Tag: clusters

The effects of methylphenidate and atomoxetine on Drosophila brain at single-cell resolution and potential drug repurposing for ADHD treatment

Both MPH and ATX increase the locomotor activity of wild-type Drosophila To investigate the cell type-specific molecular mechanisms of ADHD drugs in the brain at single-cell resolution, we conducted behavioral experiments and scRNASEQ in wild-type (WT) adult male Drosophila melanogaster following exposure to MPH, ATX, and control treatment. Here, we…

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The Imageable Genome | Nature Communications

For the Imageable Genome project, we developed a data pipeline that identifies texts containing radiotracers, recognizes and extracts names of radiotracers from texts, filters for clinically relevant radiotracers and their associated targets, and translates protein names, i.e. of radiotracer targets, to names of the coding genes. We then downloaded the…

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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…

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Scientists discover key to a potential natural cancer treatment’s potency

Within the glass vials of the Natural Products Discovery Center at The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, scientists have discovered two useful new enzymes which may help them create medicines for cancer and other conditions. Credit: Scott Wiseman Slumbering among thousands of bacterial strains in…

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How head lice reveal secrets about human origins

Sign up for CNN’s Wonder Theory science newsletter. Explore the universe with news on fascinating discoveries, scientific advancements and more. CNN  —  Head lice have been constant, if unwanted, human companions for as long as our species has been around. Evidence of this ancient connection includes a 10,000-year-old louse found on…

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Case of Spine Infection with Brucella melitensis

Introduction Brucellosis is a common zoonotic infection in most of the developing regions of the world, severely affecting livestock productivity and human health. It caused by a small, nonmotile gram-negative coccobacillus of the genus Brucella. Among reported human brucellosis cases, the pathogenic strain B. melitensis is the most frequently encountered.1,2…

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Forecasting the dynamics of a complex microbial community using integrated meta-omics

Characterization of the microbial community From the experimental period between 21 March 2011 and 3 May 2012 (ref. 27), we previously obtained and analysed 51 weekly samples, to which we added 21 samples collected in the month of June during the years 2012–2016. The 72 samples were submitted to the…

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(05) – Practical Handout 5 – Department of Computing & Information Systems CMIS 3253- Data

Preview text Department of Computing & Information Systems CMIS 3253- Data Mining Handout- 05 ——————————————————————————————————————————– Cluster Analysis Cluster is a group of objects that belongs to the same class. In other words, similar objects are grouped in one cluster and dissimilar objects are grouped in another cluster. Cluster Analysis –…

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Bioconductor – scDesign3

DOI: 10.18129/B9.bioc.scDesign3   A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics Bioconductor version: Release (3.18) We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning…

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Head of Bioinformatics Job in Greater London, Career, Permanent Jobs in Bactobio

We are looking for an exceptional microbial bioinformatician to join our leadership team at Bactobio as Head of Bioinformatics. Company Bactobio is a London-based biotechnology company founded in 2020. We use breakthrough technologies in synthetic biology, next-generation sequencing, and machine learning to cultivate the 99% previously unculturable microbes. These…

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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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Chst9 Marks a Spatially and Transcriptionally Unique Population of Oprm1 -Expressing Neurons in the Nucleus Accumbens

Abstract Opioids produce addictive, analgesic, and euphoric effects via actions at mu opioid receptors (μORs). The μOR is encoded by the Oprm1 gene and is expressed in multiple brain regions that regulate reward and motivation, such as the nucleus accumbens (NAc). Oprm1 expression in NAc medium spiny neurons (MSNs) mediates…

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python – Scikit Kmeans tutorial, n_runs and n_init different purpose?

scikit-learn.org/stable/auto_examples/text/plot_document_clustering.html In the above documentation, we are running KMeans. The KMeans class has an n_init parameter like so: kmeans = KMeans( n_clusters=true_k, max_iter=100, n_init=1, ) Additionally, the fit_and_evaluation function from the docs uses an n_runs parameter for the number of times to rerun kmeans. for seed in range(n_runs): km.set_params(random_state=seed) t0…

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Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae

Sheridan, P. O. et al. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat. Commun. 11, 1–12 (2020). Article  Google Scholar  Sheridan, P. O., Meng, Y., Williams, T. A. & Gubry-Rangin, C. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat. Commun. 13, 1–13…

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The CRTC-1 transcriptional domain is required for COMPASS complex-mediated longevity in C. elegans

