Tag: AF

Different relatedness estimates by PLINK and VCFTOOLS despite same method

According to the vcftools manual, specifying the “–relatedness2” flag allows calculating relatedness statistics using the method by Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559). That is, based on KING. According to the PLINK manual, PLINK uses the same method to calculate relatedness when specifying the flag “–make-king-table”. So, although both PLINK…

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N6-methyladenosine modification positively regulate Japanese encephalitis virus replication | Virology Journal

Burgess HM, Depledge DP, Thompson L, Srinivas KP, Grande RC, Vink EI, Abebe JS, Blackaby WP, Hendrick A, Albertella MR, Kouzarides T, Stapleford KA, Wilson AC, Mohr I. Targeting the m6A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication. Genes Dev. 2021;35:1005–19. Article  CAS  PubMed  PubMed Central  Google Scholar  Chambers…

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slurm fails on disconnected standalone computer/node

Hi, I have a setup similar to the one of the original reporter. My NodeName is localhost . The error messages at booting time scared me, so I dug the issue. I also related this issue to my observation that slurm fails to launch jobs when my standalone computer is…

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cfDNA Standards For Molecular Testing

Multiplexed ctDNA fragments (~150bp) mixed with nucleosomally fragmented wildtype cfDNA background in human plasma. The cell-derived ctDNA fragments are generated by Anchor’s unique multiplexed gene-editing method and are nucleosomally fragmented to around 150bp. The cell-derived variants are suitable for both the amplicon-based and capture-based methods. The synthetic ctDNA fragments are…

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cfDNA Extraction Sensitivity Controls – cfDNA Extraction Sensitivity Controls

Does your cfDNA extraction process affect the Limit of Detection (LOD) of a particular gene target? Our new products, cfDNA Extraction Sensitivity Panels and Extraction Low Positive Controls, can help your research and development for liquid biopsy assays. NEW PRODUCTS: cfDNA EXTRACTION SENSITIVITY PANELS &  CONTROLS The Extraction Sensitivity Controls…

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Progress of circRNA/lncRNA-miRNA-mRNA axis in atrial fibrillation [PeerJ]

Introduction The incidence and mortality rates of AF are continuously increasing, leading to serious complications such as heart failure and stroke (Fig. 1) (Sagris et al., 2021). The occurrence and development of AF involve different mechanisms and interactions (Kornej et al., 2020). AF often progresses from paroxysmal to persistent (Nattel…

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Analysis of off-tumour toxicities of T-cell-engaging bispecific antibodies via donor-matched intestinal organoids and tumouroids

Human tissue samples Tissue samples and annotated data were obtained, and experimental procedures were performed within the framework of the non-profit foundation HTCR, including informed patient consent. Intestinal organoid and tumouroid cell culture Supplementary Table 1 provides anonymized basic donor information. After isolation of intestinal crypts following a previously described…

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Analysis of biomarkers in speculative CNS-enriched extracellular vesicles for parkinsonian disorders: a comprehensive systematic review and diagnostic meta-analysis

44. Zurück zum Zitat Thery C, Witwer KW, Aikawa E, Alcaraz MJ, Anderson JD, Andriantsitohaina R, Antoniou A, Arab T, Archer F, Atkin-Smith GK, Ayre DC, Bach JM, Bachurski D, Baharvand H, Balaj L, Baldacchino S, Bauer NN, Baxter AA, Bebawy M, Beckham C, Bedina Zavec A, Benmoussa A, Berardi…

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hypothetical protein LOTGIDRAFT_99224 partial, maker-scaffold1322_size48131-snap-gene-0.13 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of hypothetical protein LOTGIDRAFT_99224 partial vs. L. salmonis genes Match: EMLSAG00000006769 (supercontig:LSalAtl2s:LSalAtl2s379:476161:478870:-1 gene:EMLSAG00000006769 transcript:EMLSAT00000006769 description:”maker-LSalAtl2s379-augustus-gene-4.10″) HSP 1 Score: 59.6918 bits (143), Expect = 4.225e-12Identity = 29/57 (50.88%), Postives = 39/57 (68.42%), Query Frame = 0 Query: 22 AANARERTRMRVLSKAFGRLKLTLPWVPPDTKLSKLDTLRLATSYISHLQRLLSDEE 78 +N +ER R + ++…

Continue Reading hypothetical protein LOTGIDRAFT_99224 partial, maker-scaffold1322_size48131-snap-gene-0.13 (gene) Tigriopus kingsejongensis

Convolution element wise with pytorch

dthanoon (david thanoon) December 16, 2023, 4:21pm 1 I have a tensor A of size [904,145] and B of size [904,1234]. Both tensor have 904 elements. I am looking to convolve element wise each element of A with their respective element of B. So basically convolve A[i,:] with B[i,:] for…

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Outcomes of allogeneic hematopoietic stem cell transplantation for relapsed or refractory diffuse large B-cell lymphoma

Coiffier B, Lepage E, Briere J, Herbrecht R, Tilly H, Bouabdallah R, et al. CHOP chemotherapy plus rituximab compared with CHOP alone in elderly patients with diffuse large-B-cell lymphoma. N Engl J Med. 2002;346:235–242. Article  CAS  PubMed  Google Scholar  Philip T, Guglielmi C, Hagenbeek A, Somers R, Van der Lelie…

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FDA Approves First Pulsed Field Ablation System for AF

The US Food and Drug Administration (FDA) has approved the PulseSelect Pulsed Field Ablation (PFA) System (Medtronic) for the treatment of both paroxysmal and persistent atrial fibrillation (AF), the manufacturer has announced. The technology uses microsecond-scale pulsed electrical fields for pulmonary vein isolation (PVI) to reduce AF and is the…

