autophagy, and enhanced cell growth under poor growth conditions.

[22795129]

Which kinase is inhibited by the small molecule KN-93?

The calcium/calmodulin-dependent protein kinase-II (CaMK-II) is inhibited by the small molecule KN-93. KN-93 is a membrane-permeant calcium/calmodulin- dependent kinase II (CaMK-II)-selective inhibitor

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What is the effect of Chk2 splice variants on wild-type Chk2 kinase activity?

Chk2 splice variants have been demonstrated to exert a dominant-negative effect on wild-type Chk2 kinase activity.

[20080130]

List genes that have been found mutated in CMT1A (Charcot-Marie-Tooth disease type 1 A).

PMP22 is the common gene found mutated through a duplication in CMT1A. Other genes are MPZ and SH3TC2

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Which viruses are best known to cause myocarditis?

The most frequent viruses causing myocarditis are Enterovirus, Adenovirus and Coxsackie B viruses.

[18039618, 8199011, 3889351, 18277927, 2641165, 14993139]

Which genes have been associated with Cerebral Cavernous Malformation?

Loss-of-function mutations in genes encoding CCM1 (also known as KRIT1), CCM2 (also known as OSM and malcavernin) or CCM3 (also known as PDCD10) cause cerebral cavernous malformations (CCMs).

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Is DITPA a thyroid hormone analog utilized in experimental and clinical studies

There is very large body of evidence that DITPA is a true thyroid hormone analog, largely utilized in experimental and clinical studies.

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What is Tarlov Cyst?

Tarlov or perineural cysts are nerve root cysts found most commonly at the sacral spine level arising between covering layers of the perineurium and the endoneurium near the dorsal root ganglion and are usually asymptomatic.

[10758434, 21139800, 21830055, 19110185, 25191117, 23400656, 25216402, 11453427, 20102100, 20712856, 19569467]

What are 'vildagliptin', 'sitagliptin', 'saxagliptin', 'alogliptin', 'linagliptin', and 'dutogliptin'?

"Sitagliptin," "vildagliptin," "saxagliptin," "alogliptin," "linagliptin," and "dutogliptin" are dipeptidyl peptidase-4 (DPP-4) inhibitors.

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Which is the most important prognosis sub-classification in Chronic Lymphocytic Leukemia?

The mutational status of the immunoglobulin heavy variable (IGHV) genes, defines two subsets: mutated and unmutated CLL. Unmutated CLL patients show a shorter progression-free and overall survival than mutated CLL patients.

[19500131, 17786276, 16014569, 23468975, 16083281, 20353875, 22560084, 16825496, 19127482, 20090781]

Is MammaPrint cleared by the United States Food and Drug Administration?

Yes. MammaPrint is cleared by the FDA for breast cancer recurrence.

[21479927, 18786252, 19506735]

Is amantadine effective for treatment of disorders conciousness?

Amantadine, a dopaminergic agent, has been shown to be effective for induction of recovery from disorders of consciousness. Amantadine is a commonly prescribed medication for patients with prolonged disorders of consciousness after traumatic brain injury. Amantadine accelerates the pace of functional recovery during active treatment in patients with post-traumatic disorders of consciousness. Higher dosing of amantadine may be considered in the setting of brain injury.

[24025056, 24025057, 19404190, 22375973, 15825541, 20129511, 20658796, 18540467, 20460949, 19894299, 15759228, 24025054]

What is needed for MMP proteins to be functional?

Extracellular matrix metalloproteinases (MMPs) are a family of zinc-dependent neutral endopeptidases.

[24570026, 26087627, 23001203, 26150355, 26013370, 25360794, 22257051]

What is hyperosmia

Hyperosmia is increased olfactory acuity

[24302690, 23520356, 21250223]

What is the number of long non coding RNAs in the human genome

Different estimates put currently the number of human long non coding RNAs between 10,000 and 20,000

[23126680, 23846593, 23369519]

Which is the most known bacterium responsible for botulism (sausage-poisoning)?

