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List features of the Kaufman Oculocerebrofacial Syndrome. | Clinical features of the Kaufman Oculocerebrofacial Syndrome include hypotonia, developmental delay, intellectual disability, low cholesterol levels, microcephaly, long narrow face, ocular anomalies, and long thin hands and feet. | Two unrelated Mexican girls, aged 14 months and 6 years respectively, with
Kaufman oculocerebrofacial syndrome, are reported. Both showed psychomotor
retardation, microcephaly, blepharophimosis and delayed growth as the main
features; the infant also presented preauricular tags and large clitoris.
Comparative analy... |
What is the role of DNA Repair Cofactors ATMIN and NBS1? | The DNA double-strand break signaling kinase ATM and its cofactor NBS1 are required during T cell development and for the maintenance of genomic stability. The role of a second ATM cofactor, ATMIN (also known as ASCIZ) in T cells is much less clear, and whether ATMIN and NBS1 function in synergy in T cells is unknown. | Proper development of the immune system is an intricate process dependent on
many factors, including an intact DNA damage response. The DNA double-strand
break signaling kinase ATM and its cofactor NBS1 are required during T cell
development and for the maintece of genomic stability. The role of a second
ATM cofact... |
The MMR vaccine protects against what 3 viruses? | The MMR vaccine provides immunity to measles, mumps and rubella. | Measles, mumps, rubella (MMR) vaccine is a live vaccine preparation containing
attenuated strains of all 3 viruses. MMR vaccine is widely used throughout the
world, with the US having the widest experience with the vaccine. In countries
where the vaccine has been introduced successfully, significant reductions in
a... |
List cardinal features of the Triple A syndrome. | Triple A syndrome, also known as Allgrove syndrome, is a rare disease, and presents mainly in children. Its cardinal symptoms are achalasia, alacrima, and adrenal insufficiency. | The triple A syndrome or Allgrove syndrome (MIM*231550) is characterized by
adrenocorticotropic hormone (ACTH) resistant Adrenal insufficiency, Achalasia of
the cardia and Alacrima. In addition to the main features, patients frequently
suffer from neurological disturbances. Dermatological abnormalities such as
palm... |
Describe the applicability of Basset in the context of deep learning | Basset is an open source package which applies CNNs to learn the functional activity of DNA sequences from genomics data. Basset was trained on a compendium of accessible genomic sites mapped in 164 cell types by DNase-seq, and demonstrated greater predictive accuracy than previous methods. Basset predictions for the c... | The complex language of eukaryotic gene expression remains incompletely
understood. Despite the importance suggested by many noncoding variants
statistically associated with human disease, nearly all such variants have
unknown mechanisms. Here, we address this challenge using an approach based on a
recent machine l... |
Does the Abelson-related gene (ARG) gene encode for a serine kinase? | No, the ARG gene encodes for a nonreceptor tyrosine kinase. | Arg encodes a protein highly related to the c-abl gene product with regard to
overall structural architecture as well as the amino acid sequences of their
tyrosine kinase, and src-homologous 2 and 3 domains. The two genes form a
distinct subfamily of non-receptor tyrosine kinases and share a common homolog
in Droso... |
What organism causes tularemia? | Francisella tularensis, the agent of tularemia, is a Gram-negative coccobacillus primarily pathogen for animals and occasionally for humans. F. tularensis is the causative agent of zoonotic tularemia. | Francisella tularensis is a highly virulent bacterium that causes tularemia, a
disease that is often fatal if untreated. A live vaccine strain (LVS) of this
bacterium is attenuated for virulence in humans but produces lethal disease in
mice. F. tularensis has been classified as a Category A agent of bioterrorism.
D... |
Is Prochlorococcus the most abundant photosynthetic organism? | Yes, the marine cyanobacterium Prochlorococcus is the smallest and most abundant photosynthetic organism on Earth. | The oceanic picoplankton Prochlorococcus - probably the most abundant
photosynthetic organism on our planet - can grow at great depths where light
intensity is very low. We have found that the chlorophyll-binding proteins in a
deep-living strain of this oxyphotobacterium form a ring around a trimer of the
photosyst... |
List 3 features of IRVAN syndrome. | Idiopathic retinal vasculitis, aneurysms, and neuroretinitis is coined as IRVAN syndrome. | PURPOSE: The authors describe the clinical feature of ten patients with a new
syndrome characterized by the presence of retinal vasculitis, multiple
macroaneurysms, neuro-retinitis, and peripheral capillary nonperfusion.
METHODS: The authors evaluated ten patients identified to have clinical features
compatible with... |
Which are the Proprotein Convertase Subtilisin Kexin 9 (PCSK9) inhibitors that are FDA approved? | The PCSK9 inhibitors that are FDA approved are:
1) Alirocumab and
2) Evolocumab. | INTRODUCTION: Reduction of plasma low-density lipoprotein (LDL) cholesterol
concentration with statins reduces adverse cardiovascular outcomes. However,
lack of efficacy and intolerance of statins in many patients requires
alternative treatments. Currently available non-statin alternatives include bile
acid sequest... |
Is dupilumab an antibody targeting the IL-1 receptor? | No, Dupilumab is a fully human monoclonal antibody directed against the IL-4 receptor α subunit that blocks the signaling of IL-4 and IL-13, both key cytokines in Th2-mediated pathways. | Collaborators: Nikolova-Pavlova E, Stoyanova B, Vlaeva T, Alavi A, Gauvreau G,
Henein S, Poulos E, Yang W, Lepage F, Wiseman M, Bissonnette R, Agner T,
Deleuran M, Jemec G, Skov L, Kingo K, Konno P, Pender K, Põder A, Vahlberg A,
Oksman R, Pasternack R, Remitz A, Bieber T, Dominicus R, Gerlach B, Kardorff B,
Toader... |
List active ingredients of the Stribild polypill. | Active ingredients of Stribild are elvitegravir, cobicistat, emtricitabine and tenofovir. It is used for treatment of HIV infection. | OBJECTIVE: To review the clinical trials, pharmacologic characteristics, safety,
and efficacy of the elvitegravir/cobicistat/emtricitabine/tenofovir single
tablet formulation (Stribild).