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Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking

Prediction with AlphaFold2 and AlphaFold-Multimer For each PDB the release date in the Protein Data Bank34 was recorded. AlphaFold 2 (2.2.2) was run setting the –max_template_date flag to be the day before the release date of the PDB and the –model_preset to be either monomer for AF or multimer for…

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The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases

Annesley SJ, Fisher PR (2019) Mitochondria in health and disease. Cells 8(7). doi.org/10.3390/cells8070680 Cannino G, Ferruggia E, Luparello C, Rinaldi AM (2009) Cadmium and mitochondria. Mitochondrion 9(6):377–384. doi.org/10.1016/j.mito.2009.08.009 Article  CAS  PubMed  Google Scholar  Bonora M, Missiroli S, Perrone M, Fiorica F, Pinton P, Giorgi C (2021) Mitochondrial control of genomic…

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INTERVAL RNA-seq Portal | eQTL

INTERVAL RNA-seq Portal | eQTL Gene ID Gene Type Range Lead RsID qVal Z-score Independent eQTL signals Rank Variant RsID Variant PosID AF Dist Beta (joint) P-val (joint) Nominal eQTL summary statistics Variant RsID Variant PosID AF Beta P-val Z-score PheWAS for lead variant (OpenTargets) Trait Author PMID Beta P-val…

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Construction of a risk stratification model integrating ctDNA to predict response and survival in neoadjuvant-treated breast cancer | BMC Medicine

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. Article  PubMed  Google Scholar  Giaquinto AN, Sung H, Miller KD, Kramer JL, Newman LA,…

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Disease signatures in the gut metagenome of a prospective family cohort of inflammatory bowel disease

Abstract Inflammatory bowel disease (IBD) is associated with dysbiotic microbiomes. However, whether microbiomes of family members of IBD patients harbour microbial disease signatures of IBD is unknown. Here, we generate shotgun metagenomic data of an IBD family cohort and treatment-naive IBD cases, which we combine with published IBD metagenomes, to…

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Transition of allele-specific DNA hydroxymethylation at regulatory loci is associated with phenotypic variation in monozygotic twins discordant for psychiatric disorders | BMC Medicine

Lichtenstein P, Yip BH, Bjork C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. Lancet. 2009;373(9659):234–9. Article  PubMed  Google Scholar  Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R,…

Continue Reading Transition of allele-specific DNA hydroxymethylation at regulatory loci is associated with phenotypic variation in monozygotic twins discordant for psychiatric disorders | BMC Medicine

Wide bovine tick-borne pathogen spectrum: Predominancy of Theileria annulata and the first molecular detection of Ehrlichia minasensis in Turkey

Agina OA, Shaari MS, Isa NMM, Ajat M, Zamri-Saad M, Hamzah H (2020) Clinical pathology, immunopathology and advanced vaccine technology in bovine theileriosis: A review. Pathogens 9:697. doi.org/10.3390/pathogens9090697 Article  PubMed  PubMed Central  CAS  Google Scholar  Aktas M (2014) A survey of ixodid tick species and molecular identification of tick-borne pathogens….

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Is Protein BLAST a thing of the past?

BLAST1 is widely used in molecular biology to search for nucleotide and protein sequences. Three decades after BLAST was introduced, there were major breakthroughs in structure prediction, and tools such as RoseTTAFold2 and AlphaFold3 emerged. Consequently, every protein sequence in the major sequence databases now comes with a model of…

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Genome sequence and characterization of a novel Pseudomonas putida phage, MiCath

Bacterial strains We used P. putida strains S12, DOT-T1E, F1 (kindly gifted by Grant Rybnicky), ATCC 12633 (purchased from ATCC), JUb85 (kindly provided by Samuel Buck), EM383 (kindly gifted by Huseyin Tas), p106 (kindly provided by Carey-Ann Burnham), and KT2440 (obtained from lab stocks). An overnight culture of each P….

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Advancements in Non-human Forensic DNA Analysis

Alahi MEE, Mukhopadhyay SC (2017) Detection methodologies for pathogen and toxins: a review. Sensors 1885:17 Google Scholar  Aly SM, Sabri DM (2015) Next generation sequencing (NGS): a golden tool in forensic toolkit. Archiwum Medycyny Sądowej i Kryminologii/Archives of Forensic Medicine and Criminology 65(4):260–271 Google Scholar  Amendt J, Richards CS, Campobasso…

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the condition has length > 1

absolute running error: Error in if (!is.na(res)) { : the condition has length > 1 0 the following are my R codes: install.packages(“numDeriv”) BiocManager::install(“DNAcopy”) install.packages(“ABSOLUTE_1.0.6.tar.gz”,repos = NULL) library(numDeriv) library(ABSOLUTE) RunAbsolute( seg.dat.fn = “P01_1_GISTIC_segment”, sigma.p = 0, max.sigma.h = 0.2, min.ploidy = 0.5, max.ploidy = 8, primary.disease = “NPC”, platform =…

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Bioinformatics analysis of immune characteristics in tumors with alternative carcinogenesis pathways induced by human papillomaviruses | Virology Journal

de Martel C, Georges D, Bray F, Ferlay J, Clifford GM. Global burden of cancer attributable to infections in 2018: a worldwide incidence analysis. Lancet Glob Health. 2020;8:e180–90. Article  PubMed  Google Scholar  McKaig RG, Baric RS, Olshan AF. Human papillomavirus and head and neck cancer: epidemiology and molecular biology. Head…

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Building reference dbSNP file using WGS samples

Building reference dbSNP file using WGS samples 2 Dear scientific community, I have to call variants from WGS samples of citrus. I used GATK pipeline for post processing of aligned reads but reference dbSNP file is not available for citrus sinensis. I am using bootstraping method. Removed duplicates and called…