CRTC-1-binding proteins To identify CRTC-1 protein interactions, we tagged endogenous CRTC-1 via clustered regularly interspaced short palindromic repeats–associated protein 9 (CRISPR–Cas9) editing to generate a crtc-1::3xFLAG strain and performed immunoprecipitation (IP) followed by liquid chromatography coupled to mass spectrometry (LC–MS). We found 137 potential CRTC-1 interacting proteins (Fig. 1a and…

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Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma

Statistical methods Statistical tests, test statistics and P values are indicated where appropriate in the main text. Categorical associations were established using the chi-squared test of independence if n > 5 for all categories and Fisherʼs exact test otherwise. For both tests, the Python package scipy.stats v1.5.3 implementation was used64. Multiple hypothesis corrections…

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Google Announces Expansion of AI Partnership with Anthropic

Partnership includes important new collaborations on AI safety standards, committing to the highest standards of AI security, and use of TPU v5e accelerators for AI inference  Google announced an expansion of its partnership with Anthropic, committing to the highest standards of AI security and safety, and that Anthropic will leverage…

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Rafay Launches AI Infrastructure Templates to Help Enterprise Platform Teams Develop AI Applications

Templates enable platform teams to build automation for cloud environments and Kubernetes, jumpstarting adoption of Large Language Models (LLMs), while supporting traditional AI applications leveraging SLURM, MLFlow and Kubeflow Rafay Systems, the leading platform provider for Cloud and Kubernetes Automation announced the availability of curated infrastructure templates for Generative AI…

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When Did Humans Arrive in the Americas? Lice Help Answer That Head-Scratcher | Science

Contact between Europeans and Native Americans is recorded in the DNA of head lice. Vincent Smith, Natural History Museum, London, CC-BY 4.0 The first humans to arrive in America left scattered evidence behind, from ancient stone tools to fossilized footprints. And among descendants on either side of the Bering Strait,…

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Single-cell RNA sequencing reveals a molecular blueprint of circuits governing locomotor speed

Researchers at Karolinska Institutet, Sweden have uncovered the molecular logic underpinning the assembly of spinal circuits that control the speed of locomotion in adult zebrafish. The study has recently been published in Nature Neuroscience. What does the study show? A fundamental hallmark of motor actions is the flexibility of their…

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WHO unveils WGS guides to help tackle foodborne disease

The World Health Organization (WHO) has released a guide for use of whole genome sequencing (WGS) in food safety. The guidance comes in three parts. The first explains the minimum capacity requirements in the foodborne disease surveillance and response system prior to considering implementation of WGS. The second discusses how…

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Vector Databases: The Engine Behind Today’s AI Revolution | by Vi Nguyen | Nov, 2023

Unlocking the power of AI: How vector databases drive today’s technological revolution. The ability to analyze vast amounts of data is crucial in the field of artificial intelligence. For many decades, traditional databases have served as the foundation of information systems for storing and retrieving data. They have been the…

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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…

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Advocating for PCR-RFLP as molecular tool within malaria programs in low endemic areas and low resource settings

Abstract The road to malaria elimination for low- and middle-income countries is paved with obstacles, including the complexity and high costs of advanced molecular methods for genomic analysis. The usefulness of PCR-RFLP as less complex and affordable molecular surveillance tool in low-endemic malaria regions was assessed in a cross-sectional study…

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Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics

Albone, E. S. Mammalian semiochemistry. The investigation of chemical signals between mammals. 2–5 (1984). Wyatt, T. D. Pheromones and Animal Behaviour: Communication by Smell and Taste (Cambridge University Press, 2003). Book  Google Scholar  Doty, R. L. Odor-guided behavior in mammals. Experientia 42, 257–271 (1986). Article  CAS  PubMed  Google Scholar  Brennan,…

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Orkes Brings Generative AI and Human-in-the-Loop Capabilities to Microservices and Workflow Orchestration

Fortune 500s and other enterprises are piloting the new features to bring AI to business workflows and deploy them at scale, routing to humans as needed Orkes, the enterprise microservices and workflow orchestration platform for Netflix Conductor used by companies like United Wholesale Insurance, Foxtel, and Normalyze, has released new…

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[slurm-users] Slurm release candidate version 23.11rc1 available for testing

We are pleased to announce the availability of Slurm release candidate version 23.11.0rc1. To highlight some new features coming in 23.11: – Substantially overhauled the SlurmDBD association management code. For clusters updated to 23.11, account and user additions or removals are significantly faster than in prior releases. – Overhauled ‘scontrol…

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Merge or integrate multiple samples and then do downstream analysis

