Tag: heatmaps

miR-195b is required for proper cellular homeostasis in the elderly

Expression pattern of miR-195 during embryonic development We analyzed the expression pattern of miR-195 by in situ hybridization at two distinct developmental stages in mouse embryos. Whole-mount in situ hybridization at E10.5, demonstrated a wide expression of miR-195 along the entire embryo, including the central nervous system, the cardiopharyngeal area,…

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Summary of Genomics and Transcriptomics – DNA sequencing I. Goal II. Methodology A. Sanger DNA

DNA sequencing I. Goal II. Methodology A. Sanger DNA sequencing ● Up to 900 base pairs ● Primer extension with labeled ddNTPs (radioactive or fluorescent) ● Prior knowledge on target needed ● Difficult to detect variation in mixtures ● High accuracy + still in use for genotyping When it is…

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Sequential deregulation of histone marks, chromatin accessibility and gene expression in response to PROTAC-induced degradation of ASH2L

Loss of ASH2L prevents cell proliferation We have studied the molecular and cellular consequences of Ash2l loss in mouse embryo fibroblasts (MEFs) with floxed Ash2l alleles and an inducible Cre-ER recombinase (iMEF-Ash2lfl/fl-Cre-ER). While the knockout of Ash2l was rapid, the downstream effects, including the decrease in promoter-associated H3K4me3, altered gene…

Continue Reading Sequential deregulation of histone marks, chromatin accessibility and gene expression in response to PROTAC-induced degradation of ASH2L

Plasma cell-free DNA 5-hydroxymethylcytosine and whole-genome sequencing signatures for early detection of esophageal cancer

Waters JK, Reznik SI. Update on management of squamous cell esophageal cancer. Curr Oncol Rep. 2022;24:375–85. Article  PubMed  Google Scholar  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…

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Genomic hypomethylation in cell-free DNA predicts responses to checkpoint blockade in lung and breast cancer

Lung cancer ICB cohort Advanced non-small cell lung carcinoma patients who were treated with anti-PD-1/PD-L1 monotherapy at Samsung Medical Center, Seoul, Republic of Korea were enrolled for this study. The present study has been reviewed and approved by the Institutional Review Board (IRB) of the Samsung Medical Center (IRB no….

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Transcription factor-mediated direct cellular reprogramming yields cell-type specific DNA methylation signature

iISC-BOs exhibit a CpG methylation signature that closely resembles ISC-BOs Genomic DNA was extracted from MEFs, iISC-BOs, and ISC-BOs, and high-resolution methylome analysis was performed using the PBAT method (Fig. 1A). The genome-wide methylation states of cytosine-containing sequences such as CpG, CHH, and CHG were compared among the samples. The data…

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Wrangling And Analyzing Data In RStudio

Article Summary Box Efficient data preparation in RStudio hinges on automated data cleaning techniques, significantly reducing manual errors and streamlining the initial stages of analysis. Vectorized operations and the apply() family functions in RStudio dramatically enhance data manipulation efficiency, especially for large datasets. Utilizing multiple linear regression and PCA in…

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Help me confirm if my reads are properly normalized and transformed or do I need to re-do

Help me confirm if my reads are properly normalized and transformed or do I need to re-do 0 Hello, can you help me confirm whether or not my reads dataset were normalized properly prior to my work on them? The data source is 40 florets from Arabidopsis for 3 replicates…

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Thyroid hormone-regulated chromatin landscape and transcriptional sensitivity of the pituitary gland

Mouse genetic models The ThrbHAB allele expresses TRβ proteins (TRβ1 and TRβ2) fused to a peptide with a hemagglutinin (HAx2) tag and a site for biotinylation by prokaryotic BirA ligase, modified from a published tag30. The tag was inserted at the endogenous Thrb gene by homologous recombination in W9.5 (129/Sv)…

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Identification and validation of key miRNAs for colon cancer

Introduction With nearly 2 million new cases and 1 million deaths worldwide in 2020, colorectal cancer is the third-most common cancer and the second leading cause of cancer-related deaths.1 According to data from the US Surveillance, Epidemiology and End Results program and the National Program of Cancer Registries program, the…

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Key Genes for Pyroptosis-induced Salivary Gland Inflammation

Kaiyuan Zhang,1,* Ziyue Luo,1,* Xinchao Zhu,1 Xinyi Yao,1 Dingqi Lu,2 Liying Chen,1 Tao Hong,1 Yating Ren,1 Xinchang Wang3 1Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China; 2First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China;…

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Borrelia puertoricensis in opossums (Didelphis marsupialis) from Colombia | Parasites & Vectors

Oppler Z, Keeffe K, McCoy K, Brisson D. Evolutionary genetics of Borrelia. Curr Issues Mol Biol. 2021;42:97–112. doi.org/10.21775/cimb.042.097.2. Article  PubMed  Google Scholar  Margos G, Fingerle V, Cutler S, Gofton A, Stevenson B, Estrada-Peña A. Controversies in bacterial taxonomy: the example of the genus Borrelia. Ticks Tick Borne Dis. 2020;11:101335. doi.org/10.1016/j.ttbdis.2019.101335….

