196 Works

Sex differences in moral judgements across 67 countries

Morteza Dehghani, Mohammad Atari, Mark Lai & Morteza Dehghani
Most of the empirical research on sex differences and cultural variations in morality has relied on within-culture analyses or small-scale cross-cultural data. To further broaden the scientific understanding of sex differences in morality, the current research relies on two international samples to provide the first large-scale examination of sex differences in moral judgements nested within cultures. Using a sample from 67 countries (Study 1; n = 336,691), we found culturally-variable sex differences in moral judgements,...

Data from: Variations of mesozoic feathers: insights from the morphogenesis of extant feather rachises

Shuo Wang, Wei-Ling Chang, Qiyue Zhang, Menglu Ma, Feng Yang, De Zhuo, Harn I-Chen Hans, Rui Yang, Ping Wu, Michael Bruce Habib, Wen-Tau Juan & Cheng-Ming Chuong
The rachises of extant feathers, composed of dense cortex and spongy internal medulla, are flexible and light, yet stiff enough to withstand the load required for flight, among other functions. Incomplete knowledge of early feathers prevents a full understanding of how cylindrical rachises have evolved. Bizarre feathers with unusually wide and flattened rachises, known as “rachis-dominated feathers” (RDFs) have been observed in fossil non-avian and avian theropods. Newly discovered RDFs embedded in early Late Cretaceous...

Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity

Feng Yang, Jinghao Zhang, Su Wang, Zhaoyang Sun, Jun Zhou, Feng Li, Yue Liu, Li Ding, Yixin Liu, Wenjing Chi, Tao Liu, Yongqun He, Ping Xiang, Zhijun Bao, Michal A. Olszewski, Hu Zhao & Yanmei Zhang
Severe Helicobacter pylori-linked gastric disorders are especially prevalent in the East Asia region. The ability of H. pylori to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked to specific gastrointestinal pathologies. Genome heterogeneity of clinical H. pylori strains from patients with four different gastric disorders was studied to explore the population structure and molecular genomic features and their...

Adaptive parameter of standard deviation enhances the power of noninvasive prenatal screens

Li Qu, Qixi Wu, Xiaoke Yang, Weiwei Wang, Bing Xu, Guangyu Shan, Lin Liang, Shaowei Wang & Jingbo Zhang
Traditional Z-test methods during noninvasive prenatal screens (NIPS) use the fixed parameter of standard deviation (SD), which ignores the influence of actual sequencing read counts of a sample on the results. The aim of this study is to eliminate the influence of the sequencing depth of individual samples on the results and enhance the power of NIPS. In this study, we propose an improved NIPS method, which calculates the SD in the Z-score process adaptively...

Data from: A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan

Imran Rahman, Jeffrey Thompson, Derek Briggs, David Siveter, Derek Siveter & Mark Sutton
Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, Sollasina cthulhu, from the Silurian Herefordshire Lagerstätte, UK. S. cthulhu belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical-optical...

Data from: Heritable variation and lack of tradeoffs suggest adaptive capacity in Acropora cervicornis despite negative synergism under climate change scenarios

Erinn Muller, Ashley Dungan, Wyatt Million, Katherine Eaton, Chelsea Petrik, Erich Bartels, Emily Hall & Carly Kenkel
Knowledge of multi-stressor interactions and the potential for trade-offs among tolerance traits is essential for developing intervention strategies for the conservation and restoration of reef ecosystems in a changing climate. Thermal extremes and acidification are two major co-occurring stresses predicted to limit the recovery of vital Caribbean reef-building corals. Here we conducted an aquaria-based experiment to quantify the effects of increased water temperatures and pCO2 individually and in concert on 12 genotypes of the endangered...

Set1-mediated H3K4 methylation is required for Candida albicans virulence by regulating intracellular level of reactive oxygen species

Jueun Kim, Shinae Park, Sohee Kwon, Eun-Jin Lee & Jung-Shin Lee
Candida albicans is an opportunistic human fungal pathogen that exists in normal flora but can cause infection in immunocompromised individuals. The transition to pathogenic C. albicans requires a change of various gene expressions. Because histone-modifying enzymes can regulate gene expression, they are thought to control the virulence of C. albicans. Indeed, the absence of H3 lysine 4 (H3K4) methyltransferase Set1 has been shown to reduce the virulence of C. albicans; however, Set1-regulated genes responsible for...

Recommended fossil calibrators for time-scaled molecular phylogenies of Afrotheria

Steven Heritage, Erik Seiffert & Matthew Borths
A phylogenetic framework provides the necessary evolutionary context for studies of comparative anatomy, life history, behavior, biogeography, systematics, and conservation. Time-scaled phylogenetic analyses require researchers to include calibration ages which are used to fit a model that transforms tree branch lengths into units of time. The inclusion of multiple calibration ages (if they are available) is a best practice that brings all the available evidence to bear on the temporal model. While selecting the appropriate...