Botulism is a severe neuroparalytic disease caused by botulinum neurotoxin (BoNT), and affects humans, all warm-blooded animals, birds, and some fishes. Botulinum toxin is produced under anaerobic conditions by the bacterium Clostridium botulinum, which is the most known etiological agent of the disease, and some other clostridia, and is one of the most dangerous toxin in the world.

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What is the association of spermidine with α-synuclein neurotoxicity?

Spermidine protects against α-synuclein neurotoxicity. In the fruit fly, simple feeding with spermidine inhibited loss of climbing activity and early organismal death upon heterologous expression of human α-synuclein, which is thought to be the principal toxic trigger of Parkinson's Disease (PD). In this line, administration of spermidine rescued α-synuclein-induced loss of dopaminergic neurons, a hallmark of PD, in nematodes. Alleviation of PD-related neurodegeneration by spermidine was accompanied by induction of autophagy, suggesting that this cytoprotective process may be responsible for the beneficial effects of spermidine administration.

[22662273, 25483063]

List symptoms of 4H leukodystrophy.

Hypomyelination, hypodontia, and hypogonadotropic hypogonadism are major symptoms of 4H leukodystrophy.

[21855841, 18671210, 25339210, 23242285, 23307887, 24190003, 22451160, 22855961]

What is the extracellular core "matrisome"?

The "matrisome" is defined as the ensemble of extracellular matrix proteins (ECM) proteins and associated factors. The core matrisome have been defined in mammals through the analysis of whole genome sequences and comprises of ~ 300 proteins.

[23539364, 22159717, 21937732]

Is GAGA associated with nucleosome-free regions (NFR)?

The GAGA factor is a protein known to be involved in the formation and/or maintenance of nucleosome-free regions of chromatin. The interactions of GAGA factor and heat shock factor with their binding sites in chromatin occurred in two modes. Their interaction with binding sites in the nucleosome-free regions did not require ATP. In the presence of ATP both factors interacted also with nucleosomal binding sites, causing nucleosome rearrangements and a refinement of nucleosome positions. While chromatin remodeling upon transcription factor interaction has previously been interpreted to involve nucleosome disruption, the data suggest energy-dependent nucleosome sliding as main principle of chromatin reorganization.

[8474442, 15579691, 11158316, 7737124]

Which are the plant DNA (cytosine-5) methyltransferase families?

The plant DNA (cytosine-5)methyltransferases are classified into the families: MET, CMT, and the de novo DRM.

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Where is the histone variant CENPA preferentially localized?

Centromere protein A (Cenpa for mouse, CENP-A for other species) is an essential histone H3-like protein that localizes to the centromeric region of eukaryotic chromosomes, where it replaces conventional histone H3 and together with centromere-specific-DNA-binding factors directs the assembly of active kinetochores.

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In which proteins is the chromodomain present?

The chromodomain (chromatin organizer modifier domain) is a highly conserved motif, 40-50 amino acids in length, present in a wide range of animal and plant proteins involved in chromatin organization. Chromodomain-containing proteins can be classified into boader families based, particularly, on the presence of other types of domains. Chromodomain is present in: the heterochromatin proteins HP1 alpha and HP1 beta, chromointgrases (e.g. Tf1 integrase) the chromodomain helicase DNA-binding proteins (CHD) and CHD 1-like (CHD1L), CReMM (chromatin-related mesenchymal modulator), dna methyltransferase 3 (cmt3), the chromointegrase of the LTR-retrotransposons, the Polycomb group (PcG) proteins, the mouse Polycomb homologs (Cbx2, Cbx4, Cbx6, Cbx7, Cbx8), the chromodomain Y chromosome (CDY) family of proteins and the CDY-like protein (CDYL), the histone acetyltransferases TgMYST-A and –B, MRG-1 and -15 (MORF4-Related Gene on chromosome 15), ADP/ATP translocase 1, MPP8, MSL3, NlMof, Chp1, Chriz, dMi-2, Corto, cpSRP43, KISMET, PICKLE (PKL), ScoHET1 and ScoHET2.

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What is Genomicus?