DATA SOURCES: Literature searches were performed in MEDLINE (1948-September
2012) and PubMed (1966-September 2012) using the searc... |
List clinical features of the IMAGe syndrome. | Clinical features of IMAGe syndrome include intra-uterine growth restriction, metaphyseal dysplasia, adrenal hypoplasia congenita and genital abnormalities. It is s caused by gain-of-function mutations of maternally expressed gene CDKN1C on chromosome 11p15.5. | IMAGe syndrome (intrauterine growth restriction, metaphyseal dysplasia, adrenal
hypoplasia congenita, genital abnormalities; MIM 300290) is a multisystem
disorder with a broad phenotype, which, if unrecognized, may result in major and
possibly life-threatening complications. Initial clinical features overlap with
t... |
Which gene mutations are predictive of response to anti-TNF therapy in Rheumatoid Arthritis patients? | Μutations in TLR5 and TLR1 genes contribute to differential response to anti-TNF treatment in RA. Variation at FCGR2A and functionally related genes such as DHX32 and RGS12 is also associated with the response to anti-TNF therapy in rheumatoid arthritis. | The introduction of anti-TNF therapy has dramatically improved the outlook for
patients suffering from a number of inflammatory conditions including rheumatoid
arthritis and inflammatory bowel disease. Despite this, a substantial proportion
of patients (approximately 30-40%) fail to respond to these potentially toxi... |
Which method is used for prediction of novel microRNA genes in cancer-associated genomic regions? | SSCprofiler is a computational tool utilizing a probabilistic method based on Profile Hidden Markov Models to predict novel miRNA precursors. Via the simultaneous integration of biological features such as sequence, structure and conservation, SSCprofiler achieves a performance accuracy of 88.95% sensitivity and 84.16%... | The majority of existing computational tools rely on sequence homology and/or
structural similarity to identify novel microRNA (miRNA) genes. Recently
supervised algorithms are utilized to address this problem, taking into account
sequence, structure and comparative genomics information. In most of these
studies mi... |
Does the histone chaperone ASF1 interact with histones H1/H2? | No, the histone chaperone ASF1 interacts with histones H3/H4. | In this issue of Cell, English et al. present the first crystal structure of a
histone chaperone (Asf1) bound to histones (the H3/H4 heterodimer). The
structure provides insights into how histone chaperones participate in
nucleosome disassembly. It reveals that Asf1 physically blocks (H3/H4)(2)
tetramer formation a... |
Is Hepatic mesenchymal hamartoma usually a malignant tumor? | Mesenchymal hamartoma of the liver (MHL) is an uncommon benign hepatic tumor typically affecting children under 2 years of age. | A case of a prenatally recognized hepatic mesenchymal hamartoma is presented and
the literature reviewed. These tumors are benign and usually present in early
infancy with symptoms that are related to the mass effect on adjacent organs.
Radiologic methods used in the past to image this tumor include angiography and ... |
List clinical features of EEM syndrome. | EEM syndrome is characterized by ectodermal dysplasia, ectrodactyly and macular dystrophy. | The authors reported a 41-year-old female patient with EEM (ectodermal
dysplasia, ectrodactyly and macular dystrophy) syndrome with hypotrichosis,
teeth anomaly, split hand complex and retinal changes with prominent
pigmentations located in the posterior pole of the retina. Retinal degeneration
had shown minimal pr... |
How many times is CLAST faster than BLAST? | was capable of identifying sequence similarities ~80.8 times faster than blast and 9.6 times faster than blat . | BACKGROUND: Metagenomics is a powerful methodology to study microbial
communities, but it is highly dependent on nucleotide sequence similarity
searching against sequence databases. Metagenomic analyses with next-generation
sequencing technologies produce enormous numbers of reads from microbial
communities, and ma... |
Which are the most common methods for circular RNA detection from RNASeq? | The main algorithms are circRNA_finder, find_circ, CIRCexplorer, CIRI, and MapSplice. | CircRNAs are novel members of the non-coding RNA family. For several decades
circRNAs have been known to exist, however only recently the widespread
abundance has become appreciated. Annotation of circRNAs depends on sequencing
reads spanning the backsplice junction and therefore map as non-linear reads in
the geno... |
From which cell type is leptin secreted? | leptin is mainly produced and secreted by adipocytes, but other tissues and gastric glands have also recently been shown to produce it in a dual (endocrine and exocrine) mode. | Leptin is a circulating hormone secreted by adipose and a few other tissues. The
leptin receptor consists of a single transmembrane-spanning polypeptide that is
present as a long physiologically important form as well as in several short
isoforms. Recent studies have suggested that the anterior pituitary may have a ... |
Which tool is used for the identification of recurrent variants in noncoding regions? | LARVA is an integrative framework for large-scale analysis of recurrent variants in noncoding annotations. It integrates variants with a comprehensive set of noncoding functional elements, modeling the mutation counts of the elements with a β-binomial distribution to handle overdispersion. LARVA, moreover, uses regiona... | In cancer research, background models for mutation rates have been extensively
calibrated in coding regions, leading to the identification of many driver
genes, recurrently mutated more than expected. Noncoding regions are also
associated with disease; however, background models for them have not been
investigated ... |
What body parts are also known as phalanges? | The anatomical structure of each finger is comprised of four phalanges (distal, middle, proximal, and metacarpal phalange). Toes are also known as phalages | The legal systems of the Germanic tribes in the early Middle Ages elaborated
detailed catalogs of forfeits in compensation for certain physical injuries. The
perpetrator had to pay the forfeit to the injured person, or in case of
manslaughter, to the tribe of the dead. By doing so he could avert the feud
which othe... |
Are selenium supplements recommended for prostate cancer prevention? | No. The SELECT study failed to show any significant risk reduction for prostate cancers ascribable to selenium and vitamin E supplementations. | BACKGROUND: Few studies have evaluated the relation between selenium
supplementation after diagnosis and prostate cancer outcomes.
