402 Works

Data from: Vocal turn-taking in a nonhuman primate is learned during ontogeny

Cecilia P. Chow, Jude F. Mitchell & Cory T. Miller
Conversational turn-taking is an integral part of language development, as it reflects a confluence of social factors that mitigate communication. Humans coordinate the timing of speech based on the behaviour of another speaker, a behaviour that is learned during infancy. While adults in several primate species engage in vocal turn-taking, the degree to which similar learning processes underlie its development in these non-human species or are unique to language is not clear. We recorded the...

Data from: Evolution of early Eocene Palaeosinopa (Mammalia, Pantolestidae) in the Willwood Formation of the Bighorn Basin, Wyoming

Rachel H. Dunn & Kenneth D. Rose
Species-level diversity and evolution of Palaeosinopa from the Willwood Formation of the Bighorn Basin is reassessed based on substantial new material from the Bighorn, Powder River, and Wind River basins. We recognize three species of Palaeosinopa in the Willwood Formation of the Bighorn Basin: P. lutreola, P. incerta, and P. veterrima. The late Wasatchian species P. didelphoides is not present in the Bighorn Basin. The Willwood species can be differentiated based only on size. P....

Data from: Hedging your bets: intermediate movements as optimal behavior in the context of an incomplete decision

Adrian M. Haith, David M. Huberdeau & John W. Krakauer
Existing theories of movement planning suggest that it takes time to select and prepare the actions required to achieve a given goal. These theories often appeal to circumstances where planning apparently goes awry. For instance, if reaction times are forced to be very low, movement trajectories are often directed between two potential targets. These intermediate movements are generally interpreted as errors of movement planning, arising either from planning being incomplete or from parallel movement plans...

Data for \"Seasonal cycle of idealized polar clouds: large eddy simulations driven by a GCM\"

Xiyue Zhang, Tapio Schneider, Zhaoyi Shen, Kyle Pressel & Ian Eisenman
We provide data sets used to produce results in the paper "Seasonal cycle of idealized polar clouds: large eddy simulations driven by a GCM". Data sets include GCM forcing files, ensemble mean LES output files, and offline RRTMG (radiative transfer) files. Update 2021-10-01: Rerun offline RRTMG for cloud liquid + ice and liquid-only cases, then calculated the ensemble average of radiative fluxes

Pig as a reservoir of CRISPR type TST4 Salmonella enterica serovar Typhimurium monophasic variant during 2009–2017 in China

Xiaolei Xie, Zhenyu Wang, Kai Zhang, Yang Li, Yachen Hu, Zhiming Pan, Xiang Chen, Qiuchun Li & Xinan Jiao
CRISPR-based typing was performed to subtype isolates of S. Typhimurium and its monophasic variant Salmonella 4,[5],12:i:- from humans and animals between 2009 and 2017 in China. CRISPR typing classified all isolates into two lineages and four sub-lineages. All isolates from Lineage II and Lineage IB-1 were Salmonella Typhimurium. All of Salmonella 4,[5],12:i: – isolates were distributed in Lineage IA and Lineage IB-2, which all belonged to ST34 by MLST typing. Only Lineage IB-2 contained ST34...

Pig as a reservoir of CRISPR type TST4 Salmonella enterica serovar Typhimurium monophasic variant during 2009–2017 in China

Xiaolei Xie, Zhenyu Wang, Kai Zhang, Yang Li, Yachen Hu, Zhiming Pan, Xiang Chen, Qiuchun Li & Xinan Jiao
CRISPR-based typing was performed to subtype isolates of S. Typhimurium and its monophasic variant Salmonella 4,[5],12:i:- from humans and animals between 2009 and 2017 in China. CRISPR typing classified all isolates into two lineages and four sub-lineages. All isolates from Lineage II and Lineage IB-1 were Salmonella Typhimurium. All of Salmonella 4,[5],12:i: – isolates were distributed in Lineage IA and Lineage IB-2, which all belonged to ST34 by MLST typing. Only Lineage IB-2 contained ST34...