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

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

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

Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato

A supply of nitrate triggers organ-specific changes of histone modifications at specific gene loci To investigate the organ specificity of dynamic histone modifications in response to N changes, we treated 3-week-old tomato seedlings (Solanum lycopersicum, cultivar M82) with four days of N starvation, followed by N-supply (2.8 mM NO3−; +N) or…

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Music compensates for altered gene expression in age-related cognitive disorders

Global impact of music on the human transcriptome We first aimed at quantifying the global effect of music on the transcriptomes of the two groups of donors separately. ACD patients exposed to music showed 2.3 times more DEGs (n = 2605) than controls (n = 1148); Table 2. Moreover, while the proportion up-regulated/down-regulated DEGs…

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Bacteriophage-host Interactions In Microgravity Onboard The International Space Station

Deep Mutational Scanning profiles beneficial substitutions in the RBP tip domain (A-B) Heatmaps showing normalized functional scores (FN) of all substitutions (red gradient) and wildtype amino acids (FN=1 and black dot upper left) at every position after incubation with E. coli BL21 in (A) microgravity and (B) after terrestrial incubation….

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DNA methylation change in blood cells of FB and CFS patients

Introduction Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) are characterized by chronic pain, fatigue, and weakness. Patients with these symptoms also suffer from sleep abnormalities and report affected cognitive processes such as memory. The diagnosis of these two syndromes is challenging and is based on questionnaires that make the diagnosis…

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Comparing 3 Data Sets using DeSeq and Heatmaps

Hi all, I am new to bioinformatics analysis, so I’d appreciate if someone could check my code for the goal I am trying to achieve. I have 3 samples – Wild Type (WT) FoxP3-TCF-HEB (I have 3 replicates of this) TCFKO I have defined these in the sample information csv…

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Genome wide analysis revealed conserved domains involved in the effector discrimination of bacterial type VI secretion system

Construction of the VgrG database Encoded as a stand-alone gene or fused at the N-terminus of the toxin, the MIX domains can assist the delivery of their cognate T6SS effector19,20. As the central component of the spike complex, VgrG is a good marker to explore the potential conserved domains involved…

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Pan-Cancer Analysis and Validation of Opioid-Related Receptors Reveals

Introduction The potential role of opioids used in oncology patients has been controversial. Epidemiological and retrospective studies have demonstrated that lower opioid doses and regional anesthesia (epidural, intrathecal, or paravertebral) for breast,1 colon,2 or melanoma3 are linked to lower rates of cancer recurrence, while general anesthesia with high opioid doses…

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Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). Article  PubMed  Google Scholar  Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). Article  PubMed  Google Scholar  Amborella Genome Project et al. The Amborella…

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Creating heatmap for ChIP-seq using deeptools

Hi all, I am a newbie in ChIP-seq, and I conducted my analysis using the nfcore ChIPseq pipeline. After reviewing the results, I now need to perform more specific analyses. With nfcore, I generated informative heatmaps that provide a general overview of my ChIP-seq data (I will upload the heatmap)….

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Elevated stress response marks deeply quiescent reserve cells of gastric chief cells

Generation of inducible H2b-GFP knock-in mice Generation of inducible H2b-GFP knock-in mice was performed by using CRISPR/Cas943. In brief, a mixture containing a sgRosa26-1 crRNA43 (8.7 ng/μl, Fasmac, Japan), a tracrRNA (14.3 ng/μl, Fasmac, Japan), a single strand oligo donor nucleotide (ssODN) composed of 5′ arm, adenovirus splicing acceptor, SV40 pA, TRE3G…

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Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles

Introduction The CRISPR-Cas system is a widely used genome engineering technology because of its simple programmability, versatile scalability, and targeting efficiency (Wang & Doudna, 2023). Although researchers are rapidly developing CRISPR-Cas9 tools, the biggest challenge remains to overcome undesired on- and off-targeting outcomes. Previous studies have reported unintended genomic alterations,…

