Tag: LD

Understanding the Role of Rare Genetic Variants and Their Impact on Health

Understanding the Role of Rare Genetic Variants Recent research on the UK Biobank cohort, a large-scale genetic data set, has shed light on the significant role of rare genetic variants (RVs) in complex trait heritability. The study confirms that these RVs account for a substantial portion of the complex trait…

Continue Reading Understanding the Role of Rare Genetic Variants and Their Impact on Health

calculated an LD matrix for a locus using plink2

Hi Everyone, I have a genotype file in  .pgen  format, that I subset and would like to calculate LD Matrix for. Previously I used a .bed file format and use plink 1.9 which worked as charm. But unfortunately my file is in Pgen format which is not supported  in plink…

Continue Reading calculated an LD matrix for a locus using plink2

Causality-enriched epigenetic age uncouples damage and adaptation

Gladyshev, V. N. et al. Molecular damage in aging. Nat. Aging 1, 1096–1106 (2021). Article  PubMed  PubMed Central  Google Scholar  Sziráki, A., Tyshkovskiy, A. & Gladyshev, V. N. Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction. Aging Cell 17, e12738 (2018). Article  PubMed …

Continue Reading Causality-enriched epigenetic age uncouples damage and adaptation

Functional-metabolic coupling in distinct renal cell types coordinates organ-wide physiology and delays premature ageing

Preferential carbohydrate import and early metabolism in PCs (but not SCs) supports renal physiology independent of ATP production Drosophila renal (Malpighian, MpT) tubules consist of two major cell types, the larger PCs and smaller SCs which perform distinct roles in ion, solute and water transport (Fig. 1a, b)16. These functional differences…

Continue Reading Functional-metabolic coupling in distinct renal cell types coordinates organ-wide physiology and delays premature ageing

Promising Biotech Selling Way Under Cash Value

Nkarta is using CRISPR technology for cell therapies for leukemia. The FDA just approved a similar cell therapy treatment for Vertex using the same CRISPR technology. Nkarta is trading well below cash value and has a significant short position sinking underwater. We did very well with Talaris as a takeover…

Continue Reading Promising Biotech Selling Way Under Cash Value

Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry

To investigate potential functional SNPs in APOBEC3 genes involved in COVID-19 severity, we evaluated the COVID-19 association signals around 7 APOBEB3 genes, comprising APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H, in the two COVID-19 hospitalization GWASs with European and African ancestries (HGI-B2-EUR and HGI-B2-AFR, respectively). Around these 7 APOBEC3…

Continue Reading Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry

PRRG4 regulates mitochondrial function and promotes migratory behaviors of breast cancer cells through the Src-STAT3-POLG axis | Cancer Cell International

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. doi.org/10.3322/caac.21660. Article  PubMed  Google Scholar  Hu G, Chong RA, Yang Q, Wei Y, Blanco…

Continue Reading PRRG4 regulates mitochondrial function and promotes migratory behaviors of breast cancer cells through the Src-STAT3-POLG axis | Cancer Cell International

Undefined reference to mbedTLS functions – Nordic Q&A – Nordic DevZone

Hi all!  So I’m trying to use mbedTLS methods in my project. I got it to work on SDK v1.9.0 but when upgrading to v.2.4.0 I get  a lot of “undefined references” to methods regarding mbedTLS.I see that there is some other issues regarding this but those haven’t solved my…

Continue Reading Undefined reference to mbedTLS functions – Nordic Q&A – Nordic DevZone

Archaic Introgression Shaped Human Circadian Traits | Genome Biology and Evolution

Abstract When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in…

Continue Reading Archaic Introgression Shaped Human Circadian Traits | Genome Biology and Evolution

Seeking Individual-Level Genotype Data for Linkage Disequilibrium Analysis Beyond 1000 Genomes Project

Seeking Individual-Level Genotype Data for Linkage Disequilibrium Analysis Beyond 1000 Genomes Project 0 Hi Biostars, I’m searching for databases with individual-level genotype data for linkage disequilibrium (LD) analysis. Already familiar with the 1000 Genomes Project, but I need more. Looking for something freely accessible, with detailed genotypic info. Any suggestions?…

Continue Reading Seeking Individual-Level Genotype Data for Linkage Disequilibrium Analysis Beyond 1000 Genomes Project

Checking my installation via serial mode of testing – LAMMPS Installation

I have installed LAMMPS 02Aug 2023 version and now from the bench directory I am running the test cases. I loaded the environmental modules and the path where lmp_nompi is oocated, but it ended up with following: /apps/lammps-2Aug2023/02082023/bench$ mpirun -np 4 /apps/lammps-2Aug2023/02082023/bin/lmp_mpi -in in.rhodo /apps/lammps-2Aug2023/02082023/bin/lmp_mpi: error while loading shared libraries:…

Continue Reading Checking my installation via serial mode of testing – LAMMPS Installation

Cannot install PyTorch on Orin AGX, with JP 5.0.2 – Jetson Orin NX

gbetsos December 12, 2023, 7:32pm 1 I have a custom Orin AGX board with L4T 35.1.0 and JetPack 5.0.2GA. I followed all steps from page: Installing PyTorch for Jetson Platform export TORCH_INSTALL=https://developer.download.nvidia.com/compute/redist/jp/v502/pytorch/torch-1.13.0a0+d0d6b1f2.nv22.10-cp38-cp38-linux_aarch64.whl $ python3 -m pip install –upgrade pip; $ python3 -m pip install aiohttp numpy==’1.19.4′ scipy==’1.5.3′ $ export “LD_LIBRARY_PATH=/usr/lib/llvm-8/lib:$LD_LIBRARY_PATH”;…

Continue Reading Cannot install PyTorch on Orin AGX, with JP 5.0.2 – Jetson Orin NX

PyTorch for JetPack 6.0DP – Jetson Orin Nano

I see that a PyTorch wheel is available for JetPack 6.0DP:developer.download.nvidia.cn/compute/redist/jp/v60dp/pytorch/ However the installation instructions seem to be out of date: NVIDIA Docs Installing PyTorch for Jetson Platform – NVIDIA Docs This guide provides instructions for installing PyTorch for Jetson Platform. The following packages are not generally available for Ubuntu…

