Tag: wilcoxon

Unravelling cell type-specific responses to Parkinson’s Disease at single cell resolution | Molecular Neurodegeneration

Single nucleus RNA-seq reveals cell type heterogeneity in human SNpc We sampled SNpc from post-mortem human brains of 15 sporadic Parkinson’s disease (PD) patients and 14 Control individuals (see Supplementary Table 1 for full pathology reports). Using a 10X Genomics Chromium platform, we performed single nucleus RNA-seq (snRNA-seq) on more than…

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Analysis of sepsis combined with pulmonary infection by mNGS

Introduction Sepsis is one of the major diseases that poses a serious threat to human health, and its incidence and in-hospital mortality rates remain high despite the continuous updating of sepsis guidelines.1 Its main clinical manifestations are elevated body temperature, chills, and rapid heart rate, and it is most common…

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CRISPR/Cas9-mediated nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo

CRISPR/Cas9-induced homozygous knockout of nexn causes progressive cardiac dysfunction without affecting skeletal muscle function in zebrafish Several studies in different animal models and cardiomyopathy patients have shown that loss of NEXN is leading to DCM which is characterized by an impaired contractility of the heart6,10,12. Homozygous loss of NEXN mostly…

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MNCLCDA: predicting circRNA-drug sensitivity associations by using mixed neighbourhood information and contrastive learning | BMC Medical Informatics and Decision Making

circRNA-drug sensitivity associations We download the circRNA-drug sensitivity association dataset from reference [17], where Deng et al. [17] collected and organized the association data between circRNA and drug sensitivity from the circRic database [16]. Here, the drug sensitivity and circRNA data come from the GDSC database [19], which provides 80,076…

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

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

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Functional alterations and predictive capacity of gut microbiome in type 2 diabetes

Diversity and compositional analyses Regarding clinical differences (Table 1), T2DM individuals (mean 69.6 (± 12.3 sd) years) were significantly (p value < 0.01; Wilcoxon rank-sum test) older than the controls (46.9 (± 17.3 sd) years), showed higher BMI (mean 30.9 (± 7.01 sd) vs. mean 26.3 (± 6.12 sd) than the control…

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r – Problem with significance test using stat_signif() coupled with a ggplot2 boxplot

I am attempting to produce a boxplot with the results of a significance text, ideally with Student’s test and/or a Wilcoxon’s test comparing two groups of concentrations between two different auto-analysers. If I run the following code (Note the code does not include the input statements for the datafiles but…

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What does each point represent in a volcano plots for RNAseq data?

What are the advantages and disadvantages of RNA-seq compared to other methods for studying gene expression?5 answersRNA-seq has several advantages over other methods for studying gene expression. Firstly, RNA-seq can detect new transcripts and coding regions, which is not possible with microarray technology. Secondly, RNA-seq provides less noisy data compared…

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Multiple host colonization and differential expansion of multidrug-resistant ST25-Acinetobacter baumannii clades

Features of animal and human isolates of this study On average, sequencing of isolates of this study generated 2.36 M of reads per genome, with an estimated genome size of 4.2 M bases, with a coverage depth of 204X (Table S1). Animal isolates included in this study (n = 33) were found mostly in…

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Generating high-quality plant and fish reference genomes from field-collected specimens by optimizing preservation

Sample collection A total of nine species of marine fish were collected across three different sampling days (September 7th, 9th, and 12th 2022) under IACUC Animal Use Protocol S12219 (Supplementary Data 1). Six species were collected using a speargun donated by a local fisher. Fish were transported back to shore, euthanized,…

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NOTCH1 mutations predict superior outcomes, NSCLC

Introduction Lung cancer remains the leading cause of cancer-related mortality worldwide, and the majority are non-small-cell lung cancer (NSCLC).1,2 Genetic variation is a typical feature of NSCLC that drives cancer initiation and progression.3 Understanding the role of mutated genes in NSCLC is the basis of the development of novel treatment…

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Lower-limb ulcers in participants with leprosy sequelae

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

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What is the best way to identify which group of genes is more highly expressed?

What is the best way to identify which group of genes is more highly expressed? 0 Hello, I am new to bioinformatics. I am trying to compare two sets of genes that belong to different subgenomes of my species to identify if one of the subgenomes is more highly expressed….

