185 Works

Senescent preosteoclast secretome promotes metabolic syndrome-associated osteoarthritis through COX2-PGE2

Weiping Su
Metabolic syndrome–associated osteoarthritis (MetS-OA) is a distinct osteoarthritis phenotype defined by the coexistence of MetS or its individual components. Despite the high prevalence of MetS-OA, its pathogenic mechanisms are unclear. Here, we report that humans and mice with MetS are more likely to develop osteoarthritis-related subchondral bone alterations than those without MetS. MetS-OA mice exhibited a rapid increase in joint subchondral bone plate and trabecular thickness before articular cartilage degeneration. Subchondral preosteoclasts undergo senescence at...

The structural basis of PTEN regulation by multi-site phosphorylation

Daniel Dempsey, Thibault Viennet, Philip Cole, Haribabu Arthanari & Sandra Gabelli
PTEN is a phosphatidylinositol-3,4,5-triphosphate (PIP3) phospholipid phosphatase that is commonly mutated or silenced in cancer. PTEN's catalytic activity, cellular membrane localization, and stability are orchestrated by a cluster of C-terminal phosphorylation events on Ser380, Thr382, Thr383, and Ser385, but the molecular details of this multifaceted regulation have remained uncertain. Here we use a combination of protein semisynthesis, biochemical analysis, NMR, X-ray crystallography, and computational simulations on human PTEN and its sea squirt homolog VSP to...

Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Hollis Dahn, Jacquelyn Mountcastle, Jennifer Balacco, Sylke Winkler, Iliana Bista, Anthony Schmitt, Olga Vinnere Pettersson, Giulio Formenti, Karen Oliver, Michelle Smith, Wenhua Tan, Anne Kraus, Stephen Mac, Lisa Komoroske, Tanya Lama, Andrew Crawford, Robert Murphy, Samara Brown, Alan Scott, Phillip Morin, Erich Jarvis & Olivier Fedrigo
Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different...

Additional file 2 of African-specific alleles modify risk for asthma at the 17q12-q21 locus in African Americans

Charles Washington, Matthew Dapas, Arjun Biddanda, Kevin M. Magnaye, Ivy Aneas, Britney A. Helling, Brooke Szczesny, Meher Preethi Boorgula, Margaret A. Taub, Eimear Kenny, Rasika A. Mathias, Kathleen C. Barnes, Gurjit K. Khurana Hershey, Carolyn M. Kercsmar, Jessica D. Gereige, Melanie Makhija, Rebecca S. Gruchalla, Michelle A. Gill, Andrew H. Liu, Deepa Rastogi, William Busse, Peter J. Gergen, Cynthia M. Visness, Diane R. Gold, Tina Hartert … & Carole Ober
Additional file 2. Region-wide eQTL results in airway epithelial cells from 189 African American children in the URECA cohort.

Additional file 2 of Transcriptome analysis of MYB transcription factors family and PgMYB genes involved in salt stress resistance in Panax ginseng

Mingming Liu, Ke Li, Shichao Sheng, Mingyu Wang, Panpan Hua, Yanfang Wang, Ping Chen, Kangyu Wang, Mingzhu Zhao, Yi Wang & Meiping Zhang
Additional file 2: Table S2. The PgMYB protein sequences for phylogenetic analysis.

Additional file 1 of Revealing the characteristics of ZIKV infection through tissue-specific transcriptome sequencing analysis

Zhi-lu Chen, Zuo-jing Yin, Tian-yi Qiu, Jian Chen, Jian Liu, Xiao-yan Zhang & Jian-qing Xu
Additional file 1.

Additional file 4 of COVID-19 vaccine update: vaccine effectiveness, SARS-CoV-2 variants, boosters, adverse effects, and immune correlates of protection

Wei-Yu Chi, Yen-Der Li, Hsin-Che Huang, Timothy En Haw Chan, Sih-Yao Chow, Jun-Han Su, Louise Ferrall, Chien-Fu Hung & T.-C. Wu
Additional file 4: Table S4. Heterologous booster lab data. Studies of heterologous vaccine boosters and their immunogenicity. Related to Table 3.