Continue Reading PyTorch for JetPack 6.0DP – Jetson Orin Nano

Genetic architecture of cardiac dynamic flow volumes

Virani, S. S. et al. Heart disease and stroke statistics-2021 update: a report from the American Heart Association. Circulation 143, e254–e743 (2021). Article  PubMed  Google Scholar  Nauffal, V. et al. Genetics of myocardial interstitial fibrosis in the human heart and association with disease. Nat. Genet. 55, 777–786 (2023). Article  CAS …

Continue Reading Genetic architecture of cardiac dynamic flow volumes

Pytorch installation error – General Topics and Other SDKs

Hi ,i have upgrade my cuda from 11,4 to 12.2 using the following steps:wget developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/arm64/cuda-keyring_1.1-1_all.debsudo dpkg -i cuda-keyring_1.1-1_all.debsudo apt-get updatesudo apt-get -y install cudasudo gedit ~/.bashrcexport PATH=/usr/local/cuda-12.2/bin${PATH:+:${PATH}}export LD_LIBRARY_PATH=/usr/local/cuda-12.2/${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}source ~/.bashrc after that i am ablr=e to clone the pytorch using the following steps: git clone –recursive –branch v2.1.1 github.com/pytorch/pytorch export USE_NCCL=0…

Continue Reading Pytorch installation error – General Topics and Other SDKs

ncs v2.5.0 linker error when setting CONFIG_BOOTLOADER_MCUBOOT – Nordic Q&A – Nordic DevZone

Hello, I currently have an app using nRF Connect SDK v2.5.0. To enable FOTA I set CONFIG_NCS_SAMPLE_MCUMGR_BT_OTA_DFU and CONFIG_BOOTLOADER_MCUBOOT in my prj.conf (following the documentation instructions). After this building the app fails during linking for 3 different undefined references: [275/280] Linking C executable zephyr/zephyr_pre0.elf FAILED: zephyr/zephyr_pre0.elf zephyr/zephyr_pre0.map : && ccache /home/q/app/zephyr_workspace/toolchains/7795df4459/opt/zephyr-sdk/arm-zephyr-eabi/bin/arm-zephyr-eabi-gcc…

Continue Reading ncs v2.5.0 linker error when setting CONFIG_BOOTLOADER_MCUBOOT – Nordic Q&A – Nordic DevZone

Installation error Gromacs 2023.3 – User discussions

GROMACS version:2023.3GROMACS modification: NoHere post your questionI am trying to install the Cuda version of Gromacs. However, I am getting the following error after executing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda. Error : [ 98%] Linking CXX executable …/…/…/bin/argon-forces-integration/bin/ld: /home/saikat/softwares/gromacs-2023.3/build/lib/libgromacs.so.8: undefined reference to srot_’ /bin/ld: /home/saikat/softwares/gromacs-2023.3/build/lib/libgromacs.so.8: undefined reference to strsm_’collect2:…

Continue Reading Installation error Gromacs 2023.3 – User discussions

Converting txt.gz to PLINK bim

Converting txt.gz to PLINK bim 0 Hello, I’m trying to do a stratified LDSC (or S-LDSC/partitioned LDSC) between locus of interest and diseases (diabetes, arthritis, etc.). For locus of interest, I have a bed file from previous research. For diseases, I have downloaded GWAS sumstats from the GWAS atlas. I…

Continue Reading Converting txt.gz to PLINK bim

Psychological impact of additional findings detected by genome-wide Non-Invasive Prenatal Testing (NIPT): TRIDENT-2 study

Lo YMD, Corbetta N, Chamberlain PF, Rai V, Sargent IL, Redman CWG, et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997;350:485–7. Article  CAS  PubMed  Google Scholar  Warsof SL, Larion S, Abuhamad AZ. Overview of the impact of noninvasive prenatal testing on diagnostic procedures. Prenat Diagn. 2015;35:972–9….

Continue Reading Psychological impact of additional findings detected by genome-wide Non-Invasive Prenatal Testing (NIPT): TRIDENT-2 study

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…

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

tensorflow – CuDNN using wrong CUDA version

I’m re-doing my CUDA/CuDNN setup on a new profile on Ubuntu 22.04.3 because Keras raised an error with libcublasLT I couldn’t fix. For project compatibility, I need to use TF 12.12 with CUDA 11.8 and CuDNN 8.6. I’m working on a machine with multiple CUDA versions already installed. $ cd…

Continue Reading tensorflow – CuDNN using wrong CUDA version

Panic: Could not run ‘torchvision::roi_pool’ with arguments from the ‘CUDA’ backend – Jetson Nano

Hi, Team! I have such errors, when I run my code in docker container: root@de87551d73cf:/app/src# ./main WARN[0032] CUDA is valid WARN[0044] CUDA is valid INFO[0044] Forwarding… [W TensorImpl.h:1156] Warning: Named tensors and all their associated APIs are an experimental feature and subject to change. Please do not use them for…

Continue Reading Panic: Could not run ‘torchvision::roi_pool’ with arguments from the ‘CUDA’ backend – Jetson Nano

locuszoom error

locuszoom error 1 Hi there, I downloaded locuszoom in it’s entirty from their github page. I have everything in order but when I attempt to run the following I get an error: locuszoom_test/bin/locuszoom –metal chr7.snx13.marker.locuszoom.metal –ld chr7.imputed.concat.sorted.nomono.80.recode.maf01.pheno.vcf.2.ld.locuszoom.input –refsnp rs1533245 –prefix chr7.snx13.rs1533245 /share/hennlab/progs/locuszoom_test/bin/../src/m2zfast.py:82: SyntaxWarning: invalid escape sequence ‘\d’ RE_SNP_1000G = re.compile(“chr(\d+|[a-zA-z]+):(\d+)$”);…

Continue Reading locuszoom error

Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes

Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…

Continue Reading Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes

The Frequency of CYP2D6 and CYP3A4/5 Genotypes and The Impact of Their Allele Translation and Phenoconversion-Predicted Enzyme Activity on Risperidone Pharmacokinetics in Saudi Children with Autism

Al-Dosari MS, Al-Jenoobi FI, Alkharfy KM, Alghamdi AM, Bagulb KM, Parvez MK, Al-Mohizea AM, Al-Muhsen S, Halwani R (2013) High prevalence of CYP2D6*41 (G2988A) allele in Saudi Arabians. Environ Toxicol Pharmacol 36:1063–1067. doi.org/10.1016/j.etap.2013.09.008 Article  PubMed  CAS  Google Scholar  Almandil NB, Alkuroud DN, AbdulAzeez S, AlSulaiman A, Elaissari A, Borgio JF…