Genomicus had been developed as a database and a browser to study gene synteny in modern and ancestral genomes. It allows easy comparative genomic visualization in >150 eukaryote genomes and in four different phyla (Vertebrate, Fungi, Metazoan and Plants). It provides a way to explore spatial information related to gene organization within and between genomes and temporal relationships related to gene and genome evolution. For the specific vertebrate phylum, it also provides access to ancestral gene order reconstructions and conserved non-coding elements information. The graphical modules of Genomicus show how it is capable of revealing differential gene loss and gain, segmental or genome duplications and facilitate the study of the evolution of a locus through homology relationships. The Genomicus server provides access to ancestral gene orders, as well as computationally predicted regulatory interactions, thanks to the representation of conserved non-coding elements with their putative gene targets.

[20185404, 23193262, 25378326]

Is amiodarone a class I anti-arrhythmic drug?

Although considered to be a class III anti-arrhythmic, amiodarone also has class I, II and IV actions, which gives it a unique pharmacological and anti-arrhythmic profile

[12491809, 17352036, 11825323, 15989900, 20041841, 21728182, 21626366]

Which is the prognostic meaning of delayed enhancement documented in patients hypertrophic cardiomyopathy?

Delayed enhancement by CMR has prognostic value in predicting adverse cardiovascular events among HCM patients, and is associated with cardiovascular mortality, heart failure death, and all-cause mortality in HCM.

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What is the COUGER tool?

COUGER takes as input two sets of genomic regions bound by paralogous TFs, and it identifies a small set of putative co-factors that best distinguish the two sets of sequences.

[24861628]

Are there drugs for Tick-borne Encephalitis?

No drug therapy available today

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Is SLC22A3 expressed in the brain?

Yes, SLC22A3 (organic cation transporter (OCT3)) is widely expressed in various organs in humans, and involved in the disposition of many exogenous and endogenous compounds. Several lines of evidence have suggested that OCT3 expressed in the brain plays an important role in the regulation of neurotransmission.

[19702534, 15028779, 19033200, 19280114, 20402963, 18513366, 21352605]

Has the protein TIEG1 been associated with apoptosis?

Yes, TIEG1 (also known as KLF10) seems to play a role in regulating apoptosis.

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Which is the cellular localization of the protein Opa1?

The Opa1 protein localizes to the mitochondria.

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Which are the drugs utilized for the burning mouth syndrome?

Dopaminergic drugs should be given in patients with BMS. Catuama reduces the symptoms of BMS and may be a novel therapeutic strategy for the treatment of this disease. Capsaicin, alpha-lipoic acid (ALA), and clonazepam were those that showed more reduction in symptoms of BMS. Treatment with placebos produced a response that was 72% as large as the response to active drugs

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Is PTEN involved in follicular thyroid carcinoma?

The PTEN mutation frequency in unselected cases of follicular thyroid carcinoma was 4.8%.

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Which genome browser database for DNA shape annotations is available?

The Genome Browser for DNA shape annotations (GBshape; freely available at http://rohslab.cmb.usc.edu/GBshape/) provides minor groove width, propeller twist, roll, helix twist and hydroxyl radical cleavage predictions for the entire genomes of 94 organisms. Additional genomes can easily be added using the GBshape framework. GBshape can be used to visualize DNA shape annotations qualitatively in a genome browser track format, and to download quantitative values of DNA shape features as a function of genomic position at nucleotide resolution.

[25326329]

What is known about clinical efficacy of ceftriaxone for treatment of amyotrophic lateral sclerosis?

There have been a few case reports to suggest that ceftriaxone can be effective for treatment of amyotrophic lateral sclerosis. However, other case reports did not report clinical benefit of ceftriaxone therapy for ALS. Ceftriaxone has been reported to reduce neuronal damage in amyotrophic lateral sclerosis a through increased expression and activity of the glutamate transporter, GLT1. Clinical trials investigating potential clinical benefits of ceftriaxone in ALS are ongoing.

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What is the relationship between TailorX and Oncotype?

The TAILORx trial uses the Oncotype DX recurrence score to assign estrogen receptor-positive (ER+), node-negative patients to chemotherapy plus hormonal therapy versus hormonal therapy alone.

[25240289, 18922117, 20665886, 23411384, 23643806]

Does strenuous physical activity affect thyroid hormone metabolism?