Data from: Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans

Ho-Yon Hwang & Jiou Wang
Genetic diversity is maintained by continuing generation and removal of variants. While examining over 800,000 DNA variants in wild isolates of Caenorhabditis elegans, we made a discovery that the proportions of variant types are not constant across the C. elegans genome. The variant proportion is defined as the fraction of a specific variant type (e.g. single nucleotide polymorphism (SNP) or indel) within a broader set of variants (e.g. all variants or all non-SNPs). The proportions...

Social bonds, social status and survival in wild baboons: a tale of two sexes

Fernando Campos, Francisco Villavicencio, Elizabeth Archie, Fernando Colchero & Susan Alberts
People who are more socially integrated or have higher socio-economic status live longer. Recent studies in nonhuman primates show striking convergences with this human pattern: female primates with more social partners, stronger social bonds or higher dominance rank all lead longer lives. However, it remains unclear whether social environments also predict survival in male nonhuman primates, as it does in men. This gap persists because, in most primates, males disperse among social groups, resulting in...

Psychological distress and state boredom during the COVID-19 outbreak in China: the role of meaning in life and media use

Miao Chao, Xueming Chen, Tour Liu, Haibo Yang & Brian J. Hall
Epidemics are associated with increased burden of psychological distress. However, the role of boredom on mental health during epidemic periods has seldom been explored. This study attempted to examine the effect of state boredom on psychological outcomes, and the role of media use and meaning in life among the indirectly exposed Chinese adults in the initial phase of the COVID-19 outbreak. An online survey was administered to 917 Chinese adults on 28 January 2020 (1...

The human origin recognition complex (ORC) is essential for pre-RC assembly, mitosis and maintenance of nuclear structure

Hsiang-Chen Chou, Kuhulika Bhalla, Osama-El Demerdesh, Olaf Klingbeil, Kaarina Hanington, Sergey Aganezov, Peter Andrews, Habeeb Alsudani, Kenneth Chang, Christopher R. Vakoc, Michael C. Schatz, Richard W. McCombie & Bruce Stillman
The origin recognition complex (ORC) cooperates with CDC6, MCM2-7, and CDT1 to form pre-RC complexes at origins of DNA replication. Here, using tiling-sgRNA CRISPR screens, we report that each subunit of ORC and CDC6 is essential in human cells. Using an auxin-inducible degradation system, we created stable cell lines capable of ablating ORC2 rapidly, revealing multiple cell division cycle phenotypes. The primary defects in the absence of ORC2 were cells encountering difficulty in initiating DNA...

Data from: Cherry-picking by trialists and meta-analysts can drive conclusions about intervention efficacy

Evan Mayo-Wilson, Tianjing Li, Nicole Fusco, Lorenzo Bertizzolo, Joseph K. Canner, Terrie Cowley, Peter Doshi, Jeffrey Ehmsen, Gillian Gresham, Nan Guo, Jennifer A. Haythornthwaite, James Heyward, Hwanhee Hong, Diana Pham, Jennifer L. Payne, Lori Rosman, Elizabeth A. Stuart, Catalina Suarez-Cuervo, Elizabeth Tolbert, Claire Twose, Swaroop Vedula & Kay Dickersin
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN SUBSEQUENT PUBLICATIONS. PLEASE SEE http://dx.doi.org/10.1016/j.jclinepi.2017.05.007 FOR MORE INFORMATION. Objectives The objective of this study was to determine whether disagreements among multiple data sources affect systematic reviews of randomized clinical trials (RCTs). Study Design and Setting Eligible RCTs examined gabapentin for neuropathic pain and quetiapine for bipolar depression, reported in public (e.g., journal articles) and nonpublic sources (clinical study reports [CSRs] and individual participant data [IPD]). Results...

