101 Works

Data from: Zooming in on mechanistic predator-prey ecology: integrating camera traps with experimental methods to reveal the drivers of ecological interactions

Justine Smith, Justin Suraci, Jennifer Hunter, Kaitlyn Gaynor, Carson Keller, Meredith Palmer, Justine Atkins, Irene Castañeda, Michael Cherry, Patrick Garvey, Sarah Huebner, Dana Morin, Lisa Teckentrup, Martijn Weterings & Lydia Beaudrot
1. Camera trap technology has galvanized the study of predator-prey ecology in wild animal communities by expanding the scale and diversity of predator-prey interactions that can be analyzed. While observational data from systematic camera arrays have informed inferences on the spatiotemporal outcomes of predator-prey interactions, the capacity for observational studies to identify mechanistic drivers of species interactions is limited. 2. Experimental study designs that utilize camera traps uniquely allow for testing hypothesized mechanisms that drive...

Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018

Yanqun Wang, Xin Li, Wenkuan Liu, Mian Gan, Lu Zhang, Jin Wang, Zhaoyong Zhang, Airu Zhu, Fang Li, Jing Sun, Guoxian Zhang, Zhen Zhuang, Jiaying Luo, Dehui Chen, Shuyan Qiu, Li Zhang, Duo Xu, Chris Ka Pun Mok, Fuchun Zhang, Jingxian Zhao, Rong Zhou & Jincun Zhao
Human coronavirus NL63 (HCoV-NL63) is primarily associated with common cold in children, elderly and immunocompromised individuals. Outbreaks caused by HCoV-NL63 are rare. Here we report a cluster of HCoV-NL63 cases with severe lower respiratory tract infection that arose in Guangzhou, China, in 2018. Twenty-three hospitalized children were confirmed to be HCoV-NL63 positive, and most of whom were hospitalized with severe pneumonia or acute bronchitis. Whole genomes of HCoV-NL63 were obtained using next-generation sequencing. Phylogenetic and...

Long-term evidence shows crop-rotation diversification increases agricultural resilience to adverse growing conditions in North America

Timothy Bowles, Maria Mooshammer, Yvonne Socolar, Franciso Calderón, Michel Cavigelli, Steve Culman, William Dean, Axel Garcia Y Garcia, Amélie Gaudin, W Scott Harkom, Michael Lehman, Shannon Osborne, G Philip Robertson, Jonathan Salerno, Marty Schmer, Jeffrey Strock, A Stuart Grandy & Craig Drury
A grand challenge facing humanity is how to produce food for a growing population in the face of a changing climate and environmental degradation. Though empirical evidence remains sparse, management strategies that increase environmental sustainability, like increasing agroecosystem diversity through crop rotations, may also increase resilience to weather extremes without sacrificing yields. We used multilevel regression analyses of long-term crop yield datasets across a continental precipitation gradient to assess how temporal crop diversification affects maize...

Habitat fragmentation influences genetic diversity and differentiation: Fine-scale population structure of Cercis canadensis (eastern redbud)

Meher Ony, Marcin Nowicki, Sarah Boggess, William Klingeman, John Zobel, Robert Trigiano & Denita Hadziabdic
Forest fragmentation may negatively affect plants through reduced genetic diversity and increased population structure due to habitat isolation, decreased population size, and disturbance of pollen-seed dispersal mechanisms. However, in the case of tree species, effective pollen-seed dispersal, mating system, and ecological dynamics may help the species overcome the negative effect of forest fragmentation. A fine-scale population genetics study can shed light on the postfragmentation genetic diversity and structure of a species. Here, we present the...

R Code and Output Supporting: Resampling-Based Methods for Biologists

John Fieberg, Kelsy Vitense & Douglas H. Johnson
This repository contains data, R code, and associated output from running R code supporting results reported in: Fieberg, J., K. Vitense, and D. H. Johnson 2020. Resampling-Based Methods for Biologists. PeerJ [In Revision]

Data and R Markdown files for: Estimating the capacity of Chamaecrista fasciculata for adaptation to change in precipitation

Anna Peschel, Emma Boehm & Ruth Shaw
Adaptation through natural selection may be the only means by which small and fragmented plant populations will persist through present day environmental change. A population’s additive genetic variance for fitness (VA(W)) represents its immediate capacity to adapt to the environment in which it exists. We evaluated this property for a population of the annual legume Chamaecrista fasciculata through a quantitative genetic experiment in the tallgrass prairie region of the Midwest USA, where changing climate is...

