Tag: AF

©santoelia/stock.adobe.com The FDA has granted fast track designation for 3 prospective indications for milvexian, an investigational oral factor Xla inhibitor, in joint development by Janssen Pharmaceutical and Bristol Myers Squibb. The indications are stroke prevention after an acute ischemic stroke or high-risk transient ischemic attack, recent acute coronary syndrome, and atrial…

Anderson IC, Campbell CD, Prosser JI (2003) Diversity of fungi in organic soils under a moorland–Scots pine (Pinus sylvestris L.) gradient. Environ Microbiol 5(11):1121–1132. doi.org/10.1046/j.1462-2920.2003.00522.x Aria M, Cuccurullo C (2017) Bibliometrix: an R-tool for comprehensive science mapping analysis. J Informetr 11(4):959–975. doi.org/10.1016/j.joi.2017.08.007 CrossRef  Google Scholar  Artursson V, Jansson JK (2003)…

WHO. World malaria report 2022. Geneva: World Health Organization; 2023. Google Scholar  Ministério da Saúde/Secretaria de Vigilância em Saúde. Malária 2021. Boletim Epidemiológico. Número especial. Brasília: MS/SVS; 2021. 100 pp. Melo JO, Padilha MAO, Barbosa RTA, Alonso WJ, Vittor AY, Laporta GZ. Evaluation of the malaria elimination policy in Brazil:…

Dear community I’m currently trying to try a GWAS for case control study using PLINK using whole exome VCF files. I understand that I need to convert these VCF files into PLINK’s binary format (bed/bim/fam) before I can proceed with the GWAS. From my literature I have to manually create…

Earlier this week, the Center for AI Safety put out a statement that’s sobering both in its content and in its brevity. Mitigating the risk of extinction from AI should be a global priority alongside other societal-scale risks such as pandemics and nuclear war. The 1,100 signatures on this statement…

Correa P, Houghton J. Carcinogenesis of Helicobacter pylori. Gastroenterology. 2007;133(2):659–72. Article  CAS  PubMed  Google Scholar  Dube C, Tanih N, Ndip R. Helicobacter pylori in water sources: a global environmental health concern. Rev Environ Health. 2009;24(1):1–14. Article  CAS  Google Scholar  Stark RM, Gerwig GJ, Pitman RS, Potts LF, Williams NA, Greenman…

SOUTH SAN FRANCISCO, Calif.–(BUSINESS WIRE)–Jun 1, 2023– Vistagen (Nasdaq: VTGN), a late clinical-stage biopharmaceutical company aiming to transform the treatment landscape for individuals living with anxiety, depression and other central nervous system (CNS) disorders, today announced that positive safety and exploratory efficacy data from its large Phase 3 open-label study…

Produced in Partnership with SPT LabtechMay 30 2023Reviewed by Aimee Molineux Next-generation sequencing (NGS) has transformed the medical and biological sciences, delivering enhanced throughput and improved affordability. The fundamentals of NGS library preparation remain mostly unchanged, despite a substantial drop in the time required (now taking less than half a…

I am trying to run MutSIgCV and got stuck with this error: MutSigCV allsamples.md.tc.ir.br.pr.ug.dbsnp.vep.maf \ “$anno”exome_full192.coverage.txt \ “$anno”gene.covariates.txt \ my_results \ “$anno”mutation_type_dictionary_file.txt \ “$anno”chr_files_hg19 ====================================== MutSigCV v1.4 (c) Mike Lawrence and Gaddy Getz Broad Institute of MIT and Harvard ====================================== MutSigCV: PREPROCESS ——————– Loading mutation_file… Error using MutSigCV>MutSig_preprocess (line 246)…

Software description This open source code provides an implementation of the AlphaFold v2.0 system. It allows users to predict the 3-D structure of arbitrary proteins with unprecedented accuracy. AlphaFold v2.0 is a completely new model that was entered in the CASP14 assessment and published in Nature (Jumper et al. 2021)….

