223 Works

Semaphorin 3A Inhibits Endoplasmic Reticulum Stress Induced by High Glucose in Müller Cells

Mengyang Li, Enzhong Jin, Li Zhu, Chi Ren, Zhiqiao Liang, Mingwei Zhao & Jinfeng Qu
This study aimed to explore the effect of the Semaphorin3A (Sema3A)/Neuropilin-1 (Nrp-1) pathway on Müller cell activities and endoplasmic reticulum (ER) stress induced by high glucose (HG) in vitro. The primary Müller cells of C57BL/6J mice were isolated and cultured in normal or high glucose medium. The expression of endogenous Sema3A and its coreceptor Nrp-1 was measured by Western blot. Müller cells were incubated with exogenous recombinant Sema3A protein or transfected with lentiviral vectors expressing...

Adverse outcome pathways and linkages to transcriptomic effects relevant to ionizing radiation injury

Jihang Yu, Wangshu Tu, Andrea Payne, Chris Rudyk, Sarita Cuadros Sanchez, Saadia Khilji, Premkumari Kumarathasan, Sanjeena Subedi, Brittany Haley, Alicia Wong, Catalina Anghel, Yi Wang & Vinita Chauhan
In the past three decades, a large body of data on the effects of exposure to ionizing radiation and the ensuing changes in gene expression has been generated. These data have allowed for an understanding of molecular-level events and shown a level of consistency in response despite the vast formats and experimental procedures being used across institutions. However, clarity on how this information may inform strategies for health risk assessment needs to be explored. An...

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 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 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.

Semantic segmentation dataset of Chinese martial arts classic movie props(part)

rongwang wang, yaqiw wang, suiyu zhang, guiping qian, Yizheng Chen, Rong Li, xiaoyu ma & xiaodiao chen
Semantic segmentation is a hot area in computer vision (CV) research. The integration of computer vision and the film and television industry has put forward higher requirements for media data. At present, the analysis of film clips integrating high dynamics and continuous frames is one of the hot spots of video semantic segmentation. High-precision, high-volume data is the basis for proposing and improving deep learning models. However, the content labels of existing datasets are disorderly,...

Non-specific binding of compounds in in vitro metabolism assays: a comparison of microsomal and hepatocyte binding in different species and an assessment of the accuracy of prediction models

Iain Gardner, Mandy Xu, Chunyan Han, Yi Wang, Xingjin Jiao, Masoud Jamei, Hiba Khalidi, Peter Kilford, Sibylle Neuhoff, Roz Southall, David B. Turner, Helen Musther, Barry Jones & Simon Taylor
Non-specific binding in in vitro metabolism systems leads to an underestimation of the true intrinsic metabolic clearance of compounds being studied. Therefore in vitro binding needs to be accounted for when extrapolating in vitro data to predict the in vivo metabolic clearance of a compound. While techniques exist for experimentally determining the fraction of a compound unbound in in vitro metabolism systems, early in drug discovery programmes computational approaches are often used to estimate the...

The effect of insulin and kruppel like factor 10 on osteoblasts in the dental implant osseointegration in diabetes mellitus patients

Chen Sheng, Yalin Guo, Wenjie Hou, Haobin Chen, Hongchen Liu & Lin Wang
Diabetes mellitus, metabolic disease, is characterized by chronic hyperglycemia. Patients with diabetes mellitus are susceptible to infection and therefore have a higher prevalence and progression rate of periodontal disease. We aimed to study the effect of insulin and kruppel like factor 10 (KLF10) on osteoblasts proliferation and differentiation, and expression of bone metabolism-related molecules and related signaling pathway molecules of AKT serine/threonine kinase 1 (AKT) and nuclear factor kappa B subunit 1 (NF-κB) through in...

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.