Continue Reading Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles

Knockdown of GNL3L alleviates the progression of COPD

Introduction Chronic obstructive pulmonary disease (COPD) is a common chronic bronchitis disease characterized by persistent airflow limitation, which can be prevented and treated. COPD is the third leading cause of death in the world reported in 2020.1 With the progression of the disease, COPD will lead to respiratory failure, pulmonary…

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Shotgun metagenomes from productive lakes in an urban region of Sweden

Williamson, C. E., Saros, J. E., Vincent, W. F. & Smol, J. P. Lakes and reservoirs as sentinels, integrators, and regulators of climate change. Limnology and Oceanography 54, 2273–2282, doi.org/10.4319/lo.2009.54.6_part_2.2273 (2009). Article  ADS  Google Scholar  Cavicchioli, R. et al. 2019. Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews…

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Transgenerational epigenetic effects imposed by neonicotinoid thiacloprid exposure

This study is aimed at revealing the transgenerational effects of thia. We chose the developmental window from embryonic days 6.5 to E15.5 because of its importance in germ cell program establishment. The mice breeding was described in the Materials and Methods section “Mouse treatment and dissection.” The design of the…

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COL10A1 promotes tumorigenesis by modulating CD276 in pancreatic adenocarcinoma | BMC Gastroenterology

Bioinformatics analysis The GEO database (www.ncbi.nlm.nih.gov/geo/) provided detailed gene expression information for the GSE62165 microarray. Differentially expressed genes were identified using the online tool Morpheus (software.broadinstitute.org/morpheus/) (fold change = normal pancreatic tissue gene expression/PDAC tissue gene expression, P value < 0.05 and |log2(fold change)|>1). The downstream analysis was based on the genes with the…

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How To Use Machine Learning In Python

Introduction Machine learning has revolutionized the way we approach problem-solving, data analysis, and decision-making. It is a branch of artificial intelligence that focuses on enabling computers to learn from data and improve their performance over time. With the growing availability of data and computing power, machine learning has become increasingly…

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Primate-specific ZNF808 is essential for pancreatic development in humans

Subjects The study was conducted in accordance with the Declaration of Helsinki and all subjects or their parents/guardian gave informed written consent for genetic testing. DNA testing and storage in the Beta Cell Research Bank was approved by the Wales Research Ethics Committee 5 Bangor (REC 17/WA/0327, IRAS project ID…

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Deep learning and single-cell phenotyping for rapid antimicrobial susceptibility detection in Escherichia coli

Detecting antibiotic susceptibility based on deep learning of single-cell subcellular phenotypes We designed a method that takes as an input bacterial cultures grown in rich medium to a consistent optical density and then treated with an antibiotic of choice for a time sufficient to produce distinct, antibiotic-specific, cellular phenotypic changes…

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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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Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance

Sample collection and spiking Chicken fecal samples were collected and processed as follows: one spoonful of fecal material (≈ 1 g) was collected and stored in a DNA/RNA Shield™ Fecal Collection Tube R1101 containing 9 ml of DNA/RNA-shield (Zymo Research, Irvine, CA, USA), according to the manufacturer’s instructions. The sample was mixed…

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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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Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms

Bond, R. & Loeffler, A. What’s happened to Staphylococcus intermedius? Taxonomic revision and emergence of multi-drug resistance. J. Small Anim. Pr. 53, 147–154 (2012). Article  CAS  Google Scholar  Carroll, K. C., Burnham, C. D. & Westblade, L. F. From canines to humans: clinical importance of Staphylococcus pseudintermedius. PLoS Pathog. 17,…

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Bioconductor – SEtools

DOI: 10.18129/B9.bioc.SEtools     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SEtools. SEtools: tools for working with SummarizedExperiment Bioconductor version: 3.12 This includes a set of tools for working with the SummarizedExperiment class, including merging, melting, aggregation and plotting functions. In particular,…

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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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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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Identification of hub genes associated with gastric cancer

Introduction GC is a common malignant tumor of digestive system. According to the International Agency for Research on Cancer (IARC) of the World Health Organization, there were 19.29 million new cancer cases and 9.96 million deaths worldwide in 2020, of which the number of new cases of GC was 1089,103…

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unbiased clustering of these top 50 genes in seurat

unbiased clustering of these top 50 genes in seurat 0 Here is a code, i have now: combined <- rbind(mutant1, mutant2, mutant3) as.data.frame(combined) data_genes <- data.frame(gene = rownames(combined), combined, row.names = NULL) View(data_genes) data_genes %>% group_by(mutant) %>% mutate(abs_lfc = abs(avg_log2FC)) %>% top_n(n = 50, wt = abs_lfc) -> top50 I…