I am doing some analysis on a public scRNAseq datasets in order to see differential gene expression between two clusters. The basal sample information about it: tissue_donor_1_treatment, tissue_donor_2_treatment, tissue_donor_1_control, tissue_donor_1_control, All of them produced under the same sequencing conditions. # In my opinion, I want to divide them into two…

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A Flexible, Modular and Scalable Approach for Building Production ML Models

Transcript Rajpal: I’m going to be talking about declarative machine learning systems, a new paradigm for flexible, modular, and scalable machine learning development. My name is Shreya. I’m a Senior Machine Learning Engineer and the Domain Lead for Machine Learning Infrastructure at Predibase. Previously, I’d spend some time at Apple…

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Characteristics of Klebsiella pneumoniae co-infections

Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tuberculosis), is a prominent issue in the field of global public health, particularly in lower-middle-income-countries. Nearly two-thirds of global TB cases come from eight countries, including China.There are 780,000 new TB cases in China every year.1 TB is characterized by increased risk…

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Targeting nucleic acid phase transitions as a mechanism of action for antimicrobial peptides

Phase separation propensity of AMPs We retrieved the sequences of previously identified AMPs deposited into the Database of Antimicrobial Activity and Structure of Peptides (DBAASP)40 and in the APD3 antimicrobial peptide database41 to analyse their predicted propensities to undergo phase separation. Interestingly, we find that some AMPs possess features42,43,44 that…

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Development of a rapid, sensitive detection method for SARS-CoV-2 and influenza virus based on recombinase polymerase amplification combined with CRISPR-Cas12a assay

. 2023 Nov;95(11):e29215. doi: 10.1002/jmv.29215. Yuning Wang  1 , Liqiang Wu  1 , Xiaomei Yu  2 , Gang Wang  1 , Ting Pan  2 , Zhao Huang  2 , Ting Cui  2 , Tianxun Huang  1 , Zhentao Huang  1 , Libo Nie  2 , Chungen Qian  3 Affiliations Expand Affiliations 1 Department of Reagent Research and Development, Shenzhen YHLO…

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Rafay Launches Infrastructure Templates for Generative AI to Help Enterprise Platform Teams Bring AI Applications to Market Faster

Templates enable platform teams to build automation for cloud environments and Kubernetes, jumpstarting adoption of Large Language Models (LLMs), while supporting traditional AI applications leveraging SLURM, MLFlow and Kubeflow SUNNYVALE, Calif. & CHICAGO, November 07, 2023–(BUSINESS WIRE)–Rafay Systems, the leading platform provider for Cloud and Kubernetes Automation, today announced the…

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Bioconductor – ClusterFoldSimilarity (development version)

DOI: 10.18129/B9.bioc.ClusterFoldSimilarity   This is the development version of ClusterFoldSimilarity; to use it, please install the devel version of Bioconductor. Calculate similarity of clusters from different single cell samples using foldchanges Bioconductor version: Development (3.19) This package calculates a similarity coefficient using the fold changes of shared features (e.g. genes)…

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Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization

Nematode materials and species identification Mi, Mj, and Mg were collected from farmlands in Wuhan city of Hubei province, Longyan city of Fujian province, and Changsha city of Hunan Provinces, respectively. Two Ma samples were collected from farmlands in Shenyang city of Liaoning province and Shiping city of Yunnan province….

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Chromosome-level genomes of three key Allium crops and their trait evolution

Chase, M. W. et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016). Article  Google Scholar  Jones, M. G. et al. Biosynthesis of the flavour precursors of onion and garlic. J. Exp. Bot….

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AWS Researchers Introduce Gemini: Pioneering Fast Failure Recovery in Large-Scale Deep Learning Training

A team of researchers from Rice University and Amazon Web Services have developed a distributed training system called GEMINI, which aims to improve failure recovery in the training of large machine learning models. The system deals with the challenges associated with using CPU memory for checkpoints, which ensures higher availability…

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Postdoc in Computational Biology at the Cardiac Genetics Group

Faculty of Health and Medical SciencesUniversity of Copenhagen The Cardiac Genetics Group is looking for a highly motivated and dynamic bioinformatics postdoc for a 2-year position to commence 1st of March 2024 or soon thereafter.  You will be part of our team leading research on elucidation the genetic mechanisms underlying complex…

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Visualize individual cell clusters colored by meta.data variable

Seurat: Visualize individual cell clusters colored by meta.data variable 0 Hello, I am analyzing a public scRNA dataset using Seurat. My goal is to observe variation inside individual cell clusters according to a condition (e.g. the diet) in a visual way using a dimensional reduction plot, e.g. observing sub-clusters of…