Diversification or collapse of self-incompatibility haplotypes as a rescue process

Alexander Harkness, Emma Goldberg & Yaniv Brandvain
In angiosperm self-incompatibility systems, pollen with an allele matching the pollen recipient at the self-incompatibility locus is rejected. Extreme allelic polymorphism is maintained by frequency-dependent selection favoring rare alleles. However, two challenges result in a "chicken-egg"problem for the spread of a new allele (a tightly linked haplotype in this case) under the widespread "collaborative non-self recognition" mechanism. A novel pollen-function mutation alone would merely grant compatibility with a nonexistent style-function allele: a neutral change at...

Development of an automatic integrated gene detection system for novel severe acute respiratory syndrome-related coronavirus (SARS-CoV2)

Yuchang Li, Jing Li, Ying Zhang, Lizhong Dai, Lin Li, Juan Liu, Sen Zhang, Xiaoyan Wu, Yi Hu, Chengfeng Qin, Tao Jiang & Xiaoping Kang
In December 2019, Wuhan, China suffered a serious outbreak of a novel coronavirus infectious disease (COVID) caused by novel severe acute respiratory syndrome-related coronavirus (SARS-CoV 2). To quickly identify the pathogen, we designed and screened primer sets, and established a sensitive and specific qRT-PCR assay for SARS-CoV 2; the lower limit of detection (LOD) was 15 (95% CI: 9.8–21) copies per reaction. We combined this qRT-PCR assay with an automatic integration system for nucleic acid...

Data from: Surf and Turf Vision: Patterns and predictors of visual acuity in compound eye evolution

Kathryn Feller, Lorian Schweikert, Camilla Sharkey, Alyssa McDuffee-Altekruse, Heather Bracken-Grissom, Nathan Lord & Megan Porter
Eyes have the flexibility to evolve to meet the ecological demands of their users. Relative to camera-type eyes, the fundamental limits of optical diffraction in arthropod compound eyes restricts the ability to resolve fine detail (visual acuity) to much lower degrees. We tested the capacity of several ecological factors to predict arthropod visual acuity, while simultaneously controlling for shared phylogenetic history. In this study, we have generated the most comprehensive review of compound eye visual...

Ictal source imaging in epilepsy patients - Supplementary Data

Shuai Ye, Lin Yang, Yunfeng Lu, Michal Kucewicz, Benjamin Brinkmann, Cindy Nelson, Abbas Sohrabpour, Gregory Worrell & Bin He
Objective Localization of seizure onset zone in focal epilepsy patients is a crucial step prior to surgical planning. Noninvasively achieving this goal would have a tremendous impact on clinical management of intractable seizure. Methods In a total of 39 focal epilepsy patients, we recorded and extracted 138 seizures and 1,325 interictal epileptic discharges using high-density EEG. We have investigated a novel approach for directly imaging sources of seizures and interictal spikes from high density EEG...

Crocin inhibits the activation of mouse hepatic stellate cells via the lnc-LFAR1/MTF-1/GDNF pathway

Ji Xuan, Dongmei Zhu, Zhengyuan Cheng, Yuping Qiu, Mei Shao, Ya Yang, Qi Zhai, Fangyu Wang & Feng Qin
Crocin is the main monomer of saffron, which is a momentous component of traditional Chinese medicine Lang Qing A Ta. Here, we tried to probe into the role of crocin in liver fibrosis. Hematoxylin-eosin staining and Sirius Red staining were used to observe the pathological changes of liver tissues. After hepatic stellate cells (HSCs) were isolated from liver tissues, lnc-LFAR1, MTF-1, GDNF, and α-SMA expressions were detected by qRT-PCR and western blot. Immunohistochemistry and immunofluorescence...

Crocin inhibits the activation of mouse hepatic stellate cells via the lnc-LFAR1/MTF-1/GDNF pathway

Ji Xuan, Dongmei Zhu, Zhengyuan Cheng, Yuping Qiu, Mei Shao, Ya Yang, Qi Zhai, Fangyu Wang & Feng Qin
Crocin is the main monomer of saffron, which is a momentous component of traditional Chinese medicine Lang Qing A Ta. Here, we tried to probe into the role of crocin in liver fibrosis. Hematoxylin-eosin staining and Sirius Red staining were used to observe the pathological changes of liver tissues. After hepatic stellate cells (HSCs) were isolated from liver tissues, lnc-LFAR1, MTF-1, GDNF, and α-SMA expressions were detected by qRT-PCR and western blot. Immunohistochemistry and immunofluorescence...

Identifying the fitness consequences of sex in complex natural environments

Catherine Rushworth, Yaniv Brandvain & Thomas Mitchell-Olds
In the natural world, sex prevails, despite its costs. While much effort has been dedicated to identifying the intrinsic costs of sex (e.g. the cost of males), few studies have identified the ecological fitness consequences of sex. Furthermore, correlated biological traits that differ between sexuals and asexuals may alter these costs, or even render the typical costs of sex irrelevant. We conducted a large-scale multi-site reciprocal transplant using multiple sexual and asexual genotypes of a...