YES

[18057380, 16175495, 2807143, 8743723, 8325717, 7198038, 596247, 14637241, 3101339]

Which is the main function of "RNA sponges"?

Natural RNA circles function as efficient microRNA sponges. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called competing endogenous RNA in humans and target mimicry in plants.

[23446346, 25957803, 23615404, 25483404, 25630703, 25404635, 26052092, 25580223]

Is the gene MAOA epigenetically modified by methylation?

In recent years, the role of epigenetic phenomenon, such as methylation, in mediating vulnerability to behavioral illness has become increasingly appreciated. One prominent locus at which epigenetic phenomena are thought to be in play is the monoamine oxidase A (MAOA) locus. We conclude that methylation of MAOA may play a significant role in common psychiatric illness and that further examination of epigenetic processes at this locus is in order.

[22198720, 20505345, 18454435, 22948232, 22906985, 20421737, 22436428, 16893905, 23116433, 22139575, 19777560]

Which mutations of phopspholamban have been found in patients with cardiomyopathy?

PLN mutation R14del [or c.40_42delAGA(p.Arg14del)] was identified in 12 (12 %) ARVC patients and in 39 (15 %) DCM patients. Another PLN mutation is a T116G point mutation, substituting a termination codon for Leu-39 (L39stop), and it was identified in two families with hereditary heart failure. Hereditary mutants of phospholamban, such as Arg(9) to Cys, Arg(9) to Leu, Arg(9) to His, cause lethal, hereditary dilated cardiomyopathy.in specific, two patients presented a G-T missense mutation at the G26 nucleotide, which encodes an Arg-Leu substitution at codon 9 (R9L).One patient presented a G-A missense mutation at the same nucleotide, which encodes an Arg-His substitution at codon 9 (R9H). A missense mutation in PLN cytoplasmic domain (R9C) triggers dilated cardiomyopathy in humans, leading to premature death.

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Which are the supplemental antioxidant in athletes?

There are several antioxidant supplements belonging to different families, i.e. Vitamins, Polyphenols, alpha-lipoic acid, ubiquinones, n-3- polyunsaturated acids (PUFAs), minerals and others. Nonetheless the widespread use of these supplements, it is still debated their true usefulness, and it is not unanimously advised their use in athletes.

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Is glycyl-tRNA synthetase gene involved in the development of Charcot-Marie-Tooth disease?

Dominant mutations in GARS, encoding the essential enzyme glycyl-tRNA synthetase (GlyRS), result in a form of Charcot-Marie-Tooth disease, type 2D (CMT2D), predominantly characterized by lower motor nerve degeneration.

[24368416, 23990368, 25168514, 17035524, 24669931, 24898252, 23279345, 16982418, 22144914, 12690580, 19470612, 25420567, 17545306]

Is there any software for automated analysis of FISH images?

FISH is a popular molecular cytogenetic method. The output of a single FISH analysis is a set of several tens or hundreds microscopic images — a single evaluated sample is of roughly 20mm diameter. The goal of an automated evaluation is to replace the subjective evaluation of images by the laboratory technician to achieve higher uniformity of results. Following explanation of the principle of the method and the typical contents of images, the processing flow of image segmentation is outlined and the results are presented on several example images. Based on results there are software for automated analysis of FISH images.

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How do histone methyltransferases cause histone modification?

Histone methyltransferases (HMTs) are responsible for the site-specific addition of covalent modifications on the histone tails, which serve as markers for the recruitment of chromatin organization complexes. There are two major types of HMTs: histone-lysine N-Methyltransferases and histone-arginine N-methyltransferases. The former methylate specific lysine (K) residues such as 4, 9, 27, 36, and 79 on histone H3 and residue 20 on histone H4. The latter methylate arginine (R) residues such as 2, 8, 17, and 26 on histone H3 and residue 3 on histone H4. Depending on what residue is modified and the degree of methylation (mono-, di- and tri-methylation), lysine methylation of histones is linked to either transcriptionally active or silent chromatin.

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Is there an increased risk for cancer in Dyskeratosis Congenita?

