145 Works

A specialist bee and its host plants experience phenological shifts at different rates in response to climate change

Sarah Weaver & Rachel Mallinger
Changes in climate can alter the phenology of organisms, potentially decoupling partners within mutualisms. Previous studies have shown that plant and pollinator phenologies are shifting over time, but these shifts have primarily been documented for generalists and within small geographic regions, and the specific climatic cues regulating these shifts are not well-understood. We examined phenological shifts in a specialist pollinator and its host plant species over a 117-year study period using a digitized dataset of...

From nature reserve to mosaic management: improving matrix survival, not permeability, benefits regional populations under habitat loss and fragmentation

Yuichi Yamaura, Robert Fletcher, Steven Lade, Motoki Higa & David Lindenmayer
Although matrix improvement in fragmented landscapes is a promising conservation measure, matrix permeability (willingness of an organism to enter the matrix) and movement survival in the matrix are usually aggregated. Consequently, it is unknown which matrix property needs to be improved. It also remains unclear whether matrix upgrading from dispersal passage to providing reproduction opportunities has large conservation benefits and whether there are interactive effects between habitat and matrix management. We examined matrix effects on...

PRMI: A dataset of minirhizotron images for diverse plant root study

Weihuang Xu, Guohao Yu, Yiming Cui, Romain Gloaguen, Alina Zare, Jason Bonnette, Joel Reyes-Cabrera, Ashish Rajurkar, Diane Rowland, Roser Matamala, Julie D. Jastrow, Thomas E. Juenger & Felix B. Fritschi
Understanding a plant's root system architecture (RSA) is crucial for a variety of plant science problem domains including sustainability and climate adaptation. Minirhizotron (MR) technology is a widely-used approach for phenotyping RSA non-destructively by capturing root imagery over time. Precisely segmenting roots from the soil in MR imagery is a critical step in studying RSA features. In this paper, we introduce a large-scale dataset of plant root images captured by MR technology. In total, there...

Human-mediated trophic mismatch between fire, plants, and herbivores

Marcus Lashley, Michael Chitwood, Jacob Dykes, Christopher DePerno & Christopher Moorman
Trophic mismatches are commonly reported across a wide array of taxa and can have important implications for species participating in the interaction. However, to date, examples of trophic mismatch have centrally focused on those induced by shifts in climate. Here we report on the potential for humans to induce trophic mismatch by shifting the phenology of fire. Globally, anthropogenic fire ignitions are phenologically mismatched to that of historic lightning ignitions but the effects of this...

Data from: Evaluating the use of lidar to discern snag characteristics important for wildlife

Jessica M. Stitt, Andrew T. Hudak, Carlos A. Silva, Lee A. Vierling & Kerri T. Vierling
Standing dead trees (known as snags) are historically difficult to map and model using airborne laser scanning (ALS), or lidar. Specific snag characteristics are important for wildlife; for instance, a larger snag with a broken top can serve as a nesting platform for raptors. The objective of this study was to evaluate whether characteristics such as top intactness could be inferred from discrete-return ALS data. We collected structural information for 198 snags in closed-canopy conifer...

Data from: Exploring conflicts in whole genome phylogenetics: A case study within Manakins (Aves: Pipridae)

Min Zhao, Sarah Kurtis, Noor White, Andre Moncrieff, Rafael Leite, Robb Brumfield, Edward Braun & Rebecca Kimball
Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using an appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising...

The extinct shark Otodus megalodon was a transoceanic super-predator: Inferences from 3D modelling

Jack Cooper, John Hutchinson, David Bernvi, Geremy Cliff, Rory Wilson, Matt Dicken, Jan Menzel, Stephen Wroe, Jeanette Pirlo & Catalina Pimiento
Although shark teeth are abundant in the fossil record, their bodies are rarely preserved. Thus, our understanding of the anatomy of the extinct Otodus megalodon remains rudimentary. We used an exceptionally preserved fossil to create the first 3D model of the body of this giant shark and used it to infer its movement and feeding ecology. We estimate that an adult O. megalodon could cruise at faster absolute speeds than any shark species today, and...