Biological mechanisms of growth performance and meat quality in porcine muscle tissue

Chen Fang, Fei Guo, Xiaoqi Zhao, Zining Zhang, Junlan Lu, Hongbin Pan, Taojie Xu, Weizhen Li, Minghua Yang, Ying Huang, Yanguang Zhao & Sumei Zhao
Growth performance and meat quality are important traits for pig production. The aim of the present study was to investigate the molecular mechanisms underlying growth performance and meat quality, and to identify novel target molecules for predicting the growth performance and meat quality. The differentially expressed genes (DEGs) in Diannan small ears pigs (DSP) and Landrace pigs (LP) were assessed by RNA-sequencing analyzing technology. A total of 339 DEGs were obtained between DSP and LP....

Jamestown Canyon virus in Massachusetts: clinical case series and vector screening

Cormac M. Kinsella, Molly L. Paras, Sandra Smole, Samar Mehta, Vijay Ganesh, Lin H. Chen, Daniel P. McQuillen, Ruta Shah, Justin Chan, Matthew Osborne, Scott Hennigan, Frederic Halpern-Smith, Catherine M. Brown, Pardis Sabeti & Anne Piantadosi
Jamestown Canyon virus (JCV) is a neuroinvasive arbovirus that is found throughout North America and increasingly recognized as a public health concern. From 2004 to 2012, an average of 1.7 confirmed cases were reported annually in the United States, whereas from 2013 to 2018 this figure increased over seventeen-fold to 29.2 cases per year. The rising number of reported human infections highlights the need for better understanding of the clinical manifestations and epidemiology of JCV....

Left ventricular MRI segmentations

Ryan O'Hara
Hypertrophic cardiomyopathy (HCM) causes sudden cardiac death (SCD) due to ventricular arrhythmias (VA) manifesting from myocardial fibrosis proliferation. Current clinical risk stratification criteria inadequately identify at-risk patients in need of primary prevention of VA. Here, we use mechanistic computational modeling of the heart to analyze how HCM-specific remodeling of the heart promotes arrhythmogenesis and to develop a personalized strategy to forecast risk of VAs in these patients. We combine contrast-enhanced cardiac magnetic-resonance (CMR) imaging and...

Genetic regulation of the development of mating projections in Candida albicans

Weihong Liang, Guobo Guan, Chao Li, Clarissa J. Nobile, Li Tao & Guanghua Huang
Candida albicans is a major human fungal pathogen, capable of switching among a range of morphological types, such as the yeast form, including white and opaque cell types and the GUT (gastrointestinally induced transition) cell type, the filamentous form, including hyphal and pseudohyphal cell types, and chlamydospores. This ability is associated with its commensal and pathogenic life styles. In response to pheromone, C. albicans cells are able to form long mating projections resembling filaments. This...

2-back task in split-belt adaptation

Cristina Rossi, Ryan Roemmich, Nicolas Schweighofer, Amy Bastian & Kristan Leech
We studied split-belt treadmill adaptation and savings in young (21±2 y/o) and older (56±6 y/o) adults with or without a secondary 2-back task during adaptation. We here provide here kinematic data for split-belt treadmill walking - specifically, step length asymmetry, double support asymmetry, and limb excursion asymmetry measure. We provide raw response data (button presses and reaction time) for performance in the 2-back cognitive task. We also provide scripts that can be used to analyse...

Quantitative assessment of agricultural sustainability reveals divergent priorities among nations

Guolin Yao, Xin Zhang, Srishti Vishwakarma, Carole Dalin, Adam Komarek, David Kanter, Kyle Davis, Kimberly Pfeifer, Jing Zhao, Tan Zou, Paolo D'Odorico, Christian Folberth, Fernando Galeana Rodriguez, Jessica Fanzo, Lorenzo Rosa, William Dennison, Mark Musumba, Amy Heyman & Eric Davidson
Agriculture is fundamental to all three pillars of sustainability, environment, society, and economy. However, the definition of sustainable agriculture and capacities to measure it remain elusive. Independent and transparent measurements of national sustainability are needed to gauge progress, encourage accountability, and inform policy. Here, we developed a Sustainable Agriculture Matrix (SAM) to quantify national performance indicators in agriculture and to investigate the tradeoffs and synergies based on historical data for most countries of the world....