METHODS: We prospectively followed 4459 men initially diagnosed with
nonmetastatic prostate cancer in the Health Professionals Follow-Up Study from
1988 through 2010 and examined whether... |
Which disease is treated with lucinactant? | Lucinactant us used for the prevention of respiratory distress syndrome in premature infants. | BACKGROUND AND OBJECTIVE: Evidence suggests that synthetic surfactants
consisting solely of phospholipids can be improved through the addition of
peptides, such as sinapultide, that mimic the action of human surfactant
protein-B (SP-B). A synthetic surfactant containing a mimic of SP-B may also
reduce the potential... |
Which proteins control the degradation of cryptic unstable transcripts (CUTs) in yeast? | Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. These cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome. Key substrates for exosomal degradation include aberrant functional RNAs and cryptic unstable transcripts (CUTs). Yeast RNA binding ... | Studies of yeast transcription have revealed the widespread distribution of
intergenic RNA polymerase II transcripts. These cryptic unstable transcripts
(CUTs) are rapidly degraded by the nuclear exosome. Yeast RNA binding proteins
Nrd1 and Nab3 direct termination of sn/snoRNAs and recently have also been
implicate... |
Is there any involvement of L1 retrotransposition in the Rett syndrome? | Yes. Recent studies indicate that long interspersed nuclear element-1 (L1) are mobilized in the genome of human neural progenitor cells and enhanced in Rett syndrome and ataxia telangiectasia. | Long interspersed element-1 (L1) retrotransposons compose ∼20% of the mammalian
genome, and ongoing L1 retrotransposition events can impact genetic diversity by
various mechanisms. Previous studies have demonstrated that endogenous L1
retrotransposition can occur in the germ line and during early embryonic
developm... |
Is Downs syndrome associated with decreased risk of leukemia? | No, multiple studies have established the incidence of leukemia in Down's syndrome patients to be 10- to 20-fold higher than that in the general population. | The association of Down's syndrome and leukemia has been documented for over 50
years. Multiple studies have established the incidence of leukemia in Down's
syndrome patients to be 10- to 20-fold higher than that in the general
population. The age of onset for leukemia in these children is bimodal, peaking
first in... |
Which enzyme is inhibited by ixazomib? | Ixazomib is proteasome inhibitor. It is used for treatment of multiple myeloma. | Medicinal chemists try to avoid certain organic functional groups, summarized in
an ever-growing list, in order to avoid the potential bioactivation to reactive
metabolites. To add to that alert list, we report herein that boronic
acid-containing compound structures, such as those found in proteasome
inhibitors bor... |
Does PCSK9 (Proprotein convertase subtilisin/kexin type 9) binds with HDL-receptor (HDL-R)? | No, Proprotein Convertase Subtilisin Kexin 9 (PCSK9) binds with LDL-receptor (LDL-R) causing its degradation in the lysosome with the result of LDL-C accumulating in the blood. | Mutations within PCSK9 (proprotein convertase subtilisin/kexin type 9) are
associated with domit forms of familial hyper- and hypocholesterolemia.
Although PCSK9 controls low density lipoprotein (LDL) receptor (LDLR) levels
post-transcriptionally, several questions concerning its mode of action remain
uswered. We s... |
Hy's law measures failure for what organ? | Hy's law correlates enzyme elevations with liver injury ad subsequent failure. | BACKGROUND AND AIM: The genotype-phenotype interaction in drug-induced liver
injury (DILI) is a subject of growing interest. Previous studies have linked
amoxicillin-clavulanate (AC) hepatotoxicity susceptibility to specific HLA
alleles. In this study we aimed to examine potential associations between HLA
class I a... |
Is apremilast effective for psoriatic arthritis? | Yes, apremilast, an oral phosphodiesterase 4 inhibitor, is effective for psoriatic arthritis. | BACKGROUND: Discoid lupus erythematosus (DLE) is a chronic inflammatory disorder
mediated by Th1 cells. Apremilast is a novel oral PDE4 enzyme inhibitor capable
of blocking leukocyte production of IL-12, IL-23, TNF-a, INF- with subsequent
suppression of Th1 and Th17-mediated immune responses, and proven clinical
ef... |
Is there any role of TBR1 in autism? | Yes. Exome sequencing studies have identified multiple genes harboring de novo loss-of-function (LoF) variants in individuals with autism spectrum disorders (ASD), including T-Brain-1 (TBR1), a master regulator of cortical development. T-brain-1 (TBR1) is a brain-specific T-box transcription factor. In 1995, Tbr1 was f... | The neuron-specific transcription factor T-box brain 1 (TBR1) regulates brain
development. Disruptive mutations in the TBR1 gene have been repeatedly
identified in patients with autism spectrum disorders (ASDs). Here, we show that
Tbr1 haploinsufficiency results in defective axonal projections of amygdalar
neurons ... |
What is the role of the MCM2-7 complex? | The MCM2-7 complex is a ring-shaped heterohexamer helicase, that unwinds the DNA double helix ahead of the other replication machinery. During pre-replication complex (pre-RC) formation, origin recognition complex (ORC), Cdc6, and Cdt1 cooperatively load a double-hexameric MCM2-7 complex onto DNA. Loading of MCM2-7 is ... | To maintain genome integrity in eukaryotes, DNA must be duplicated precisely
once before cell division occurs. A process called replication licensing ensures
that chromosomes are replicated only once per cell cycle. Its control has been
uncovered by the discovery of the CDKs (cyclin dependent kinases) as master
reg... |
In which fields of DNA sequencing are Bloom filters applied? | A novel algorithm, fast and accurate classification of sequences (FACSs), is introduced that can accurately and rapidly classify sequences as belonging or not belonging to a reference sequence. Classification of DNA sequences using Bloom filters Lighter is a fast, memory-efficient tool for correcting sequencing errors... | MOTIVATION: New generation sequencing technologies producing increasingly
complex datasets demand new efficient and specialized sequence analysis
algorithms. Often, it is only the 'novel' sequences in a complex dataset that
are of interest and the superfluous sequences need to be removed.