People with DC are at increased risk for progressive bone marrow failure (BMF), myelodysplastic syndrome (MDS) or acute myelogenous leukemia (AML), solid tumors (usually squamous cell carcinoma of the head/neck or anogenital cancer), and pulmonary fibrosis

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Does MicroRNA-21 (miR-21) contribute to cardiovascular disease?

MicroRNA-21 (miR-21) is a highly expressed microRNA (miRNA) in cardiovascular system. Recent studies have revealed that its expression is deregulated in heart and vasculature under cardiovascular disease conditions such as proliferative vascular disease, cardiac hypertrophy and heart failure, and ischemic heart disease. miR-21 is found to play important roles in vascular smooth muscle cell proliferation and apoptosis, cardiac cell growth and death, and cardiac fibroblast functions. Accordingly, miR-21 is proven to be involved in the pathogenesis of the above-mentioned cardiovascular diseases as demonstrated by both loss-of-function and gain-of-function approaches

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What is the enzymatic activity of the breast cancer associated gene BRCA1?

E3-ubiquitin ligase activity is the only known enzymatic activity of BRCA1, which is mediated by the N-terminal RING finger domain.BRCA1 nuclear transport and ubiquitin E3 ligase enzymatic activity are tightly regulated by the BRCA1 dimeric binding partner BARD1 and further modulated by cancer mutations and diverse signaling pathways.

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List markers for autophagy.

Expression of LC3-II and BECN1 as well as SQSTM1 are used as markers of autophagy activity.

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Are there any statistical methods for normalizing and identifying differential regions in histone modification ChIP-seq data?

Yes. ChIPnorm is a two-stage statistical method to normalize ChIP-seq data, and to find differential regions in the genome, given two libraries of histone modifications of different cell types.

[22870189]

Is CD84 genetically associated with arthritis?

Three members of this gene family, Ly108, Ly9, and CD84, exhibit polymorphisms that strongly influence susceptibility to systemic autoimmunity, notably in mice, but also in some human populations. Our study demonstrates that an allele associated with response to etanercept therapy is also associated with CD84 gene expression, and further that CD84 expression correlates with Rheumatoid Arthritis disease activity.

[21094032, 23555300, 21255096]

What is the function of Neu5Gc (N-Glycolylneuraminic acid)?

N-glycolylneuraminic acid (Neu5Gc) is an immunogenic sugar of dietary origin that metabolically incorporates into diverse native glycoconjugates in humans. Humans lack a functional cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH) protein and cannot synthesize the sugar Neu5Gc, an innate mammalian signal of self. N-Glycolylneuraminic acid (Neu5Gc) can be incorporated in human cells and can trigger immune response, a response that is diverse and polyclonal. As dietary Neu5Gc is primarily found in red meat and milk products, it is suggested that this ongoing antigen-antibody reaction may generate chronic inflammation, possibly contributing to the high frequency of diet-related carcinomas and other diseases in humans.

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Are there any specific antidotes for rivaroxaban?

Currently, there is no specific antidote for rivaroxaban

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Which metabolite activates AtxA?

Upon infection of a mammalian host, Bacillus anthracis responds to host cues, and particularly to elevated temperature (37°C) and bicarbonate/CO2 concentrations, with increased expression of virulence factors that include the anthrax toxins and extracellular capsular layer. Cultures grown with elevated CO(2) /bicarbonate exhibited increased AtxA dimer/monomer ratios and increased AtxA activity, relative to cultures grown without added CO(2) /bicarbonate, suggesting that this host-associated signal enhances AtxA function by shifting the dimer/monomer equilibrium towards the dimeric state. CO2-enhanced toxin gene transcription is not observed in atx4-null mutants. Overall data indicate a clear association of atxA with CO2-enhanced gene expression in B. anthracis and provide evidence that atxA regulates genes other than the structural genes for the anthrax toxin proteins.

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What is the function of 6SRNA in bacteria?

6S RNA, first described as a ncRNA in E. coli, mimics an open promoter structure, which has a large bulge with two hairpin/stalk structures that regulate transcription through interactions with RNA polymerase. Escherichia coli 6S RNA represents a non-coding RNA (ncRNA), which, based on the conserved secondary structure and previous functional studies, had been suggested to interfere with transcription. The carboxy terminus containing the Arg-Gly-Gly (RGG) repeat domains in these proteins are necessary for cis-repression of transcription activation and HAT activity by the N-terminal glutamine-rich domain.