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DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle

Overview of this study In this study, we measured the DNA methylome from mouse liver and skeletal muscle, integrated the data with the transcriptome and proteome of these mouse tissues22,23, and examined how tissue-dominant protein and gene expression were associated with DNA hypomethylation (Fig. 1). In this study, we measured DNA…

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University of Oklahoma hiring Postdoctoral Researcher in Bioinformatics & Computational Biology in Norman, OK

Description Description The candidate is responsible for analyzing and mining multi-omics data using computational techniques, such as deep learning, generalized linear mixed models, and biological network analysis. This may require development of new computer algorithms and/or construction of computational workflows on computer clusters. The types of multi-omics data will include…

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hpc – how start_time is calculated for slurm multi-cluster

I’m having a hard time figuring out the distribution of jobs between 2 clusters in a Slurm multi-cluster environment. The documentation says that each job is submitted to the cluster that provides the earliest start time, and once the task is submitted to a cluster, it can’t be re-distributed to…

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Detection and characterization of putative hypervirulent Klebsiella pneumoniae isolates in microbiological diagnostics

Navon-Venezia, S., Kondratyeva, K. & Carattoli, A. Klebsiella pneumoniae: A major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol. Rev. 41(3), 252–275 (2017). Article  CAS  PubMed  Google Scholar  Marr, C. M. & Russo, T. A. Hypervirulent Klebsiella pneumoniae: A new public health threat. Expert Rev. Anti Infect. Ther. 17(2),…

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Evolutionary insights into 3D genome organization and epigenetic landscape of Vigna mungo

Introduction The non-random packaging of chromatin within the nucleus is a universal feature of eukaryotic genomes. The three-dimensional (3D) spatial organization of chromatin could be partitioned at different levels based on the interaction frequency between two given loci in the genome. Advances in sequencing technologies have led to the identification…

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Single-cell transcriptomics reveals the brain evolution of web-building spiders

Animals for single-cell sequencing Adult samples of the aerial web-building spider (Hylyphantes graminicola) were collected from Anci district, Langfang, Hebei, China (39° 31.90’ N, 116° 38.15’ E) between September and October 2020. Collected spiders used for brain dissection were housed individually in a glass tube (Φ12 mm × 80 mm) at temperature- and humidity-controlled condition (24–26 °C and 50–60%…

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Genes | Free Full-Text | Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley

1. Introduction The Antioquia region has played a pivotal role in the pre-Hispanic history of South America, serving as a gateway for the initial human migrations to the continent and as a hub for the development of a sophisticated culture deeply rooted in the utilization of natural resources and advanced…

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Job submission on HPC using pbs script – User discussions

GROMACS version:2022.1GROMACS modification: YesRespected expert, I am using our institute HPC for mdrun. I can utilise one node but cannot utilise multiple nodes. I have learnt that PBS.sh script(image attached)is used for job submission on our institute’s HPC Even though i have tried modifications like varying number of nodes, process…

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Create Custom Multimodal AI Apps Easily

Create Custom Multimodal AI Apps Easily Table of Contents: Introduction Building a Custom Multimodal AI Application using Google Cloud’s AI suite 2.1 Setting up the Environment 2.2 Crafting the Custom Web Application 2.3 Powering the System with Python Code 2.4 Utilizing the Flask Web Application Framework Incorporating the Multimodal Embeddings…

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Researchers develop new method to analyze proteins in ecologically significant moss

The Sphagnum genus of mosses absorbs carbon from the atmosphere, storing it in peat bogs. Credit: Genevieve Martin/ORNL, U.S. Dept. of Energy Though the changing climate threatens the world’s vegetation, a type of peat moss has surprised scientists with its resilience: Sphagnum divinum is actively evolving in response to hot,…

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Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria

Isolation of phyllosphere isolates All bacterial strains were isolated in June 2021 from the flag leaves of four wheat cultivars (Sheriff, Heerup, Rembrandt and Kvium) grown in an experimental field in Høje Taastrup, near Copenhagen, Denmark. Wheat flag leaves were picked, pooled, and either washed or blended prior to dilution…

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Why Databricks is Using AMD GPUs

While the world is hell-bent on getting their hands on NVIDIA GPUs such as H100, Databricks has made a strategic move towards utilising AMD GPUs to elevate their LLM training capabilities, and it is working marvellously for the company. Last year, Databricks partnered with AMD for using its 3rd Gen…

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Comparative transcriptome analysis reveals candidate genes for cold stress response and early flowering in pineapple

Phenotypic response of two pineapple varieties to cold stress Notable differences in flowering time were observed for the two genotypes used in this study. The first signs of flowering were observed up to two weeks later in Dole-17 (precocious flowering tolerant) than in MD2 (precocious flowering susceptible) (Supplementary Figure S1)….