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Allelic hierarchy for USH2A influences auditory and visual phenotypes in South Korean patients

Genotypes of USH2A-related disorders We identified 14 biallelic variants in USH2A, either homozygous or compound heterozygous, in a trans configuration. The segregation of these variants was confirmed by Sanger sequencing. Overall, 18 mutant alleles were implicated in the diagnosis of USH2A-related phenotypes, including c.251G > A:p.Cys84Tyr, c.2209C > T:p.Arg737*, c.2802 T > G:p.Cys934Trp, c.4372C > T:p.Arg1578Cys, c.4858C > T:p.Gln1620*, c.7120 + 1475A > G, c.8232G > C:p.Trp2744Cys,…

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Bioinformatics analysis of immune cell infiltration patterns and potential diagnostic markers in atherosclerosis

A database in the Gene Set Enrichment Analysis (GSEA; www.gsea-msigdb.org/gsea/msigdb/index.jsp) platform10,11 was used to identify 134 GLN metabolism-associated genes. Weighted gene co-expression network analysis (WGCNA) and module screening GLN-associated gene sets were investigated using WGCNA. The results demonstrated that when the weighted value was 24 (Fig. 1A), scale independence was greater…

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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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Additional file 1 of Anti-diarrheal drug loperamide induces dysbiosis in zebrafish microbiota via bacterial inhibition

journal contribution posted on 2023-11-12, 04:20 authored by Rebecca J. Stevick, Bianca Audrain, Sébastien Bedu, Nicolas Dray, Jean-Marc Ghigo, David Pérez-Pascual Additional file 1: Supplementary figures: Fig. S1. Sequencing depth and coverage for 16S rRNA gene amplicon data from conventional zebrafish larvae. (A) Number of quality-controlled bacterial sequences per sample. (B)….

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

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

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

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

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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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Clonal Hematopoiesis and Cardiovascular Disease in Patients With Multiple Myeloma Undergoing Hematopoietic Cell Transplant | Cardiology | JAMA Cardiology

Key Points Question  Is clonal hematopoiesis of indeterminate potential (CHIP) detected at the time of hematopoietic stem transplant (HCT) associated with increased rates of cardiovascular disease (CVD) among patients with multiple myeloma (MM) following HCT? Finding  In this cohort study of patients with MM undergoing HCT, CHIP was highly prevalent…

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ggplot2 – add increase change value between control and treatment in ggplot from a second dataframe R

I have this example dataframe with samestructure of my real one. I calculate the increase change in a second dataframe and then I need to add this value to this boxplots: test <- data.frame(city=c(rep(“city1”, 6), rep(“city2”, 6)), Treatment=c(rep(“control”, 3), rep(“treat”, 3)), replicate=c(1,2,3,1,2,3,1,2,3,1,2,3), y=c(12,24,13,15,26,16,13,23,45,34,12,24) ) test1 <- test %>%pivot_wider(names_from = “Treatment”,…

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Resurgence of SARS-CoV-2 Delta after Omicron variant superinfection in an immunocompromised pediatric patient | Virology Journal

Patient history The patient was a school-aged child previously diagnosed with a neuroinflammatory condition initially treated with the IFN-γ blocking antibody emapalumab-Iszg and ongoing therapy with steroids and monthly etoposide. The patient had a history of varicella encephalitis and remained on suppressive valacyclovir therapy. In early January 2022, the child…

Continue Reading Resurgence of SARS-CoV-2 Delta after Omicron variant superinfection in an immunocompromised pediatric patient | Virology Journal

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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Uncovering the relationship between gut microbial dysbiosis, metabolomics, and dietary intake in type 2 diabetes mellitus and in healthy volunteers: a multi-omics analysis

After processing the data, 20 control samples and 21 Type 2 Diabetes Mellitus samples contained data from all three collected assays (bacteriome, mycobiome, metabolome). The bacteriome data comprised on average 9534 contigs (s.d. ± 3465), ranging from 2032 to 18,320 contigs (786 ASVs). The mycobiome data contained on average 5450 contigs (s.d. ± 4964),…

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Passive diffusion accounts for the majority of intracellular nanovesicle transport

Introduction Trafficking of proteins, lipids, and other molecules between cellular compartments is carried out by vesicular carriers. Material destined for transfer is packaged into a small trafficking vesicle at the donor compartment; the vesicle must then travel to its destination, before fusing with the target compartment to deliver the material…

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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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Characterizing the regulatory Fas (CD95) epitope critical for agonist antibody targeting and CAR-T bystander function in ovarian cancer

Mice strains Six- to eight-week-old (age), 20–25-g (weight), both male and female (sex) mice were used for tumor xenografts generation and in vivo efficacy studies as described in the text (see Table 3). Athymic Nude (Envigo) Foxn1nu/Foxn1+ or NOD.Cg Prkdcscid Il2rgtm1Wjl/SzJ also called NSG mice were used. All animal procedures were…

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Simulation of undiagnosed patients with novel genetic conditions