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HOXC-AS3 as an Oncological Biomarker and Therapeutic Target

1Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330008, People’s Republic of China; 2Department of General Surgery, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang, Jiangxi, 332007, People’s Republic of China; 3Queen Mary School, Nanchang University, Nanchang, Jiangxi, 330038, People’s Republic of China Correspondence: Hongliang Luo,…

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A spatial sequencing atlas of age-induced changes in the lung during influenza infection

Single-cell RNA sequencing reveals cellular heterogeneity among young and aged lungs post-influenza infection In order to investigate age-induced alterations in the host response to influenza A virus (IAV) infection, we infected groups of three young (16–18-week-old) and three aged (80–82-week-old) female C57Bl/6 mice intranasally with 50 PFU of the PR8…

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Pathway-driven analysis of synthetic lethal interactions in cancer using perturbation screens

Introduction Cancer cells are characterized by unrestrained proliferation and dysregulated growth, which lead to the formation of malignant neoplasms (Hanahan & Weinberg, 2023). The development and progression of cancer have been linked to the dysregulation of multiple signaling pathways, including MAPK/ERK, Wnt/β-catenin, PI3K/AKT/mTOR, and NF-kB, which are among crucial pathways…

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seurat-creating heatmaps

seurat-creating heatmaps 1 I have three tables (results from differential expression in seurat): Table 1 is for mutant 1 vs WT Table 2 is for mutant 2 vs WT Table 3 is for mutant 3 vs WT I would like to create a heatmap that shows all the genes combined(mutant…

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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…

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Adding a Dendrogram to a ggplot2 Heatmap in R

A potent technique that improves the visualisation of hierarchical clustering patterns inside data is to add a dendrogram to a ggplot2 heatmap in R. Dendrograms shed light on the connections and resemblances among data points, assisting in the discovery of distinct clusters or groups. We will examine how to combine…

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Signatures of necroptosis-related genes as diagnostic markers of endometriosis and their correlation with immune infiltration | BMC Women’s Health

Technical roadmap Figure 1. Fig. 1 Analysis of endometriosis-related differentially expressed genes Using the limma package, we first normalized the expression profile data of the endometriosis datasets, GSE7305 and GSE11691. The data distribution before and after standardized treatment is revealed in a box plot (Figs. 2A–D). We found that the data after…

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Virulence Characteristics of Salmonella Enteritidis

Introduction As an important zoonosis pathogen, Salmonella is widely distributed in nature and one of the four major pathogens causing global diarrhea diseases.1 Salmonella has six subspecies and 2659 serotypes, among which Salmonella Enteritidis (S. Enteritidis) are the most common serotypes causing Salmonella outbreaks.1 S. Enteritidis has a wide variety…

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plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style | BMC Genomics

Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990;18(20):6097–100. Article  CAS  PubMed  PubMed Central  Google Scholar  Colaert N, Helsens K, Martens L, Vandekerckhove J, Gevaert K. Improved visualization of protein consensus sequences by iceLogo. Nat Methods. 2009;6(11):786–7. Article  CAS  PubMed  Google Scholar …

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Purpose, Types, Applications, Bioinformatics and more

Next-Generation Sequencing (NGS), also known as high-throughput sequencing, is a revolutionary technology used for determining the sequence of DNA or RNA molecules. It has significantly advanced the field of genomics and has numerous applications in various biological and medical fields. Key Points of Next-Generation Sequencing (NGS): Revolutionary Technology: NGS represents…

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DNA-bridging by an archaeal histone variant via a unique tetramerisation interface

Chromatin isolation and MNase digestion M. jannaschii DSM 2661 cells were grown in 100 l fermenters in minimal medium containing 0.3 mM K2HPO4, 0.4 mM KH2PO4, 3.6 mM KCl, 0.4 M NaCl, 10 mM NaHCO3, 2.5 mM CaCl2, 38 mM MgCl2, 22 mM NH4Cl, 31 µM Fe(NH4)2(SO4)2, 1 mM C6H9NO6, 1.2 µM MgSO4, 0.4 mM CuSO4, 0.3 µM MnSO4, 36 nM FeSO4, 36 nM CoSO4, 3.5 nM…

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AlphaMissense: DeepMind’s New AI Tool Sheds Light on Genetic Mutations

Google’s DeepMind has unveiled a new artificial intelligence tool, AlphaMissense, capable of predicting the potential harm of millions of genetic mutations. This tool aims to expedite research and enhance the diagnosis of rare disorders. Specifically, AlphaMissense focuses on missense mutations, which involve a single letter alteration in the DNA code….