Continue Reading The Frequency of CYP2D6 and CYP3A4/5 Genotypes and The Impact of Their Allele Translation and Phenoconversion-Predicted Enzyme Activity on Risperidone Pharmacokinetics in Saudi Children with Autism

Performance evaluation of core genome multilocus sequence typing for genotyping of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection

Jagielski T, Minias A, van Ingen J, Rastogi N, Brzostek A, Żaczek A, Dziadek J (2016) Methodological and clinical aspects of the molecular epidemiology of Mycobacterium tuberculosis and other mycobacteria. Clin Microbiol Rev 29:239–290. doi.org/10.1128/cmr.00055-15 Article  PubMed  PubMed Central  CAS  Google Scholar  Niemann S, Merker M, Kohl T, Supply P…

Continue Reading Performance evaluation of core genome multilocus sequence typing for genotyping of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection

Identification of constrained sequence elements across 239 primate genomes

De novo assembly and repeat-masking To maximize the species diversity of primates in our analyses, we newly sequenced and assembled the genomes of 187 different primate species, initially presented in refs. 11,23, for which no other reference genome assembly was available. In brief, each individual was sequenced with 150 bp paired…

Continue Reading Identification of constrained sequence elements across 239 primate genomes

nrfConnect 2.5.0: mbedTLS fails to compile (calloc()) – Nordic Q&A – Nordic DevZone

Hi there: we’ve just updated from nrfConnect 2.3.0 to nrfConnect 2.5.0 and mbedTLS (which seems to have been modified in nrfConnect 2.5.0) now fails to link (in platform.c) because it needs and is unable to find calloc(): /home/arm_embedded_gcc-10-2020-q4-major/bin/ld.bfd: modules/mbedtls/libmbedTLSBase.a(platform.c.obj):/home/nrfconnectsdk-v2.5.0/modules/crypto/mbedtls/library/platform.c:56: undefined reference to `calloc’ As you can see, we are just compiling…

Continue Reading nrfConnect 2.5.0: mbedTLS fails to compile (calloc()) – Nordic Q&A – Nordic DevZone

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 …

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

East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease

We conducted a three-stage genome-wide analysis of PUD and its subtypes. An overview of the workflow is provided in Fig. 1 and Supplementary Fig. 1. PUD cases in the east Asian populations were obtained by combining individuals with any of the two major PUD subtypes (DU and GU), which were…

Continue Reading East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease

Population-specific distribution of TPMT deficiency variants

Introduction Thiopurine S-methyltransferase (TPMT) is a cytoplasmic enzyme that catalyzes the S-methylation of purine analogs, including azathioprine, 6-mercaptopurine (6-MP), and thioguanine.1 The metabolism of these drugs results in two types of metabolites: S-methylmercaptopurine and S-methylthioguanine, which are generally described as inactive metabolites, and S-methyl-thioinosine monophosphate, an inhibitor of de novo…

Continue Reading Population-specific distribution of TPMT deficiency variants

PyTorch 2.1 compatibility with CUDA 12.3

llama fails running on the GPU.Traced it to torch! Torch is using CUDA 12.1.Tried multiple different approaches where I removed 12.1 to make it use 12.3 downgraded the Nvidia driver. No joy! All help is appreciated. Running on a openSUSE tumbleweed.PyTorch Version: 2.1.1CUDA Version: 12.1CUDA Available: False | NVIDIA-SMI 545.29.06…

Continue Reading PyTorch 2.1 compatibility with CUDA 12.3

python – Different behavior in the same conda-pytorch env on different GPUs

Want to improve this question? Add details and clarify the problem by editing this post. I have a project that uses conda env with old pytorch version. It works smoothly if I use Nvidia V100, but it won’t run on other GPUs (I’ve tried RTX3080, TeslaA10, RTX2080TI, TeslaA2, TeslaT4) using…

Continue Reading python – Different behavior in the same conda-pytorch env on different GPUs

Error: Atomtype N3 not found while trying to obtain ions.tpr – User discussions

sam13 November 27, 2023, 12:33am 1 GROMACS version: 🙂 GROMACS – gmx grompp, 2023.3-Homebrew (-:GROMACS modification: No Hello,I have been trying to do MD simulation for a protein whose 3D structure is predicted by AlphaFold. The ligand is Aspartate molecule. I am following a similar approach to the Protein-Ligand GROMACS…

Continue Reading Error: Atomtype N3 not found while trying to obtain ions.tpr – User discussions

Evaluating 17 methods incorporating biological function with GWAS summary statistics to accelerate discovery demonstrates a tradeoff between high sensitivity and high positive predictive value

Method selection We reviewed the published literature through February 2020 to identify methods that met the following criteria: i. Descriptively categorized as (a) annotation-based; (b) pleiotropy-based; or (c) eQTL-based. ii. Utilized GWAS summary statistics, as opposed to individual-level genotype data. iii. Implemented using freely-available software or packages. iv. Provided either…

Continue Reading Evaluating 17 methods incorporating biological function with GWAS summary statistics to accelerate discovery demonstrates a tradeoff between high sensitivity and high positive predictive value

Decline of DNA damage response along with myogenic differentiation

Introduction Proper functioning of all living organisms depends on the faithful maintenance and transmission of genomic information stored in the molecule of DNA. However, DNA integrity is continuously challenged by a variety of endogenous and exogenous agents causing DNA lesions which have a critical impact on cellular activities and homeostasis….