Simulated patient initialization We simulate patients for each of the 2134 diseases in Orphanet20 (orphadata.org, accessed October 29, 2019) that do not correspond to a group of clinically heterogeneous disorders (i.e., Orphanet’s “Category” classification31), have at least one associated phenotype, and have at least one causal gene. For Orphanet diseases…

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Distribution tendencies of pathogens causing LRTI

Introduction Lower respiratory tract infection (LRTI) remains one of the leading causes of death worldwide.1 Several well-known pathogens, including Streptococcus pneumoniae, Pseudomonas aeruginosa, Klebsiella pneumoniae, Candida, Herpesvirus, and others, have been identified as significant causes of infection.2 Nonetheless, nearly half of the cases still have an undetermined etiology,3,4 despite the…

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Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin

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

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Filter, Plot, and Explore with Seurat in RStudio

First thing’s first, we need to load the packages we will be using. In order to use any functions of a package, we must first call the library of that package. In your console (likely in the lower left corner of your RStudio window), run the following lines of code…

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PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant chemotherapy for colorectal cancer: a retrospective study | BMC Gastroenterology

Tissue samples A total of 84 analytic samples from surgical or biopsy specimens were collected from 84 patients who underwent radical surgery for CRC at Saitama Medical University International Medical Center between January and December 2016. One case was excluded because the specimen was too small; therefore, we used a…

Continue Reading PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant chemotherapy for colorectal cancer: a retrospective study | BMC Gastroenterology

scRNAseq Differential expression analysis

Forum:scRNAseq Differential expression analysis 0 Hello everyone! I am a student that recently started working with transcriptomics data. I am trying to conduct my first single cell data analysis of an organoid model using mainly Seurat. I tried to conduct a differential expression analysis between different clusters using the FindMarkers()…

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Reconstructing the cytokine view for the multi-view prediction of COVID-19 mortality | BMC Infectious Diseases

Li H, Liu SM, Yu XH, Tang SL, Tang CK. Coronavirus disease 2019 (COVID-19): current status and future perspectives. Int J Antimicrob Agents. 2020;55(5):105951. Article  CAS  PubMed  PubMed Central  Google Scholar  . virusncov.com/. Iwendi C, Bashir AK, Peshkar A, Sujatha R, Chatterjee JM, Pasupuleti S, et al. COVID-19 Patient Health…

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Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts

Study population Among the 60 cases, 28 were male (46.7%) and 32 were female (53.3%) ranging between 1.5 and 90 years of age; most patients were between 19 and 64 years (n = 26; 43.3%) or less than 9 years (n = 16; 26.7%). No difference in the proportion of stool submissions was observed by year, though…

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Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli

PPTP-seq development and validation PPTP-seq uses plasmid to integrate each CRISPRi-based TF perturbation and each promoter activity reporter into one construct. Each plasmid contains a CRISPRi cassette that constitutively expresses a single guide RNA (sgRNA) to repress a specific TF in the genome19 and a promoter-reporter cassette to measure the…

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The impact of mutational clonality in predicting the response to immune checkpoint inhibitors in advanced urothelial cancer

Genomic analysis and cohort description We generated whole-exome sequencing (WES) and RNA sequencing (RNA-Seq) data from tumors and blood samples from 27 advanced urothelial cancer patients treated with anti-PD-1/PD-L1 ICIs at Hospital del Mar (Fig. 1a). WES data was obtained from the tumors before treatment as well as from blood samples,…

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Comparative evaluation of 16S rRNA metagenomic sequencing in the diagnosis and understanding of bacterial endophthalmitis

Introduction Endophthalmitis is a severe infection in the eye that can occur as a consequence of intraocular surgery, intraocular injections, trauma, the presence of a central venous catheter and systemic infectious diseases such as sepsis, abscesses or urinary tract infection.1 2 Acute bacterial endophthalmitis represents a significant ocular pathology that…

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Genomic profiling of post-transplant lymphoproliferative disorders using cell-free DNA | Journal of Hematology & Oncology

The median age of the patients was 55 years (range 13–74). Median time between SOT and PTLD was 95 months (range 2–338). Most patients had stage IV disease (n = 13, 76%) with a median metabolic tumor volume (MTV) of 302 mL (range 5–2070 mL). Lactate dehydrogenase (LDH) levels ranged from 210 to 5068 (Additional file…

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Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution

Consensus MTG taxonomy across primates The BRAIN Initiative Cell Census Network26 generated high-resolution transcriptomic maps of the MTG in human, chimpanzee, gorilla, macaque and marmoset by applying single-nucleus transcriptomic (snRNA-seq) assays to samples isolated from between three and seven donor brains in each species (plate-based SMART-seq v4 (SSv4) for great…

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Can one sample t.test be used to determine statistical significance for log2FC values?