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 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 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 1 of Plasma metabolomics provides new insights into the relationship between metabolites and outcomes and left ventricular remodeling of coronary artery disease

Qian Zhu, Min Qin, Zixian Wang, Yonglin Wu, Xiaoping Chen, Chen Liu, Qilin Ma, Yibin Liu, Weihua Lai, Hui Chen, Jingjing Cai, Yemao Liu, Fang Lei, Bin Zhang, Shuyao Zhang, Guodong He, Hanping Li, Mingliang Zhang, Hui Zheng, Jiyan Chen, Min Huang & Shilong Zhong
Additional file 1: Table S1. Baseline characteristics on death and MACE risks. Table S2. Baseline characteristics on LVEF and LVMI. Table S3. Relationship between metabolites and death risk. Table S4. Relationship between metabolites and MACE risk. Table S5. Multivariate Cox proportional hazards model for clinical outcomes. Table S6. Spearman correlation analysis between clinical factors and those metabolites associated with death risk. Table S7. Spearman correlation analysis between clinical factors and those metabolites associated with death...

Genome-wide identification of genes critical for in vivo fitness of multi-drug resistant porcine extraintestinal pathogenic Escherichia coli by transposon-directed insertion site sequencing using a mouse infection model

Fan Yin, Yan Hu, Zixuan Bu, Yuying Liu, Hui Zhang, Yawen Hu, Ying Xue, Shaowen Li, Chen Tan, Xiabing Chen, Lu Li, Rui Zhou & Qi Huang
Extraintestinal pathogenic Escherichia coli (ExPEC) is an important zoonotic pathogen. Recently, ExPEC has been reported to be an emerging problem in pig farming. However, the mechanism of pathogenicity of porcine ExPEC remains to be revealed. In this study, we constructed a transposon (Tn) mutagenesis library covering Tn insertion in over 72% of the chromosome-encoded genes of a virulent and multi-drug resistant porcine ExPEC strain PCN033. By using a mouse infection model, a transposon-directed insertion site...

Morphology and phylogeny of two new Thalassiosiroid taxa (Bacillariophyceae), with two marginal rimoportulae

Biaobiao Niu, Yaqiong Guo, Nina Lundholm & Yang Li
Thalassiosira and related taxa i.e. the taxa within Thalassiosirales are among the most abundant and widespread diatoms. The vast majority have one marginal rimoportula, but very few always have two. The knowledge on Thalassiosiroid taxa in Chinese waters is restricted, and to explore the diversity, monoclonal strains were established from southern Chinese coastal waters. Morphological data were based on light and scanning electron microscopy. The D1‒D3 region of the ribosomal large subunit (LSU) and the...

Transcriptome analysis of adipocytokines and their-related LncRNAs in lung adenocarcinoma revealing the association with prognosis, immune infiltration, and metabolic characteristics

Jie Ren, Hui Zhang, Jinna Wang, Yingsong Xu, Lei Zhao & Qihang Yuan
Lung adenocarcinoma (LUAD) is amongst the major contributors to cancer-related deaths on a global scale. Adipocytokines and long non-coding RNAs (lncRNAs) are indispensable participants in cancer. We performed a pan-cancer analysis of the mRNA expression, single nucleotide variation, copy number variation, and prognostic value of adipocytokines. LUAD samples were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Simultaneously, train, internal and external cohorts were grouped. After a stepwise screening...

MeCP2-induced heterochromatin organization is driven by oligomerization-based liquid–liquid phase separation and restricted by DNA methylation

Hui Zhang, Hector Romero, Annika Schmidt, Katalina Gagova, Weihua Qin, Bianca Bertulat, Anne Lehmkuhl, Manuela Milden, Malte Eck, Tobias Meckel, Heinrich Leonhardt & M. Cristina Cardoso
Heterochromatin is the highly compacted form of chromatin with various condensation levels hallmarked by high DNA methylation. MeCP2 is mostly known as a DNA methylation reader but has also been reported as a heterochromatin organizer. Here, we combine liquid–liquid phase separation (LLPS) analysis and single-molecule tracking with quantification of local MeCP2 concentrations in vitro and in vivo to explore the mechanism of MeCP2-driven heterochromatin organization and dynamics. We show that MeCP2 alone forms liquid-like spherical...

A temperate Siphoviridae bacteriophage isolate from Siberian tiger enhances the virulence of methicillin-resistant Staphylococcus aureus through distinct mechanisms

Dan Yang, Shuang Wang, Erchao Sun, Yibao Chen, Lin Hua, Xiangru Wang, Rui Zhou, Huanchun Chen, Zhong Peng & Bin Wu
The emergence and worldwide spread of Methicillin-resistant Staphylococcus aureus (MRSA) pose a threat to human health. While bacteriophages are recognized as an effective alternative to treat infections caused by drug resistant pathogens, some bacteriophages in particular the temperate bacteriophage may also influence the virulence of the host bacteria in distinct ways. In this study, we isolated a bacteriophage vB_Saus_PHB21 from an epidermal sample of Siberian tiger (Panthera tigris altaica) using an MRSA strain SA14 as...