Continue Reading Decline of DNA damage response along with myogenic differentiation

Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost

Tarnocai C, Canadell JG, Schuur EA, Kuhry P, Mazhitova G, Zimov S. Soil organic carbon pools in the northern circumpolar permafrost region. Global Biogeochem Cycles. 2009;23:1–11. Article  Google Scholar  Hugelius G, Strauss J, Zubrzycki S, Harden JW, Schuur EA, Ping CL, et al. Estimated stocks of circumpolar permafrost carbon with…

Continue Reading Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost

merge .pdata and .xdata sections from host object files

diff –git a/src/cmd/cgo/internal/test/callback_windows.go b/src/cmd/cgo/internal/test/callback_windows.gonew file mode 100644index 0000000..95e97c9— /dev/null+++ b/src/cmd/cgo/internal/test/callback_windows.go@@ -0,0 +1,133 @@+// Copyright 2023 The Go Authors. All rights reserved.+// Use of this source code is governed by a BSD-style+// license that can be found in the LICENSE file.++package cgotest++/*+#include <windows.h>+USHORT backtrace(ULONG FramesToCapture, PVOID *BackTrace) {+#ifdef _AMD64_+ CONTEXT context;+…

Continue Reading merge .pdata and .xdata sections from host object files

GenAlEx Haploid Data Detecting Recombination

GenAlEx Haploid Data Detecting Recombination 0 Hello, I am currently using GenAlEx to try and detect if recombination is present in both of my populations. My data consists of 4 Loci with one allele per locus. GenAlEx seems to have options for Paired biallelic LD, but I am struggling with…

Continue Reading GenAlEx Haploid Data Detecting Recombination

ARFID Genes and Environment (ARFID-GEN): study protocol | BMC Psychiatry

Dinkler L, Bryant-Waugh R. Assessment of avoidant restrictive food intake disorder, pica and rumination disorder: interview and questionnaire measures. Curr Opin Psychiatry. 2021;34(6):532–42. Article  Google Scholar  American Psychiatric Association. Diagnostic and Statistical Manual of Mental Disorders (5th ed.). Arlington, VA: American Psychiatric Publishing; 2013. Thomas JJ, Lawson EA, Micali N, Misra…

Continue Reading ARFID Genes and Environment (ARFID-GEN): study protocol | BMC Psychiatry

Multi-ancestry genome-wide association study of cannabis use disorder yields insight into disease biology and public health implications

Inclusion and ethics statement We included researchers from the iPSYCH biobank and the PGC, who played a role in study design. This research was not restricted or prohibited in the setting of any of the included researchers. All studies were approved by local instituational research boards and ethics review committees….

Continue Reading Multi-ancestry genome-wide association study of cannabis use disorder yields insight into disease biology and public health implications

Nccl_external fails while trying to compile pytroch from source – torch.compile

Hello, I’m trying to compile pytorch from source and encountering the following build error. $ CC=gcc-10 CXX=g++-10 python setup.py develop … [5995/6841] Linking CXX executable bin/HashStoreTest Warning: Unused direct dependencies: /home/netfpga/research/collective/pytorch/build/lib/libc10.so /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_intel_lp64.so.1 /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_gnu_thread.so.1 /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_core.so.1 /lib/x86_64-linux-gnu/libdl.so.2 /home/netfpga/anaconda3/envs/pytorch_base/lib/libgomp.so.1 [5996/6841] Performing build step for ‘nccl_external’ FAILED: nccl_external-prefix/src/nccl_external-stamp/nccl_external-build nccl/lib/libnccl_static.a /home/netfpga/research/collective/pytorch/build/nccl_external-prefix/src/nccl_external-stamp/nccl_external-build /home/netfpga/research/collective/pytorch/build/nccl/lib/libnccl_static.a cd /home/netfpga/research/collective/pytorch/third_party/nccl/nccl &&…

Continue Reading Nccl_external fails while trying to compile pytroch from source – torch.compile

Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance

De novo genome assemblies and genome annotation We assembled a de novo genome of a seven-year-old male SED from Ubon Ratchathani Zoo using a combination of Illumina short-reads (92.94 × coverage) and PacBio long-reads (61.6 × coverage) (GenBank accession number: JACCHN000000000). Additionally, we used MGI short-reads (52.15 × coverage) to assemble a de novo genome of…

Continue Reading Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance

python – Docker with Rstudio & conda virtual env – unable to load R packages

I have this dockerfile: # Use the rocker/rstudio image with R version 4.1.2 FROM rocker/rstudio:4.1.2 # Install deps RUN apt-get update && apt-get install -y \ wget \ bzip2 \ bash-completion \ libxml2-dev \ zlib1g-dev \ libxtst6 \ libxt6 \ libhdf5-dev \ libcurl4-openssl-dev \ libssl-dev \ libfontconfig1-dev \ libcairo2-dev \…

Continue Reading python – Docker with Rstudio & conda virtual env – unable to load R packages

Error in compiling lammps after interfacing with AENET

Dear Dr. Artrith and team, Greetings! I’m new to aenet. Thank you Dr. Artrith and team for develping aenet and opensourcing it.  I downloaded USER-AENET and interfaced with lammps 4Feb2020-version. However, I’m getting the following error (complete error response attached ) when I compile the lammps using “make mpi”. Kindly…

Continue Reading Error in compiling lammps after interfacing with AENET

Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis

Rg3 elicits protection against local and systemic enteric virus infection by regulating the intestinal microbiome To assess the antiviral effects of Rg3 in vivo, groups of C57BL/6J mice (referred to as WT B6 hereafter) were orally administered Rg3 for 3 consecutive days, inoculated with MNV-1 by the peroral route, and…

Continue Reading Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis

132arm64-default][science/votca] Failed for votca-2022.1_1 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere3/data/132arm64-default/d5268d5f7157/logs/votca-2022.1_1.log Build URL: pkg-status.freebsd.org/ampere3/build.html?mastername=132arm64-default&build=d5268d5f7157 Log: =>> Building science/votca build started at Fri Nov 10…

Continue Reading 132arm64-default][science/votca] Failed for votca-2022.1_1 in build

A software tool to adjust codeine dose based on CYP2D6 gene-pair polymorphisms and drug-drug interactions

Review doi: 10.1038/s41397-023-00318-7. Online ahead of print. Affiliations Expand Affiliations 1 Pharmaceutical Sciences Department, School of Pharmacy, Lebanese American University, Byblos, Lebanon. ysaab@lau.edu.lb. 2 Electrical and Computer Engineering Department, School of Engineering, Lebanese American University, Byblos, Lebanon. zahi.nakad@lau.edu.lb. Item in Clipboard Review Yolande Saab et al. Pharmacogenomics J. 2023. Show details…

Continue Reading A software tool to adjust codeine dose based on CYP2D6 gene-pair polymorphisms and drug-drug interactions

Genome-wide meta-analysis, functional genomics and integrative analyses implicate new risk genes and therapeutic targets for anxiety disorders

Kessler, R. C. et al. Lifetime prevalence and age-of-onset distributions of DSM-IV disorders in the National Comorbidity Survey Replication. Arch. Gen. Psychiatry 62, 593–602 (2005). Article  PubMed  Google Scholar  Kessler, R. C. et al. Prevalence, persistence, and sociodemographic correlates of DSM-IV disorders in the National Comorbidity Survey Replication Adolescent Supplement….