Data from: Temporal scale-dependence of plant-pollinator networks

Benjamin Schwarz, Diego Vázquez, Paul CaraDonna, Tiffany Knight, Gita Benadi, Carsten Dormann, Benoit Gauzens, Elena Motivans, Julian Resasco, Nico Blüthgen, Laura Burkle, Qiang Fang, Christopher Kaiser-Bunbury, Ruben Alarcón, Justin Bain, Natacha Chacoff, Shuang-Quan Huang, Gretchen LeBuhn, Molly MacLeod, Theodora Petanidou, Claus Rasmussen, Michael Simanonok, Amibeth Thompson, Daniel Cariveau, Michael Roswell … & Jochen Fründ
The study of mutualistic interaction networks has led to valuable insights into ecological and evolutionary processes. However, our understanding of network structure may depend upon the temporal scale at which we sample and analyze network data. To date, we lack a comprehensive assessment of the temporal scale-dependence of network structure across a wide range of temporal scales and geographic locations. If network structure is temporally scale-dependent, networks constructed over different temporal scales may provide very...

Molecular characteristics of eae-positive clinical Shiga toxin-producing Escherichia coli in Sweden

Ying Hua, Xiangning Bai, Ji Zhang, Cecilia Jernberg, Milan Chromek, Sverker Hansson, Anne Frykman, Xi Yang, Yanwen Xiong, Chengsong Wan & Andreas Matussek
Shiga toxin (Stx)-producing Escherichia coli (STEC) can cause a wide range of symptoms from asymptomatic carriage, mild diarrhea to bloody diarrhea (BD) and hemolytic uremic syndrome (HUS). Intimin, encoded by the eae gene, also plays a critical role in STEC pathogenesis. Herein, we investigated the prevalence and genetic diversity of eae among clinical STEC isolates from patients with diarrhea, BD, HUS as well as from asymptomatic STEC-positive individuals in Sweden with whole-genome sequencing. We found...

Parasite intensity and the evolution of migratory behavior

Laurinne Balstad, Sandra Binning, Meggan Craft, Marlene Zuk & Allison Shaw
Migration can allow individuals to escape parasite infection, which can lead to a lower infection probability (prevalence) in a population and/or fewer parasites per individual (intensity). Since individuals with more parasites often have lower survival and/or fecundity, infection intensity shapes the life-history tradeoffs determining when migration is favored as a strategy to escape infection. Yet, most theory relies on susceptible-infected (SI) modeling frameworks, defining individuals as either healthy or infected, ignoring details of infection intensity....

Data supporting “Data Sharing Readiness in Academic Institutions” Version 1

Lisa R Johnston & Elizabeth Coburn
To address how the academic landscape for data repository and curation services changed since 2017 Spec Kit for Data Curation (Hudson-Vitale et al., 2017a), we used website content analysis to better understand data repository services in academic research libraries. Of the 124 ARL institutions we chose to focus on academic institutions and therefore excluded 10 civic libraries. For each of the remaining 114 ARL institutions we asked four research questions: Do they support data sharing...

Partial migration alters population ecology and food chain length: evidence from a salmonid fish

Suzanne Kelson, Mary Power, Jacques Finlay & Stephanie Carlson
Many migratory species, from monarch butterflies to wildebeest, express partial migration, where only a subset of a population migrates. This intraspecific variation is likely to have large ecological consequences. We studied the ecological consequences of partial migration in a salmonid fish, Oncorhynchus mykiss, in coastal streams in California, USA. One ecotype, steelhead trout, migrates to the ocean, whereas the other, rainbow trout, completes its lifecycle in freshwater. Migration has a strong genetic basis in O....

Data from: Climate and local environment structure asynchrony and the stability of primary production in grasslands

Benjamin Gilbert, Andrew MacDougall, Taku Kadoya, Munemitsu Akasaka, Joseph Bennett, Eric Lind, Habacuc Flores-Moreno, Jennifer Firn, Yann Hautier, Elizabeth Borer, Eric Seabloom, Peter Adler, Elsa Cleland, James Grace, W. Harpole, Ellen Esch, Joslin Moore, Jean Knops, Rebecca McCulley, B. Mortensen, J. Bakker & Philip Fay
Aim: Climate variability threatens to destabilize production in many ecosystems. Asynchronous species dynamics may buffer against such variability when decreased performance by some species is offset by increased performance of others. However, high climatic variability can eliminate species through stochastic extinctions or cause similar stress responses among species, reducing buffering. Local conditions, such as soil nutrients, can further alter production stability directly or by influencing asynchrony. We test these hypotheses using a globally distributed sampling...