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Postdoctoral Scholar – Bioinformatics at Syngenta, Durham, UK

Postdoctoral Scholar – Bioinformatics: Syngenta, a global leader in agriculture, is seeking a dedicated Postdoctoral Scholar in Bioinformatics to join our mission of safely feeding the world and caring for our planet. Located in Durham, North Carolina, this role offers a unique opportunity to contribute to biological research in agriculture…

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Insights into expression patterns and immunotherapy response prediction

[1] D. Schadendorf, D. E. Fisher, C. Garbe, J. E. Gershenwald, J. Grob, A. Halpern, et al., Melanoma, Nat. Rev. Dis. Primers, 1 (2015), 15003. doi.org/10.1038/nrdp.2015.3 doi: 10.1038/nrdp.2015.3 [2] A. M. M. Eggermont, A. Spatz, C….

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Glycoengineered keratinocyte library reveals essential functions of specific glycans for all stages of HSV-1 infection

Generation of a glycogene knock out library in HaCaT keratinocytes HaCaT is a human keratinocyte cell line capable of forming a stratified squamous epithelium, and thus allows evaluating the infection of the skin tropic HSV-1 in both cell and organotypic tissue culture. In order to address the role of specific…

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Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection

Bacterial strains and phages Escherichia coli DH5a was routinely grown in Lysogeny broth (LB) medium and used for plasmid cloning, while E. coli BL21 (DE3) was used for protein production and the in vivo assays. E. coli phages T5, T7 and Lambda-vir are gifts from Shi Chen lab (Wuhan University,…

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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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Fasting-Mimicking Diet Drives Antitumor Immunity against Colorectal Cancer by Reducing IgA-Producing Cells | Cancer Research

Fasting-mimicking diet (FMD) is emerging as an effective dietary intervention with the potential to prolong life span in healthy people and boost antitumor immunity in patients with cancer. FMD refers to a medically designed fasting-like state that allows periodic consumption of a very-low-calorie and low-protein diet (1, 2). Compared with…

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When Glia Meet Induced Pluripotent Stem Cells (iPSCs)

Abstract The importance of glial cells, mainly astrocytes, oligodendrocytes, and microglia, in the central nervous system (CNS) has been increasingly appreciated. Recent advances have demonstrated the diversity of glial cells and their contribution to human CNS development, normal CNS functions, and disease progression. The uniqueness of human glial cells is…

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Reproducible seurat clustering

Dear all fellows, What is the standard way for reproducible Seurat clustering in single cell? I have been trying to use set.seed function like library(tidyverse) library(Seurat) library(patchwork) set.seed(198752) However, once it comes to running the following script, I get new shape of cluster all the time I rerun it. How…

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Genomic disturbance of vitellogenin 2 (vtg2) leads to vitellin membrane deficiencies and significant mortalities at early stages of embryonic development in zebrafish (Danio rerio)

A large deletion mutation of 2811 bp of gDNA was introduced into zebrafish vtg2 via CRISPR/Cas9 genome editing. A schematic representation of the general strategy for CRISPR target design and application is given in Fig. 1A–C. The introduced deletion involved 1692 bp of the vtg2 transcript, encoding 564 aa of its respective protein, and…

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What are some of the recent insights from CO2 mineralization simulations using LAMMPS with calcium?

Recent insights from CO2 mineralization simulations using LAMMPS with calcium include the elucidation of the CO2 mineralization mechanism with Mg-rich forsterite. The simulations revealed a two-step process involving ion dissolution from the forsterite surface and the agglomeration of ion pairs into MgCO3 clusters in aqueous solution. The effects of pH,…

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The metagenomic and metabolomic profile of the gut microbes in Chinese full-term and late preterm infants treated with Clostridium butyricum

Ethics approval and consent to participate The study was approved by the Human Research Ethics Committees of the Children’s Hospital of Soochow University (Reference 2020CS017). All specimens were collected according to the guidelines set by the Children’s Hospital of Soochow University. All authors confirm that all methods were performed in…

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epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data | GigaScience

Abstract Low-level mosaic epimutations within the BRCA1 gene promoter occur in 5–8% of healthy individuals and are associated with a significantly elevated risk of breast and ovarian cancer. Similar events may also affect other tumor suppressor genes, potentially being a significant contributor to cancer burden. While this opens a new…