RESULTS: A novel algorithm,... |
Which 2 medications are included in the Qsymia pill? | Qsymia pill includes phentermine and topiramate. It is used for treatment of obesity. | Obesity is a world-wide epidemic associated with significant morbidity and
mortality which costs billions of dollars per year. The associated related
conditions are many and include heart disease, stroke, type II diabetes
mellitus, sleep apnea and certain types of cancer. Given that it is a
multifactorial problem, ... |
Is sonidegib effective for basal cell carcinoma? | Yes. Sonidegib, an oral smoothened antagonist, is indicated for the treatment of adults with locally advanced basal cell carcinoma (laBCC) who are not candidates for surgery or radiation therapy, or adults with recurrent laBCC following surgery or radiation therapy. | PURPOSE: This phase I trial was undertaken to determine the maximum tolerated
dose (MTD), dose-limiting toxicities (DLT), safety, tolerability,
pharmacokinetics, pharmacodynamics, and preliminary antitumor activity of the
novel smoothened inhibitor sonidegib (LDE225), a potent inhibitor of hedgehog
signaling, in pa... |
Which R package could be used for the identification of pediatric brain tumors? | MethPed | |
Describe the usefulness of CAMUR in The Cancer Genome Atlas (TCGA) | CAMUR is a new method that extracts multiple and equivalent classification models. CAMUR iteratively computes a rule-based classification model, calculates the power set of the genes present in the rules, iteratively eliminates those combinations from the data set, and performs again the classification procedure until ... | MOTIVATION: Nowadays, knowledge extraction methods from Next Generation
Sequencing data are highly requested. In this work, we focus on RNA-seq gene
expression analysis and specifically on case-control studies with rule-based
supervised classification algorithms that build a model able to discriminate
cases from co... |
Which markers are screened with the triple test for the detection of syndromes in fetus? | The markers that are screened with the triple test for the detection of syndromes in fetus are:
1) alpha-fetoprotein (AFP),
2) beta-chorionic gonadotrophin (beta-CG) and
3) unconjugated oestriol (uE3). | OBJECTIVE: Our purpose was to compare the efficacy of triple-marker screening
(alpha-fetoprotein, unconjugated estriol, human chorionic gonadotropin) with
alpha-fetoprotein plus free beta-human chorionic gonadotropin.
STUDY DESIGN: Free beta-human chorionic gonadotropin was concurrently assayed in
2349 maternal seru... |
What is the role of TAD protein domain? | TAD domain is a transcription activation domain found in transcription factors. | The amino terminus of the avian myelocytomatosis virus MC29 v-Myc oncoprotein
contains sequences that are essential for cellular transformation (S. Farina, et
al. J. Virol., 66: 2698-2708, 1992; S. Min and E. J. Taparowsky. Oncogene,
7:1531-1540, 1992) and for the ability to activate gene transcription (S. Min
and ... |
What is the function of lncRNA? | Long noncoding RNAs (lncRNAs) are involved in a variety of biological processes, including the epigenetic control of gene expression, post-transcriptional regulation of mRNA, and cellular proliferation and differentiation | BACKGROUND: Though most of the transcripts are long non-coding RNAs (lncRNAs),
little is known about their functions. lncRNAs usually function through
interactions with proteins, which implies the importance of identifying the
binding proteins of lncRNAs in understanding the molecular mechanisms underlying
the func... |
What is the function of the exosome? | Exosomes are 40-100-nm vesicles released by most cell types after fusion of multivesicular endosomes with the plasma membrane. Exosomes contain proteins and RNA species and can mediate communication and immune responses. | Exosomes are small membrane vesicles originating from late endosomes and
secreted by hematopoietic and epithelial cells in culture. Exosome proteic and
lipid composition is unique and might shed some light into exosome biogenesis
and function. Exosomes secreted from professional antigen-presenting cells
(i.e., B ly... |
Which factors drive replisome disassembly during DNA replication termination and mitosis? | CUL-2LRR-1 and UBXN-3. | Replisome disassembly is the final step of DNA replication in eukaryotes,
involving the ubiquitylation and CDC48-dependent dissolution of the CMG helicase
(CDC45-MCM-GINS). Using Caenorhabditis elegans early embryos and Xenopus laevis
egg extracts, we show that the E3 ligase CUL-2LRR-1 associates with the
replisome... |
Does RNA polymerase II have RNA cleavage activity? | In addition to RNA synthesis, multisubunit RNA polymerases (msRNAPs) support enzymatic reactions such as intrinsic transcript cleavage. The eukaryotic transcription factor TFIIS enhances elongation and nascent transcript cleavage activities of RNA polymerase II in a stalled elongation complex. | In addition to polynucleotide polymerization, DNA polymerases and bacterial RNA
polymerase can also remove nucleotides from the growing end of nucleic acid
chains. For DNA polymerases this activity is an important factor in establishing
fidelity in DNA synthesis. This report describes a novel in vitro activity of
R... |
Is there a sequence bias in MNase digestion patterns? | The cutting preference of MNase in combination with size selection generates a sequence-dependent bias in the resulting fragments. | We have mapped sequence-directed nucleosome positioning on genomic DNA molecules
using high-throughput sequencing. Chromatins, prepared by reconstitution with
either chicken or frog histones, were separately digested to mononucleosomes
using either micrococcal nuclease (MNase) or caspase-activated DNase (CAD). Both ... |
Is NEMO a zinc finger protein? | NEMO function is mediated by two distal ubiquitin binding domains located in the regulatory C-terminal domain of the protein: the coiled-coil 2-leucine zipper (CC2-LZ) domain and the zinc finger (ZF) domain. | Molecular dynamics (MD) simulation methods have seen significant improvement
since their inception in the late 1950s. Constraints of simulation size and
duration that once impeded the field have lessened with the advent of better
algorithms, faster processors, and parallel computing. With newer techniques and
hardw... |
Does TFIIS affect nucleosome positioning? | Transcript cleavage factor TFIIS reactivates the backtracked complexes and promotes pol II transcription through the nucleosome. The same nucleosomes transcribed in the opposite orientation form a weaker, more diffuse barrier that is largely relieved by higher salt, TFIIS, or FACT | Transcriptional elongation involves dynamic interactions among RNA polymerase
and single-stranded and double-stranded nucleic acids in the ternary complex. In
prokaryotes its regulation provides an important mechanism of genetic control.