Can one sample t.test be used to determine statistical significance for log2FC values? 1 I downloaded proteomic data from CPTAC, but it is already in log2FC form, [while the spectral count lacks the sample mapping]. Now, I want to determine which genes are statistically significant, what test can be applied?…

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Genomic diversity of Yersinia pestis from Yunnan Province, China, implies a potential common ancestor as the source of two plague epidemics

Sampling of Y. pestis in Yunnan Province spanning two epidemic-silent cycles In this study, 356 strains were isolated from 11 prefectures or cities in Yunnan Province, China, and Myanmar, near the China-Myanmar border, between 1952 and 2016, spanning two epidemic-silent cycles (Fig. 1a). Among them, 70 strains were isolated from the…

Continue Reading Genomic diversity of Yersinia pestis from Yunnan Province, China, implies a potential common ancestor as the source of two plague epidemics

Characterization of the pig lower respiratory tract antibiotic resistome

Composition and distribution of ARGs in the pig lower respiratory tract microbiome Using 745 metagenome data of the lower respiratory tract microbiome from 675 experimental pigs across five populations, we constructed a swine respiratory microbial gene catalog containing 10,337,194 non-redundant genes. Of these, 1228 open reading frames (ORFs) were identified…

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Unreprogrammed H3K9me3 prevents minor zygotic genome activation and lineage commitment in SCNT embryos

doi: 10.1038/s41467-023-40496-3. Ruimin Xu #  1   2   3 , Qianshu Zhu #  3   4 , Yuyan Zhao  1 , Mo Chen  2   5 , Lingyue Yang  1   2 , Shijun Shen  3   4 , Guang Yang  3   4 , Zhifei Shi  1 , Xiaolei Zhang  1 , Qi Shi  1   2 , Xiaochen Kou …

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Nutrients | Free Full-Text | Association of Maternal Folate Intake and Offspring MTHFD1 and MTHFD2 Genes with Congenital Heart Disease

1. Introduction Congenital heart defect (CHD) is the most prevalent congenital malformation worldwide and has emerged as the leading cause of death among children under five years old in China [1,2]. While surgical interventions have improved survival rates, CHD patients often experience long-term cardiovascular and systemic complications, leading to substantial…

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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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16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling

The problem of off-target amplification The widely used standardized protocol for 16S rRNA gene amplicon sequencing7,14 turned out to be inadequate due to robust off-target amplification of human DNA during the analysis of bacteriome in samples of different biopsy sites from the upper gastrointestinal (GI) tract. In samples from all…

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Liftedover vcf header/contig compatibility

I have a collaborator that has lifted over their hg19 files to hg38 using Crossmap. The first step in the workflow they need to run is a simple bcftools filter for variant quality. They are getting an unknown file type error. Are there any obvious problems with this header that…

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Single-molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer

Genome-wide somatic mutation analyses of cancer tissues To develop this method, we examined whole-genome sequences of cancers from 2,511 individuals across 25 different cancers from the PCAWG study25,26, identifying distinct mutation frequencies across the genome in different tumor types (Extended Data Fig. 1). For example, analysis of lung tumor and…

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Vascular level inflammatory response induced by COVID-19

Runlong Lin,1,2 Jing Yu,2 Aijuan Tian,2 Xiaomei Wang,2 Xin Yuan,2 Wengui Xu,1 Wenli Xie3 1Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s…

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A universal tool for predicting differentially active features in single-cell and spatial genomics data

singleCellHaystack methodology For a detailed description of the original singleCellHaystack implementation (version 0.3.2) we refer to Vandenbon and Diez19. In brief, singleCellHaystack uses the distribution of cells inside an input space to predict DAFs. First, it infers a reference distribution \(Q\) of all cells in the space by estimating the…

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Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution

Isolation of crAss-like phages CrAss-like phages were searched in 12 sewage samples from five wastewater treatment plants using three different qPCR assays, the one designed from ΦCrAss001 genome in this study and two previously described12,19. Depending on the qPCR assay employed and the samples, values in wastewater ranged from 103−106…

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HIV-1 promotes ubiquitination of the amyloidogenic C-terminal fragment of APP to support viral replication

Ethics Statement LifeSource Buffy Coat blood obtained from New York blood center was used for isolation of peripheral blood mononuclear cells using Ficoll-Plaque (GE). Ethical approval for the study was obtained from the Institutional Review Board of Northwestern University and all donors provided their written, informed consent. Cell cultures HEK293T…