Data from: Temporal and spatial comparisons of angiosperm diversity between eastern Asia and North America

Haihua Hu, Jianfei Ye, Bing Liu, Lingfeng Mao, Stephen A. Smith, Russell L. Barrett, Pamela S. Soltis, Douglas E. Soltis, Zhiduan Chen & Limin Lu
Eastern Asia (EA) and North America north of Mexico (NA) have comparable latitude, land area, and climate, but the overall plant diversity is much higher in EA than in NA. Despite intensive studies on disjunct taxa of the two regions, the temporal and spatial diversity patterns between the two floras remain unclear. Here we explore the floristic differences between EA and NA using the well-studied floras of China and the United States of America (USA)...

Dexmedetomidine protects cells from Angiotensin II-induced smooth muscle cell phenotype switch and endothelial cell dysfunction

Min Dai, Xiaohong Zhu, Simin Zeng, Qiang Liu, Ruilin Hu, Lianghui Huang, Yu Wang, Jun Deng & Qi Yu
Abdominal aortic aneurysm (AAA) is a vascular disorder greatly threatening life of the elderly population. Dexmedetomidine (DEX), an α2-adrenergic receptor agonist, has been shown to suppress AAA development. Nevertheless, the signaling pathways that might be mediated by DEX in AAA has not been clarified. Vascular smooth muscle cells (VSMCs) and endothelial cells (ECs) were treated with Angiotensin II (Ang II) to mimic AAA in vitro. BrdU, wound healing, and Transwell assays were utilized for measuring...

Unoccupied aerial systems imagery from Camas, Cedar Gulch and Rocky Canyon Idaho

Peter Olsoy, Matthew Burgess, Jennifer Sorensen Forbey, Janet Rachlow, Lisa Shipley & Daniel Thornton
UAS imagery data and data products from Camas, Cedar Gulch and Rocky Canyon Idaho. Data were collected in both summer and winter seasons between 2013-2015. Data products include digital surface models (DSM), orthorectified color imagery (Ortho), and las point cloud files for each site and season; the dataset also contains 5-cm and 25-cm resolution canopy height models (CHM) for the Camas and Cedar Gulch sites during the summer sampling season. Processing reports are provided for...

Additional file 2 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

Yang Yang, Yiqi Wu, Mengting Ji, Xiaoyin Rong, Yanwei Zhang, Shuai Yang, Chang Lu, Chunbo Cai, Pengfei Gao, Xiaohong Guo, Bugao Li & Guoqing Cao
Additional file 2.

Additional file 3 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

Yang Yang, Yiqi Wu, Mengting Ji, Xiaoyin Rong, Yanwei Zhang, Shuai Yang, Chang Lu, Chunbo Cai, Pengfei Gao, Xiaohong Guo, Bugao Li & Guoqing Cao
Additional file 3.

Additional file 3 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

Yang Yang, Yiqi Wu, Mengting Ji, Xiaoyin Rong, Yanwei Zhang, Shuai Yang, Chang Lu, Chunbo Cai, Pengfei Gao, Xiaohong Guo, Bugao Li & Guoqing Cao
Additional file 3.

Additional file 4 of A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng … & Barry Smith
Additional file 4: Supplemental Table 3. Protein Ontology representation of SARS-CoV-2 proteins. Comparative information in RefSeq and UniProtKB is also provided.

Additional file 2 of Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula

Sara A. Knaack, Daniel Conde, Sanhita Chakraborty, Kelly M. Balmant, Thomas B. Irving, Lucas Gontijo Silva Maia, Paolo M. Triozzi, Christopher Dervinis, Wendell J. Pereira, Junko Maeda, Henry W. Schmidt, Jean-Michel Ané, Matias Kirst & Sushmita Roy
Additional file 2: Table S1. DRMN module assignments (all genes, all time points). Table S2. Inferred module-network edge-weights from DRMN. Table S3. Module motif enrichments. Table S4. MTG-LASSO target predictions. Table S5. RNAi validation results.

Agricultural Crop- and Animal-specific Ammonia Emission Inventory

Yuyu Yang, Lei Liu, Pu Liu, Jia Ding, Hang Xu & Sheng Liu
All products (crop- and animal- specific NH3 emission inventories in the time span of 1961-2018) are provided in TIFF format at a spatial resolution of 0.5 degree by 0.5 degree (latitude by longitude) at figshare. The unit is kg N yr-1, stored in two folders (cropland and livestock).

Additional file 6 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 6: Table S5. Relative abundance of families detected through 16S rRNA gene sequencing using fecal DNA.

Additional file 10 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 10: Table S8. Gene coverage of various functional KEGG genes detected through shotgun sequencing.

Additional file 11 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 11: Table S9. KEGG orthology IDs.

CCMI nursery coral disease 2019

Anya Brown, Dagny-Elyse Anastasiou, Monica Schul, Sophia MacVittie, Lindsay Spiers, Julie Meyer, Carrie Manfrino & Thomas Frazer
Marine infectious diseases are a leading cause of population declines globally due, in large part, to challenges in diagnosis and limited treatment options. Mitigating disease spread is particularly important for species targeted for conservation. In some systems, the strategic arrangement of organisms in space can constrain disease outbreaks, however, this approach has not been used in marine restoration. Reef-building corals have been particularly devastated by disease and continue to experience catastrophic population declines. Here, we...

C Type Natriuretic Peptide Receptor Activation Inhibits Sodium Channel Activity in Human Aortic Endothelial Cells by Activating the Diacylglycerol and Protein Kinase C Pathway

Ling Yu, Mohammad-Zaman Nouri, Lauren P. Liu, Niharika Bala, Nancy Denslow, John F. LaDisa Jr. & Abdel Alli
Supplementary Table 1: Lipidomics raw data.

C Type Natriuretic Peptide Receptor Activation Inhibits Sodium Channel Activity in Human Aortic Endothelial Cells by Activating the Diacylglycerol and Protein Kinase C Pathway

Ling Yu, Mohammad-Zaman Nouri, Lauren P. Liu, Niharika Bala, Nancy Denslow, John F. LaDisa Jr. & Abdel Alli
Supplementary Table 1: Lipidomics raw data.

Additional file 11 of FMO3 deficiency of duck leads to decreased lipid deposition and increased antibacterial activity

Xingzheng Li, Jianlou Song, Xuefeng Shi, Mingyi Huang, Lei Liu, Guoqiang Yi, Ning Yang, Guiyun Xu & Jiangxia Zheng
Additional file 11: Table S4. Taxa associated with TMA metabolism using the Mann-Whitney U-test.

Additional file 12 of FMO3 deficiency of duck leads to decreased lipid deposition and increased antibacterial activity

Xingzheng Li, Jianlou Song, Xuefeng Shi, Mingyi Huang, Lei Liu, Guoqiang Yi, Ning Yang, Guiyun Xu & Jiangxia Zheng
Additional file 12: Table S5. Taxa associated with TMA metabolism using LEfSe analysis.

Whole-exome sequencing reveals novel variants associated with abnormal uterine bleeding caused by copper intrauterine device Supplementary Materials

Yupei Shen, Xiaoli Liu, Linfen Xu, Weiqiang Zhu, Zhaofeng Zhang, Junwei Liu, Lifang Jiang, Yanyan Mao, Jianhua Xu, Xiaoqin Yan, Junjie Sun, Fang Liu, Xiumei Xiong, Xiujuan Chen, Yan Che & Jing Du
Aim: This study aimed to explore the genetic risk factors and validate variants of abnormal uterine bleeding after copper intrauterine device insertion. Methods: Whole-exome sequencing was performed and several variants were validated by Sequenom MassARRAY. Results: Eight variants showed potential clinical damage according to American College of Medical Genetics and Genomics criteria. By combined analysis of screening and validation, NFASC RS2802808 C>G p.Ile971Met (Pallele = 0.009 and Pgenotype = 0.027) and PIGR RS2275531 C>T p.Gly365Ser...

Registration Year

  • 2022
    145

Resource Types

  • Dataset
    145

Affiliations

  • University of Florida
    145
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    56
  • Chinese Academy of Agricultural Sciences
    56
  • Shanghai Jiao Tong University
    47
  • Sichuan University
    46
  • Ministry of Agriculture and Rural Affairs
    45
  • Soochow University
    44
  • West China Hospital of Sichuan University
    43
  • Zhejiang University
    43
  • Nantong University
    40