Additional file 2 of Causality of genetically determined metabolites on anxiety disorders: a two-sample Mendelian randomization study

Gui Xiao, Qingnan He, Li Liu, Tingting Zhang, Mengjia Zhou, Xingxing Li, Yijun Chen, Yanyi Chen & Chunxiang Qin
Additional file 2: Table S1. The formula used to calculate R2 and F statistic between exposure and outcome; Table S2. Summary statistics of the anxiety disorders; Table S3–S12. Mendelian Randomization estimation for Amino acid(Table S3); Carbohydrate (Table S4); Co-factor or vitamin(Table S5);Energy(Table S6); Lipid(Table S7); Nucleotide (Table S8); Peptide (Table S9); Xenobiotic(Table S10);X(unknow metabolites) (Table S11);known metabolites (Table S12) on the risk of anxiety disorders; Table S13. The characteristics of SNPs and their genetic associations...

Efficacy and safety of osimertinib for patients with EGFR-mutated NSCLC: a systematic review and meta-analysis of randomized controlled studies

Li Li, Qin Huang, Jianhai Sun, Fei Yan, Wujie Wei, Zihui Li, Li Liu & Jie Deng
Osimertinib is a recently approved third-generation epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) that selectively inhibits both EGFR-TKI-sensitizing and EGFR-T790M resistance mutations. The aim of the present meta-analysis was to investigate the efficacy and safety of osimertinib for patients with EGFR-mutated non-small-cell lung cancer (NSCLC). Databases were searched for randomized controlled studies that reported the efficacy and safety of osimertinib versus other treatments (chemotherapy, other EGFR-TKIs, etc.) in treating EGFR-mutated NSCLC. The measured effects...

Additional file 1 of Integrated proteomic and metabolomic modules identified as biomarkers of mortality in the Atherosclerosis Risk in Communities study and the African American Study of Kidney Disease and Hypertension

Linda Zhou, Aditya Surapaneni, Eugene P. Rhee, Bing Yu, Eric Boerwinkle, Josef Coresh, Morgan E. Grams & Pascal Schlosser
Additional file 1. Additional materials including the module memberships and annotations of proteins/metabolites; the cross-sectional associations of modules and participant characteristics; the mortality associations of modules; and network representations of module 42 and 98.

Additional file 2 of Three-dimensional microenvironment regulates gene expression, function, and tight junction dynamics of iPSC-derived blood–brain barrier microvessels

Raleigh M. Linville, Matthew B. Sklar, Gabrielle N. Grifno, Renée F. Nerenberg, Justin Zhou, Robert Ye, Jackson G. DeStefano, Zhaobin Guo, Ria Jha, John J. Jamieson, Nan Zhao & Peter C. Searson
Additional file 2. Summary of bulk RNA-sequencing data.

Additional file 10 of Carbohydrates and ginsenosides in shenmai injection jointly improve hematopoietic function during chemotherapy-induced myelosuppression in mice

Shiyu Zhang, Yinxiao Mi, Tingting Ye, Xiaoyan Lu, Li Liu, Jing Qian & Xiaohui Fan
Additional file 10: Table S7. GO analysis of DEGs uniquely regulated in the S+Rg group.

Additional file 11 of Carbohydrates and ginsenosides in shenmai injection jointly improve hematopoietic function during chemotherapy-induced myelosuppression in mice

Shiyu Zhang, Yinxiao Mi, Tingting Ye, Xiaoyan Lu, Li Liu, Jing Qian & Xiaohui Fan
Additional file 11: Table S8. KEGG pathway analysis of Model, S+Rg, S, and Rg groups.

Additional file 2 of Network reconstruction for trans acting genetic loci using multi-omics data and prior information

Johann S. Hawe, Ashis Saha, Melanie Waldenberger, Sonja Kunze, Simone Wahl, Martina Müller-Nurasyid, Holger Prokisch, Harald Grallert, Christian Herder, Annette Peters, Konstantin Strauch, Fabian J. Theis, Christian Gieger, John Chambers, Alexis Battle & Matthias Heinig
Additional file 2 Supplementary tables, large supporting tables with table titles as tabs.