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Unraveling the mystery of brain infections

Credit: CC0 Public Domain In April 1997, a one-year-old child was admitted to Sibu Hospital in Sarawak, Malaysia with fever and mouth ulcers, symptoms suggestive of an illness known as hand, foot, and mouth disease (HFMD). HFMD is typically a mild disease, but the infant developed cardiovascular complications and died…

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Distributed Training on GPU Clusters with PyTorch & TensorFlow

Distributed training is a technique that allows you to train deep learning models on multiple GPUs or machines in parallel. This can speed up the training process, reduce the memory usage, and enable you to train larger and more complex models. However, distributed training also introduces some challenges, such as…

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Hubble Captures the Enigmatic Beauty of the “Spanish Dancer Galaxy”

The Hubble Space Telescope captured this stunning image of NGC 1566, dubbed the ‘Spanish Dancer Galaxy’, a member of the Dorado galaxy group. Distinguishing members within such groups poses intricate challenges for astronomers. Credit: ESA/Hubble & NASA, D. Calzetti and the LEGUS team, R. Chandar Captured by the Hubble Space…

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X-chromosome inactivation in human iPSCs provides insight into escape-regulated gene expression.

Abstract Epigenetic variation in the X chromosome inactivation (XCI) of human induced pluripotent stem cells (hiPSCs) can impact their ability to accurately model biological sex biases. However, the gene-wise landscape of escape from XCI remains unresolved in female hiPSCs. To characterize the patterns of escape from inactivation, we performed a…

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Transform Your Business with Google Cloud’s AI Platform

Transform Your Business with Google Cloud’s AI Platform Introduction Google’s AI Platform Vertex AI Enterprise Search Generative AI Technologies Google Cloud Partnerships New Models in Vertex Reinforcement Learning in Vertex AI Duet AI for Google Cloud AI-Optimized Infrastructure A3 Virtual Machines Google Cloud is using the power of AI to…

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Fix Shake takes forever to run – LAMMPS General Discussion

m.adibi October 27, 2023, 11:57pm 1 I am running molecular simulations using EPM2 model of CO2. This is the force field data: units real atom_style full bond_style harmonic angle_style harmonic pair_style lj/cut/coul/long 10.0 kspace_style pppm 1.0e-5 pair_modify mix arithmetic bond_coeff 1 450 1.149 angle_coeff 1 147 180 # explanation: lammps.sandia.gov/doc/angle_harmonic.html

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Screening of genes interacting with high myopia and neuropsychiatric disorders

Studies have shown that patients with high myopia have structural changes in their brain white matter, which are important factors contributing to neuropsychiatric disorders16,17. In this study, causative genes for neuropsychiatric disorders were found to account for 22.69% of strongly pathogenic genes in patients with HM, which represents the highest…

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Clustering while deforming stulls the run – LAMMPS Development

I have a script where I first create a system in a grid, then deform it under NVE+langevin to the desired dimensions, then relax it under NPH+langevin. I want to track certain cluster sizes so it is implemented in LAMMPS. The issue is the following. The run stulls at a…

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Genetic diversity and phylogenetic analyses of Asian lineage Zika virus whole genome sequences derived from Culex quinquefasciatus mosquitoes and urine of patients during the 2020 epidemic in Thailand

Hayes, E. B. Zika virus outside Africa. Emerg. Infect. Dis. 15(9), 1347–1350. doi.org/10.3201/eid1509.090442 (2009). Article  PubMed  PubMed Central  Google Scholar  Faye, O. et al. Molecular evolution of Zika virus during its emergence in the 20th century. PLoS Negl. Trop. Dis. 8(1), e2636. doi.org/10.1371/journal.pntd.0002636 (2014). Article  CAS  PubMed  PubMed Central  Google…

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KEGG tools for classification and analysis of viral proteins

doi: 10.1002/pro.4820. Online ahead of print. Affiliations Expand Affiliations 1 Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan. 2 Pathway Solutions Inc., 2-16-3 Higashi-Shinbashi, Minato-ku, Tokyo, Japan. 3 Network Support Co. Ltd., Hakata-ku, Fukuoka, Japan. Item in Clipboard Zhao Jin et al. Protein Sci. 2023. Show details Display options Display…

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NERSC Collaborations Help Illuminate Earth’s Biodiversity

Oct. 26, 2023 — How do we know who’s in our world? Genomics researchers study and map the genomes of all kinds of genetic entities, from the blue whale all the way down to mobile genetic elements (MGEs), which have genetic material but are not considered living. But many organisms…