Effect of stressors on the carrying capacity of spatially distributed metapopulations

Bo Zhang, Donald DeAngelis, Wei-Ming Ni, Yuanshi Wang, Lu Zhai, Alex Kula, Shuang Xu & David Van Dyken
Stressors such as antibiotics, herbicides and pollutants are becoming increasingly common in the environment. The effects of stressors on populations are typically studied in homogeneous, non-spatial settings. However, most populations in nature are spatially distributed over environmentally heterogeneous landscapes with spatially-restricted dispersal. Little is known about the effects of stressors in these more realistic settings. Here, we combine laboratory experiments with novel mathematical theory to rigorously investigate how a stressor’s physiological effect and spatial distribution...

Recovery from infection is more likely to favor the evolution of migration than social escape from infection

Allison Shaw & Sandra Binning
1. Pathogen and parasite infections are increasingly recognized as powerful drivers of animal movement, including migration. Yet, infection-related migration benefits can result from a combination of environmental and/or social conditions, which can be difficult to disentangle. 2. Here, we focus on two infection-related mechanisms that can favor migration: moving to escape versus recover from infection. By directly comparing the evolution of migration in response to each mechanism, we can evaluate the likely importance of changing...

Experimental alluvial-river and landsliding response to base-level fall

Andrew D. Wickert, Olivia P Beaulieu, Elizabeth D Witte & Stefanie Tofelde
We observed the incisional response of an alluvial river to base-level fall. We conducted the experiment in a 3.9 × 2.4 × 0.4 m box that we filled with uniform 0.140±0.04 mm sand. We dropped base level by lowering the elevation of an "ocean" pool at the river outlet. As the initial condition, we cut a 10±2 cm wide channel to a steadily increasing depth, from 3±0.5 cm at the inlet, where we supplied water...

Isolation of Infectious SARS-CoV-2 from Urine of a COVID-19 Patient

Jing Sun, Airu Zhu, Heying Li, Kui Zheng, Zhen Zhuang, Zhao Chen, Yongxia Shi, Zhaoyong Zhang, Si-bei Chen, Xuesong Liu, Jun Dai, Xiaobo Li, Shuxiang Huang, Xiaofang Huang, Ling Luo, Liyan Wen, Jianfen Zhuo, Yuming Li, Yanqun Wang, Lu Zhang, Yanjun Zhang, Fang Li, Liqiang Feng, Xinwen Chen, Nanshan Zhong … & Yi-min Li
SARS-CoV-2 caused a major outbreak of severe pneumonia (COVID-19) in humans. Viral RNA was detected in multiple organs in COVID-19 patients. However, infectious SARS-CoV-2 was only isolated from respiratory specimens. Here, infectious SARS-CoV-2 was successfully isolated from urine of a COVID-19 patient. The virus isolated could infect new susceptible cells and was recognized by its’ own patient sera. Appropriate precautions should be taken to avoid transmission from urine.

Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient

Jing Sun, Airu Zhu, Heying Li, Kui Zheng, Zhen Zhuang, Zhao Chen, Yongxia Shi, Zhaoyong Zhang, Si-bei Chen, Xuesong Liu, Jun Dai, Xiaobo Li, Shuxiang Huang, Xiaofang Huang, Ling Luo, Liyan Wen, Jianfen Zhuo, Yuming Li, Yanqun Wang, Lu Zhang, Yanjun Zhang, Fang Li, Liqiang Feng, Xinwen Chen, Nanshan Zhong … & Yi-min Li
SARS-CoV-2 caused a major outbreak of severe pneumonia (COVID-19) in humans. Viral RNA was detected in multiple organs in COVID-19 patients. However, infectious SARS-CoV-2 was only isolated from respiratory specimens. Here, infectious SARS-CoV-2 was successfully isolated from urine of a COVID-19 patient. The virus isolated could infect new susceptible cells and was recognized by its’ own patient sera. Appropriate precautions should be taken to avoid transmission from urine.

Pilgrim 2020.1

David Ferro-Costas, Donald G. Truhlar & Antonio Fernandez-Ramos
Pilgrim is a program written in Python and designed to use direct dynamics in the calculation of thermal rate constants of chemical reactions by the variational transition state theory (VTST), based on electronic structure calculations for the potential energy surface. Pilgrim can also simulate reaction mechanisms using kinetic Monte Carlo (KMC). For reaction processes with many elementary steps, the rate constant of each of these steps can be calculated by means of conventional transition state...

Registration Year

  • 2020
    101

Resource Types

  • Dataset
    94
  • Text
    6
  • Other
    1

Affiliations

  • University of Minnesota
    101
  • Zhejiang University
    12
  • Fudan University
    12
  • Sichuan University
    10
  • Southern Medical University
    10
  • Shanghai Jiao Tong University
    10
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    10
  • Chinese Academy of Sciences
    10
  • West China Hospital of Sichuan University
    9
  • Jiangxi Agricultural University
    8