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Genetic strategies for sex-biased persistence of gut microbes across human life

Strain dynamics of the gut-associated microbiota within the first 24 months of life Shotgun metagenomics sequencing approaches were applied to the microbiomes of 11 healthy, vaginally delivered, full-term (>37 weeks of gestation) newborns, which were longitudinally sampled at 1-, 6-, 12-, and 24-months following birth (Figs. S1, S2, Supplementary Data 1). Consistent with…

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Differentially expressed gene analysis in Python with omicverse

An important task of bulk rna-seq analysis is the different expression , which we can perform with omicverse. For different expression analysis, ov change the gene_id to gene_name of matrix first. When our dataset existed the batch effect, we can use the SizeFactors of DEseq2 to normalize it, and use…

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Neutrophil extracellular traps predict postoperative pulmonary complications in paediatric patients undergoing parental liver transplantation | BMC Gastroenterology

Study design and subjects This prospective study was conducted at Renji Hospital, School of Medicine, Shanghai Jiaotong University from July 1, 2019, to October 10, 2020. The study protocol was approved by the Renji Hospital Ethics Committee and adhered to the principles of the Declaration of Helsinki. Written informed consent…

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Individualized dynamic methylation-based analysis of cell-free DNA in postoperative monitoring of lung cancer | BMC Medicine

Patient characteristics and tumor-informed methylation analysis Of the 387 consecutive patients with suspected NSCLC, a total of 195 patients (stage I-II 165, 84.6%) were included in the MEDAL cohort. The clinicopathological features of the MEDAL cohort were comparable to that of the independent DYNAMIC cohort [2] (Table 1; Additional file…

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FindAllMarkers in Seurat and statistical problem

FindAllMarkers in Seurat and statistical problem 1 I used to use FindAllMarkers in Seurat for finding the differentially expressed genes (DEGs) across all clusters. The default statistical testing that Seurat use to calculate the DEGs via Wilcoxon Rank Sum Test which is also known as Mann-Whitney U test. As we…

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Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering

Predominant bacteria in sewage do likely not originate from the human gut To identify bacterial genomes from sewage across the world, we used a combination of two different metagenomics genome binners (VAMB24 and MetaBAT225). From 757 samples across 101 different countries (Fig. 1a and Supplementary Fig. 1), we were able to create…

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An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis | Malaria Journal

Optimization of the pipeline on monoclonal and simulated mixed infection samples Towards optimizing GATK4 for P. falciparum, the creation of an improved training “truth set” for the pipeline was key. To filter raw VCFs with a high quality truth callset, which is difficult to obtain using wet laboratory methods, a…

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Genetic characterization of primary and metastatic high-grade serous ovarian cancer tumors reveals distinct features associated with survival

Characterization of genomic landscape We compared somatic variants, copy number alterations, and mutational burden between the primary and metastatic tumors of the ST and LT survival groups. Our cohort of patient tumors exhibited characteristics typical of those seen in previously sequenced HGSC tumors, such as nearly ubiquitous TP53 mutations, high…

Continue Reading Genetic characterization of primary and metastatic high-grade serous ovarian cancer tumors reveals distinct features associated with survival

Mann Whitney U Test with Rstudio: A Comprehensive Guide

Introduction A statistical technique used to assess if there is a significant difference in the distributions of two independent groups is the Mann-Whitney U test, commonly referred to as the Mann-Whitney-Wilcoxon test. Unlike parametric tests, the Mann-Whitney U test is appropriate for non-normal data since it does not require that…

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Genomic characteristics of triple negative apocrine carcinoma: a comparison to triple negative breast cancer

Baseline characteristics We described the baseline clinical and pathological characteristics of TNAC and LK-TNBC in Supplementary Table 1. Only stage at diagnosis was different between TNAC and LK-TNBC (P = 0.03), while no significant differences were observed in other characteristics, including nuclear grade, histologic grade, Ki-67, and status of (neo)adjuvant treatment. Somatic…

Continue Reading Genomic characteristics of triple negative apocrine carcinoma: a comparison to triple negative breast cancer

Patterns and determinants of the global herbivorous mycobiome

Sampling overview A total of 661 samples belonging to 34 species and 9 families of foregut-fermenting ruminant (thereafter ruminant, n = 468), foregut-fermenting pseudoruminant (thereafter pseudoruminant, n = 17), and hindgut fermenters (n = 176) were examined (Fig. 1a, b, Supplementary Data 1). The dataset also provides a high level of replication for a variety of animals (229…

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Nitrate and a nitrate-reducing Rothia aeria strain as potential prebiotic or synbiotic treatments for periodontitis