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Is cytisine superior to nicotine replacement therapy for smoking cessation?

Yes, one clinical trial that directly compared smoking cessation rates with cytisine versus nicotine replacement therapy reported that cytisine was superior to nicotine-replacement therapy in helping smokers quit smoking, but it was associated with a higher frequency of self-reported adverse events.

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Which amino acid residue appears mutated in most of the cases reported with cadasil syndrome?

CADASIL is caused mostly by missense mutations in the NOTCH3 gene, invariably involving a cysteine residue.

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Which syndromes are associated with mutations in the EZH2 gene?

EZH2 mutations that cause Weaver syndrome are primarily missense variants and the rare truncating mutations reported to date are in the last exon, suggesting that simple haploinsufficiency is unlikely to be generating the overgrowth phenotype although the exact mechanism has not yet been determined. Recent studies have shown that EZH2 mutations are often associated with RUNX1 mutations in MDS patients, although its pathological function remains to be addressed. These data show that mutations in EZH2 cause Weaver syndrome. The EZH2 gene is a homolog of the Drosophila Polycomb group (PcG) gene enhancer of zest, a crucial regulator of homeotic gene expression.

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Which databases exist for experimentally determined topologies of α-helical transmembrane proteins ?

ExTopoDB and TMPDB.

[12520035, 20601677]

Which disease is characterized by congenital absence of intrinsic ganglion cells of the gastrointestinal tract?

Hirschsprung disease (HSCR, aganglionic megacolon) is a common congenital malformation leading to bowel obstruction, with an incidence of 1/5,000 live births. It is characterized by the absence of intrinsic ganglion cells in the myenteric and submucosal plexuses along variable lengths of the gastrointestinal tract.

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What is the disease in which patients are sensitive to DNA crosslinking agents, presenting with a high frequency of chromosomal aberrations?

Fanconi anemia (FA) is an autosomal disorder that causes genome instability and manifests by defects in DNA repair, hypersensitivity to DNA crosslinking agents, and a high degree of chromosomal aberrations.

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How is oprozomib administered?

Oprozomib is administered orally.

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What is a Caveolae?

Caveolae, plasma membrane invaginations of 60-80nm in diameter, are a subset of lipid rafts enriched in cholesterol and sphingolipids.

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Which are the roles of chromatin compartments in the eukaryotic nucleus?

The complexity in composition and function of the eukaryotic nucleus is achieved through its organization in specialized nuclear compartments. Chromosome conformation capture approaches have shown that interphase chromatin is partitioned into spatially segregated Mb-sized compartments and sub-Mb-sized topological domains. This compartmentalization is thought to facilitate the matching of genes and regulatory elements. Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Therefore, concentrating proteins needed to perform different steps of RNA synthesis within specialized nuclear compartments is important in orchestrating events required for efficient gene expression.

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Is the abnormal dosage of ultraconserved elements disfavored in cancer cells?

No. Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells.

[25340765]

Does thyroid hormone regulate calcium transient in the myocardium?

YES

[9875761, 19298522, 9773867, 2428004]

What are the biological roles proposed for proteins containing the SPRY domain?

defence against retroviral infection innate and adaptative immunity vesicular trafficking neural differentiation embryonic development

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How could we infer functional associations from gene fusion events?

The detection of gene fusion events across genomes can be used for the prediction of functional associations of proteins, based on the observation that related proteins in one organism (including physically interacting proteins/members of complexes, proteins involved in the same pathway) tend to be found in other species as a fused composite gene encoding a single multifunctional protein. For this purpose, gene fusion events may be used as the sole evidence or as independent information combined with other 'genome-aware' or similarity-based methods, and functional association may be predicted at different levels. An advantage of this approach is that it is not necessary to know the function of the composite/components to infer association.

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The protein NONO forms heterodimers. With which proteins?

The protein NONO forms heterodimers with PSPC1, SFPQ.

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Which syndrome is associated with mutant DVL1?