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Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression

B cells undergo a series of programmed genomic alterations that enable the immunoglobulin light and heavy chain loci to generate high-affinity antibodies against invading pathogens. First, B cells undergo variability, diversity and joining (VDJ) recombination in the bone marrow with subsequent somatic hypermutation (SHM) and class switch recombination (CSR) occurring…

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Lower-limb ulcers in participants with leprosy sequelae

Introduction Leprosy is a disabling infectious disease that predominantly occurs in the skin and peripheral nerves and is transmitted by contact with pathogenic bacteria through the respiratory tract and broken skin. Leprosy is attributed to infection with Mycobacterium leprae (M. leprae)1 and the more recently discovered Mycobacterium lepromatosis.2 In addition,…

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Mitophagy in human health, ageing and disease

Palikaras, K., Lionaki, E. & Tavernarakis, N. Mechanisms of mitophagy in cellular homeostasis, physiology and pathology. Nat. Cell Biol. 20, 1013–1022 (2018). Article  CAS  PubMed  Google Scholar  Palikaras, K., Lionaki, E. & Tavernarakis, N. Coordination of mitophagy and mitochondrial biogenesis during ageing in C. elegans. Nature 521, 525–528 (2015). Article …

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Potential use of iPSCs for disease modeling, drug screening, and cell-based therapy for Alzheimer’s disease | Cellular & Molecular Biology Letters

Tarawneh R, Holtzman DM. The clinical problem of symptomatic Alzheimer disease and mild cognitive impairment. Cold Spring Harb Perspect Med. 2012;2(5): a006148. Article  PubMed  PubMed Central  Google Scholar  van der Flier WM, Scheltens P. Epidemiology and risk factors of dementia. J Neurol Neurosurg Psychiatry. 2005;76(suppl 5):v2-7. Article  PubMed  PubMed Central …

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BBtools bug in reporting the number of substitutions in the console output, it seems to report insanely high rates of heterozygosity

Hello, I know Brian is sometimes around, but here is my command: while read p; do callvariants.sh in=${p}.recal.bam ploidy=2 vcf=${p}.20score.vcf useidentity=f overwrite=true ref=ref.fsa -Xmx50g ; done <ID java -ea -Xmx50g -Xms50g -cp /home/alessandro/software/bbmap/current/ var2.CallVariants in=ancestor.recal.bam ploidy=2 vcf=ancestor.20score.vcf useidentity=f overwrite=true ref=ref.fsa -Xmx50g Executing var2.CallVariants [in=ancestor.recal.bam, ploidy=2, vcf=ancestor.20score.vcf, useiden tity=f, overwrite=true, ref=Adineta_vaga.fsa,…

Continue Reading BBtools bug in reporting the number of substitutions in the console output, it seems to report insanely high rates of heterozygosity

GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data

GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data 0 Dear all, Is there any best practice for the mouse snp indel vcf files using GATK Mutect2 for mouse whole exome data? For mm10, it seems have several available, for mm39, it seems the newest is from…

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Longitudinal detection of circulating tumor DNA

Analysis of Roche KAPA Target Enrichment kit experimental data obtained on an Illumina sequencing system is most frequently performed using a variety of publicly available, open-source analysis tools. The typical variant calling analysis workflow consists of sequencing read quality assessment, read filtering, mapping against the reference genome, duplicate removal, coverage…

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Germline PTEN genotype-dependent phenotypic divergence during the early neural developmental process of forebrain organoids

American Psychiatric Association Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5). Arlington, VA: American Psychiatric Publishing; 2013. Lewis MH, Bodfish JW. Repetitive behavior disorders in autism. Ment Retard Dev D R. 1998;4:80–9. Article  Google Scholar  Bodfish JW, Symons FJ, Parker DE, Lewis MH. Varieties of repetitive behavior in…

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Chromosome-scale genome of the human blood fluke Schistosoma mekongi and its implications for public health | Infectious Diseases of Poverty

Barnett R. Schistosomiasis. (1474–547X (Electronic)). Steinmann P, Keiser J, Bos R, Tanner M, Utzinger J. Schistosomiasis and water resources development: systematic review, meta-analysis, and estimates of people at risk. Lancet Infect Dis. 2006;6(7):411–25. Article  PubMed  Google Scholar  Uthailak N, Adisakwattana P, Thiangtrongjit T, Limpanont Y, Chusongsang P, Chusongsang Y, et…

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Exploring the promising potential of induced pluripotent stem cells in cancer research and therapy | Molecular Cancer

Rowe RG, Daley GQ. Induced pluripotent stem cells in disease modelling and drug discovery. Nat Rev Genet. 2019;20:377–88. Article  CAS  PubMed  PubMed Central  Google Scholar  Li L, Papadopoulos V. Advances in stem cell research for the treatment of primary hypogonadism. Nat Rev Urol. 2021;18:487–507. Article  CAS  PubMed  Google Scholar  Lawrence…

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Sequence-Based Classification and Identification | SpringerLink

Adékambi T, Drancourt M, Raoult D (2009) The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 17:37–45 CrossRef  PubMed  Google Scholar  Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef  CAS  PubMed  Google Scholar  Arahal DR,…

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Making Tile plots to show Synonymous Non-Synonymous mutation fraction

There are times when you have fractions across genomic ranges and you want to plot them. A line plot is fine for plotting fractions or absolute counts, but if the range is large, the per-base resolution is poor, and line plots look like spikes, as can be seen below: The…

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normalize not left-normalizing?