Overexpression of LtKNOX1 from Lilium tsingtauense in Nicotiana benthamiana affects the development of leaf morphology

Rui Zhou, Menglong Fan, Mei Zhao, Xinqiang Jiang & Qinghua Liu
Leaves are the main vegetative organs of the aboveground part of plants and play an important role in plant morphogenesis. KNOTTED-LIKE HOMEOBOX (KNOX) plays a crucial role in regulating leaf cell fate and maintaining leaf development. In this study, we analyzed LtKNOX1 from Lilium tsingtauense and illustrated its function in transgenic plants. Tissue-specific expression analysis indicated that LtKNOX1 was highly expressed in stems, young flower buds, and shoot apical meristems (SAMs). Ectopic overexpression of LtKNOX1...

Data for: Neuromuscular embodiment of feedback control elements in Drosophila flight

Samuel Whitehead, Sofia Leone, Theodore Lindsay, Matthew Meiselman, Noah Cowan, michael dickinson, Nilay Yapici, David Stern, Troy Shirangi & Itai Cohen

Clinical features of the first critical case of acute encephalitis caused by the avian influenza A (H5N6) virus

Libing Zhang, Kaituo Liu, Qin Su, Xiao Chen, Xiaoquan Wang, Qingfeng Li, Wenlei Wang, Xuhua Mao, Jinmei Xu, Xin Zhou, Qin Xu, Le Zhou, Xiufan Liu & Pinghu Zhang
Highly pathogenic avian influenza viruses (HPAIV), such as H5N1, H5N6, and H7N9, have been reported to frequently infect humans, but acute encephalitis caused by HPAIV in humans has been rarely reported. We report the first critical case of acute encephalitis with mild pneumonia caused by the H5N6 virus. On January 25 of 2022, a 6-year-old girl with severe neurological symptoms was admitted to our hospital and rapidly developed into seizures and coma. Brain imaging showed...

Additional file 1 of Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma

Qing Kay Li, Yingwei Hu, Lijun Chen, Michael Schnaubelt, Daniel Cui Zhou, Yize Li, Rita Jui-Hsien Lu, Mathangi Thiagarajan, Galen Hostetter, Chelsea J. Newton, Scott D. Jewell, Gil Omenn, Ana I. Robles, Mehdi Mesri, Oliver F. Bathe, Bing Zhang, Li Ding, Ralph H. Hruban, Daniel W. Chan & Hui Zhang
Additional file 1: Table S1. Clinical information of study cases. Table S2. Expression of proteins from the PDAC tumors and NATs

Additional file 2 of Direct identification of HLA class I and class II-restricted T cell epitopes in pancreatic cancer tissues by mass spectrometry

Kenji Fujiwara, Yingkuan Shao, Nan Niu, Tengyi Zhang, Brian Herbst, Mackenzie Henderson, Stephen Muth, Pingbo Zhang & Lei Zheng
Additional file 2: Supplemental Table S2, PDAC peptidome.

Spectral estimation of large stochastic blockmodels with discrete nodal covariates

Angelo Mele, Lingxin Hao, Joshua Cape & Carey E. Priebe
In many applications of network analysis, it is important to distinguish between observed and unobserved factors affecting network structure. We show that a network model with discrete unobserved link heterogeneity and binary (or discrete) covariates corresponds to a stochastic blockmodel (SBM). We develop a spectral estimator for the effect of covariates on link probabilities, exploiting the correspondence of SBMs and generalized random dot product graphs (GRDPG). We show that computing our estimator is much faster...

Registration Year

  • 2022
    223

Resource Types

  • Dataset
    223

Affiliations

  • Johns Hopkins University
    223
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    126
  • Fudan University
    120
  • Capital Medical University
    102
  • Sichuan University
    101
  • Sun Yat-sen University
    91
  • Zhejiang University
    91
  • Huazhong University of Science and Technology
    91
  • Peking University
    86
  • Chinese Academy of Sciences
    84