Targeted Ablation of Epicardial Ganglionated Plexi During Cardiac Surgery with Pulsed Field Electroporation ( NEURAL AF ) Abstract Background: Modulation of the cardiac autonomic nervous system (ANS) is a promising adjuvant therapy in the treatment of atrial fibrillation (AF). In pre-clinical models, pulsed field (PF) energy has the advantage of…

I am encountering “Error: Frequency/count too large on line XXX of –read-freq file” when applying a score using plink2.  As far as I can tell, this seems to be happening where the site is multiallelic in the cohort that I’m applying the score in. (The derivation cohort data where the…

Preuss TM. The human brain: rewired and running hot. Ann N Y Acad Sci. 2011;1225 Suppl 1(Suppl 1):E182-191. Article  PubMed  Google Scholar  Roth G, Dicke U. Evolution of the brain and intelligence in primates. Prog Brain Res. 2012;195:413–30. Article  PubMed  Google Scholar  Laland K, Seed A. Understanding human cognitive uniqueness….

So I was able to retrieve this information using bcftools query. As stated in the bcftools documentation, the FORMAT fields can be accessed if they are declared in square brackets. I stored the values for AF and DP in a csv file (stats.csv) using this command: bcftools query -f'[%CHROM,%POS,%AF,%DP\n]’ SAMPLE_3.vcf…

New data from three late-breaking clinical trials has demonstrated the safety and efficacy of pulsed field ablation (PFA) as a viable, non-thermal treatment option for atrial fibrillation (AF) and were presented at the 2023 Heart Rhythm (May 19–21, New Orleans, USA) annual meeting. Today, the standard approaches to AF treatment…

Messina JP, Brady OJ, Golding N, Kraemer MUG, Wint GRW, Ray SE, Pigott DM, Shearer FM, Johnson K, Earl L, et al. The current and future global distribution and population at risk of dengue. Nat Microbiol. 2019;4(9):1508–15. Article  CAS  PubMed  PubMed Central  Google Scholar  Zeng Z, Zhan J, Chen L,…

Catheter ablation using pulsed field energy leads to freedom from atrial arrhythmia in many patients with atrial fibrillation (AF), according to data from MANIFEST-PF*. MANIFEST-PF was a retrospective, multinational, patient-level registry that included all patients undergoing postapproval treatment with a multielectrode 5-spline pulsed field ablation catheter for AF. Pulsed field…

Aase K, Jensen H, Muff S (2022) Genomic estimation of quantitative genetic parameters in wild admixed populations. Meth Ecol Evol 13:1014–1026 Article  Google Scholar  Aitken SN, Bemmels JB (2015) Time to get moving: Assisted gene flow of forest trees. Evol Appl 9:271–290 Article  PubMed  PubMed Central  Google Scholar  Alberto F…

VCF file will be having seven fixed columns and INFO column. Chromosome, position, ID, ref, alt, qual, filter, and INFO column. This INFO column will be having the variant related information. In the INFO column CSQ field will be having multiple fields – 82 fields fixed with the delimeter “|”…

Dubilier N, Bergin C, Lott C. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nat Rev Microbiol. 2008;6:725–40. Article  CAS  PubMed  Google Scholar  Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the dark: phylogenetic and physiological diversity of chemosynthetic symbioses. Annu Rev Microbiol. 2021;75:695–718….

Heo J, Cho H, Kim MA, Hamada M, Tamura T, Saitou S, Kim SJ, Kwon SW. Protaetiibacter intestinalis gen. nov., of the family Microbacteriaceae, isolated from gut of Protaetia brevitarsis seulensis, reclassification of Lysinimonas kribbensis Jang et al. 2013 as Pseudolysinimonas kribbensis gen. nov., comb. nov. and emended description of…

National Cancer Institute (2020) Cancer stat facts: diffuse large B-cell lymphoma. seer.cancer.gov/statfacts/html/dlbcl.html. Accessed 9 Nov 2022 Sant M, Allemani C, Tereanu C et al (2010) Incidence of hematologic malignancies in Europe by morphologic subtype: results of the HAEMACARE project. Blood 116(19):3724–3734 Article  CAS  PubMed  Google Scholar  Al-Hamadani M, Habermann TM,…

Fleischhacker WW, Arango C, Arteel P, Barnes TR, Carpenter W, Duckworth K, et al. Schizophrenia-time to commit to policy change. Schizophr Bull. 2014;40:S165–S94. Article  PubMed  PubMed Central  Google Scholar  Cirulli ET, Guo L, Leon Swisher C, Shah N, Huang L, Napier LA, et al. Profound perturbation of the metabolome in…