I’m running plink2 to convert a vcf to a pgen with pseudobiallelic variants. Calling –normalize does not seem to left-normalize as I would expect, at least when I look at the .pvar. Log PLINK v2.00a6LM AVX2 Intel (21 Nov 2023)       www.cog-genomics.org/plink/2.0/(C) 2005-2023 Shaun Purcell, Christopher Chang  …

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Whole mitochondrial genome sequencing provides new insights into the phylogeography of loggerhead turtles (Caretta caretta) in the Mediterranean Sea

Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc Avise JC (1986) Mitochondrial DNA and the evolutionary genetics of higher animals. Philos Trans R Soc Lond B 312:325–342. doi.org/10.1098/rstb.1986.0011 Article  CAS  Google Scholar  Baker CS, Steel D, Calambokidis J, Falcone E, González-Peral U, Barlow J,…

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Phase 3 Trial of Factor XIa Inhibitor Asundexian Halted for Lack of Efficacy

Bayer announced earlier this week it has stopped the OCEANIC-AF phase 3 clinical trial investigating the factor FXIa inhibitor asundexian for the agent’s lack of efficacy compared to apixaban, a factor Xa inhibitor, in patients with atrial fibrillation (AF) at risk for stroke or systemic embolism.1 The decision to halt…

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All variants in a VCF register as “invalid genotype records in input file”

ANNOVAR Error: All variants in a VCF register as “invalid genotype records in input file” 0 Hello, I am running into an error with convert2annovar.pl where it is registering all of the variants in my VCF as invalid. My VCF is 1925 variants plus the header with the following format:…

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Asundexian Phase 3 AF Study Halted for Lack of Efficacy

The phase 3 OCEANIC-AF trial of the investigational oral factor XI inhibitor asundexian (Bayer) has been stopped early owing to inferior efficacy of the drug in comparison with apixaban for the prevention of stroke and systemic embolism in patients with atrial fibrillation (AF). This decision is based on the recommendation…

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Bayer Falls Short in Bid to Beat Eliquis in Afib, But Key Stroke Study Continues

Bayer is stopping a pivotal clinical trial for its experimental treatment for atrial fibrillation at the recommendation of an independent committee that concluded the drug would not be more effective than a Bristol Myers Squibb and Pfizer product widely used to treat the heart condition. The Bayer drug, asundexian, was…

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Mitochondrial DNA Oxidation, Methylation, and Copy Number Alterations in Major and Bipolar Depression

1Koç University Research Center for Translational Medicine, Affective Laboratory, Türkiye 2Department of Psychiatry, Koç University Hospital, Türkiye 3Izmir Biomedicine and Genome Center, Genç Lab, Türkiye 4Izmir Demokrasi University, Brain and Neuroscience Research and Application Center, Türkiye 5Vocational School of Health…

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Molecular detection and whole genome sequencing of Pectobacterium and Dickeya, the casual agents of soft rot disease in lettuce

Azadmanesh S, Marefat A (2013) and Kayhan Azadmanesh. Detection of Pectobacteria causal agents of potato soft rot in north-western provinces of Iran. J Plant Pathol Microbiol 4(1) Babadoost M (1990) Bacterial soft rot of vegetables, fruits and ornamentals. Rep Plant Dis 943:7 Google Scholar  Ben Fekih I, Zhang C, Li…

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What AlphaFold tells us about cohesin’s retention on and release from chromosomes

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 hook-shaped…

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What AlphaFold tells us about cohesin’s retention on and release from chromosomes

If ATP-dependent dissociation of Scc1’s NTD from the Smc3 neck is a feature intrinsic to Smc-kleisin trimers, then how might Wapl enhance this process? To address this, we used AF to explore how Wapl is first recruited to cohesin and second what effect it has on the configuration of cohesin’s…

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RStudio – Statistik – Create the dataset dset

Create the dataset dset &lt;- 1 : 100 Calculate mean mean_bp &lt;- mean(dset) Calculate median median_bp &lt;- median(dset) Calculate minimum min_bp &lt;- min(dset) Calculate maximum max_bp &lt;- max(dset) Calculate variance variance_bp &lt;- var(dset) Calculate standard deviation std_dev_bp &lt;- sd(dset) Print the results print(paste(&quot;Mean:&quot;, mean_bp)) print(paste(&quot;Median:&quot;, median_bp)) print(paste(&quot;Minimum:&quot;, min_bp)) print(paste(&quot;Maximum:&quot;, max_bp))…

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Inhibition of providencia vermicola FabD

Introduction Microbial resistance has become a problem in the contemporary medical environment due to the inadequate development of new antibiotics and the asinine prescription of antibiotics in both developed and developing nations. Antimicrobial resistance (AMR), which affects wealthy and developing nations, is a global concern.1 AMR is a problem for…

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Diagnosis of Two meningitis Cases caused by Rickettsia felis

Introduction Rickettsia felis belongs to the transitional group in the genus Rickettsia and is mainly transmitted by the cat flea (Ctenocephalides felis) but has been detected in a variety of arthropods including mosquitoes, ticks, and mites.1 Flea-borne spotted fever is caused by R. felis, with symptoms including fever, headache, and…

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Predicting multiple conformations via sequence clustering and AlphaFold2

AlphaFold2 (AF2) 1 has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein’s biological function often depends on multiple conformational substates2, and disease-causing point mutations often cause population changes within these substates3,4. We demonstrate that clustering a multiple sequence alignment (MSA) by sequence similarity enables AF2…

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GATK SelectVariants –remove-unused-alternates dropping real INDELs?

I’m using a VCF that is generated by GenotypeGVCFs (so doing calibration based on a larger cohort of samples) and my goal is to only extract variants of interest to one specific sample. The VCF in the subset tends to include some variants that were present in the original joint…

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A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

40,039 MAGs reconstructed from large-scale genome-resolved metagenomics To reconstruct previously unexplored bacterial and archaeal genomes, we performed a large-scale single-sample metagenomic assembly on 3304 soil metagenomes across the globe (Fig. 1a), including 363 metagenomes from the in-house dataset and 2941 from publicly available metagenomes. The soil samples were mainly collected from…

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Myeloid/Lymphoid Neoplasms with ETV6::PDGFRB Fusion Gene

Introduction The ETV6::PDGFRB fusion gene is commonly associated with myeloid neoplasms with monocytosis (such as CMML), and with eosinophilia.1 The PDGFRB gene, located on 5q33, encodes PDGFRβ, a type III tyrosine kinase comprising an extracellular domain consisting of five immunoglobulin (Ig)-like domains, a single-transmembrane helix domain, a juxtamembrance domain, and…

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Recovery of microbial DNA by agar-containing solution from extremely low-biomass specimens including skin

Ethical considerations This study complies with relevant institutional, national, and international guidelines and legislation. The Ethics Committee at the RIKEN Center for Integrative Medical Sciences (H30-4) approved this study, and written informed consent was obtained from all volunteers who provided specimens. Sampling solutions The AgST solution was prepared as follows:…

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Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

The comparison between MULTICOM servers and other CASP15 server assembly predictors According to the CASP15 official assessment (see the official ranking predictioncenter.org/casp15/zscores_multimer.cgi), MULTICOM_qa and MULTICOM_deep servers ranked 3rd and 5th among all CASP15 assembly server predictors. The MULTICOM human predictors (MULTICOM_human and MULTICOM) ranked 7th and 10th among all CASP15…

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filtering SNV/INDEL in tumor-only WGS samples

filtering SNV/INDEL in tumor-only WGS samples 0 Dear all, To the cancer genomics community on Biostars that worked with tumor-only samples, a question please : which criteria do you apply to identify the most reliable somatic mutations ? I would appreciate having your suggestions. <> my colleagues performed somatic mutation…

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Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques

Victora CG, Bahl R, Barros AJD, França GVA, Horton S, Krasevec J, et al. Breastfeeding in the 21st century: Epidemiology, mechanisms, and lifelong effect. Lancet. 2016;387:475–90. Article  PubMed  Google Scholar  Bardanzellu F, Fanos V, Strigini FAL, Artini PG, Peroni DG. Human breast milk: Exploring the linking ring among emerging components….

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Global Metagenomics Sequencing Market Trends, Opportunities, Competition and Forecasts, 2018-2022 & 2023-2028 – ResearchAndMarkets.com | Business

DUBLIN–(BUSINESS WIRE)–Nov 8, 2023– The “Metagenomics Sequencing Market – Global Industry Size, Share, Trends, Opportunity, and Forecast, 2018-2028 Segmented By Product and Service (Reagents & consumables, Instruments, Services), By Technology, By Application, By Region, and By Competition” report has been added to ResearchAndMarkets.com‘s offering. × This page requires Javascript. …

Continue Reading Global Metagenomics Sequencing Market Trends, Opportunities, Competition and Forecasts, 2018-2022 & 2023-2028 – ResearchAndMarkets.com | Business

The correlation between gut microbiome and atrial fibrillation: pathophysiology and therapeutic perspectives | Military Medical Research

Kim JE, Li B, Fei L, Horne R, Lee D, Loe AK, et al. Gut microbiota promotes stem cell differentiation through macrophage and mesenchymal niches in early postnatal development. Immunity. 2022;55(12):2300-17.e6. Article  CAS  PubMed  Google Scholar  Xiao W, Su J, Gao X, Yang H, Weng R, Ni W, et al….

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Patient-derived xenograft models of ALK+ ALCL reveal preclinical promise for therapy with brigatinib

. 2023 Sep;202(5):985-994. doi: 10.1111/bjh.18953. Epub 2023 Jun 25. Nina Prokoph  1 , Jamie D Matthews  1 , Ricky M Trigg  1 , Ivonne A Montes-Mojarro  2 , G A Amos Burke  3 , Falko Fend  2 , Olaf Merkel  4 , Lukas Kenner  4   5   6   7 , Birgit Geoerger  8   9 , Robert…

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vcf – VEP annotation INFO field Ensembl IDs and locations

I have a vcf file that I annoteted with VEP, for human data. I have run VEP to annotate my files with some additional parameters (as shown below in the ##VEP-command-line). However, my output is rather strange (mainly the INFO column). ##VEP=”v108″ time=”2023-04-27 15:13:08″ cache=”workflow/resources/variants/cache_vep/homo_sapiens/108_GRCh38″ ensembl-funcgen=108.56bb136 ensembl-variation=108.a885ada ensembl-io=108.58d13c1 ensembl=108.d8a9c80 1000genomes=”phase3″…

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Molecular diagnosis, phylogenetic analysis, and antifungal susceptibility profiles of Candida species isolated from neutropenic oncological patients | BMC Infectious Diseases

Eissa S, Khedr R, Romeih M, Halaby L, Elanany M, Madney Y. Clinical characteristics and outcome of invasive fungal sinusitis in children with hematological malignancies. Med Mycol. 2022;60(4):myac010. Article  PubMed  Google Scholar  Lin G-L, Chang H-H, Lu C-Y, Chen C-M, Lu M-Y, Lee P-I, Jou S-T, Yang Y-L, Huang L-M,…

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Bayer doubles down on Factor XIa with new phase 3 trial

Bayer has added another phase 3 trial into its registration programme for oral Factor XIa inhibitor asundexian, signalling growing confidence in a drug that generated mixed results in phase 2. The new OCEANIC-AFINA study will enrol patients aged 65 and over with atrial fibrillation (AF) and at high risk of…

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HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases

HLA allele calling from WES HLA-HD was used to call HLA alleles for 454,824 participants at 3-field resolution (representing the allele’s serological specificity, HLA protein, and synonymous variants). We used the UKB whole-genome genotyping (unavailable in 1283 participants) projected on the 1000 Genome reference to estimate genetic ancestry. We found…

Continue Reading HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases

Domain definition and preliminary functional exploration of the endonuclease NOBP-1 in Strongyloides stercoralis | Parasites & Vectors

Boes J, Slotved HC, Murrell KD, Eriksen L, Roepstorff A, Nansen P, et al. Alternative migration routes of Ascaris suum in the pig. J Parasitol. 2002;88:180–3. Article  CAS  PubMed  Google Scholar  Nikolaou S, Gasser RB. Prospects for exploring molecular developmental processes in Haemonchus contortus. Int J Parasitol. 2006;36:859–68. Article  CAS …

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Structural Variants in gnomAD v4

Today, we are thrilled to announce the release of genome-wide structural variants (SVs) for 63,046 unrelated samples with genome sequencing (GS) data. All site-level information for 1,199,117 high-quality SVs discovered in these samples is browsable in the gnomAD browser (gnomAD SV v4) and downloadable from the gnomAD downloads page. For…

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Geron IMerge Phase 3 Presentations at Upcoming ASH Annual Meeting Reinforce Significant Durability and Breadth of Effect of Imetelstat in Lower Risk MDS | Business

FOSTER CITY, Calif.–(BUSINESS WIRE)–Nov 2, 2023– Geron Corporation (Nasdaq: GERN), a late-stage clinical biopharmaceutical company, today announced the publication of abstracts from the IMerge Phase 3 clinical trial evaluating its first-in-class investigational telomerase inhibitor imetelstat in patients with lower risk myelodysplastic syndromes (MDS). Four abstracts have been accepted for presentation…

Continue Reading Geron IMerge Phase 3 Presentations at Upcoming ASH Annual Meeting Reinforce Significant Durability and Breadth of Effect of Imetelstat in Lower Risk MDS | Business

Epigenetic regulation during cancer transitions across 11 tumour types

Specimen data All samples for MM, OV, BRCA, PDAC, UCEC, CRC, CESC/AD, SKCM and HNSCC, as well as 2 NATs for GBM and 1 NAT for ccRCC were collected with informed consent in concordance with Institutional Review Board (IRB) approval at the School of Medicine at Washington University in St…

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DNA damage response(DDR): a link between cellular senescence and human cytomegalovirus | Virology Journal

Hayflick L, Moorhead PS. The serial cultivation of human diploid cell strains. Exp Cell Res. 1961;25:585–621. Article  CAS  PubMed  Google Scholar  Hayflick L. THE LIMITED IN VITRO LIFETIME OF HUMAN DIPLOID CELL STRAINS. Exp Cell Res. 1965;37:614–36. Article  CAS  PubMed  Google Scholar  Schmitt CA, Tchkonia T, Niedernhofer LJ, Robbins PD,…

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papain family cysteine protease containing protein, maker-scaffold1702_size30647-snap-gene-0.14 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of papain family cysteine protease containing protein vs. L. salmonis genes Match: EMLSAG00000006045 (supercontig:LSalAtl2s:LSalAtl2s327:400616:404607:-1 gene:EMLSAG00000006045 transcript:EMLSAT00000006045 description:”augustus_masked-LSalAtl2s327-processed-gene-4.0″) HSP 1 Score: 590.497 bits (1521), Expect = 0.000e+0Identity = 283/525 (53.90%), Postives = 368/525 (70.10%), Query Frame = 0 Query: 49 GHVARPLGKSPPNFVRDPPPRTTPPAQWLWNNVNETNFLTVSRNQHLPTYCGSCWAHAATSSLSDRIKIARQGAWPDINLAPQVLISCGPGDGCHGGEAGDANAYMHAQGITDETCSIYRARGQDNGLPCSKLEICSTCE—SKCYQPQHFFTYRVDEFHDVEGESNGEQEANMMAEIHHRGPISCGIAVTQALV-NYTGGLFHDKTGAQEIDHDISVVGYGVDEGTQEKYWLIRNSWGTYWGEQGFFRLIRGVNNLGIESGTCSWATPADTWSDAARE—RAAILSNEITLQKP——LWKQLWTVVADFVDNTRDTDLFRRLKLMQKGCKKLSSPRVPVVNIRPRPQDYVSTADLPEALDWRSVNGTNFLSWSVNQHLPVYCGSCWAQAGLSSLADRFTIADRKRFANLALSVQYILNCQAGGSCHGGDAFPLYAFIQKQGVPDVTCQPYEALDEGPLTDCSKPSKLVCKDCTWPPPEPGQEGNCWAKEKFHRYYVDEYNGVEGADNMKKEILERGPVT 560 GH+ R G+…

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Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species

Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, et al. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Arch Virol. 2021;166:2633–48. Article  CAS  PubMed  Google Scholar  Koonin EV, Dolja VV,…

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coatomer subunit alpha, maker-scaffold52_size450388-snap-gene-3.16 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of coatomer subunit alpha vs. L. salmonis genes Match: EMLSAG00000004199 (supercontig:LSalAtl2s:LSalAtl2s221:488387:561813:1 gene:EMLSAG00000004199 transcript:EMLSAT00000004199 description:”maker-LSalAtl2s221-augustus-gene-5.19″) HSP 1 Score: 208.379 bits (529), Expect = 8.743e-63Identity = 95/135 (70.37%), Postives = 99/135 (73.33%), Query Frame = 0 Query: 1 MLTKFETKSPRVKGLAFHPQRPWILASLHNGVIQLWDYRMCTLLEKFDEHEGPVRGIGFHAQQPLFVSGGDDYKIKVWNYKLKRCLFHLLGHLDYIRTTVFHAPVPHARRISPAGPAESSTYLAKIHGLWGWKAR 135 MLTKFETKSPRVKGLAFHP+RPWILASLHNGVIQLWDYRMC LLEKFDEHEGP GI H QPLFVSGGDDYKIKVWNYKLKRCLF LLGHLDYIR…

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BDQ resistance and molecular characterization of RR-TB

Enyu Tong,1,&ast; Ying Zhou,1,&ast; Zhengwei Liu,2 Yelei Zhu,2 Mingwu Zhang,2 Kunyang Wu,2 Junhang Pan,2 Jianmin Jiang1– 3 1School of Public Health, Hangzhou Normal University, Hangzhou, 311100, People’s Republic of China; 2Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China; 3Key Laboratory of…

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AlphaFold model used for docking? and it is ggod?

AlphaFold, an artificial intelligence-based protein structure prediction method, has been evaluated for its accuracy in docking-based drug discovery. The performance of AlphaFold (AF) models in high-throughput docking (HTD) was compared to experimental PDB structures using various docking programs and consensus techniques. The results consistently showed that AF models had worse…

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No samples in .vcf file.

I am trying to convert my vcf file into a BED format file.  When I use this command: plink –vcf merge.bacteria.vcf.gz –make-bed –out merge.bacteria.vcf.bed  I get the following error stating:  PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License…

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How to run multiple jobs, one per GPU, with SLURM?

Apologies if this has be asked/answered before, but even after reading everything I can find, I am struggling to get SLURM to do what I want. Let’s say I have a machine with 4 GPUs. I want to train 4 models in parallel, each job running on a single GPU….

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NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology

Patient characteristics and tissue context The clinical interpretation of molecular alterations starts with evaluating relevant patient characteristics and the tissue context in which a genetic profile occurs. The former relates, in particular, to previous therapies, in addition to disease stage and clinical performance status. For example, prior targeted therapies warrant…

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Bioconductor – Bioconductor 3.18 Released

Home Bioconductor 3.18 Released October 25, 2023 Bioconductors: We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books. There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows,…

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NGS one-liner to call variants

Tutorial:NGS one-liner to call variants 0 This is a tutorial about creating a pipeline for sequence analysis in a single line. It is made for capture/amplicon short read sequencing in mind for human DNA and tested with reference exome sequencing data described here. I share the process and debuging steps…

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NGS oneliner

Tutorial:NGS oneliner 0 This is a tutorial about creating a pipeline for sequence analysis in a single line.I share the process and debuging steps gone through while putting it together.Source is available at: github.com/barslmn/ngsoneliner/I couldn’t make a longer post, complete version of this post: omics.sbs/blog/NGSoneliner/NGSoneliner.html Pipeline # fastp –in1 “$R1″…

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Chromatin compartmentalization regulates the response to DNA damage

Cell culture and treatments DIvA (AsiSI-ER-U2OS)19, AID-DIvA (AID-AsiSI-ER-U2OS)23 and 53BP1-GFP DIvA20 cells were developed in U2OS (ATCC HTB-96) cells and were previously described. Authentication of the U2OS cell line was performed by the provider ATCC, which uses morphology and short tandem repeat profiling to confirm the identity of human cell…

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Allele numbers and frequencies in X and Y chr?

Allele numbers and frequencies in X and Y chr? 1 I’m new to a lot of this and I’ve been looking through the X and Y chromosome regions of a WGS vcf file. I’m confused. How are variant calls made on X and Y? I have a few examples: X…

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Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans

Protein sequence and prediction analysis The amino acid sequence of FcR was deduced from the F. cylindrus genome sequence33. Protein alignments with characterized microbial rhodopsins were performed using the MUSCLE algorithm implemented in Geneious (v.5.6)69. Predictions of subcellular location were performed with SignalP v.4.0 and TargetP (v.1.1)70. Putative transmembrane domains…

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Aligner with statistics included?

Aligner with statistics included? 1 Hello, Is there a long range aligner that could make a statistics outlook listing how many SNP, indels etc are observed in the alignment itself? Thank you aligner alignment • 203 views BBTools’ callvariants.sh calls variants only from the alignments. So: callvariants.sh in=nxyxx.bam ref=ref.fa yields:…

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Advances in Polatuzumab Vedotin-PIIQ Therapy

Introduction Between 30 to 40% of non-Hodgkin lymphoma cases globally are diffuse B-cell lymphoma (DLBCL), the most prevalent disease. Patients often have a rapidly expanding nodal or extranodal tumor mass in one or more locations.1 The concept of “high-grade B-cell lymphoma” has historically been used to refer to B-cell lymphomas…

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filter multisample VCF based on Altered AD values

I have a multisample VCF, ex. of a line: 1 14464 . A T . . ECNT=1;PON;DP=67;MBQ=0,36;MFRL=0,278;MMQ=60,28;MPOS=23;POPAF=0.69;TLOD=29.47 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,17:0.947:17:0,9:0,8:0,0,14,3 ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. 0/1:1,25:0.929:26:1,14:0,10:1,0,17,8 ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. 0/1:1,12:0.866:13:0,5:1,6:1,0,5,7 ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. 0/1:0,9:0.912:9:0,4:0,5:0,0,7,2 ./.:.:.:.:.:.:. What I need is to filter samples based on their…

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Integration of phenotypic, qPCR and genome sequencing methodologies for the detection of antimicrobial resistance and virulence in clinical isolates of a tertiary hospital, India

Azimi A, Peymani A, Pour PK (2018) Phenotypic and molecular detection of metallo-β-lactamase-producing Pseudomonas aeruginosa isolates from patients with burns in Tehran. Iran Rev Soc Bras Med Tro 51:610–615. doi.org/10.1590/0037-8682-0174-2017 Article  Google Scholar  Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology….

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AlphaFold-predicted deformation probes changes in protein stability

Abstract AlphaFold2 (AF) is an excellent structure predictor, but it does not unambiguously indicate whether the predicted structure is stable. Could it be that AF contains sufficient information to predict protein stability, and one just needs a way to extract it? To address this question, we investigate single-mutation effects on…

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A cytoskeleton-membrane interaction conserved in fast-spiking neurons controls movement, emotion, and memory

Trubetskoy V, Pardiñas AF, Qi T, Panagiotaropoulou G, Awasthi S, Bigdeli TB, et al. Mapping genomic loci implicates genes and synaptic biology in schizophrenia. Nature. 2022;604:502–8. Article  CAS  PubMed  PubMed Central  Google Scholar  Singh T, Poterba T, Curtis D, Akil H, Al Eissa M, Barchas JD, et al. Rare coding…

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public databases – Converting VCF format to text for use with PLINK and understanding column mapping

I successfully completed Nature PRS tutorial, which is based on PLINK. Turning to my real data, I downloaded ukb-d-20544_1.vcf.gz. Now I’m facing the problem that I seem to be unable to use it in PLINK or find the correct data format to download at all, and I am a bit…

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Genotyping, sequencing and analysis of 140,000 adults from Mexico City

Recruitment of study participants The MCPS was established in the late 1990s following discussions between Mexican scientists at the National Autonomous University of Mexico (UNAM) and British scientists at the University of Oxford about how best to measure the changing health effects of tobacco in Mexico. These discussions evolved into…

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Z2jh 500 : Internal Server Error – Zero to JupyterHub on Kubernetes

I have installed z2jh on a local k8s cluster. Sometimes I get 500 error, other times it works fine.I’m using jupyterhub Version 3.0.0, helm chart 2.0.0 500 : Internal Server ErrorThe error was:Failed to connect to Hub API at ‘hub:8081/hub/api’. Is the Hub accessible at this URL (from host: jupyter-hammad-20ali-20baig)?…

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The effect of vitrification on blastocyst mitochondrial DNA dynamics and gene expression profiles

Bosch E, De Vos M, Humaidan P. The future of cryopreservation in assisted reproductive technologies. Front Endocrinol (Lausanne). 2020;11:1–15. Article  Google Scholar  De Geyter C, Calhaz-Jorge C, Kupka MS, Wyns C, Mocanu E, Motrenko T, et al. ART in Europe, 2015: results generated from European registries by ESHRE†. Hum Reprod…

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Unable to spawn server after login JupyterHub on EKS cluster – Zero to JupyterHub on Kubernetes

HiI have installed jupyterhub with my newly created EKS Cluster with helm install, Installation was success and able to get the login page, while login with admin userI’m getting error message like below Your server is starting up. You will be redirected automatically when it’s ready for you. 100% Complete…

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BriaCell Partners with New York Cancer & Blood Specialists for Pivotal Phase 3 Study of Bria-IMT in Advanced Breast Cancer

In patients treated in the first-line setting (n=20), the confirmed objective response rate (ORR) was 65%, with a 100% disease control rate (DCR) (95% CI: 83.2, 100). In assessable patients in the second-line setting (n=13), the ORR was 54%, with a DCR of 85% (95% CI: 54.6, 98.1). Among patients…

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Filter vcf SNPs by sample GT value

Filter vcf SNPs by sample GT value 1 I have a merged VCF file with multiple samples on joined SNP set, where original genotypes have a 0|0 / 0|1 / 1|0 / 1|1 genotype (GT) and merged are fomatted as 0/0 if SNP was missing (–missing-ref option of bcftools merge)….

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Histone regulator KAT2A acts as a potential biomarker related to tumor microenvironment and prognosis of diffuse large B cell lymphoma | BMC Cancer

Zhang Y, Tan H, Daniels JD, Zandkarimi F, Liu H, Brown LM, et al. Imidazole Ketone Erastin induces ferroptosis and slows Tumor Growth in a mouse lymphoma model. Cell Chem Biol. 2019;26(5):623–33e9. Article  CAS  PubMed  PubMed Central  Google Scholar  Hartert KT, Wenzl K, Krull JE, Manske M, Sarangi V, Asmann…

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Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains | Cell & Bioscience

Lo MT, Kauppi K, Fan CC, Sanyal N, Reas ET, Sundar VS, Lee WC, Desikan RS, McEvoy LK, Chen CH, Alzheimer’s Disease Genetics, C. Identification of genetic heterogeneity of Alzheimer’s disease across age. Neurobiol Aging. 2019;84(243):e241-243. doi.org/10.1016/j.neurobiolaging.2019.02.022. Article  Google Scholar  Nacmias B, Bagnoli S, Piaceri I, Sorbi S. Genetic heterogeneity…

Continue Reading Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains | Cell & Bioscience

BriaCell Initiates Pivotal Phase 3 Study of Bria-IMT in Advanced Metastatic Breast Cancer

In patients treated in the first-line setting (n=20), the confirmed objective response rate (ORR) was 65%, with a 100% disease control rate (DCR) (95% CI: 83.2, 100). In assessable patients in the second-line setting (n=13), the ORR was 54%, with a DCR of 85% (95% CI: 54.6, 98.1). Among patients…

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