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A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

Field sample collection Topsoil samples (0–15 cm, roughly 0.5 m3) from replicate field plots were collected from the Hopland Research and Extension Center (HREC) in Northern California, which is unceded land of the Shóqowa and Hopland People, on August 28th, 2018 after experiencing mean annual precipitation during the rainy season, see our…

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How to use attention and encoding layers in pytorch

Neskelogth (Samuel Kostadinov) September 19, 2023, 11:38am 1 I have a working neural network with two data streams as a backbone network. Now I’m working on the classification head and would like to sum the features extracted from the two streams in the backbone using an attention mechanism, but unfortunately…

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Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation

Cultivations and harvest Cupriavidus necator strain DSMZ 428 was grown in Ralstonia Minimal Media (RMM) with 100 mM HEPES pH 7.5 under chemostat conditions in a Photon Systems Instruments Multi-Cultivator MC-1000 OD. Each reactor tube was set up to a volume of 55 mL, OD600 0.05 and 3.5 g/L fructose. Once growth ceased,…

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Real-time Analytics News for the Week Ending September 16

In this week’s real-time analytics news: MLCommons released its latest machine learning benchmark testing results. Keeping pace with news and developments in the real-time analytics market can be a daunting task. We want to help by providing a summary of some of the important real-time analytics news items our staff…

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What is R? | CellularNews

What is R? A Comprehensive Definition Welcome to our “DEFINITIONS” blog series, where we provide clear and concise explanations of various terms and concepts. In this edition, we will demystify the powerful programming language known as R. So, if you’ve ever wondered, “What is R?” or “How is R used?”,…

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Chipseq analysis on repeat genes

Chipseq analysis on repeat genes 0 Hello everyone I am in need of some tips to analyze and make heatmaps as shown in this figure C and G. I already have downloaded the repeatmasker list. I want to compare my chromatin data with repeat elements and see their enrichment. I…

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Somatic SLC30A1 mutations altering zinc transporter ZnT1 cause aldosterone-producing adenomas and primary aldosteronism

Young, W. F. Primary aldosteronism: renaissance of a syndrome. Clin. Endocrinol. 66, 607–618 (2007). Article  CAS  Google Scholar  Rossi, G. P. et al. A prospective study of the prevalence of primary aldosteronism in 1,125 hypertensive patients. J. Am. Coll. Cardiol. 48, 2293–2300 (2006). Article  CAS  PubMed  Google Scholar  Fardella, C….

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Top 25 Bioconductor Interview Questions and Answers

Bioconductor is an open-source software project that provides tools for the analysis and comprehension of high-throughput genomic data. It’s a powerful tool, widely used in bioinformatics and computational biology to process and analyze intricate biological data. Bioconductor’s strength lies in its vast array of packages specifically tailored for genomics research,…

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Identification of co-diagnostic effect genes for aortic dissection and metabolic syndrome by multiple machine learning algorithms

Identification and functional enrichment analysis of common DEGs Batch effects had been eliminated with Rank-In in all samples from the AD combined dataset and GSE98895 dataset, as shown in Fig. 2A,B. The 3023 DEGs (1376 up- and 1647 down-regulated) were screened between AD and control subjects using the ‘limma’ package in…

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RnBeads Differential Methylation

Hi, I am trying to run a Differential methylation analysis with RnBeads as I have done previously on a similar fashion. This time I am just running it on my HPC and it seems to run just fine until it arrives to the differential methylation step. See the error output…

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Google adds AI-infused sustainability tools to Google Maps Platform

Google is equipping developers with three environment APIs for the Google Maps Platform to help them create new sustainability tools. The company made the announcement Wednesday at Google Next 2023 in San Francisco. Saleem Van Groenou, product manager, environment APIs at Google, explained during a breakout session that the launch…

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Getting Started with Python for Data Science

Image by Author   Summer is over and it’s back to studying or working on your self-development plan. Many of you may have had the summertime to think about what your next steps will be, and if that involves anything to do with Data Science – you need to read…

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Multiplexed transcriptomic profiling of the fate of human CAR T cells in vivo via genetic barcoding with shielded small nucleotides

Wagner, A., Regev, A. & Yosef, N. Revealing the vectors of cellular identity with single-cell genomics. Nat. Biotechnol. 34, 1145–1160 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Gehring, J., Hwee Park, J., Chen, S., Thomson, M. & Pachter, L. Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular…