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University of Oklahoma hiring Senior Bioinformatics Analyst in Oklahoma City Metropolitan Area

Senior Bioinformatics Analyst – Job Number: 232353 Organization : Core Facilities Job Location : Oklahoma-Oklahoma City-Health Sciences Center Schedule : Full-time Work Schedule : 40 Work Type : Onsite Salary Range : Commensurate With Experience Benefits Provided : Yes Required Attachments : Resume, Cover Letter Job Description – – –…

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Breast implant-associated anaplastic large cell lymphoma

INTRODUCTION — Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is an uncommon and still emerging peripheral T cell lymphoma caused by and arising around textured-surface breast implants placed for either reconstructive or cosmetic indications. The association of breast implants with a cancer of the immune system has created understandable concern among patients,…

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Structure and electromechanical coupling of a voltage-gated Na+/H+ exchanger

Expression and purification of SLC9C1 The gene encoding the S. purpuratus SLC9C1 protein (NP_001091927.1), referred to as SLC9C1, was synthesized (Thermo Fisher Scientific) and subcloned into the pcDNA3.1(+) vector followed by a TEV (Tobacco Etch Virus nuclear-inclusion-a endopeptidase) recognition site, eGFP and a TwinStrep tag at the C terminus. An…

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Construction of a novel prognostic model in skin cutaneous melanoma based on chemokines-related gene signature

Skin cutaneous melanoma, SKCM, is one of the most aggressive treatment-resistant tumours. Despite the fact that the BRAF oncogene and immunological checkpoints such as PD-1/PD-L1 and CTLA-4 have enhanced the therapeutic efficacy of SKCM, the subsequent resistance mechanisms and remedies have raised concerns. Chemokines have a significant role in the…

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EM Algorithm for Gaussian Mixture Model with PyTorch

import torch from torch.distributions import MultivariateNormal def em_algorithm(data, num_components, num_iterations): “”” Function to implement the Expectation-Maximization (EM) algorithm for solving the Gaussian Mixture Model (GMM). Parameters: – data: torch.Tensor The input data on which the GMM is to be trained. It should be a 2D tensor of shape (num_samples, num_features)….

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DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages

Parasite culture, maintenance, synchronization and transfection The DiCre-expressing P. falciparum clone II3 (ref. 10) was maintained in human A+ erythrocytes at 37 °C in Roswell Park Memorial Institute 1640 medium containing AlbumaxII (Invitrogen) supplemented with 2 mM l-glutamine. Parasites were either synchronized by sorbitol treatment or by purifying mature schizont stages using…

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Mycobacterium tuberculosis Sub Lineage 4.2.2/SIT149 as DR

Introduction Antimicrobial resistance is a hidden global pandemic that shattered over 4.9 million people in 2019 alone, and the burden is highest, mainly in low-resource settings.1 Drug-resistant tuberculosis (DR-TB) caused by Mycobacterium tuberculosis (Mtb) complex (MTBC), which is resistant to one or more anti-TB drugs, is a leading global public…

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How do I add sample annotations to this data?

How do I add sample annotations to this data? 0 I was able to generate this dot plot using ggplot2 from scratch. I would like to add sample annotations (similar to the ones you’d see in heat maps where they annotate clusters). I have another data frame containing sample IDs…

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Unlocking the Power of Kubeflow Pipelines v2 for ML Efficiency | by Vishnu Adithyan | SquareShift | Oct, 2023

In today’s tech-driven world, machine learning is a vital tool for businesses of all sizes. However, getting from concept to reality with ML models can be a challenging journey. That’s where Kubeflow Pipelines (KFP) v2 comes in, promising to make this journey smoother. Let’s explore what’s new and exciting in…

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Roles of SNORD115 and SNORD116 ncRNA clusters in neuronal differentiation

Abstract Prader-Willi syndrome shows features linked to brain development and hypothalamus-related endocrine abnormalities. The smallest clinical deletions fall within the large (~650Kb) SNHG14 gene, removing 29 consecutive introns that each generate SNORD116. SNHG14 also includes 48 tandem introns encoding SNORD115 and generates multiple, extended snoRNA-related species. SNORD115 and SNORD116 resemble…

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Summer of intense field-work for GreenFjord project

GreenFjord is a four-year research program intended to investigate how climate change is affecting ecosystems in southern Greenland. The scientists just completed a first intensive field season where they won over the local residents. The next step will be to analyze the millions of datapoints they collected. Julia Schmale is…

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Using SAM for the Prediction of Segmentations on the Kaggle Football Player Segmentation Dataset

Welcome to the latest installment of our ongoing blog series where we highlight notebooks and datasets from the FiftyOne Examples GitHub repository. The fiftyone-examples repository contains over 30 notebooks that make it easy to try various computer vision workflows and explore their associated datasets. In this post, we take a…

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kubernetes – Load balancing between Slurm clusters

What strategy of load balancing in k8s would be recommended between Slurm (think SGE) clusters? The reason I raise this is Slurm has a Pythonic API governing the queuing system. Information can freely pass from the queuing system to the load balancer in Nginx (k8s) via the API. The load…

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NGS Training | Top NGS Courses | Online Training | RNASeq | Genome Variant Detection

        NGS Training Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which…

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Postdoctoral studies in bioinformatics, focusing on molecular sub-phenotyping of obstructive lung diseases including post-COVID and COPD (scholarship)

Do you want to contribute to top quality medical research? We have an opening for 1-2 post-doctoral researcher in bioinformatics to join a multidisciplinary systems medicine team investigating the molecular mechanisms of obstructive lung diseases, particularly long-COVID and COPD in non-smokers. The successful candidate will have a leading role in…

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The Age of Aquarius – RNA, the Epicenter of Genetic Information

The veil on genetic information was lifted by the advent of gene cloning and sequencing technologies in the 1970s. The discovery and purification of bacterial nucleases capable of cutting DNA at specific sequences and ligases capable of joining them enabled DNA from any species – or mRNAs converted to complementary…

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How-to: NGS Quality Control

Thanks to the introduction of high-throughput next generation sequencing (NGS) methods, generating nucleic acid sequencing data has never been easier. Now, DNA and RNA samples can be sequenced within hours, creating millions of DNA fragments (known as reads), which can then be aligned to a reference genome.  Quality control is…

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SPOTlight error with Visium data

SPOTlight error with Visium data 0 Hi, could anyone help to fix the error with SPOTlight command? I have one reference from single cell experiment (cortex_sc) and one data from h5 file with Visium Spatial transcriptome. I have the gene markers based on clusters from cortex_sc with the tutorial from…

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Aculys Reports Positive Phase 3 Findings of Diazepam Nasal Spray in Epilepsy

Recently announced interim findings from a Japanese-based phase 3 study assessing Aculys Pharma’s diazepam nasal spray showed that the antiseizure medication was effective across multiple clinical end points, demonstrating efficacy and safety. Based on these data, the company plans to intend to submit a new drug application in Japan for…

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Solved R/Rstudio question:I have this R code and I am

R/Rstudio question: I have this R code and I am supposed to write a Market Segmentation Analysis​ based on the data I extract out of the SAS file I loaded into my R code. I also have the CSV file I want my data loaded into. My question is how…

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Gnome Home Crisis | Devpost

Inspiration We were inspired by the recent surge in world events caused by climate change, such as the wild fires in Canada and the recent hurricanes. What it does We created a python program that analyzes public sentiment through a dataset of Reddit posts using pandas. We then created a…

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Unraveling Genomic Mysteries: A Conversation with Neil Ward, VP and GM of PacBio in EMEA

Neil Ward is the Vice President and General Manager for PacBio in EMEA. His role is to expand PacBio’s EMEA footprint, developing the team and its research partnerships to capitalise on the immense potential for genomics.  He spoke exclusively with Healthcare Digital to discuss the latest in rare disease diagnosis…

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hclust with similar data gives different

hclust with similar data gives different 0 I have RNAseq data with expression in ensembl ID and I convert them into gene symbol and for further analysis. I had performed hclustering and then cut tree using dynamicTreeCut with a geneset of 20010 genes and got 27 different gene-clusters. Now after…

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What can you expect from Ubuntu 23.10?

• Ubuntu 21.10 focuses on stronger security.• It also includes smoother app discovery processes.• In advance of next year’s bigger update, Ubuntu 23.10 offers a surprising amount of additional refinement. On October 12th, Canonical announced the release of Ubuntu 23.10. It’s not exactly “lines around the Apple store” time, but…

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Adversarial and variational autoencoders improve metagenomic binning

Overview of AAMB The AAMB workflow consists of the following main steps (Fig. 1a). First, Tetra Nucleotide Frequencies (TNF) and per sample co-abundances (Coab) are extracted from the contigs and BAM files of reads mapped to contigs, and input to the AAMB model as a concatenated vector. The AAMB model encodes…

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