Data from: FOXP2 exhibits neuron class specific expression, but is not required for multiple aspects of cortical histogenesis

Ryan J. Kast, Alexandra L. Lanjewar, Colton D. Smith & Pat Levitt
The expression patterns of the transcription factor FOXP2 in the developing mammalian forebrain have been described, and some studies have tested the role of this protein in the development and function of specific forebrain circuits by diverse methods and in multiple species. Clinically, mutations in FOXP2 are associated with severe developmental speech disturbances, and molecular studies indicate that impairment of Foxp2 may lead to dysregulation of genes involved in forebrain histogenesis. Here, anatomical and molecular...

Intentional Control of Type I Error Over Unconscious Data Distortion: A Neyman–Pearson Approach to Text Classification

Lucy Xia, Richard Zhao, Yanhui Wu & Xin Tong
This article addresses the challenges in classifying textual data obtained from open online platforms, which are vulnerable to distortion. Most existing classification methods minimize the overall classification error and may yield an undesirably large Type I error (relevant textual messages are classified as irrelevant), particularly when available data exhibit an asymmetry between relevant and irrelevant information. Data distortion exacerbates this situation and often leads to fallacious prediction. To deal with inestimable data distortion, we propose...

Food deprivation exposes sex-specific trade-offs between stress tolerance and lifespan in the copepod Tigriopus californicus

Ning Li, Ben A Flanagan & Suzanne Edmands
Long life is standardly assumed to be associated with high stress tolerance. Previous work shows that the copepod Tigriopus californicus breaks this rule, with longer lifespan under benign conditions found in males, the sex with lower stress tolerance. Here we extended this previous work, raising animals from the same families in food-replete conditions until adulthood and then transferring them to food-limited conditions until all animals perished. As in previous work, survivorship under food-replete conditions favored...

Multivariate trait analysis reveals diatom plasticity constrained to a reduced set of biological axes

Phoebe Argyle, Nathan G. Walworth, Jana Hinners, Sinéad Collins, Naomi M. Levine & Martina A. Doblin
Trait-based approaches to phytoplankton ecology have gained traction in recent decades as phenotypic traits are incorporated into ecological and biogeochemical models. Here, we use high-throughput phenotyping to explore both intra- and interspecific constraints on trait combinations that are expressed in the cosmopolitan marine diatom genus Thalassiosira. We demonstrate that within Thalassiosira, phenotypic diversity cannot be predicted from genotypic diversity, and moreover, plasticity can create highly divergent phenotypes that are incongruent with taxonomic grouping. Significantly, multivariate...

A high-throughput assay for quantifying phenotypic traits of microalgae

Phoebe Argyle, Jana Hinners, Nathan G. Walworth, Sinead Collins, Naomi M. Levine & Martina A. Doblin
High-throughput methods for phenotyping microalgae are in demand across a variety of research and commercial purposes. Many microalgae can be readily cultivated in multi-well plates for experimental studies which can reduce overall costs, while measuring traits from low volume samples can reduce handling. Here we develop a high-throughput quantitative phenotypic assay (QPA) that can be used to phenotype microalgae grown in multi-well plates. The QPA integrates 10 low-volume, relatively high-throughput trait measurements (growth rate, cell...

Set1-mediated H3K4 methylation is required for Candida albicans virulence by regulating intracellular level of reactive oxygen species

Jueun Kim, Shinae Park, So Hee Kwon, Eun-Jin Lee & Jung-Shin Lee
Candida albicans is an opportunistic human fungal pathogen that exists in normal flora but can cause infection in immunocompromised individuals. The transition to pathogenic C. albicans requires a change of various gene expressions. Because histone-modifying enzymes can regulate gene expression, they are thought to control the virulence of C. albicans. Indeed, the absence of H3 lysine 4 (H3K4) methyltransferase Set1 has been shown to reduce the virulence of C. albicans; however, Set1-regulated genes responsible for...

Additional file 3 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 3. Table S3: Performance of three strategies.

Impacts of menopause hormone therapy on mood disorders among postmenopausal women

P. Feng, L. Lin, Y. Wang, L. Chen, J. Min, Y. Xie, M. Liu, S. Wei, S. Lin & Q. Yu
This study aimed to explore the modulatory effects of menopause hormone therapy (MHT) on mood disorders among postmenopausal women. A cross-sectional study was conducted to recruit postmenopausal women, including patients (arranged MHT for over 3 years as the medication group) and non-MHT controls. All participants were asked to respond to the Center for Epidemiological Studies Depression Scale (CES-D) and Generalized Anxiety Disorder Screener (GAD-7) questionnaires to assess their depression and anxiety status. A total of...

Additional file 2 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 2: Supplementary Table 1. TOGA status of 18430 ancestral placental mammal genes in muroid rodent genome assemblies. Supplementary Table 2. Positively selected genes and their mutation tolerance in humans according to gnomAD.