Continue Reading Genome-wide meta-analysis, functional genomics and integrative analyses implicate new risk genes and therapeutic targets for anxiety disorders

Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network | Genome 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  Llovet JM, Kelley RK, Villanueva A, Singal AG, Pikarsky E,…

Continue Reading Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network | Genome Medicine

RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome | Briefings in Bioinformatics

Abstract Bacterial infections often involve virulence factors that play a crucial role in the pathogenicity of bacteria. Accurate detection of virulence factor genes (VFGs) is essential for precise treatment and prognostic management of hypervirulent bacterial infections. However, there is a lack of rapid and accurate methods for VFG identification from…

Continue Reading RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome | Briefings in Bioinformatics

Go Lang Developer to fix one rest API issue

I have a Go Lang Project where it creates tickets by using JSON LD objects. The requirements are : -1. Currently the JSONLD data is stored in “Content” field in string format, while creating the ticket , we are sending the jsonld in string format only as its expecting in…

Continue Reading Go Lang Developer to fix one rest API issue

Pytorch installation error – Jetson Xavier NX

I am installing pytorch. While installing according to the installation guide, an error such as a photo occurred. Hi @seongone.156, there appears to be a missing semicolon between scipy==’1.5.3′ and export “LD_LIBRARY_PATH=…” Also set export TORCH_INSTALL=https://developer.download.nvidia.cn/compute/redist/jp/v511/pytorch/torch-2.0.0+nv23.05-cp38-cp38-linux_aarch64.whl first, or set it to the path of the whl file that you downloaded….

Continue Reading Pytorch installation error – Jetson Xavier NX

Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis

Identification of CH cases from WGS in ISL and UKB We used WGS from 45,510 Icelanders and 130,709 British ancestry participants from the UKB17,18. Average sequencing depth was 33× for UKB and 38× for ISL. Participants with prior diagnoses of hematological disorders or grossly abnormal hematology measurements on entry were…

Continue Reading Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis

significant SNPs from per-phenotype GWAS summary statistics

significant SNPs from per-phenotype GWAS summary statistics 0 I performed an analysis for a specific gene/region of interest using GWAS summary statistics for a binary phenotype (+/- disease). Using the corrected p values in the summary statistics and mapping in FUMA, I found a significant missense/coding SNP, with p=0.025. Other…

Continue Reading significant SNPs from per-phenotype GWAS summary statistics

Figure S12 – compa WG

%PDF-1.7 % 1 0 obj <>/OCGs[9 0 R 59 0 R 108 0 R 158 0 R 207 0 R 256 0 R 305 0 R]>>/Pages 3 0 R/Type/Catalog>> endobj 2 0 obj <>stream 2018-07-03T11:32:26+02:00 Adobe Illustrator CC 22.1 (Macintosh) 2019-05-14T19:51:08+02:00 2019-05-14T19:51:08+02:00 184 256 JPEG /9j/4AAQSkZJRgABAgEASABIAAD/7QAsUGhvdG9zaG9wIDMuMAA4QklNA+0AAAAAABAASAAAAAEA AQBIAAAAAQAB/+4ADkFkb2JlAGTAAAAAAf/bAIQABgQEBAUEBgUFBgkGBQYJCwgGBggLDAoKCwoK DBAMDAwMDAwQDA4PEA8ODBMTFBQTExwbGxscHx8fHx8fHx8fHwEHBwcNDA0YEBAYGhURFRofHx8f Hx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8f/8AAEQgBAAC4AwER AAIRAQMRAf/EAaIAAAAHAQEBAQEAAAAAAAAAAAQFAwIGAQAHCAkKCwEAAgIDAQEBAQEAAAAAAAAA AQACAwQFBgcICQoLEAACAQMDAgQCBgcDBAIGAnMBAgMRBAAFIRIxQVEGE2EicYEUMpGhBxWxQiPB UtHhMxZi8CRygvElQzRTkqKyY3PCNUQnk6OzNhdUZHTD0uIIJoMJChgZhJRFRqS0VtNVKBry4/PE 1OT0ZXWFlaW1xdXl9WZ2hpamtsbW5vY3R1dnd4eXp7fH1+f3OEhYaHiImKi4yNjo+Ck5SVlpeYmZ qbnJ2en5KjpKWmp6ipqqusra6voRAAICAQIDBQUEBQYECAMDbQEAAhEDBCESMUEFURNhIgZxgZEy obHwFMHR4SNCFVJicvEzJDRDghaSUyWiY7LCB3PSNeJEgxdUkwgJChgZJjZFGidkdFU38qOzwygp…

Continue Reading Figure S12 – compa WG

Non-coding RNA-mediated endothelial-to-mesenchymal transition in human diabetic cardiomyopathy, potential regulation by DNA methylation | Cardiovascular Diabetology

Raghavan S, Vassy JL, Ho Y, Song RJ, Gagnon DR, Cho K, et al. Diabetes mellitus-related all-cause and cardiovascular mortality in a national cohort of adults. J Am Heart Assoc. 2019;8(4): e011295. Article  PubMed  PubMed Central  Google Scholar  Jia G, Whaley-Connell A, Sowers JR. Diabetic cardiomyopathy: a hyperglycaemia—and insulin-resistance-induced heart…

Continue Reading Non-coding RNA-mediated endothelial-to-mesenchymal transition in human diabetic cardiomyopathy, potential regulation by DNA methylation | Cardiovascular Diabetology

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

Plink2 –extract not working

Hi Chris,         This problem seems so silly but I just got stuck here for a long time.         I tried to extract a set of SNPs (I’m pretty sure they all appear in the .bim file) and rename their IDs with –set-all-var-ids, and…

Continue Reading Plink2 –extract not working

LD D-prime (D’) calculation

LD D-prime (D’) calculation 0 Hi all, I am trying to compute LD statistics with gaston package in R and plotting them, but I do not know how to obtain D’ values. I do obtain r2 and D values but I would very interested in D’ statistic. Is it possible…

Continue Reading LD D-prime (D’) calculation

Production of leishmanin skin test antigen from Leishmania donovani for future reintroduction in the field

Study design and ethical statement All research complies with all relevant ethical regulations. Animal experiments in this study were reviewed and approved by the Animal Care and Use Committee of the Center for Biologics Evaluation and Research, U.S. Food and Drug Administration (ASP-1999#23 and ASP-1995#26) and the National Institute of…