Analogous eukaryotic mechanisms are not well understood, but may control
expre... |
Which two cotransporters are inhibited by sotagliflozin? | Sotagliflozin works by inhibiting sodium-glucose cotransporter 1 (SGLT1) and sodium-glucose cotransporter 2 (SGLT2). It is used for treatment of diabetes. | The sodium-dependent glucose transporter 2 (SGLT2) inhibitors are an important
emerging class for the treatment of diabetes. Development of SGLT2 inhibitors
has been oriented around a desire for high selectivity for the SGLT2 protein
relative to the SGLT1 protein. More recently, genetic and pharmacology research
in... |
What is the administration route of IVIG in Alzheimer's disease patients? | IVIG is administered intravenously. | |
What is metaSPAdes? | MetaSPAdes is a new versatile metagenomic assembler. | MOTIVATION: We present Faucet, a two-pass streaming algorithm for assembly graph
construction. Faucet builds an assembly graph incrementally as each read is
processed. Thus, reads need not be stored locally, as they can be processed
while downloading data and then discarded. We demonstrate this functionality by
per... |
What is measured through the NOMe-Seq methodology? | We have developed a method (NOMe-seq) that uses a GpC methyltransferase (M.CviPI) and next generation sequencing to generate a high resolution footprint of nucleosome positioning genome-wide using less than 1 million cells while retaining endogenous DNA methylation information from the same DNA strand. DNaseI-seq and N... | Despite the fact that 45% of all human gene promoters do not contain CpG
islands, the role of DNA methylation in control of non-CpG island promoters is
controversial and its relevance in normal and pathological processes is poorly
understood. Among the few studies which investigate the correlation between DNA
methy... |
What is the function of the dormancy survival regulator (DosR) in Mycobacterium tuberculosis? | During this phase, at least 48 genes, collectively named Dormancy survival regulator (DosR) regulon, are important for the long-term survival of bacilli under a non-respiring state. | Mycobacterium tuberculosis residing within pulmonary granulomas and cavities
represents an important reservoir of persistent organisms during human latent
tuberculosis infection. We present a novel in vivo model of tuberculosis
involving the encapsulation of bacilli in semidiffusible hollow fibers that are
implante... |
Which are the effects of ALDH2 deficiency? | In alcohol drinkers, ALDH2-deficiency is a well-known risk factor for upper aerodigestive tract cancers, i.e., head and neck cancer and esophageal cancer. Diabetic patients with ALDH2 mutations are predisposed to worse diastolic dysfunction.
These data demonstrate that ALDH2 deficiency enhances EtOH-induced disruption ... | Acetaldehyde (ACH) associated with alcoholic beverages is Group 1 carcinogen to
humans (IARC/WHO). Aldehyde dehydrogenase (ALDH2), a major ACH eliminating
enzyme, is genetically deficient in 30-50% of Eastern Asians. In alcohol
drinkers, ALDH2-deficiency is a well-known risk factor for upper aerodigestive
tract can... |
What is the role of the positive effector of transcription (pet) in the hepatitis B virus? | This element, which we have named pet (positive effector of transcription), exerts its effect in cis in a position and orientation-dependent manner, suggesting that it may function as part of the nascent pregenome transcript. In the presence of this region, deletion of pet activates transcription from downstream promo... | We report the presence of two elements, pet and net, that are required for
proper transcription of the duck hepatitis B virus (DHBV). These regions were
previously identified by using plasmid clones of the virus in transient
expression assays (M. Huang and J. Summers, J. Virol. 68:1564-1572, 1994). In
this study, w... |
What is the role of Kmt5a in liver? | H4K20 monomethylation maintains genome integrity by regulating proper mitotic condensation, DNA damage response, and replication licensing. In non-dividing hepatic cells, H4K20Me1 is specifically enriched in active gene bodies and dynamically regulated by the antagonistic action of Kmt5a methylase and Kdm7b demethylase... | H4K20 monomethylation maintains genome integrity by regulating proper mitotic
condensation, DNA damage response, and replication licensing. Here, we show
that, in non-dividing hepatic cells, H4K20Me1 is specifically enriched in active
gene bodies and dynamically regulated by the antagonistic action of Kmt5a
methyla... |
Is tretinoin effective for photoaging? | Yes, Tretinoin is commonly used topically in the treatment of photoaging. | Tretinoin was shown in the late 1960s to be useful for the treatment of
disorders associated with abnormal epithelial differentiation; however, because
of irritation, retinoids were only slowly accepted. In the 1970s, evidence
accumulated to show that topical tretinoin could modulate many of the
abnormalities in th... |
What is the difference between ganglion mother cells (GMC) and intermediate neural precursor cells (INP) in Drosophila? | GMC divides only once to give rise to two post-mitotic cells (neurons or glia), whereas the INP can also self-renew, albeit for fewer rounds than a NSC, and generate GMCs | The approximately 300 distinct neurons comprising each hemineuromere of the
Drosophila embryonic central nervous system are derived from a segmentally
reiterated array of approximately 30 progenitor cells, neuroblasts (NBs). Each
NB has a unique identity and undergoes repeated cell divisions to produce
several smal... |
What is the FIRE (Functional Inference of Regulators of Expression) tool? | FIRE (Functional Inference of Regulators of Expression) is a tool to score both noncoding and coding SNVs based on their potential to regulate the expression levels of nearby genes. | |
Does TUC.338 inhibit colorectal cancer? | No. TUC.338 is significantly up-regulated in colorectal cancers (CRC) tissue and CRC cell lines, and the up-regulated TUC.338 is associated with lymph node metastasis. TUC.338 acts as a novel oncogene by targeting the TIMP-1 gene thus promoting colorectal cancer cell migration and invasion. | |