Additional file 10 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 10: Table S3: Succinylated proteins and succinylated peptides identified in this study.

Additional file 16 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 16: Table S9: Conserved succinylated proteins and succinylated sites in three grasses.

Vegetation and vantage point influence visibility across diverse ecosystems: implications for animal ecology

Rachel Stein, Bastien Lecigne, Eitel Jan, Timothy Johnson, Craig McGowan & Janet Rachlow
Visual information can influence animal behavior and habitat use in diverse ways. Visibility is the property that relates 3D habitat structure to accessibility of visual information. Despite the importance of visibility in animal ecology, this property remains largely unstudied. Our objective was to assess how habitat structure from diverse environments and animal position within that structure can influence visibility. We gathered terrestrial lidar data (1 cm at 10 m) in four ecosystems (forest, shrub-steppe, prairie,...

Harmonized HRS COVID, Version A

Hunter Green, Jenny Wilkens, Codi Young & Jinkook Lee

Data for: Occupancy–detection models with museum specimen data: Promise and pitfalls

Vaughn Shirey, Rassim Khelifa, Leithen M'Gonigle & Laura Melissa Guzman
Historical museum records provide potentially useful data for identifying drivers of change in species occupancy. However, because museum records are typically obtained via many collection methods, methodological developments are needed in order to enable robust inferences. Occupancy-detection models, a relatively new and powerful suite of statistical methods, are a potentially promising avenue because they can account for changes in collection effort through space and time. We use simulated datasets to identify how and when patterns...

Additional file 2 of PredictCBC-2.0: a contralateral breast cancer risk prediction model developed and validated in ~ 200,000 patients

Daniele Giardiello, Maartje J. Hooning, Michael Hauptmann, Renske Keeman, B. A. M. Heemskerk-Gerritsen, Heiko Becher, Carl Blomqvist, Stig E. Bojesen, Manjeet K. Bolla, Nicola J. Camp, Kamila Czene, Peter Devilee, Diana M. Eccles, Peter A. Fasching, Jonine D. Figueroa, Henrik Flyger, Montserrat García-Closas, Christopher A. Haiman, Ute Hamann, John L. Hopper, Anna Jakubowska, Floor E. Leeuwen, Annika Lindblom, Jan Lubiński, Sara Margolin … & Marjanka K. Schmidt
Additional file 2: Table S1. Description of the studies included in the analyses.

Additional file 3 of PredictCBC-2.0: a contralateral breast cancer risk prediction model developed and validated in ~ 200,000 patients

Daniele Giardiello, Maartje J. Hooning, Michael Hauptmann, Renske Keeman, B. A. M. Heemskerk-Gerritsen, Heiko Becher, Carl Blomqvist, Stig E. Bojesen, Manjeet K. Bolla, Nicola J. Camp, Kamila Czene, Peter Devilee, Diana M. Eccles, Peter A. Fasching, Jonine D. Figueroa, Henrik Flyger, Montserrat García-Closas, Christopher A. Haiman, Ute Hamann, John L. Hopper, Anna Jakubowska, Floor E. Leeuwen, Annika Lindblom, Jan Lubiński, Sara Margolin … & Marjanka K. Schmidt
Additional file 1: Table S3. Patient and primary breast cancer characteristics per study.

Additional file 3 of PredictCBC-2.0: a contralateral breast cancer risk prediction model developed and validated in ~ 200,000 patients

Daniele Giardiello, Maartje J. Hooning, Michael Hauptmann, Renske Keeman, B. A. M. Heemskerk-Gerritsen, Heiko Becher, Carl Blomqvist, Stig E. Bojesen, Manjeet K. Bolla, Nicola J. Camp, Kamila Czene, Peter Devilee, Diana M. Eccles, Peter A. Fasching, Jonine D. Figueroa, Henrik Flyger, Montserrat García-Closas, Christopher A. Haiman, Ute Hamann, John L. Hopper, Anna Jakubowska, Floor E. Leeuwen, Annika Lindblom, Jan Lubiński, Sara Margolin … & Marjanka K. Schmidt
Additional file 1: Table S3. Patient and primary breast cancer characteristics per study.

Registration Year

  • 2023
    7
  • 2022
    81
  • 2021
    26
  • 2020
    15
  • 2019
    16
  • 2018
    11
  • 2017
    8
  • 2016
    7
  • 2015
    7
  • 2014
    4

Resource Types

  • Dataset
    196

Affiliations

  • University of Southern California
    196
  • China Agricultural University
    22
  • Sun Yat-sen University
    21
  • Chinese Academy of Sciences
    21
  • Tianjin University of Traditional Chinese Medicine
    20
  • Fudan University
    19
  • Yangzhou University
    19
  • Chinese Center For Disease Control and Prevention
    19
  • University of Michigan–Ann Arbor
    18
  • University of Queensland
    18