Bacterial strains and growth conditions Rothia aeria CECT9999 (Ra9, isolate D1P7 described in24), was used as a nitrate-reducing probiotic candidate. Prior to the experiment, Brain Heart Infusion (BHI) (Biolife, Deerfield, Illinois, USA) agar plates were inoculated with the strain, incubated for 48 h at 37 °C, and stored at 4 °C for up…

Continue Reading Nitrate and a nitrate-reducing Rothia aeria strain as potential prebiotic or synbiotic treatments for periodontitis

Technique may restore healthy bacterial balance in C-section babies

Differences in bacterial DNA load and composition between treatment groups at differing body sites, collection types, and times. (A) Bacterial DNA load in maternal vaginal swabs (both inoculated with vaginal fluids), gauze (control gauze not inoculated with vaginal fluids), infant skin (forearm), and infant stool. (B) Bacterial load of the…

Continue Reading Technique may restore healthy bacterial balance in C-section babies

Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems

Geochemical evolution of groundwater in the Canadian Prairie The mean residence time of water in an aquifer is a very important factor influencing its geochemical composition (or facies) (Fig. 2a). Mean residence time, or groundwater age, is determined using radioisotopes such as tritium and 14C and refers to the travel time…

Continue Reading Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems

Genome-wide association study of thoracic aortic aneurysm and dissection in the Million Veteran Program

Common variants associated with TAAD We designed a two-phased GWAS. The initial MVP discovery analysis was composed of 8,626 individuals (7,050 European, 1,266 African and 310 Hispanic ancestry participants) with TAAD and 453,043 disease-free individuals from the same ancestral groups (Supplementary Fig. 1); their baseline characteristics are presented in Supplementary…

Continue Reading Genome-wide association study of thoracic aortic aneurysm and dissection in the Million Veteran Program

Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics

Construction of proteomic content networks from an ultra-deep metaproteomic approach We define the proteomic content network (PCN) of a microbiome sample as a bipartite graph connecting each microbial taxon to all expressed functions from the taxon’s proteome. In order to gain the deepest possible understanding of sample-specific PCN of the…

Continue Reading Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics

A graph-based genome and pan-genome variation of the model plant Setaria

Variation and evolution in Setaria We collected genome-wide resequencing data for 630 wild (S. viridis), 829 landrace and 385 modern cultivated accessions from the Setaria genus with an average sequencing depth of ~15×, of which 1,004 were newly generated and 840 were from previous studies16,21 (Supplementary Table 1). After aligning…

Continue Reading A graph-based genome and pan-genome variation of the model plant Setaria

Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil

Study sites Soils were collected from two different sites (ARDEC: Colorado State University’s Agricultural Research, Development and Education Center in Fort Collins, CO; and CPCRC: USDA Columbia Plateau Conservation Research Center in Pendleton, OR). At each site, four replicate plots of no-till corn (ARDEC) or no-till annual wheat (CPCRC) were…

Continue Reading Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil

Tox4 regulates transcriptional elongation and reinitiation during murine T cell development

Pan-hematopoietic Tox4 deletion reduces number of multipotential progenitors and impairs T cell development To understand the role of TOX4 in development, we generated Tox4 conditional knockout mice by the CRISPR-Cas9 methodology, and two loxP sites in the same orientation were inserted upstream and downstream of exons 4–6, respectively (Supplementary Fig. 1a). Considering…

Continue Reading Tox4 regulates transcriptional elongation and reinitiation during murine T cell development

The Biostar Herald for Monday, June 05, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

Continue Reading The Biostar Herald for Monday, June 05, 2023

Microbial diversity in the vaginal microbiota and its link to pregnancy outcomes

A prospective study of pregnant women We established a prospective cohort of 2313 pregnant women with the goal of studying the vaginal microbiota, its community composition and the presence of pathogenic bacteria in the peripartum period. Inclusions and data collection were performed in accordance with applicable laws and ethical standards. Ethical…

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Dissecting the impact of dietary fiber type on atherosclerosis in mice colonized with different gut microbial communities

Engraftment of donor communities prior to dietary treatment Germ-free (GF) female ApoE−/− mice were colonized with fecal samples from one of three human donors (Supplementary Fig. 1). These samples were selected from a repository of fecal specimens previously collected from adults in their mid-seventies36 and were chosen based on (i)…

Continue Reading Dissecting the impact of dietary fiber type on atherosclerosis in mice colonized with different gut microbial communities

Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing | BMC Cancer

Single-cell and single-nucleus RNA sequencing of sarcoma subtypes In this work, we studied sarcomas from varying tissue origins, including osteosarcoma (OS), Ewing sarcoma (ES), and desmoplastic small round cell tumor (DSRCT) (Fig. 1). We used different dissociation protocols: Miltenyi Tumor Dissociation Kit, cold-active protease derived from Bacillus licheniformis, and Nuclei EZ…