Describe mechanism of action of Napabucasin. | Napabucasin (BBI608) is an orally administered small molecule that blocks stem cell activity in cancer cells by targeting the signal transducer and activator of transcription 3 (STAT3) pathway. | A small population of cells with stem cell-like properties in prostate cancer
(PCa), called prostate cancer stem cells (PrCSCs) or prostate stemness-high
cancer cells, displays highly tumorigenic and metastatic features and may be
responsible for the therapy resistance. A small molecule, napabucasin (BBI608),
recen... |
Has ruxolitinib received FDA approval? | Yes, ruxolitinib is FDA approved. In 2011 the oral JAK2 kinase inhibitor ruxolitinib became the first Food and Drug Administration (FDA)-approved drug for the treatment of myelofibrosis. | Chronic myeloproliferative neoplasms (MPN) comprise a spectrum of clonal
neoplastic disorders characterized by overproduction of terminally
differentiated cells of the myeloid lineage. A common genetic basis for the
BCR-ABL-negative MPN disorders was elucidated in 2005 with the identification of
the JAK2V617F mutat... |
Do origins of replication close to yeast centromeres fire early or late? | Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase we discovered that each centromere is associated with a replication origin that is the first to fire on its respective chromosome. | In the yeast Saccharomyces cerevisiae, origins of replication (autonomously
replicating sequences; ARSs), centromeres, and telomeres have been isolated and
characterized. The identification of these structures allows the construction of
artificial chromosomes in which the architecture of eukaryotic chromosomes may
... |
Is scuba diving safe during pregnancy? | No, scuba diving should be avoided throughout pregnancy because the fetus is at an increased risk for decompression sickness during this activity. | Scuba diving is a leisure activity increasingly popular amongst women. Many
women are concerned about the risks associated with diving and a known or
planned pregcy. In order to advise these young women, we have reviewed the
literature concerning women and diving as well as animal studies on the subject.
The differ... |
Does deflazacort have more side effects than prednisone? | Deflazacort produces fewer side effects than Prednisone in DMD patients. | Though Deflazacort and prednisone improve clinical endpoints in Duchenne
muscular dystrophy (DMD) patients, Deflazacort produces fewer side effects. As
mechanisms of improvement and side effect differences remain unknown, we
evaluated effects of corticosteroid administration on gene expression in blood
of DMD patie... |
Does echinacea increase anaphylaxis risk? | Yes, there is evidence that echinacea use is associated with anaphylaxis. | A woman with atopy experienced anaphylaxis after taking, among other dietary
supplements, a commercial extract of echinacea. Hypersensitivity was confirmed
by skinprick and RAST testing. Regular ingestion of echinacea by up to 5% of
surveyed patients with atopy, combined with detection of echinacea-binding IgE
in a... |
Are neurexins localized at pre-synapses? | Yes, neurexins are localized at pre-synapses. | Neurexins and neuroligins are two distinct families of single-pass transmembrane
proteins localized at pre- and postsynapses, respectively. They
trans-synaptically interact with each other and induce synapse formation and
maturation. Common variants and rare mutations, including copy number
variations, short deleti... |
Is there any role of 5hmC in T-cell development and differentiation? | Yes. 5hmC is enriched in the gene body of highly expressed genes at all different stages of T-cell development in the thymus and that its presence correlates positively with gene expression. Further emphasizing the connection with gene expression, 5hmC is enriched in active thymus-specific enhancers and genes encoding ... | Author information:
(1)Department of Signaling and Gene Expression, La Jolla Institute for Allergy
and Immunology, La Jolla, CA 92034;
(2)Department of Signaling and Gene Expression, La Jolla Institute for Allergy
and Immunology, La Jolla, CA 92034;Department of Information and Computer
Science, Aalto University Sch... |
Which are the properties of mammalian GA-sequences? | In this article we identify for the first time explicitly the GA-sequences as a class of fractal genomic sequences that are easy to recognize and to extract, and are scattered densely throughout the chromosomes of a large number of genomes from different species and kingdoms including the human genome. most GA-sequen... | Pyrimidine-purine DNAs with repeating sequences can be made to undergo a
reversible transition to possibly a tetra-stranded complex. Physicochemical
characterization of the new structures and model building are consistent with,
in the case of d(TC)n-d(GA)n, a tetra-stranded complex forming by the addition
of d(GA)n... |
What is the main focus of the CVE R/Bioconductor package? | The CVE package allows interactive variant prioritisation to expedite the analysis of cancer sequencing studies. | |
Are there ultraconserved genomic regions in the budding yeast? | Yes. In addition to some fundamental biological functions, ultraconserved genomic regions play an important role in the adaptation of S. cerevisiae to the acidic environment. | MOTIVATION: In the evolution of species, a kind of special sequences, termed
ultraconserved sequences (UCSs), have been inherited without any change, which
strongly suggests those sequences should be crucial for the species to survive
or adapt to the environment. However, the UCSs are still regarded as mysterious
g... |
Is davunetide being considered for the treatment of progressive supranuclear palsy? | Yes, Davunetide's efficacy and tolerability are being tested in a placebo-controlled study in PSP patients. | Progressive supranuclear palsy (PSP) is a rare neurodegenerative disease
characterized by the accumulation of tau protein aggregates in the basal
ganglia, brainstem and cerebral cortex leading to rapid disease progression and
death. The neurofibrillary tangles that define the neuropathology of PSP are
comprised of ... |
What is the origin of XUT transcripts in yeast? | XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast | Non-coding (nc)RNAs are key players in numerous biological processes such as
gene regulation, chromatin domain formation and genome stability. Large ncRNAs