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Metabolic programs of T cell tissue residency empower tumour immunity

Masopust, D. & Soerens, A. G. Tissue-resident T cells and other resident leukocytes. Annu. Rev. Immunol. doi.org/10.1146/annurev-immunol-042617-053214 (2019). Park, S. L., Gebhardt, T. & Mackay, L. K. Tissue-resident memory T cells in cancer immunosurveillance. Trends Immunol. 40, 735–747 (2019). Article  CAS  PubMed  Google Scholar  Byrne, A. et al. Tissue-resident memory…

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KRTA6A and FA2H Are Hub Genes Associated With Cgas-STING-related Immunogenic Cell Death in Lung Adenocarcinoma

Abstract Background/Aim: The immunogenic cell death (ICD) pathway plays a crucial prognostic role in lung adenocarcinoma (LUAD) therapy. The cyclic GMP–AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway is an upstream mechanism that drives ICD activation, but the interaction of hub genes remains unclear. The present study aimed to investigate…

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Mycobacterial DNA-binding protein 1 is critical for BCG survival in stressful environments and simultaneously regulates gene expression

Koul, A. et al. Delayed bactericidal response of Mycobacterium tuberculosis to bedaquiline involves remodelling of bacterial metabolism. Nat. Commun. doi.org/10.1038/ncomms4369 (2014). Article  PubMed  Google Scholar  Global Tuberculosis Report 2021. www.who.int/publications/digital/global-tuberculosis-report-2021. Colditz, G. A. et al. Efficacy of BCG vaccine in the prevention of tuberculosis: Meta-analysis of the published literature. JAMA…

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Interrogating the viral dark matter of the rumen ecosystem with a global virome database

Gregory, A. C. et al. Marine DNA viral macro-and microdiversity from pole to pole. Cell 177, 1109–1123.e1114 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016). Article  CAS  PubMed  Google Scholar  Camarillo-Guerrero, L….

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Get the “average” of a column in a heatmap, combine 3 heatmaps into 1?

Get the “average” of a column in a heatmap, combine 3 heatmaps into 1? 1 Hey guys, So I have 3 gene signatures that I wanna look into on my own RNASeq data. I’ve created hierarchal clustering heatmaps for these gene signatures, and I want to get the “average” expression…

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Combine 3 heatmaps into 1? Get the “average” of a column

Combine 3 heatmaps into 1? Get the “average” of a column 0 Hey guys, So I have 3 gene signatures that I wanna look into on my own RNASeq data. I’ve created hierarchal clustering heatmaps for these gene signatures, and I want to get the “average” expression of a sample/column,…

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Non-cell-autonomous cancer progression from chromosomal instability

Cell culture IMR90, 4T1, CT26, RAW264.7 and B16F10 cell lines were purchased from the American Type Culture Collection and cultured in MEM (IMR90), DMEM (B16F10, RAW264.7) or RPMI (4T1, IMR90, CT26) supplemented with 10% FBS in the presence of penicillin (50 U ml−1) and streptomycin (50 μg ml−1). All cells were found to be…

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Assembly of 43 human Y chromosomes reveals extensive complexity and variation

Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003). Article  ADS  CAS  PubMed  Google Scholar  Porubsky, D. et al. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell 185, 1986–2005 (2022). Article …

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Data Visualization in R

Data visualization in R programming involves creating graphical representations of data to gain insights, communicate findings, and explore patterns. R offers a wide range of packages and functions for creating various types of visualizations, from basic plots to complex interactive charts. When choosing a data visualization package, it is important…

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Senior Scientist in Gaithersburg, Maryland

EMPLOYER: AstraZeneca Pharmaceuticals LP TITLE: Senior Scientist LOCATION: Gaithersburg, MD HOURS: Full-Time; Mon-Fri (40 hours/week) DUTIES: Develop new image analysis solutions to measure biomarkers in clinical tissues, and use data science techniques to provide statistical insights. Utilize bioinformatics and data science techniques to generate disease linkage data to guide indication,…

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Multidrug-resistant Providencia rettgeri strain YQ150713.