Additional file 1 of Transcriptional dynamics of transposable elements when converting fibroblast cells of Macaca mulatta to neuroepithelial stem cells

Dahai Liu, Li Liu, Kui Duan, Junqiang Guo, Shipeng Li, Zhigang Zhao, Xiaotuo Zhang, Nan Zhou & Yun Zheng
Additional file 1 Supplementary Table S1. The expression levels of 1627 dynamically expressed genes in the reprogramming procedure of rhesus monkey fibroblast cells toward neuroephithelia stem cells. Supplementary Table S2 to S17. The enriched GO terms of genes in Cluster G0 to G15 of Figure 1A, respectively. Supplementary Table S18. The expression levels of 495 dynamically expressed TEs in the reprogramming procedure of rhesus monkey fibroblast cells toward neuroephithelia stem cells. Supplementary Table S19. The...

Robust and distributed neural representation of action values

Eunju Shin, YunSil Jang, Soyoun Kim, Hoseok Kim, Xinying Cai, Hyunjung Lee, Jung Hoon Sul, Sung-Hyun Lee, Yeonseung Chung, Daeyeol Lee & Min Whan Jung
Studies in rats, monkeys, and humans have found action-value signals in multiple regions of the brain. These findings suggest that action-value signals encoded in these brain structures bias choices toward higher expected rewards. However, previous estimates of action-value signals might have been inflated by serial correlations in neural activity and also by activity related to other decision variables. Here, we applied several statistical tests based on permutation and surrogate data to analyze neural activity recorded...

Genome-wide analysis of the GRF gene family and their expression profiling in peach (Prunus persica)

Li Liu, Xiu-jie Li, Bo Li, Ming-yue Sun & Shao-xuan Li
Growth-regulating factors (GRFs) are plant-specific transcription factors with vital roles in multiple biological processes. Although GRFs have been identified in various plant species, a comprehensive analysis of GRF genes in peach (Prunus persica) has not yet been reported. In this study, 10 PpGRF genes distributed on 6 chromosomes were identified in peach genome and their properties were analyzed systematically. Expression pattern analysis suggested that most PpGRFs were preferentially expressed in young tissues. Multiple types of...

Genome-wide analysis of the GRF gene family their expression profiling in peach (Prunus persica)

Li Liu, Xiu-jie Li, Bo Li, Ming-yue Sun & Shao-xuan Li
Growth-regulating factors (GRFs) are plant-specific transcription factors with vital roles in multiple biological processes. Although GRFs have been identified in various plant species, a comprehensive analysis of GRF genes in peach (Prunus persica) has not yet been reported. In this study, 10 PpGRF genes distributed on 6 chromosomes were identified in peach genome and their properties were analyzed systematically. Expression pattern analysis suggested that most PpGRFs were preferentially expressed in young tissues. Multiple types of...

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...

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

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...

Registration Year

  • 2023
    47
  • 2022
    234
  • 2021
    53
  • 2020
    26
  • 2019
    12
  • 2018
    12
  • 2017
    3
  • 2016
    4
  • 2015
    5
  • 2014
    5

Resource Types

  • Dataset
    402

Affiliations

  • Johns Hopkins University
    402
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    199
  • Fudan University
    193
  • Sichuan University
    174
  • Zhejiang University
    161
  • Capital Medical University
    161
  • Sun Yat-sen University
    148
  • Chinese Academy of Sciences
    139
  • Huazhong University of Science and Technology
    137
  • Peking University
    137