interact with histone modifiers and are involved in cancer development,
X-chromosome inactivation and autosomal gene imprinting. However, despite recent
evidenc... |
How many genes constitute the DosR regulon, controlled by the dormancy survival regulator (DosR) in Mycobacterium tuberculosis? | The Mycobacterium dormancy survival regulator (DosR) regulon is composed of 48 co-regulated genes. | Mycobacterium bovis BCG is widely used as a vaccine against tuberculosis (TB),
despite its variable protective efficacy. Relatively little is known about the
immune response profiles following BCG vaccination in relation to protection
against TB. Here we tested whether BCG vaccination results in immune responses
to... |
Is autophagy modulated in a circadian fashion? | Yes, metabolic pathways, bile acid synthesis, and autophagic and immune/inflammatory processes are driven by the biological clock. | Autophagy is a highly conserved intracellular degradation system, and recently
was shown to display circadian rhythms in mice. The mechanisms underlying
circadian regulation of autophagy, however, are still unclear. Here, we observed
that numbers of autophagosomes and autolysosomes exhibit daily rhythms in the
zebr... |
Is Drk essential for anesthesia-resistant memory (ARM) in Drosophila? | Yes. Drk, the Drosophila ortholog of the adaptor protein Grb2, is essential for ARM within adult mushroom body neurons in Drosophila. | Anesthesia-resistant memory (ARM) was described decades ago, but the mechanisms
that underlie this protein synthesis-independent form of consolidated memory in
Drosophila remain poorly understood. Whether the several signaling molecules,
receptors, and synaptic proteins currently implicated in ARM operate in one or ... |
What is oclacitinib? | Oclacitinib (APOQUEL(®)) is a Janus kinase inhibitor with activity against cytokines involved in allergy. It is a potent inhibitor of JAK1. It effectively controls clinical signs associated with allergic skin disease in dogs. | |
Are TAD boundaries in Drosophila depleted in highly-expressed genes? | Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. | The spatial arrangement of interphase chromosomes in the nucleus is important
for gene expression and genome function in animals and in plants. The recently
developed Hi-C technology is an efficacious method to investigate genome
packing. Here we present a detailed Hi-C map of the three-dimensional genome
organizat... |
List the two most important hematological features of the Evans syndrome | Evans syndrome is a rare autoimmune disorder, which is characterized by immune thrombocytopenia and autoimmune hemolytic anemia. | Evans' syndrome is an unusual illness of autoimmune etiology, characterized by
thrombocytopenia and hemolytic anemia. This is more frequent in females
throughout first half of the life and during pregcy. The present paper
describes two pregt women with Evans syndrome associated to preeclampsia.
This report emphasiz... |
Is there increased recombination rate in human regulatory domains? | No. There is evidence of significantly reduced recombination rate compared to matched control regions at human regulatory domains. | |
Is enzastaurin effective treatment of glioblastoma? | No. Enzastaurin does not improve prognosis of glioblastoma patients. | The prognosis of patients with glioblastoma, anaplastic astrocytoma, and
anaplastic oligodendroglioma remains poor despite standard treatment with
radiotherapy and temozolomide. Molecular targeted therapy holds the promise of
providing new, more effective treatment options with minimal toxicity. However,
the develo... |
Which yeast nucleosomes are preferentially marked by H2A.Z? | Yeast nucleosomes containing histone variant H2A.Z (Htz1p in yeast) are primarily composed of H4 K12ac and H3 K4me3. | Nucleosome positioning maps of several organisms have shown that Transcription
Start Sites (TSSs) are marked by nucleosome depleted regions flanked by strongly
positioned nucleosomes. Using genome-wide nucleosome maps and histone variant
occupancy in the mouse liver, we show that the majority of genes were associate... |
Is dasatinib effective for treatment of glioblastoma? | No, dasatinib is ineffective for treatment of glioblastoma and is associated with significant toxicity. | There is no effective treatment for recurrent glioblastoma (GBM) after
bevacizumab failure. Putative mechanisms of resistance to bevacizumab include
increased pericyte coverage, mediated partly by platelet-derived growth factor
receptor (PDGFR) signaling, and an infiltrative tumor growth pattern potentially
depende... |
Which algorithm is available for computing minimal absent words using external memory? | emMAW | |
Has IVIG been tested in clinical trials for the treatment of Alzheimer's disease? | Yes, IVIG has been tested in clinical trials for the treatment of Alzheimer's disease. | |
Which type of urinary incontinence is diagnosed with the Q tip test? | Stress urinary incontinence is diagnosed with the Q tip test. The test evaluates urethral mobility. | Thirty-two female patients with clinical and urodynamic findings of genuine
stress urinary incontinence were evaluated before and 6 months after surgery for
stress urinary incontinence. Twenty-nine control patients had identical
evaluations before and 6 months after surgery which did not involve the
urethrovesical ... |
Does a tonsillectomy affect the patient's voice? | Some patients complaint for dry throat, foreign body sensation or voice change after tonsillectomy. Group B had a better awareness of tooth damage . There were no differences in secondary outcomes across treatment groups. The incidence rates of voice change, velopharyngeal insufficiency, bleeding, constipation, dehydr... | This paper reports about a female mutational falsetto, that means an unusual
high (309 Hz base frequency) fundamental frequency of the speaking voice in a
19-year-old girl. The psychological background and the epicrisis as well as the
practical negative result of the hormon- and metabolism examination allow the
dia... |
List the four most important interferonopathies | Aicardi-Goutières syndrome
chilblain lupus
ubiquitin specific peptidase 18 (USP18)-deficiency
Singleton-Merten syndrome | Autoinflammatory disorders are sterile inflammatory conditions characterized by
