Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in riceMichael Thomson, Ranjita Thapa & Endang Septiningsih
To investigate the genetic architecture underlying cold tolerance during germination in rice (Oryza sativa), we conducted a genome-wide association study (GWAS) using a novel diversity panel of 257 rice accessions from around the world and 5,185 SNP markers from a 7K SNP marker array. Genotyping was performed using a 7K Illumina iSelect custom-designed array by following the Infinium HD Array Ultra Protocol. The 7K array, called the C7AIR, was designed by Dr. Susan McCouch’s Lab...
Data from: External temperature and distance from nearest entrance influence microclimates of cave and culvert roosting tri-colored bats Perimyotis subflavusSamantha Leivers, Melissa Meierhofer, Brian Pierce, Jonah Evans & Michael Morrison
Many North American bat species hibernate in both natural and artificial roosts. Although hibernacula can have high internal climate stability, they still retain spatial variability in their thermal regimes, resulting in various ‘microclimates’ throughout the roost that differ in their characteristics (e.g., temperature, air moisture). These microclimate components can be influenced by factors such as the number of entrances, the depth of the roost, and distance to the nearest entrance of the roost. Tri-colored bats...
Data from: Spatial phylogenetics reveals evolutionary constraints on the assembly of a large regional floraDaniel Spalink, Ricardo Kriebel, Pan Li, Matthew C. Pace, Bryan T. Drew, John G. Zaborsky, Jeffrey R. Rose, Chloe P. Drummond, Mary Ann Feist, William S. Alverson, Donald M. Waller, Kenneth M. Cameron, Thomas J. Givnish & Kenneth J. Sytsma
Premise of the study: We use spatial phylogenetics to analyze the assembly of the Wisconsin flora, linking processes of dispersal and niche evolution to spatial patterns in floristic and phylogenetic diversity, and testing whether phylogenetic niche conservatism can account for these patterns. Methods: We use digitized records and a new molecular phylogeny for all vascular plants in Wisconsin to estimate spatial variation in species richness and phylogenetic and diversity in a native flora...
1. Knowledge of the spatial distribution of populations is fundamental to management plans for any species. When tracking data are used to describe distributions, it is sometimes assumed that the reported locations of individuals delineate the spatial extent of areas used by the target population. 2. Here, we examine existing approaches to validate this assumption, highlight caveats, and propose a new method for a more informative assessment of the number of tracked animals (i.e. sample...
Raw in vitro screening data and R scripts for: A Bayesian method for population-wide cardiotoxicity hazard and risk characterization using an in vitro human modelAlexander Blanchette, Sarah Burnett, Fabian Grimm, Ivan Rusyn & Weihsueh Chiu
Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes are an established model for testing potential chemical hazards. Inter-individual variability in toxicodynamic sensitivity has also been demonstrated in vitro; however, quantitative characterization of the population-wide variability has not been fully explored. We sought to develop a method to address this gap by combining a population-based iPSC-derived cardiomyocyte model with Bayesian concentration-response modeling. A total of 136 compounds, including 44 pharmaceuticals and 82 environmental chemicals, were tested in...
In a coal mine, natural gas can leak through walls and accumulate in enclosed regions that are no longer being mined or ventilated. If there is an accidental spark in the region containing this gas, it can ignite a flame that may transition to detonation (DDT). An important problem is to assess if, when, and where DDT can occur, and thus provide information needed to design strong enough barriers to protect active mining areas. We...
The increased severity and frequency of elevated temperatures due to climate change is changing species distributions and driving thermal selection for several species, but many potential effects are still unknown. Here, we investigated the effects of an acute thermal stress on the oviposition performance of the hairy maggot blow fly Chrysomya rufifacies (Macquart), an introduced species of ecological, economic, and forensic importance. Adult virgins were exposed to 25°C, 42°C, or 44°C for 1-h, and then...
Data from: Widespread variation in stable isotope trophic position estimates: patterns, causes, and potential consequencesMackenzie Kjeldgaard, Jeremy Hewlett & Micky Eubanks
Stable isotope analysis is one of the most widely used techniques to estimate trophic position and provides fundamental insight into the structure and management of ecological communities. To account for the effects of geographic variation in isotope levels, trophic position is typically estimated relative to an isotope “baseline” (i.e., material representing geographic variation) using a methodology such as a formula or statistical analysis. There is, however, remarkable variation in the baselines and methodologies used to...