Introduction Providencia rettgeri is a Gram-negative opportunistic human pathogenic bacterium that belongs to the Proteae bacteria. It is a pathogen commonly found in the hospitals that mainly cause urinary tract infections, pneumonia, bacteremia, neonatal sepsis, eye infections, meningitis, endocarditis, and diarrhea.1–3 The pathogen Providencia rettgeri demonstrates inherent resistance to numerous…

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Dynamic thresholding and tissue dissociation optimization for CITE-seq identifies differential surface protein abundance in metastatic melanoma

Workflow overview CITE-seq and cell hashing were performed on liquid and solid tissue biopsies (Fig. 1a, b). Experimentally, cells from 17 samples (Supplementary Data 2) were hashed and stained with a panel of 97 antibodies (Supplementary Data 2) covering key as well as exploratory immuno-oncology markers resulting in 57,261 cells after preprocessing and…

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Cas9-mediated knockout of Ndrg2 enhances the regenerative potential of dendritic cells for wound healing

Ndrg2 expression is reduced in tolerogenic DCs To identify potential targets for gene editing in DCs, we compared transcriptomic profiles of treatment induced tolerogenic DCs, which confer a variety of clinical benefits11,12,13,14,15,16,17 with untreated DCs. Bone marrow-derived DCs were cultivated from wild-type (WT) mice (C57/BL6) according to standard protocols25. Vitamin…

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How to Improve Return on Ad Spend Using R (ggplot2)

In today’s digital age, advertising has become an essential component of any marketing strategy. Companies invest significant resources in ad campaigns to attract and retain customers. However, tracking the effectiveness of these campaigns and ensuring a positive Return on Ad Spend (ROAS) can be challenging. Fortunately, with the power of…

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Transcriptome sequencing reveals circRNA expression profile in Parkinson’s disease-like mice after aerobic exercise

. 2022 Mar 21;46(3):227-238. doi: 10.55730/1300-0152.2611. eCollection 2022. Affiliations Expand Affiliation 1 The First Affiliated Hospital of Hainan Medical College, Hainan, China. Item in Clipboard Tianlun Fan et al. Turk J Biol. 2022. Show details Display options Display options Format AbstractPubMedPMID . 2022 Mar 21;46(3):227-238. doi: 10.55730/1300-0152.2611. eCollection 2022. Affiliation 1…

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ComplexHeatmap with anno_barplot

I’ve been making various heatmaps for different gene sets and I added the log2FoldChange values as an extra column, but I need to leave it as a barplot, but I’ve been lost on how to put those log2FoldChange values to appear as bars. Any help is appreciated, thanks 😉 “`r…

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Machine learning prediction and classification of behavioral selection in a canine olfactory detection program

2013 TSA cohort traits The traits scored in the cohort represent measures of confidence/fear, quality of hunting related behaviors, and dog-trainer interaction characteristics19,20. The traits Chase/Retrieve, Physical Possession, and Independent Possession were measured in both the Airport Terminal and Environmental tests whereas five and seven other traits were specific to…

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R Heatmap

R Heatmap A short tutorial for decent heat maps in R 图片 How to Create a Beautiful Interactive Heatmap in R – Datanovia 图片 Heatmap in R: Static and Interactive Visualization – Datanovia 图片 A short tutorial for decent heat maps in R 图片 How To Make a Heatmap in…

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Unusual pattern in heatmap from ChIP-seq

Unusual pattern in heatmap from ChIP-seq 0 Hello! I am plotting some heatmaps for a certain histone mark from a ChIP-seq experiment. I am producing the heatmaps using both computeMatrix and plotHeatmap functions from deeptools. The coordinates regions used for computeMatrix are all coding regions for the mouse genome, sorted…

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Differential exon usage of developmental genes is associated with deregulated epigenetic marks

H3K36me3 mark is most relevant to AS events The first task was to prepare a suitable data set where differentially used exons (DEUs) can be clearly associated with individual genes. Hence, out of 19,240 clusters of protein coding genes generated for the DEXSeq analysis (see “Materials and methods” section), we…

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DESeq2 analysis

Hi, I have a dataset including 2 variables, pH (8 values) and strains consortium (5 values) all in triplicate. The pH variable can be seen as a time because I took samples during fermentation. I would like to answer two questions: 1- For a given strains consortium do I have…

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Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct

Cell culture HCC2429 cells were a kind gift from the Hamon Center for Therapeutic Oncology Research at UT Southwestern Medical Center. The cells were grown in RPMI 1640 medium (Thermo Fisher Scientific, #11875119) with addition of 10% heat-inactivated Fetal Bovine Serum (Thermo Fisher Scientific, #10-438-026) and 1% penicillin—streptomycin (Thermo Fisher…

Continue Reading Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct

Zfp296 knockout enhances chromatin accessibility and induces a unique state of pluripotency in embryonic stem cells