WHO. Word Malaria Report 2021. Geneva: World Health Organization; 2021. Google Scholar  White NJ, Nosten F. Artemisinin-based combination treatment of falciparum malaria. Am J Trop Med Hyg. 2007;77(Suppl 6):181–92. PubMed  Google Scholar  Amato R, Pearson RD, Almagro-Garcia J, Amaratunga C, Lim P, Suon S, et al. Origins of the current…

Wastewater sample collection, RNA extraction, and sequencing Houston Water collected and provided weekly 24-hour time-weighted composite influent (raw wastewater) samples from 39 wastewater treatment plants (WWTPs) in Houston covering a service area of approximately 580 miles2 and serving over 2.3 million people. In total, 2637 samples were analyzed. Untreated wastewater…

I downloaded s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph/hprc-v1.0-minigraph-grch38.gfa.gz which contains hg38, chm13, and other assemblies, and now am trying to use vg to generate a VCF with the variants in CHM13 relative to hg38. After converting to vg format, by running vg convert <(gunzip -c hprc-v1.0-minigraph-grch38.gfa.gz) > hprc-v1.0-minigraph-grch38.vg, I tried a few different variations of…

Hello Team, I am trying to add an authentication header in the OpenAPI Job from the AF. The import is working great and also the active scan but i need to authenticate via Authorization Header. I tried using the -configfile conf option but it seems nothing is happening. the conf…

Haplotype specific alleles 0 Dear all, Do you know of any tool that provides allelic frequency information within a haplotype? > Input: Bam files > Output: allele1 – pos A/T AF=0.5, pos A/C AF=0.3, pos C/G AF=0.98 allele2 – pos A/C AF=0.3, pos………. I tried Shorah tool, but if I…

Dick G, Anantharaman K, Baker B, Li M, Reed D, Sheik C. The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Front Microbiol. 2013;4:124. Dick GJ. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat Rev Microbiol. 2019;17:271–83. Article  CAS …

Credit: AF-studio/Getty Images The National Institutes of Health (NIH) announced Thursday a new program dubbed the Common Fund’s Somatic Mosaicism Across Human Tissues (SMaHT) Network, a five-year $140 million effort to better understand the level of genetic variation present in cells throughout the human body. The SMaHT Network will be…

Dear Biostars, I am having a confusing issue with my CADD plugin. This is confusing because when I run VEP for my whole trio – all the plugins work fine. However when I try to run CADD for individual – pivoted files – it no longer does and I get…

Ettinger DS, Wood DE, Aisner DL, Akerley W, Bauman JR, Bharat A, Bruno DS, Chang JY, Chirieac LR, D’Amico TA, et al. NCCN Guidelines Insights: Non-Small Cell Lung Cancer, Version 2.2021. J Natl Compr Canc Netw. 2021;19(3):254–66. Article  CAS  PubMed  Google Scholar  Aberle DR, Adams AM, Berg CD, Black WC,…

Chenxing Wei,1,&ast; Jian Chen,1,&ast; Tanveer Muhammad Anwar,2,&ast; Lingling Huang,1 Wenjie Yang,3 Xueyan Dong,1 Qiong Chen,1 Min Yue,2,4,5 Daojun Yu1,3 1Department of Medical Laboratory, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People’s Republic of China; 2Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University…

Removing multi-variant records from vcf file 3 I am using gatk ASEReadCounter to get the read counts per allele. To do so, I used the following command: gatk ASEReadCounter -R /path_to_genome/hg38_genome/GRCh38.p13.genome.fa -I sample.sorted.bam -V sample.vcf.gz -O output.table I used GATK4. but I realized In my VCF at position chr1:1574033, there…

Baumgart DC, Sandborn WJ. Crohn’s disease. Lancet. 2012;380(9853):1590–605. Article  PubMed  Google Scholar  Bernstein CN. Treatment of IBD: where we are and where we are going. Am J Gastroenterol. 2015;110(1):114–26. Article  PubMed  Google Scholar  Sies H. Oxidative stress: a concept in redox biology and medicine. Redox Biol. 2015;4:180–3. Article  CAS  PubMed …

Sample selection We identified parent–child trios from the 1KG in which the child cell line banked within the NHGRI Sample Repository for Human Genetic Research at the Coriell Institute for Medical Research was listed as having zero expansions and two or fewer passages, and rank-ordered representative individuals as follows. Loci…