Additional file 2 of Network reconstruction for trans acting genetic loci using multi-omics data and prior information

Johann S. Hawe, Ashis Saha, Melanie Waldenberger, Sonja Kunze, Simone Wahl, Martina Müller-Nurasyid, Holger Prokisch, Harald Grallert, Christian Herder, Annette Peters, Konstantin Strauch, Fabian J. Theis, Christian Gieger, John Chambers, Alexis Battle & Matthias Heinig
Additional file 2 Supplementary tables, large supporting tables with table titles as tabs.

Data from: Pathogen spillover driven by rapid changes in bat ecology. Dataset G: Assessments of pre-weaning reproductive output

Peggy Eby, Alison Peel, Andrew Hoegh, Wyatt Madden, John Giles, Peter Hudson & Raina Plowright

Data from: Pathogen spillover driven by rapid changes in bat ecology. Dataset A: Register of Hendra virus spillovers to horses

Peggy Eby, Alison Peel, Andrew Hoegh, Wyatt Madden, John Giles, Peter Hudson & Raina Plowright

Maximum One-Factor-At-A-Time Designs for Screening in Computer Experiments

Qian Xiao, V. Roshan Joseph & Douglas M. Ray
Identifying important factors from a large number of potentially important factors of a highly nonlinear and computationally expensive black box model is a difficult problem. Morris screening and Sobol’ design are two commonly used model-free methods for doing this. In this article, we establish a connection between these two seemingly different methods in terms of their underlying experimental design structure and further exploit this connection to develop an improved design for screening called Maximum One-Factor-At-A-Time...

Data involved in this article from A game theoretical model for the stimulation of public cooperation in environmental collaborative governance

Yinhai Fang, Matjaž Perc & Hui Zhang
This file provides the data for figures in this paper, as well as the code that generates the data.

Additional file 15 of A comprehensive pan-cancer analysis of necroptosis molecules in four gynecologic cancers

Jianfeng Zheng, Xintong Cai, Yu Zhang, Huihui Wang, Li Liu, Fengling Tang, Linying Liu & Yang Sun
Additional file 15: Supplementary Table 3. The results of Univariate Cox regression analysis for pan-cancer.

Additional file 2 of Cytomegalovirus infection reduced CD70 expression, signaling and expansion of viral specific memory CD8+ T cells in healthy human adults

Jian Lu, Guobing Chen, Arina Sorokina, Thomas Nguyen, Tonya Wallace, Cuong Nguyen, Christopher Dunn, Stephanie Wang, Samantha Ellis, Guixin Shi, Julia McKelvey, Alexei Sharov, Yu-Tsueng Liu, Jonathan Schneck & Nan-ping Weng
Additional file 2: Supplementary Table 1. Demographics of study subjects used in the figures(experiments). Supplementary Table 2. GO pathways identified by GSEA analysis. Supplementary Table 3. Antibody list and information used in flowcytometry analysis.

Additional file 2 of Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson & Abhinav Nellore
Additional file 2. This file includes performance benchmarks applying tool-specific filtering criteria.

Additional file 2 of Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson & Abhinav Nellore
Additional file 2. This file includes performance benchmarks applying tool-specific filtering criteria.

Additional file 7 of Evolution patterns of NBS genes in the genus Dendrobium and NBS-LRR gene expression in D. officinale by salicylic acid treatment

Jiapeng Yang, Caijun Xiong, Siyuan Li, Cheng Zhou, Lingli Li, Qingyun Xue, Wei Liu, Zhitao Niu & Xiaoyu Ding
Additional file 7.

Additional file 10 of Evolution patterns of NBS genes in the genus Dendrobium and NBS-LRR gene expression in D. officinale by salicylic acid treatment

Jiapeng Yang, Caijun Xiong, Siyuan Li, Cheng Zhou, Lingli Li, Qingyun Xue, Wei Liu, Zhitao Niu & Xiaoyu Ding
Additional file 10.

Registration Year

  • 2022
    185

Resource Types

  • Dataset
    185

Affiliations

  • Johns Hopkins University
    185
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    101
  • Fudan University
    97
  • Capital Medical University
    92
  • Sichuan University
    76
  • Peking University
    74
  • Sun Yat-sen University
    73
  • Huazhong University of Science and Technology
    72
  • Central South University
    68
  • Jiangsu Province Hospital
    68