Continue Reading Production of leishmanin skin test antigen from Leishmania donovani for future reintroduction in the field

140releng-armv7-default][misc/py-pytorch] Failed for py39-pytorch-2.0.1 in configure

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere3/data/140releng-armv7-default/08943441f26e/logs/py39-pytorch-2.0.1.log Build URL: pkg-status.freebsd.org/ampere3/build.html?mastername=140releng-armv7-default&build=08943441f26e Log: =>> Building misc/py-pytorch build started at Thu Nov 2…

Continue Reading 140releng-armv7-default][misc/py-pytorch] Failed for py39-pytorch-2.0.1 in configure

Get errors in loading packages/ calling functions in sc-seq data analysis

Get errors in loading packages/ calling functions in sc-seq data analysis 1 Hi, I am learning to process sc-seq data in Rstudio. There are 2 problems I have: I tried to install scater package using BiocManager::install(“scater”) but it failed. This is the error message: ld: warning: directory not found for…

Continue Reading Get errors in loading packages/ calling functions in sc-seq data analysis

Generating ion.tpr file – User discussions

AF1 November 1, 2023, 11:49am 1 Hi I am getting the following error from Lysozyme in water tutorial. I successfully completed this tutorial a few months ago but this week it seems the file gets broken at the ions.tpr output step. Please see message and file generated. Command line:gmx grompp…

Continue Reading Generating ion.tpr file – User discussions

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+…

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

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,…

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

Do different microarray chips yield different accuracy of polygenic scores?

When replicating a polygenic score, labs have multiple microarray chips to choose from. (E.g., GSA, GDA, UK Biobank Axiom Array, UK BiLEVE Axiom array, GeneChip 2.0 array, Infinium Core-24 Kit, etc.). Will using different chips impact the accuracy of the polygenic score? If so, by how much? I’ve been unable…

Continue Reading Do different microarray chips yield different accuracy of polygenic scores?

CYP1A2 expression rather than genotype is associated with olanzapine concentration in psychiatric patients

Owen, M. J., Sawa, A. & Mortensen, P. B. Schizophrenia. Lancet 388, 86–97 (2016). Article  PubMed  PubMed Central  Google Scholar  Bhana, N., Foster, R. H., Olney, R. & Plosker, G. L. Olanzapine: An updated review of its use in the management of schizophrenia. Drugs 61, 111–161 (2001). Article  CAS  PubMed …

Continue Reading CYP1A2 expression rather than genotype is associated with olanzapine concentration in psychiatric patients

Bi-allelic truncating variants in CASP2 underlie a neurodevelopmental disorder with lissencephaly

Di Donato N, Chiari S, Mirzaa GM, Aldinger K, Parrini E, Olds C, et al. Lissencephaly: expanded imaging and clinical classification. Am J Med Genet A. 2017;173:1473–88. Article  PubMed  PubMed Central  Google Scholar  Guerrini R, Dobyns WB. Malformations of cortical development: clinical features and genetic causes. Lancet Neurol. 2014;13:710–26. Article …

Continue Reading Bi-allelic truncating variants in CASP2 underlie a neurodevelopmental disorder with lissencephaly

main-powerpc64le-default][misc/pytorch] Failed for pytorch-1.13.1_1 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/main-powerpc64le-default/pbc0e38d0f08e_s0afcac3e37/logs/pytorch-1.13.1_1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=main-powerpc64le-default&build=pbc0e38d0f08e_s0afcac3e37 Log: =>> Building misc/pytorch build started at Tue Oct 24…

Continue Reading main-powerpc64le-default][misc/pytorch] Failed for pytorch-1.13.1_1 in build

Genome-wide association study of traumatic brain injury in U.S. military veterans enrolled in the VA million veteran program

Helmick KM, Spells CA, Malik SZ, Davies CA, Marion DW, Hinds SR. Traumatic brain injury in the US military: Epidemiology and key clinical and research programs. Brain Imaging Behav. 2015;9:358–66. Article  PubMed  Google Scholar  DoD Numbers for Traumatic Brain Injury Worldwide – Totals (Defense Health Agency) (2021). Karr JE, Areshenkoff…

Continue Reading Genome-wide association study of traumatic brain injury in U.S. military veterans enrolled in the VA million veteran program

Expanding causal genes for Parkinson’s disease via multi-omics analysis

Proteins causally associated with PD in the brain MR analysis of brain dorsolateral prefrontal cortex (dlPFC) pQTLs identified six genetically determined significant proteins on PD after multiple testing corrections (P < 8.55E-05 (0.05/585)). Specifically, the increased abundance of 3 proteins was significantly associated with an increased risk of PD, including GPNMB (OR:1.464,…

Continue Reading Expanding causal genes for Parkinson’s disease via multi-omics analysis

Genome-wide association study in 404,302 individuals identifies 7 significant loci for reaction time variability

MacDonald SW, Li SC, Bäckman L. Neural underpinnings of within-person variability in cognitive functioning. Psychol Aging. 2009;24:792–808. Article  PubMed  Google Scholar  Haynes BI, Bunce D, Kochan NA, Wen W, Brodaty H, Sachdev PS. Associations between reaction time measures and white matter hyperintensities in very old age. Neuropsychologia. 2017;96:249–55. Article  PubMed …

Continue Reading Genome-wide association study in 404,302 individuals identifies 7 significant loci for reaction time variability

Systematic differences in discovery of genetic effects on gene expression and complex traits

Claussnitzer, M. et al. A brief history of human disease genetics. Nature 577, 179–189 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Gusev, A. et…

Continue Reading Systematic differences in discovery of genetic effects on gene expression and complex traits

IJMS | Free Full-Text | Whole-Genome Sequencing of 502 Individuals from Latvia: The First Step towards a Population-Specific Reference of Genetic Variation

1. Introduction Human population genetics benefitted from the completion of the human genome sequence [1], which was further advanced by creating the reference of global genome variation [2] and, finally, the establishment of regional references assessing fine details of local variation in whole-genome sequences. Although European populations are relatively well…

Continue Reading IJMS | Free Full-Text | Whole-Genome Sequencing of 502 Individuals from Latvia: The First Step towards a Population-Specific Reference of Genetic Variation