Establishment of Zfp296-deficient ESCs The expression of Zfp296 during ESC differentiation into trophectoderm was examined using the ZHBTc4 ESC line, in which expression of Pou5f1 encoding Oct3/4 can be downregulated by tetracycline20. As shown in Supplementary Fig. 1a, Zfp296 expression rapidly decreased, suggesting that Zfp296 is downstream of Oct3/4. To generate…

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Decreased left heart flow in fetal lambs causes left heart hypoplasia and pro-fibrotic tissue remodeling

Coil implantation in fetal lambs We have complied with all relevant ethical regulations for animal testing. All procedures followed the Canadian Council on Animal Care guidelines and were approved by the University of Western Ontario Council on Animal Care (protocol 2010-257). Time-dated pregnant Dorset × Rideau Arcott ewes (gestational age 76 days,…

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How to Improve Sales Revenue Using R (ggplot2)

In today’s data-driven business world, companies are constantly striving to find ways to improve their sales revenue. One powerful tool that has gained popularity in recent years is the R programming language, particularly when used in conjunction with the ggplot2 package. In this article, we will explore how R and…

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Upcycling rice yield trial data using a weather-driven crop growth model

Phenotype data We obtained yield datasets for rice (Oryza sativa L.) from 207,331 trials with 8524 cultivars during the 38 years from 1980 to 2017. The data were obtained from field trials at 110 public agricultural experimental stations in Japan conducted by the Institute of Crop Science of the National…

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How to Integrate AT Internet Into R (ggplot2)

In today’s data-driven world, organizations rely heavily on web analytics to make informed decisions. One popular web analytics tool is AT Internet, which provides valuable insights into website traffic, user behavior, and conversion rates. While AT Internet offers its own data visualization capabilities, many data professionals prefer integrating it with…

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How to Improve Organic Search Traffic Using R (ggplot2)

In today’s digital landscape, improving organic search traffic is crucial for the success of any website or online business. With the help of advanced data analytics and visualization tools like R and ggplot2, SEO professionals can delve deep into website metrics, uncover hidden insights, and make data-driven decisions to enhance…

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Creating heatmaps with 2 Log Fold Changes in DESEQ2

I am a new learner of DESEQ2 and have seen similar posts on this forum but could not find clear answers. What would be the best way to create heatmaps specifically with 2 log fold change(base 2) in DESEQ2 or R in general? In DESEQ2, heatmaps are created based on…

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CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter

Collins FS, Green ED, Guttmacher AE, Guyer MS. US National Human Genome Research Institute. A vision for the future of genomics research. Nature. 2003;422(6934):835–47. Article  CAS  PubMed  Google Scholar  Slatko BE, Gardner AF, Ausubel FM. Overview of next-generation sequencing technologies. Curr Protoc Mol Biol. 2018;122(1):e59. Article  PubMed  PubMed Central  Google…

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Molecular features driving cellular complexity of human brain evolution

King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107–116 (1975). Article  ADS  CAS  PubMed  Google Scholar  Konopka, G. et al. Human-specific transcriptional networks in the brain. Neuron 75, 601–617 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Liu, X. et al….

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Chip-Seq replicates from different experiments

Chip-Seq replicates from different experiments 1 Hi, I have two replicate Chip-seq samples of H3K27Ac in the same condition. However, they are from two experiments carried out at different times and on different mice. I would like to compare/merge them in order to create heatmaps etc. The correlation is high…

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Discovery of chemical means to reverse aging and restore cellular function

Reprogramming small molecule cocktails restore NCC alterations in senescent cells. (A) Chemical structures of small molecules of basal cocktails used to generate induced pluripotent stem cells (iPSCs) from mouse (left) or human (right) somatic cells. (B) Correlation heatmaps showing eGFP and mCherry colocalization in human senescent fibroblasts demonstrate the effects…

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Differential contribution of nitrifying prokaryotes to groundwater nitrification

Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol. 2018;16:263–76. Article  CAS  PubMed  Google Scholar  Koch H, van Kessel MAHJ, Lücker S. Complete nitrification: insights into the ecophysiology of comammox Nitrospira. Appl Microbiol Biotechnol. 2018;103:177–89. Article  PubMed  PubMed Central  Google Scholar  Lehtovirta-Morley LE Ammonia oxidation: ecology,…

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Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities

Rantanen M, Karpechko AY, Lipponen A, Nordling K, Hyvärinen O, Ruosteenoja K, et al. The Arctic has warmed nearly four times faster than the globe since 1979. Commun Earth Environ. 2022;3:1–10. Article  Google Scholar  Kwok R. Arctic sea ice thickness, volume, and multiyear ice coverage: losses and coupled variability (1958–2018)….

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