Mutations in DVL1 cause an osteosclerotic form of Robinow syndrome.

[25817016, 25817014]

Are proteasome inhibitors good candidates for treatment of leukemia and solid tumors?

Yes, several compounds that inhibit different members of the proteasome pathway (for example Bortezomib) are on trial for treatment of leukemia and solid tumors. It seems that a combination with other drugs may be a useful therapy for solid tumors.

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Is there any link between CTF4 and CTF18 during sister chromatid cohesion?

Yes. CTF4 and CTF18 are required for high-fidelity chromosome segregation. Both exhibit genetic and physical ties to replication fork constituents. Absence of either CTF4 or CTF18 causes sister chromatid cohesion failure and leads to a preanaphase accumulation of cells that depends on the spindle assembly checkpoint. The physical and genetic interactions between CTF4, CTF18, and core components of replication fork complexes suggest that both gene products act in association with the replication fork to facilitate sister chromatid cohesion.

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What is the Genomic Regions Enrichment of Annotations Tool (GREAT)?

Genomic Regions Enrichment of Annotations Tool (GREAT) is a tool to analyse the functional significance of cis-regulatory regions identified by localised measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. Applying GREAT to data sets from chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) of multiple transcription-associated factors, including SRF, NRSF, GABP, Stat3 and p300 in different developmental contexts, many functions of these factors are recovered that are missed by existing gene-based tools, and testable hypotheses are generated. The utility of GREAT is not limited to ChIP-seq, as it could also be applied to open chromatin, localized epigenomic markers and similar functional data sets, as well as comparative genomics sets.

[20436461]

What is the target of the drug Olaparib?

The drug Olaparib target the protein poly(ADP-ribose) polymerase.

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Are thyroid hormone receptor alpha1 mutations implicated in thyroid hormone resistance syndrome?

The lack of TR alpha1 exacerbates the manifestation of RTH in TR betaPV mice. Therefore, TR alpha1 could play a compensatory role in mediating the functions of T3 in heterozygous patients with RTH

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What is the role of RhoA in bladder cancer?

In urinary bladder cancer, RhoA was more commonly found to be activated in the later stages of the disease. This activation was related to poor tumor differentiation, muscle invasion, lymph node metastasis, and shortened disease-free and overall survival.

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List human proteins that are subject to a dimer-to-tetramer transition.

GAC SHMT2 AMPAR Orai1 Orai3

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Inhibition of which transporter is the mechanism of action of drug Canagliflozin?

Inhibition of sodium glucose co-transporter 2 (SGLT2) is the major mechanism of action of canagliflozin. Canagliflozin is the first SGLT2 inhibitor to be approved in the USA for the treatment of type 2 diabetes and is under regulatory review in the EU. Other SGLT2 inhibitors include dapagliflozin and empagliflozin.

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What is the prognostic role of thyroid hormone in patients with heart failure?

Altered thyroid profile, particularly sick euthyroid syndrome, is an independent predictor of mortality in patients with chronic heart failure, adding prognostic information to conventional clinical and functional cardiac parameters.

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which mutations of phospholamban gene have been found to cause hypertrophic cardiomyopathy?

The following mutations of the phospholamban gene have been found to be associated with hypertrophic cardiomyopathy: PLN L39X nonsense mutation; PLN Leu39Ter; PLN -42 C>G and PLN -77A-->G

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Which gene strand is targeted by transcription-coupled repair (TCR)?

Nucleotide Excision Repair (NER) removes a variety of helix-distorting lesions from DNA. It has two sub-pathways, the global genome (gg) NER and the transcription-coupled repair (TCR). TCR is triggered when a RNA polymerase, translocating along the transcribed strand, is arrested at a lesion or unusual structure in the DNA. TCR is dedicated to target and repair the transcribed strand of an active gene.

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Abnormalities in which chromosomes were linked to the Moyamoya disease?

chromosomes 3, 6, 8, 12, 15, 17, 21, X and Y were implicated in the Moyamoya disease.

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Which is the branch site consensus sequence in U12-dependent introns?

The branch site consensus sequence in U12-dependent introns is UUCCUUAAC.

[18824513]