episodes of early-onset fever and disease-specific patterns of organ
inflammation. Recently, the discoveries of monogenic disorders with strong type
I interferon (IFN) signatures caused by mutations in proteasome degradation and
cytopla... |
List the partners of budding yeast Cdc48 that are important for disassembly of ubiquitylated CMG helicase at the end of chromosome replication | The ubiquitin-binding Ufd1-Npl4 complex recruits Cdc48 to ubiquitylated CMG helicase at the end of chromosome replication. | Disassembly of the Cdc45-MCM-GINS (CMG) DNA helicase is the key regulated step
during DNA replication termination in eukaryotes, involving ubiquitylation of
the Mcm7 helicase subunit, leading to a disassembly process that requires the
Cdc48 "segregase". Here, we employ a screen to identify partners of budding
yeast... |
How are topologically associating domains (TAD) associated with replication timing? | Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program. Topologically associating domains are stable units of replication-timing regulation. | Mammalian genomes are partitioned into domains that replicate in a defined
temporal order. These domains can replicate at similar times in all cell types
(constitutive) or at cell type-specific times (developmental). Genome-wide
chromatin conformation capture (Hi-C) has revealed sub-megabase topologically
associati... |
How are cryptic unstable transcripts (CUTs) defined? | This resource includes deletions of small nuclear RNAs (snRNAs), transfer RNAs (tRNAs), small nucleolar RNAs (snoRNAs), and other annotated ncRNAs as well as the more recently identified stable unannotated transcripts (SUTs) and cryptic unstable transcripts (CUTs) whose functions are largely unknown There is extensive ... | Studies of yeast transcription have revealed the widespread distribution of
intergenic RNA polymerase II transcripts. These cryptic unstable transcripts
(CUTs) are rapidly degraded by the nuclear exosome. Yeast RNA binding proteins
Nrd1 and Nab3 direct termination of sn/snoRNAs and recently have also been
implicate... |
How many Groucho-related genes (GRG) are contained in the mouse genome? | It spans approximately 7 kb on chromosome 10 and consists of seven exons. The groucho-related genes (Grg) of the mouse comprise at least four family members. | The Grg gene encodes a 197-amino-acid protein homologous to the amino-terminal
domain of the product of the groucho gene of the Drosophila Enhancer of split
complex. We describe here the genomic organization of the mouse Grg gene. It
spans approximately 7 kb on chromosome 10 and consists of seven exons. The 3'
regi... |
What is mechanism of action of galunisertib? | Galunisertib is a transforming growth factor-β receptor type I kinase inhibitor (TGF-βRI). It was tested for treatment of solid cancers, including glioblastoma and neuroblastoma, and liver fibrosis. | BACKGROUND: The combination of galunisertib, a transforming growth factor
(TGF)-β receptor (R)1 kinase inhibitor, and lomustine was found to have
antitumor activity in murine models of glioblastoma.
METHODS: Galunisertib (300 mg/day) was given orally 14 days on/14 days off
(intermittent dosing). Lomustine was given ... |
What is a coligo? | Coligos are circularized oligodeoxynucleotides | Chemically synthesized DNA can carry small RNA sequence information but
converting that information into small RNA is generally thought to require large
double-stranded promoters in the context of plasmids, viruses and genes. We
previously found evidence that circularized oligodeoxynucleotides (coligos)
containing ... |
What is the relationship of fyn kinase and tau? | The Fyn kinase interacts with tau. The activated Fyn kinase hyperphosphorylates the tau protein. | The past decade has brought tremendous progress in unraveling the
pathophysiology of Alzheimer's disease (AD). While increasingly sophisticated
immunotherapy targeting soluble and aggregated brain amyloid-beta (Aβ) continues
to dominate clinical research in AD, a deeper understanding of Aβ physiology has
led to the... |
Which are the main manifestations of Ohdo syndrome? | Severe ID, absent or deficient language, skeletal manifestations including bilateral patella dislocations. | We report on a girl with growth and mental retardation, peculiar face with
ptosis, epicanthus, broad nasal bridge, low-set and abnormal ears, cleft uvula,
congenital heart defect, and anal atresia. A similar condition was reported
previously by Wiedemann et al. [1982: An atlas of characteristic syndromes: a
visual ... |
Which algorithm is used by the UCSC Genome Browser? | The UCSC Genome Browser organizes data and annotations (called tracks) around the reference sequences or draft assemblies of many eukaryotic genomes and presents them using a powerful web-based graphical interface. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser,... | The University of California Santa Cruz (UCSC) Genome Browser Database is an up
to date source for genome sequence data integrated with a large collection of
related annotations. The database is optimized to support fast interactive
performance with the web-based UCSC Genome Browser, a tool built on top of the
data... |
Which aminoacid position in the human CREB protein is phosphorylated? | pCREB is phosphorylated at its Serine 133. | Cyclic-AMP response element-binding protein (CREB) signaling has a critical role
in the formation of memories. CREB signaling is dysfunctional in the brains of
mouse models of Alzheimer's disease (AD), and evidence suggests that CREB
signaling may be disrupted in human AD brains as well. Here, we show that both
CRE... |
Which gene is the paralog of yeast UPC2? | the related transcription factors Ecm22 and Upc2 play a crucial role in Saccharomyces cerevisiae filamentation. | We have expressed a cDNA to human apolipoprotein E (apoE) in Saccharomyces
cerevisiae. Secretion of apoE was achieved only by the use of a mutant (upc2)
strain of yeast with the phenotype of enhanced uptake and intracellular
esterification of exogenous cholesterol. Approximately 40 ng/ml apoE was
secreted by upc2 m... |
Where is the enzyme PM20D1 localized? | PM20D1 is enriched in UCP1+ adipocytes |
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