Using cmdstanr crashing RStudio – Interfaces

I’ve recently updated to macOS Sonoma and started using {renv} when using cmdstanr started causing fatal errors and crashing RStudio (i.e., loading it using library(cmdstanr) or just making function calls using cmdstanr::). After lots of trial and error, it appears to be an RStudio thing since I can run the…

Continue Reading Using cmdstanr crashing RStudio – Interfaces

Analysis of gut bacteriome of in utero arsenic-exposed mice using 16S rRNA-based metagenomic approach

. 2023 Sep 29:14:1147505. doi: 10.3389/fmicb.2023.1147505. eCollection 2023. Affiliations Expand Affiliations 1 Department of Microbiology, Dr. Shakuntala Misra National Rehabilitation University, Lucknow, Uttar Pradesh, India. 2 Systems Toxicology and Health Risk Assessment Group, Council of Scientific & Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, Uttar Pradesh, India. 3 Department…

Continue Reading Analysis of gut bacteriome of in utero arsenic-exposed mice using 16S rRNA-based metagenomic approach

main-armv7-default][biology/viennarna] Failed for viennarna-2.6.3 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere2/data/main-armv7-default/p08943441f26e_s6e92fc9309/logs/viennarna-2.6.3.log Build URL: pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p08943441f26e_s6e92fc9309 Log: =>> Building biology/viennarna build started at Mon Oct 16…

Continue Reading main-armv7-default][biology/viennarna] Failed for viennarna-2.6.3 in build

Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton

Gene expression atlas in fiber development To uncover the genetic regulation of gene expression in fiber development, we collected 376 diverse G. hirsutum accessions for genome and transcriptome analysis. A total of 13.5 Tb of genome resequencing data were generated, with an average depth of 15.6× (Supplementary Table 1). Accessions were…

Continue Reading Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton

eQTL-seq: a Rapid Genome-Wide Integrative Genetical Genomics Strategy to Dissect Complex Regulatory Architecture of Gene Expression Underlying Quantitative Trait Variation in Crop Plants

Bajaj D, Upadhyaya HD, Khan Y, Das S, Badoni S, Shree T, Kumar V, Tripathi S, Gowda CL, Singh S, Sharma S, Tyagi AK, Chattopdhyay D, Parida SK (2015) A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea. Sci…

Continue Reading eQTL-seq: a Rapid Genome-Wide Integrative Genetical Genomics Strategy to Dissect Complex Regulatory Architecture of Gene Expression Underlying Quantitative Trait Variation in Crop Plants

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…

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

The activation of cGAS-STING in acute kidney injury

Introduction AKI, which is characterised by necroinflammation due to damage and necrosis of the kidney’s intrinsic cells,1 is a common clinical syndrome, occurring in 10–15% of hospitalized patients, whereas in the ICU this percentage is as high as 50%.2 The development of AKI is involved in the production of reactive…

Continue Reading The activation of cGAS-STING in acute kidney injury

Fatal Error: Too many warnings (1) Use -maxwarn option in gromacs 2023.2 – User discussions

Respected Sir/Ma’am,I am getting an error as shown below.🙂 GROMACS – gmx grompp, 2023.2 (-: Executable: /usr/local/gromacs/bin/gmxData prefix: /usr/local/gromacsWorking dir: /home/drr-18/Complex_02_EMinimizedCommand line:gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr Ignoring obsolete mdp entry ‘title’Ignoring obsolete mdp entry ‘ns_type’ WARNING 1 [file npt.mdp]:The…

Continue Reading Fatal Error: Too many warnings (1) Use -maxwarn option in gromacs 2023.2 – User discussions

Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin

Mapping eQTLs in patients with psoriasis We obtained longitudinal lesional and non-lesional skin biopsies from participants at baseline, during treatment, and at the time of psoriasis relapse after study medication withdrawal over a course of 22 months. We used genome-wide genotyping and RNA-seq to assay samples. After stringent quality control,…

Continue Reading Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin

Identification of eQTL from porcine muscle and liver mRNA sequencing

Master’s Dissertation DOI doi.org/10.11606/D.11.2023.tde-02102023-151405 Document Author Freitas, Felipe André Oliveira (Catálogo USP) Full name Felipe André Oliveira Freitas E-mail Institute/School/College Escola Superior de Agricultura Luiz de Queiroz Knowledge Area Animal Science and Pastures Date of Defense Published Piracicaba, 2023 Supervisor Cesar, Aline Silva Mello (Catálogo USP) Committee Cesar, Aline Silva…

Continue Reading Identification of eQTL from porcine muscle and liver mRNA sequencing

The effect of oleic acid supplementation on lipid droplet production, betaoxidation and rotavirus replication

Abstract Rotavirus (RV) is the most common cause of severe acute gastroenteritis in infants and young children globally. Rotavirus infections induce cytoplasmic inclusion bodies called viroplasms serving as a site of RV genome replication and assembly. Viroplasms recruit lipid droplets (LDs), which play major roles in energy homeostasis and is…

Continue Reading The effect of oleic acid supplementation on lipid droplet production, betaoxidation and rotavirus replication

“Installing PyTorch for Jetson Platform”: Error in pytorch install instructions? (Missing semicolon?) – Jetson Nano

Tried to install PyTorch for Jetson Platform using the command shown on Installing PyTorch for Jetson Platform – NVIDIA Docs and got errors about LD_LIBRARY_PATH . I’m not a PIP expert, but it looks to me like that export was intended to be a separate command and a semicolon was…

Continue Reading “Installing PyTorch for Jetson Platform”: Error in pytorch install instructions? (Missing semicolon?) – Jetson Nano

The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons

The genome assembly was performed with the pipeline v1.5 of the Vertebrate Genomes Project (VGP) and can be found under NCBI BioProject PRJNA558064, accession number GCA_009819655.1, for further details on the sample collection and assembly see Ishigohoka et al.9. In brief, a female blackcap from mainland Spain was caught to…

Continue Reading The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons

Multi-ancestry genome-wide study identifies effector genes and druggable pathways for coronary artery calcification

Timmis, A. et al. European Society of Cardiology: Cardiovascular Disease Statistics 2017. Eur. Heart J. 39, 508–579 (2018). Article  PubMed  Google Scholar  Tsao, C. W. et al. Heart Disease and Stroke Statistics—2022 Update: a report from the American Heart Association. Circulation 145, e153–e639 (2022). Article  PubMed  Google Scholar  Libby, P.,…

Continue Reading Multi-ancestry genome-wide study identifies effector genes and druggable pathways for coronary artery calcification

Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease

Samples for H3K27ac ChIP–seq Samples were collected by the GTEx Consortium. The donor enrollment and consent, informed consent approval, histopathological review procedures, and biospecimen procurement methods and fixation were the same as previously described22. No compensation was provided to the families of participants. Massachusetts Institute of Technology Committee on the…

Continue Reading Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease

RPM Search opensuse slurm-plugins-18.08.9-lp152.2.1.x86_64.rpm

Content of RPM slurm-plugins-18.08.9-lp152.2.1.x86_64.rpm : /etc/ld.so.conf.d/slurm.conf /usr/lib64/slurm /usr/lib64/slurm/accounting_storage_filetxt.so /usr/lib64/slurm/accounting_storage_none.so /usr/lib64/slurm/accounting_storage_slurmdbd.so /usr/lib64/slurm/acct_gather_energy_ibmaem.so /usr/lib64/slurm/acct_gather_energy_ipmi.so /usr/lib64/slurm/acct_gather_energy_none.so /usr/lib64/slurm/acct_gather_energy_rapl.so /usr/lib64/slurm/acct_gather_energy_xcc.so /usr/lib64/slurm/acct_gather_filesystem_lustre.so /usr/lib64/slurm/acct_gather_filesystem_none.so /usr/lib64/slurm/acct_gather_interconnect_none.so /usr/lib64/slurm/acct_gather_interconnect_ofed.so /usr/lib64/slurm/acct_gather_profile_influxdb.so /usr/lib64/slurm/acct_gather_profile_none.so /usr/lib64/slurm/burst_buffer_generic.so /usr/lib64/slurm/checkpoint_none.so /usr/lib64/slurm/checkpoint_ompi.so /usr/lib64/slurm/core_spec_none.so /usr/lib64/slurm/crypto_openssl.so /usr/lib64/slurm/ext_sensors_none.so /usr/lib64/slurm/ext_sensors_rrd.so /usr/lib64/slurm/gres_gpu.so /usr/lib64/slurm/gres_mic.so /usr/lib64/slurm/gres_nic.so /usr/lib64/slurm/job_container_cncu.so /usr/lib64/slurm/job_container_none.so /usr/lib64/slurm/job_submit_all_partitions.so /usr/lib64/slurm/job_submit_defaults.so /usr/lib64/slurm/job_submit_logging.so /usr/lib64/slurm/job_submit_partition.so /usr/lib64/slurm/job_submit_require_timelimit.so /usr/lib64/slurm/job_submit_throttle.so /usr/lib64/slurm/jobacct_gather_cgroup.so /usr/lib64/slurm/jobacct_gather_linux.so /usr/lib64/slurm/jobacct_gather_none.so /usr/lib64/slurm/jobcomp_elasticsearch.so /usr/lib64/slurm/jobcomp_filetxt.so /usr/lib64/slurm/jobcomp_none.so /usr/lib64/slurm/jobcomp_script.so /usr/lib64/slurm/launch_slurm.so /usr/lib64/slurm/layouts_power_cpufreq.so /usr/lib64/slurm/layouts_power_default.so /usr/lib64/slurm/layouts_unit_default.so…

Continue Reading RPM Search opensuse slurm-plugins-18.08.9-lp152.2.1.x86_64.rpm

Saving the output of LD pruning from SNPRelate package as a new GDS file

Saving the output of LD pruning from SNPRelate package as a new GDS file 1 I successfully ran LD pruning from SNPRelate package and obtained the selected SNPs IDs. I would like to create a new GDS file with only the pruned SNPs so I can use it in another…

Continue Reading Saving the output of LD pruning from SNPRelate package as a new GDS file

132releng-armv7-quarterly][misc/pytorch] Failed for pytorch-1.13.1_1 in configure

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere1/data/132releng-armv7-quarterly/2be22e0743b5/logs/pytorch-1.13.1_1.log Build URL: pkg-status.freebsd.org/ampere1/build.html?mastername=132releng-armv7-quarterly&build=2be22e0743b5 Log: =>> Building misc/pytorch build started at Mon Sep 25…

Continue Reading 132releng-armv7-quarterly][misc/pytorch] Failed for pytorch-1.13.1_1 in configure

r – How to align weeks in different years in ggplot2?

How can I align the weeks from different years on the x-axis so that weeks occurring in the same month, like June, are aligned? Please note that data was not collected during same weeks in different years, so some weeks can’t be aligned, and that’s okay. I just wish to…

Continue Reading r – How to align weeks in different years in ggplot2?

main-arm64-default][biology/viennarna] Failed for viennarna-2.6.3 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere2/data/main-arm64-default/p85ccf094713a_sc584bb9cac1/logs/viennarna-2.6.3.log Build URL: pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p85ccf094713a_sc584bb9cac1 Log: =>> Building biology/viennarna build started at Sat Sep 23…

Continue Reading main-arm64-default][biology/viennarna] Failed for viennarna-2.6.3 in build

CP2K version 2023.2 compile error

Thank you for helping me, Mishra. However, I still got problems. I modified the script according to my architecture, as below:“spack -d install cp2k@2023.1+elpa %g…@8.3.1 target=icelake ^elpa+openmp ^ope…@4.1.4 fabrics=auto”Then I got very, very long error message below and I dont’ know what is the reason. ———————————————————————————————————————————————————————————– ==> [2023-09-22-11:22:05.969419] Error: ProcessError:…

Continue Reading CP2K version 2023.2 compile error

Functional characterization of Alzheimer’s disease genetic variants in microglia

Nott, A. et al. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science 366, 1134–1139 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  Neuner, S. M., Tcw, J. & Goate, A. M. Genetic architecture of Alzheimer’s disease. Neurobiol. Dis. 143, 104976 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar …

Continue Reading Functional characterization of Alzheimer’s disease genetic variants in microglia

KidneyGPS: a user-friendly web application to help prioritize kidney function genes and variants based on evidence from genome-wide association studies | BMC Bioinformatics

User interface The user interface of KidneyGPS is organized into five tabs: Three tabs enable the specific search for genes, variants and regions (underlying data structure shown in Additional file 1: Fig. S4): (1) “gene search” tab: search for genes using their gene names (synonyms automatically mapped to their official HGNC…

Continue Reading KidneyGPS: a user-friendly web application to help prioritize kidney function genes and variants based on evidence from genome-wide association studies | BMC Bioinformatics