Continue Reading Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing | BMC Cancer

The menstrual cycle regularity and skin: irregular menstrual cycle affects skin physiological properties and skin bacterial microbiome in urban Chinese women | BMC Women’s Health

General characteristics of the participants The menstrual cycle regularity of the female participants and menstrual cycle-associated skin characteristics were obtained from the self-evaluation questionnaire. Nearly 9% of the participants reported an irregular menstrual cycle, and 66.5% reported a less regular menstrual cycle (Table 2). Thus, most of the women reported…

Continue Reading The menstrual cycle regularity and skin: irregular menstrual cycle affects skin physiological properties and skin bacterial microbiome in urban Chinese women | BMC Women’s Health

Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum

CRISPR editing of DNA polymerase δ To increase the genetic repertoire of P. falciparum parasites in culture, we aimed to generate parasites with impaired 3ʹ−5ʹ proof-reading activity from the catalytic subunit of DNA polymerase δ (PF3D7_1017000) in order to increase the level of basal spontaneous mutations, based on prior work…

Continue Reading Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum

Weak phylogenetic and habitat effects on root trait variation of 218 Neotropical tree species

Introduction Tropical rainforests in the Amazon basin harbor the highest tree diversity on earth (Ter Steege et al., 2020). Most of this diversity is concentrated in a relatively small number of plant families, including Chrysobalanaceae, Fabaceae, Lauraceae, Lecythidaceae, Malvaceae (sensu lato), Myrtaceae, Rubiaceae, and Sapotaceae, that can comprise > 60%…

Continue Reading Weak phylogenetic and habitat effects on root trait variation of 218 Neotropical tree species

IL5RA as an immunogenic cell death-related predictor in progression and therapeutic response of multiple myeloma

Differential expression analysis We downloaded GSE125361 (n = 48) microarray data from the Gene Expression Omnibus (GEO) database, which included 45 myeloma samples and 3 controls, for expression analysis of IL5RA in cancer16. Additionally, we analyzed the expression of IL5RA in smoldering myeloma (SMM) patients who progressed to active MM (n = 10) and…

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Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture

We analyzed data from a total of 2,733 participants from the GALA II16 and SAGE17 asthma case–control studies who self-identified as African American (AA; n = 757), Puerto Rican (PR; n = 893), Mexican American (MX; n = 784) or other Latino American (LA; n = 299) (Table 1 and Supplementary Table 1). The median age of the…

Continue Reading Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture

Gut microbiome signatures of extreme environment adaption in Tibetan pig

1050 SGBs clustered from 8210 high-medium quality metagenome-assembled genomes (MAGs) Over 779 Gb metagenomic sequence data was generated by Illumina HiSeq × Ten platform from 65 TPs samples (Supplementary Table 1). We integrated the above sequencing raw reads with a published metagenomic sequence dataset of 287 captive pigs from Denmark, France…

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Comparative resistome, virulome and mobilome analysis of metagenomes from wild and farm animals

Resumo:  Although (in the context of bacterial infections) the goal of antibiotic use is to combat and eliminate pathogenic bacteria, hundreds of non-pathogenic bacterial species are also affected when antibiotics are administrated. This results in a selection of bacteria resistant to the class of antibiotic applied. Additionally, with the ability…

Continue Reading Comparative resistome, virulome and mobilome analysis of metagenomes from wild and farm animals

Copy number alteration features in pan-cancer homologous recombination deficiency prediction and biology

Data collection for HRD prediction model training and validation For the development of the HRD prediction model, 1854 samples (WGS data) from the pan-cancer analysis of whole genomes9 (PCAWG) and 560 breast cancer samples (SNP array data)16 are collected. To obtain a high-confidence training dataset of HRD, samples with BRCA1/2…

Continue Reading Copy number alteration features in pan-cancer homologous recombination deficiency prediction and biology

Downsampling of cells in scRNAseq DE analysis

Downsampling of cells in scRNAseq DE analysis 0 Hello, this is a general question with no specific example concerning differential gene expression analysis in scRNAseq data. We sometimes want to compare two conditions in our DE** analysis but we see the the sample size of these groups greatly differ. For…

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Basin-wide variation in tree hydraulic safety margins predicts the carbon balance of Amazon forests

Site description We assemble a pan-Amazon dataset of key HTs (\(\varPsi \)50, HSM50 and \(\varPsi \)dry), including 129 species distributed across 11 forest sites (Fig. 1 and Extended Data Fig. 1). The sites are old-growth lowland forests (less than 400 m of elevation), with no evidence of significant human disturbance, located…