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Hi, I use a loop for that. Something like this to inspire you: # Enter folder where gnomAD data are here: gnomAD=”/path/to/gnomAD/database/release/3.1.2/gnomad.genomes.v3.1.2.sites.” # Enter the folder where your results are and will be annotated further cd /path/to/your/results/folder/ # Enter the name of the final results’ file from SnpSift ann=”results.ann.gnomAD.genomes.v3.1.2.vcf” #…

Using GATK Mutect2, we collected several variants in EGFR region. However, one variants NM_005228.5(EGFR):c.2239_2248delinsC (p.Leu747_Ala750delinsPro) were called as two separated ones. The two variants can not combined even we set the -max-mnp-distance to 20. 7 55242465 . GGAATTAAGA G . .AS_SB_TABLE=5567,5732|44,36;DP=11794;ECNT=2;MBQ=20,20;MFRL=188,168;MMQ=60,60;MPOS=39;NALOD=3.85;NLOD=1755.82;POPAF=4.52;TLOD=256.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB0|1:2957,80:0.027:3037:1304,28:1306,51:0|1:55242465_GGAATTAAGA_G:55242465:1402,1555,44,36 0|0:8342,0:1.710e-04:8342:3598,0:4195,0:0|1:55242465_GGAATTAAGA_G:55242465:4165,4177,0,0 7 55242478 . G C . .AS_SB_TABLE=5360,5529|44,36;DP=11030;ECNT=2;MBQ=20,20;MFRL=189,168;MMQ=60,60;MPOS=43;NALOD=3.93;NLOD=1686.18;POPAF=4.52;TLOD=256.12…

X-ray image of the catheter introduced into the pulmonary veins as far as the foci to be destroyed by electroporation. Photo DR. High-voltage electrical impulses applied for a few seconds to open pores in the membranes of targeted heart cells and destroy them: the Arnault-Tzanck Institute, in Saint-Laurent-du-Var, is one…

You can check out these services: * myvariant.info/v1/api#/ * api.ncbi.nlm.nih.gov/variation/v0/ * rest.ensembl.org/#VEP As far as I know they all return JSON. You can check out a tool like jq or a package in your fav language to parse JSON. **Example:** curl -s ‘rest.ensembl.org/vep/human/id/rs2656176?&#8217; -H ‘Content-type:application/json’ | jq ‘.[].colocated_variants[].frequencies’ { “A”:…

La Rosa SL, Ostrowski MP, Vera-Ponce de León A, McKee LS, Larsbrink J, Eijsink VG, Lowe EC, Martens EC, Pope PB (2022) Glycan processing in gut microbiomes. Curr Opin Microbiol 67:102143. doi.org/10.1016/j.mib.2022.102143 CrossRef  CAS  PubMed  Google Scholar  Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette…

GROMACS version:2018.1-1GROMACS modification: Yes/NoHere post your questionhelloi have done 3 to 4 simulation on gromacs and gives good results. but now i am trying to increase the the ns so its show error when I apply every force field. i have checked it on other than my protein and the…

Double Alleles in gVCF file for ChrX, ChrY & ChrM 1 Hello, I understand for that for men X,Y, mitochondria chromosomes should be represented by a single allele. but I have a gVCF file that has 2 alleles (homozygous or heterozygous) for each position under these chromosomes, mostly with GT:…

Introduction Hyperuricemia is a disease caused by irregular purine metabolism, which is always accompanied by excessive production or abnormal excretion of uric acid (UA).1 Most notably, the overall incidence of hyperuricemia in China has been increasing over the past decade with the westernization of eating habits.2,3 However, there are blind…

scEC&T sequencing A detailed, step-by-step protocol of scEC&T-seq is available on the Nature Protocol Exchange46 and is described below. The duration of the protocol is approximately 8 days per 96-well plate. Cell culture Human tumor cell lines were obtained from ATCC (CHP-212) or were provided by J. J. Molenaar (TR14; Princess…

Alkooranee JT, Liu S, Aledan TR, Yin Y, Li M (2015) First report of powdery mildew caused by erysiphe cruciferarum on brassica napus in China. Plant Dis 99(11):1651 CrossRef  Google Scholar  Al-Lami HFD, You MP, Barbetti MJ (2019a) Incidence, pathogenicity and diversity of Alternaria spp. associated with alternaria leaf spot…

I have 6 files which I want to compare to two other files and if a match is found in file1 plot red dots if it is found in file2 plot green dots and if found in none plot grey dots. I have the following code however no results are…

Allis CD, Jenuwein T. The molecular hallmarks of epigenetic control. Nat Rev Genet. 2016;17:487–500. Article  CAS  PubMed  Google Scholar  Boccaletto P, Stefaniak F, Ray A, Cappannini A, Mukherjee S, Purta E, et al. MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic Acids Res. 2022;50:D231–D235. Article  CAS  PubMed  Google…

Hepatitis E. [www.who.int/news-room/fact-sheets/detail/hepatitis-e. Nan Y, Wu C, Zhao Q, Zhou EM. Zoonotic Hepatitis E virus: an ignored risk for Public Health. Front Microbiol. 2017;8:2396. Article  PubMed  PubMed Central  Google Scholar  Kenney SP. The Current Host Range of Hepatitis E Viruses. Viruses 2019, 11. Purdy MA, Drexler JF, Meng XJ, Norder…

I have a dataframe in R #creating a dataset codigo <- paste0(“COD”, sprintf(“%03d”, 1:4)) vgene <- paste0(“VG”, LETTERS[1:8]) set.seed(123) codigo <- sample(codigos, 40, replace = TRUE) vgene <- sample(vgene, 40, replace = TRUE) datos_vgene <- data.frame(codigo, vgene) codigo vgene 1 COD001 VGG 2 COD002 VGG 3 COD003 VGC 4 COD004…

I’ve downloaded the CEL files from GSE154619 and want to run a DE test for multiple contrasts. In essence, this data has two treatments(drug vs control) in two tissues. Here’s my code: suppressPackageStartupMessages({ library(affy) library(oligo) library(limma) library(pd.clariom.s.mouse) library(clariomsmousetranscriptcluster.db) library(biomaRt) }) data_dir <- ‘./data/DpQ/GSE154619/’ metadata <- data.frame( treatment = factor(ifelse(grepl(‘DQ’, all_files),…

Mice Trex1+/– mice (C57BL/6) were gifts from D. Barnes and T. Lindahl (Cancer Research UK). All animal experiments were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals and with the approval of the Institutional Animal Care and Use Committee (IACUC-DWZX-2020-511)….

The addition of crizotinib (CZ) to a standard chemotherapy backbone for anaplastic large-cell lymphoma (ALCL) in children prevented on-therapy disease relapse but was associated with an unexpected increase in the number of thromboembolic events, according to research published in Journal of Clinical Oncology. The findings are from arm CZ of…

Home Bioconductor 3.17 Released April 26, 2023 Bioconductors: We are pleased to announce Bioconductor 3.17, consisting of 2230 software packages, 419 experiment data packages, 912 annotation packages, 27 workflows and 3 books. There are 79 new software packages, 7 new data experiment packages, no new annotation packages, 2 new workflows,…

Typhoid GBD, Paratyphoid C. The global burden of typhoid and paratyphoid fevers: a systematic analysis for the Global Burden of Disease Study 2017. Lancet Infect Dis. 2019;19(4):369–81. Article  Google Scholar  Arndt MB, Mosites EM, Tian M, Forouzanfar MH, Mokhdad AH, Meller M, Ochiai RL, Walson JL. Estimating the burden of…

Hi Simon! I ran into a problem when importing swagger into AF. When I import a swagger that contains “$” in its methods, the import fails with an error Job openapi target: domain.com/swagger/… error: components.schemas.Schema name $somemethod-name doesn’t adhere to regular expression ^[a-zA-Z0-9\.\-_]+$, after which the job fails, but the…

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doi: 10.3389/fphar.2023.1160445. eCollection 2023. Affiliations Expand Affiliations 1 School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China. 2 Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China. 3 Military Institute of Chinese Materia, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China. 4…

VJToday On April 19, 2023, the U.S. Food and Drug Administration (FDA) approved the use of polatuzumab vedotin with rituximab, cyclophosphamide, doxorubicin, and prednisone (pola + R-CHP) for adults with previously untreated diffuse large B-cell lymphoma (DLBCL), not otherwise specified (NOS), or high-grade B-cell lymphoma (HGBL), and…

The global genomics market is anticipated to grow at a considerable CAGR of 15.3% during the forecast period. The key factors that are contributing to the market growth are key players operating in the market are adopting various strategies such as acquisition, mergers, new product launches, and other are such…

Introduction Ischemic cardiomyopathy (ICM), characterized by high mobility and high mortality, is so far one of the most prevalent etiologies of congestive heart failure.1 The development of left ventricular (LV) systolic dysfunction, which is typically brought on by prior acute myocardial infarction(s), or, alternatively, a sneaky process of gradual deterioration…

Case Reports . 2023 Apr 12;11(4):e7156. doi: 10.1002/ccr3.7156. eCollection 2023 Apr. Affiliations Expand Affiliations 1 Department of Pathology University of California San Francisco USA. 2 Helen Diller Family Comprehensive Cancer Center University of California San Francisco USA. Item in Clipboard Case Reports Alexander Craig et al. Clin Case Rep. 2023. Show…

Study population and cell isolation PBMCs were obtained from leukocyte reduction chambers of 57 young (20–35 years old) and 64 older (65–85 years old) healthy blood donors of both sexes, purchased from the Stanford Blood Center and the Mayo Clinic Blood Center. The study was conducted in accordance with the…

1Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China; 2Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China Background: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon and rectum that has no exact cause and…

Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, et al. Complete nitrification by Nitrospira bacteria. Nature 2015;528:504. Article  CAS  PubMed  PubMed Central  Google Scholar  van Kessel MA, Speth DR, Albertsen M, Nielsen PH, den Camp HJO, Kartal B, et al. Complete nitrification by a single microorganism….

Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol. 2006;4:102–12. Article  CAS  PubMed  Google Scholar  Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JBH. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol. 2012;10:497–506….

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Abstract Cohesin is a trimeric complex containing a pair of SMC proteins (Smc1 and Smc3) whose ATPase domains at the end of long coiled coils (CC) are interconnected by Scc1. During interphase, it organizes chromosomal DNA topology by extruding loops in a manner dependent on Scc1’s association with two large…

Why is Beagle v5.4 (imputation) not giving Allele Frequencies (AF) and DR2 in my output? 0 Hi there! I have just imputed some low-coverage (<4x) whole genome sequencing samples using a WGS reference panel (>10x) and Beagle v5.4: java -jar beagle.22Jul22.46e.jar gt=${file} impute=true gp=true ne=100 nthreads=16 ref=${refvcf} out=${outfile} However, the…

Rojansky R, Cha M-Y, Chan DC (2016) Elimination of paternal mitochondria in mouse embryos occurs through autophagic degradation dependent on PARKIN and MUL1. eLife 5:e17896. doi.org/10.7554/eLife.17896 CrossRef  CAS  PubMed  PubMed Central  Google Scholar  Wei W, Pagnamenta AT, Gleadall N et al (2020) Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA…

The info column of raw-snps-filtered.ann.vcf file showing more than one gene for a single position of RNA editing sites. 1 Hi All, I am first time trying to identify the RNA editing sites from (A TO I )changes.I have used GATK pipeline and at the very end when I have…

Allele Frequency >0.5 for cancer somatic mutations? 0 Hello, I am analyzing WES VCF files for tumor and matched non-tumor samples and noticed that the allele frequency (AF) values in the files are quite high for the variants (>0.5 and close to 1 for a lot of the variants). This…

AF column in VCF file 1 Hi , I’m new to genetics . I have a VCF file and for each sample I need to identify if it is heterozygous or homozygous. For example, if AF=0.5 is it herto or homo? Thank you VCF AF heterozygous • 244 views AF…

Bisoffi Z, Buonfrate D, Montresor A, Requena-Méndez A, Muñoz J, Krolewiecki AJ, et al. Strongyloides stercoralis: a plea for action. PLoS Negl Trop Dis. 2013;7:5. Google Scholar  Schär F, Trostdorf U, Giardina F, Khieu V, Muth S, Marti H, et al. Strongyloides stercoralis: global distribution and risk factors. PLoS Negl…

Ann F. Mohrbacher, MD Associate Professor of Clinical Medicine Medical Director, Autologous Bone Marrow Transplant Keck School of Medicine of USC Los Angeles, CA Targeted OncologyTM: What are the recommended second-line therapy regimens for patients with relapsed or refractory DLBCL who will proceed to transplant? MOHRBACHER: Based on the NCCN…

Hi, I am performing filter based annotation using Annovar for my vcf file generated using GATK4. The command used is: annotate_variation.pl -filter -out sample -build hg19 -dbtype clinvar_20221231 sample.avinput humandb/ The output I got the following output: clinvar_20221231 192257 1 100316 100317 C G 1 100316 . C G 250.64…

allelic copy number variation 0 Dear all, I am working with sequenza output that has the following format – 1st line (www.ncbi.nlm.nih.gov/pmc/articles/PMC4269342/ ; Sequenza estimates the allelic specific copy numbers). How can I transform this output into numerical allele specific copy-numbers shown on the 2nd line ? chromosome position base.ref…

why CombineGCVFs in gatk not showing all the samples name? 0 Hi, I combined the 64 .vcf files using the CombineGVCFs in gatk. The command was completed successfully but its showing the output with only one column and why not rest of the 64 samples? The output is here #CHROM…

Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, et al. Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun. 2021;12:4774. Article  CAS  PubMed  PubMed Central  Google Scholar  Xiong Y, Guilbaud R, Peacock CL, Cox RP, Canfield DE, Krom MD,…

Background Cell-free DNA (cfDNA) refers to fragments of DNA released into the circulation by endothelial cells and white blood cells by active release or passively through apoptosis and necrosis.1,2 The fraction of cfDNA that originates from tumor is known as circulating tumor DNA (ctDNA). In 2016 the first commercial ctDNA…

I’m trying to annotate genes onto a VCF file with bcftools. My annotation file is a .bed file that originally was a hg38 UCSC knownGene gtf file, converted by BEDOPS: hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/ Original GTF file: chr1 11868 12227 . . + knownGene exon . gene_id “ENST00000456328.2”; transcript_id “ENST00000456328.2”; exon_number “1”; exon_id…

Almazán C, González-Álvarez VH, Fernández de Mera IG, Cabezas-Cruz A, Rodríguez-Martínez R, De la Fuente J (2016) Molecular identification and characterization of Anaplasma platys and Ehrlichia canis in dogs in Mexico. Ticks Tick Borne Dis 7:276–283. doi.org/10.1016/j.ttbdis.2015.11.002 Article  PubMed  Google Scholar  Aman R, Mahas A, Marsic T, Hassan N, Mahfouz…

Mertens F, Johansson B, Fioretos T, Mitelman F. The emerging complexity of gene fusions in cancer. Nat Rev Cancer. 2015;15(6):371–81. Article  CAS  PubMed  Google Scholar  Peters S, Camidge DR, Shaw AT, Gadgeel S, Ahn JS, Kim DW, et al. Alectinib versus crizotinib in untreated ALK-positive non-small-cell lung cancer. N Engl…

Trim gnomAD v3.1.2 1 Hello! I’m wondering if anyone has written code, or knows of BCFTools/VCFTools/other published tool, to trim gnomAD v3.1.2 down from its current monstrosity (~3Tb for the all chromosomes) into a smaller utility for purposes of variant filtering in rare disease variant annotation. Essentially I want to…

I had a vcf file with imputed genotypes from beagle like this: ##fileformat=VCFv4.2 ##filedate=20210504 ##source=”beagle.18May20.d20.jar” ##INFO=<ID=AF,Number=A,Type=Float,Description=”Estimated ALT Allele Frequencies”> ##INFO=<ID=DR2,Number=1,Type=Float,Description=”Dosage R-Squared: estimated squared correlation between estimated REF dose [P(RA) + 2*P(RR)] and true REF dose”> ##INFO=<ID=IMP,Number=0,Type=Flag,Description=”Imputed marker”> ##FORMAT=<ID=GT,Number=1,Type=String,Description=”Genotype”> ##FORMAT=<ID=DS,Number=A,Type=Float,Description=”estimated ALT dose [P(RA) + 2*P(AA)]”> ##FORMAT=<ID=GP,Number=G,Type=Float,Description=”Estimated Genotype Probability”> #CHROM POS ID…

alelle – specific CNA/LOH 0 Dear all, I would appreciate having your help on the following : I would like to use a software that is called scarHRD to measure the degree of homologous recombination deficiency (HRD) in cancer cells. The link to the scarHRD package is : github.com/sztup/scarHRD ScarHRD…

Human samples Placental and decidual samples used for the in vivo and in vitro profiling were obtained from elective terminations from: The MRC and Wellcome-funded Human Developmental Biology Resource (HDBR, www.hdbr.org), with appropriate maternal written consent and approval from the Fulham Research Ethics Committee (REC reference 18/LO/0822) and Newcastle and…

Kirchberger PC, Schmidt ML, Ochman H. The ingenuity of bacterial genomes. Annu Rev Microbiol. 2020;74:815–34. Article  CAS  PubMed  Google Scholar  Rodríguez-Gijón A, Nuy JK, Mehrshad M, Buck M, Schulz F, Woyke T, et al. A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked…

The new technology delivers short-duration electrical pulses to the cardiac tissue that causes pores, or holes, to form in the cellular walls of the myocytes. This irreversible electroporation process kills the cells without excess heat or cold, which can adversely effect healthy underlying tissues. This has a lot of appeal…

MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW. The database of genomic variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 2014;42(Database issue):D986–992. Article  CAS  PubMed  Google Scholar  Zarrei M, MacDonald JR, Merico D, Scherer SW. A copy number variation map of the…

Patient samples and RNA-seq analysis RNA-seq data from 395 patients with PDA was obtained from the University Health Network (Toronto), Sunnybrook Health Sciences Centre (Toronto), Kingston General Hospital (Kingston), McGill University (Montreal), Mayo Clinic (Rochester), Massachusetts General Hospital (Boston) and Sheba Medical Center (Tel Aviv) and has been described previously1,12,13,14….

Provided by: samtools_1.16.1-1_amd64 NAME samtools-phase – call and phase heterozygous SNPs SYNOPSIS samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] in.bam DESCRIPTION Call and phase heterozygous SNPs. OPTIONS -A Drop reads with ambiguous phase. -b STR Prefix of BAM output. When this option is in use, phase-0…

New Orleans, USA — New electroporation ablation technique has been shown to be as safe and effective in treating atrial fibrillation (AF) as standard thermal ablation techniques (radiofrequency or cryotherapy), according to trial results PULSED OFF presented at the congress of theAmerican College of Cardiology (ACC 2023) [] 1]. Since this…

I use python package to load and analysis vcf.gz files, for ch in chs: vcf_to_1240K_hdf(in_vcf_path = f”/mnt/gpfs/Users/wangjincheng/aDNA/All_data/Analysis4/19.genotype_imputation/GLIMPSE_test/GLIMPSE_ligated/merged_chr{ch}.vcf.gz”, path_vcf = f”/mnt/gpfs/Users/wangjincheng/aDNA/All_data/Analysis4/19.genotype_imputation/GLIMPSE_test/ancIBD/chr{ch}.vcf”, path_h5 = f”/mnt/gpfs/Users/wangjincheng/aDNA/All_data/Analysis4/19.genotype_imputation/GLIMPSE_test/ancIBD/chr{ch}.h5″, marker_path = f”/mnt/gpfs/Users/wangjincheng/aDNA/reference/data/filters/snps_bcftools_ch{ch}.csv”, map_path = f”/mnt/gpfs/Users/wangjincheng/aDNA/reference/data/afs/v51.1_1240k.snp”, af_path = f”/mnt/gpfs/Users/wangjincheng/aDNA/reference/data/afs/v51.1_1240k_AF_ch{ch}.tsv”, col_sample_af = “”, buffer_size=20000, chunk_width=8, chunk_length=20000, ch=ch) but get this error below: UnicodeDecodeError Traceback (most recent call last)…

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Andersen LO, Stensvold CR. Blastocystis in health and disease: are we moving from a clinical to a public health perspective? J Clin Microbiol. 2016;54:524–8. Article  CAS  PubMed  PubMed Central  Google Scholar  Hublin JSY, Maloney JG, Santin M. Blastocystis in domesticated and wild mammals and birds. Res Vet Sci. 2021;135:260–82. Article …

Cell culture hTERT-RPE-1 WT and hTERT RPE-1 TP53−/− (46, XX)27 cells were a gift from J. Korbel. The cells were grown in DMEM/F-12, GlutaMAX (10565018) supplemented with 10% FBS (Thermo Fisher Scientific, 10270106) and 1% antibiotic–antimycotic (Thermo Fisher Scientific, 15240062). CP-A (KR-42421) (47, XY) cells were purchased from the American Type…

Goldberg JL, Klassen MP, Hua Y, Barres BA. Amacrine-signaled loss of intrinsic axon growth ability by retinal ganglion cells. Science. 2002;296:1860–4. Article  CAS  PubMed  Google Scholar  Blackmore M, Letourneau PC. Changes within maturing neurons limit axonal regeneration in the developing spinal cord. J Neurobiol. 2006;66:348–60. Article  CAS  PubMed  Google Scholar …

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