Data from: Disparate patterns of movements and visits to points of interest located in urban hotspots across U.S. metropolitan cities during COVID-19Qingchun Li
We examined the effect of social distancing on changes in visits to urban hotspot points of interest. In a pandemic situation, urban hotspots could be potential superspreader areas as visits to urban hotspots can increase the risk of contact and transmission of a disease among a population. We mapped origin-destination networks from census block groups to points of interest (POIs), such as restaurants, museums, and schools, in sixteen cities in the United States. We adopted...
PLANT BREEDING PARTNERSHIP: A Metabolic Modeling-Based Strategy to Accelerate the Citrus Genetic Engineering ProcessJames Borneman
This is a New Investigator proposal led by Cristal Zuniga. The Long-Term Goal of this proposed project is to improve the economics, productivity, and sustainability of U.S. agriculture by using metabolic models to accelerate the engineering process of all crops. To demonstrate the feasibility of this approach, the Objective of this project is to use metabolic models to speed up the growth rate of two specific steps of the citrus engineering process in two commonly...
Artificial light at night (ALAN) is a rapidly intensifying form of environmental degradation that can impact wildlife by altering light-mediated physiological processes that control a broad range of behaviors. Although nocturnal animals are most vulnerable, ALAN’s effects on North American bats have been surprisingly understudied. Most of what is known is based on decades-old observations of bats around street lights with traditional lighting technologies that have been increasingly replaced by energy-efficient broad-spectrum lighting, rendering our...
Understanding mechanism of performance improvement in nitrogen-doped niobium superconducting radio frequency cavityXiaotian Fang, Jin-Su Oh, Matt Kramer, A. Romanenko, A. Grassellino, John Zasadzinski & Lin Zhou
Niobium superconducting radiofrequency cavities enable applications in modern accelerators and quantum computers. However, the surface resistance significantly deteriorates the cavities’ performance. Nitrogen doping surface treatment can consistently increase cavity performance by reducing surface resistance, but the improvement mechanism is not fully understood. Herein, we employed transmission electron microscopy and spectroscopy to uncover the structural and chemical differences of the Nb/air interface between the non-doped and nitrogen-doped cavities. The results indicate that nitrogen doping passivates the...
Additional file 1 of Attitudes and personal beliefs about the COVID-19 vaccine among people with COVID-19: a mixed-methods analysisMonica M. Bennett, Megan Douglas, Briget da Graca, Katherine Sanchez, Mark B. Powers & Ann Marie Warren
Supplementary Material 1
Additional file 4 of Senescence-accelerated mice prone 8 (SAMP8) in male as a spontaneous osteoarthritis modelYohei Sanada, Yasunari Ikuta, Chenyang Ding, Masahiro Shinohara, Dilimulati Yimiti, Hiroyuki Ishitobi, Keita Nagira, Minjung Lee, Takayuki Akimoto, Sachi Shibata, Masakazu Ishikawa, Tomoyuki Nakasa, Kiminori Matsubara, Martin K. Lotz, Nobuo Adachi & Shigeru Miyaki
Additional file 4: Fig. S4. ADAMTS-5 and MMP-13-positive in medial and lateral compartment of the knee from SAMR1 and SAMP8.
Additional file 1 of Molecular characteristics of global β-lactamase-producing Enterobacter cloacae by genomic analysisJincao Hu, Jia Li, Chang Liu, Yan Zhang, Hui Xie, Chuchu Li, Han Shen & Xiaoli Cao
Additional file 1.
sj-docx-1-tej-10.1177_20417314221132093 – Supplemental material for A new cell-free therapeutic strategy for liver regeneration: Human placental mesenchymal stem cell-derived extracellular vesiclesTing Li, Yu Fu, Zeyi Guo, Honglei Zhu, Hangyu Liao, Xiaoge Niu, Lin Zhou, Shunjun Fu, Yang Li, Shao Li, Lujia Wang, Yizhou Zheng, Lei Feng, Yi Gao & Guolin He
Supplemental material, sj-docx-1-tej-10.1177_20417314221132093 for A new cell-free therapeutic strategy for liver regeneration: Human placental mesenchymal stem cell-derived extracellular vesicles by Ting Li, Yu Fu, Zeyi Guo, Honglei Zhu, Hangyu Liao, Xiaoge Niu, Lin Zhou, Shunjun Fu, Yang Li, Shao Li, Lujia Wang, Yizhou Zheng, Lei Feng, Yi Gao and Guolin He in Journal of Tissue Engineering
sj-rar-3-tej-10.1177_20417314221132093 – Supplemental material for A new cell-free therapeutic strategy for liver regeneration: Human placental mesenchymal stem cell-derived extracellular vesiclesTing Li, Yu Fu, Zeyi Guo, Honglei Zhu, Hangyu Liao, Xiaoge Niu, Lin Zhou, Shunjun Fu, Yang Li, Shao Li, Lujia Wang, Yizhou Zheng, Lei Feng, Yi Gao & Guolin He
Supplemental material, sj-rar-3-tej-10.1177_20417314221132093 for A new cell-free therapeutic strategy for liver regeneration: Human placental mesenchymal stem cell-derived extracellular vesicles by Ting Li, Yu Fu, Zeyi Guo, Honglei Zhu, Hangyu Liao, Xiaoge Niu, Lin Zhou, Shunjun Fu, Yang Li, Shao Li, Lujia Wang, Yizhou Zheng, Lei Feng, Yi Gao and Guolin He in Journal of Tissue Engineering
A new cell-free therapeutic strategy for liver regeneration: Human placental mesenchymal stem cell-derived extracellular vesiclesTing Li, Yu Fu, Zeyi Guo, Honglei Zhu, Hangyu Liao, Xiaoge Niu, Lin Zhou, Shunjun Fu, Yang Li, Shao Li, Lujia Wang, Yizhou Zheng, Lei Feng, Yi Gao & Guolin He
Mesenchymal stem cells (MSCs) have potential role in organ regeneration therapy. Previous work indicating that MSCs confer protection against liver disease. Here, we aimed to determine the potential application in liver regeneration of human placenta-derived MSCs extracellular vesicles (hPMSCs-EVs) via experimental hepatectomy. hPMSCs-EVs were administered intravenously 24 h before 70% partial hepatectomy, the specific composition of hPMSCs-EVs was identified by sequencing and validated by the quantitative polymerase chain reaction, including circ-RBM23. The role of circ-RBM23...
Load and hold conical indentation responses calculated for materials having creep stress exponents of 1.15, 3.59 and 6.60 are regarded as input “experimental” responses. The creep parameters are identified using the Bayesian-type statistical approach of Zhang et al.  for noise-free and noise-contaminated data. A database for the Bayesian-type analysis is created using finite element calculations for a relatively coarse set of parameter values with interpolation used to create the refined database used for parameter...
Size normalized shell weights and measurements for Neogloboquadrina pachyderma and Uvigerina peregrina from the Gulf of Alaska (IODP Exp 341) and associated environmental proxy dataChristina Belanger & Calie Payne
Here we use volume density (ρV) measurements as a metric of size-normalized weights for Neogloboquadrina pachyderma, a planktonic foraminifer, from upper OMZ and abyssal depth sites in the Gulf of Alaska over the past ~20,000 years to test for covariation between carbonate preservation and OMZ intensity. We find that dissolution of N. pachyderma is most intense at the upper OMZ site where oxygenation is generally lower than at the abyssal site. We also examine Uvigerina...
This data set contain raw data associated with the manuscript titled "Silencing the alarm: An insect salivary enzyme closes plant stomata and inhibits volatile release". Herbivore-induced plant volatiles (HIPVs) are widely recognized as ecologically important to plant. While the majority of studies focused on the induction of this “cry for help”, little is known about whether insect herbivores have evolved mechanisms to reduce the release of HIPVs. Here we show that a caterpillar (Helicoverpa zea)...
Texas A&M University618
Southern Medical University119
Capital Medical University117
Chinese Academy of Sciences107
Chinese PLA General Hospital101
First Affiliated Hospital of Soochow University87
First Affiliated Hospital of Chongqing Medical University69
Chongqing Medical University64