Continue Reading Basin-wide variation in tree hydraulic safety margins predicts the carbon balance of Amazon forests

PAI-1 4G/5G polymorphism in patients with DM & hypertension

Introduction Diabetes mellitus (DM) is a group of metabolic syndromes characterized by disorders of glucose metabolism, including type 1 DM, type 2 DM, gestational DM, and specific types of DM due to other causes. DM is closely associated with abnormal cardiac electrophysiological signal conduction and arrhythmias, whereby it triggers sudden…

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Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data | Genome Biology

Overview of the study To uncover the contexts and biological processes that affect gene expression regulation, this study took advantage of both the resolution of single-cell data and the directionality captured by co-eQTLs. First, we constructed cell-type-specific co-expression networks using five scRNA-seq PBMC datasets from three recently generated PBMC scRNA-seq…

Continue Reading Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data | Genome Biology

r – Issues with my output. Did I mess up my RStudio settings?

When I first downloaded R, every time I ran a t.test or wilcox.test, the output would include not only the p-value but also the mean of the two groups being compared, class-interval etc. I have tried using the summary function but it doesn’t provide any extra detail. Now all I…

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Measuring antigen expression of cancer cell lines and circulating tumour cells

To quantify the expression of different antigens, cells were stained using monoclonal antibodies coupled to phycoerythrin (PE), after which the number of PE molecules per cell was determined using quantitative flow cytometry. Although the number of PE molecules will not be exactly equal to the number of antigens, in this…

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The evolution of non-small cell lung cancer metastases in TRACERx

The TRACERx 421 cohort The TRACERx study (clinicaltrials.gov/ct2/show/NCT01888601) is a prospective observational cohort study that aims to transform our understanding of NSCLC, the design of which has been approved by an independent research ethics committee (13/LO/1546). Informed consent for entry into the TRACERx study was mandatory and obtained from every…

Continue Reading The evolution of non-small cell lung cancer metastases in TRACERx

Optogenetic stimulation of mouse Hoxb8 microglia in specific regions of the brain induces anxiety, grooming, or both

Induction of grooming by optogenetic activation of Hoxb8 microglia in the DMS and mPFC The components that are critical for achieving Hoxb8 microglia dependent induction of anxiety and/or grooming in wildtype C57Bl/6 mice are: Hoxb8 microglia, Hoxb8IRESCre (a Cre driver specific to Hoxb8 microglia within the CNS), Ai32 (a Cre…

Continue Reading Optogenetic stimulation of mouse Hoxb8 microglia in specific regions of the brain induces anxiety, grooming, or both

PUREE: accurate pan-cancer tumor purity estimation from gene expression data

Genomics-based consensus tumor purity estimates For TCGA samples, genomic-based consensus tumor purities were computed as a mean of predictions from ABSOLUTE17, AbsCNSeq18, ASCAT15, and PurBayes16 following the approach reported in Ghoshdastider et al. 41. AbsCNSeq and PurBayes estimates are based on mutation variant allele frequency data, and ASCAT and ABSOLUTE…

Continue Reading PUREE: accurate pan-cancer tumor purity estimation from gene expression data

Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism

Weight loss and clinical improvements after IF intervention We performed a three-week intervention study on 72 adult Chinese volunteers subjected to a 5:2 program as detailed in Fig. 1a. The volunteers comprised individuals ranging from regular to obese (Supplementary Table 1). Seventeen clinical parameters were determined both before and after…

Continue Reading Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism

High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias

Nanopore reads coupled to a novel computational method extends analyses of differential methylation to sparse CpGs (outside CpG islands) We analyzed tumor samples at diagnosis (T) and relapse (R) from three AML patients (UD5, UD10 and AML2) who received standard chemotherapy and relapsed with chemoresistant disease (supplementary Table 1). DNA from…

Continue Reading High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias

Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals

Diversity of within-host mutations in SARS-CoV-2 samples We analysed SARS-CoV-2 samples from 2,820 different individuals, alongside 29 other samples for quality control of the analysis (see Methods). The samples were collected from June-2020 to September-2022, covering the third to the fifth COVID-19 waves in HK. All samples had \(\ge\)90% genome…

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Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation

Introduction Infections are the major cause of human deaths worldwide and present a rising threat to public security.1 Antimicrobial resistance is a major concern that is threatening our ability to treat bacterial infections.2 Delayed administration of antibiotics significantly increases the in-hospital mortality rate.3 The tragic outcome of infection highlights the…

Continue Reading Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation