233 Works

Census and phenotype data supporting Drosophila adaptive tracking

Seth Rudman, Paul Schmidt, Subhash Rajpurohit, Sharon Greenblum & Dmitri Petrov
Direct observation of evolution in response to natural environmental change can resolve fundamental questions about adaptation including its pace, temporal dynamics, and underlying phenotypic and genomic architecture. We tracked evolution of fitness-associated phenotypes and allele frequencies genome-wide in ten replicate field populations of Drosophila melanogaster over ten generations from summer to late fall. Adaptation was evident over each sampling interval (1-4 generations) with exceptionally rapid phenotypic adaptation and large allele frequency shifts at many independent...

Resilient consumers accelerate the plant decomposition in a naturally acidified seagrass ecosystem

Juhyung Lee, Maria Cristina Gambi, Kristy Kroeker, Marco Munari, Kabir Peay & Fiorenza Micheli
Anthropogenic stressors are predicted to alter biodiversity and ecosystem functioning worldwide. However, scaling up from species to ecosystem responses poses a challenge, as species and functional groups can exhibit different capacities to adapt, acclimate, and compensate under changing environments. We used a naturally acidified seagrass ecosystem (the endemic Mediterranean Posidonia oceanica) as a model system to examine how ocean acidification (OA) modifies the community structure and functioning of plant detritivores, which play vital roles in...

Flash sequence duration

Jamie Zeitzer, Daniel Joyce & Manuel Spitschan
Unlike light input for forming images, non-image forming retinal pathways are optimized to convey information about the total light environment, integrating over time and space. It has been demonstrated in a variety of species that the retinohypothalamic pathway underlying circadian entrainment can effectively integrate the impact of individual flashes over time and convey this information as if continuous light exposure had occurred. In this study, we examine the extent to which this temporal integration can...

A dataset of 5 million city trees from 63 US cities: species, location, nativity status, health, and more.

Dakota McCoy, Benjamin Goulet-Scott, Weilin Meng, Bulent Atahan, Hana Kiros, Misako Nishino & John Kartesz
Sustainable cities depend on urban forests. City trees -- a pillar of urban forests -- improve our health, clean the air, store CO2, and cool local temperatures. Comparatively less is known about urban forests as ecosystems, particularly their spatial composition, nativity statuses, biodiversity, and tree health. Here, we assembled and standardized a new dataset of N=5,660,237 trees from 63 of the largest US cities. The data comes from tree inventories conducted at the level of...

Flexible hyperspectral surface plasmon resonance microscopy

Ziwei Liu, Jingning Wu, Chen Cai, Bo Yang & Zhi-mei Qi
Dataset of the raw hyperspectral SPR datacube supporting the article titled 'Flexible Hyperspectral Surface Plasmon Resonance Microscopy'.

Additional file 1 of Assessment of genetic susceptibility to multiple primary cancers through whole-exome sequencing in two large multi-ancestry studies

Taylor B. Cavazos, Linda Kachuri, Rebecca E. Graff, Jovia L. Nierenberg, Khanh K. Thai, Stacey Alexeeff, Stephen Van Den Eeden, Douglas A. Corley, Lawrence H. Kushi, Thomas J. Hoffmann, Elad Ziv, Laurel A. Habel, Eric Jorgenson, Lori C. Sakoda & John S. Witte
Additional file 1: Table S1. Cancer Site Coding Following SEER and WHO Guidelines. Table S2. Unique Cancer Pairs and Sample Counts in the Kaiser Permanente Research Bank and UK Biobank. Table S3. Sample Counts for Shared Index Cancers Across All Diagnoses in the Kaiser Permanente Research Bank and UK Biobank. Table S4. Single Variant Association Summary Statistics for Multiple Primary Cancers Combined or Grouped by Organ Site. Table S5. Gene-Based Association Summary Statistics for Multiple...

Additional file 1 of Assessment of genetic susceptibility to multiple primary cancers through whole-exome sequencing in two large multi-ancestry studies

Taylor B. Cavazos, Linda Kachuri, Rebecca E. Graff, Jovia L. Nierenberg, Khanh K. Thai, Stacey Alexeeff, Stephen Van Den Eeden, Douglas A. Corley, Lawrence H. Kushi, Thomas J. Hoffmann, Elad Ziv, Laurel A. Habel, Eric Jorgenson, Lori C. Sakoda & John S. Witte
Additional file 1: Table S1. Cancer Site Coding Following SEER and WHO Guidelines. Table S2. Unique Cancer Pairs and Sample Counts in the Kaiser Permanente Research Bank and UK Biobank. Table S3. Sample Counts for Shared Index Cancers Across All Diagnoses in the Kaiser Permanente Research Bank and UK Biobank. Table S4. Single Variant Association Summary Statistics for Multiple Primary Cancers Combined or Grouped by Organ Site. Table S5. Gene-Based Association Summary Statistics for Multiple...

Additional file 2 of Histological and molecular responses of Vigna angularis to Uromyces vignae infection

Xiwang Ke, Jie Wang, Xiaodan Xu, Yongxia Guo, Yuhu Zuo & Lihua Yin
Supplementary Material 2

Additional file 2 of Histological and molecular responses of Vigna angularis to Uromyces vignae infection

Xiwang Ke, Jie Wang, Xiaodan Xu, Yongxia Guo, Yuhu Zuo & Lihua Yin
Supplementary Material 2

Data from: Changes in Invertebrate Food Web Structure Between High- and Low-productivity Environments are Driven by Intermediate but Not Top Predator Diet Shifts

Ana Miller-Ter Kuile, Austen Apigo, An Bui, Kirsten Butner, Jasmine Childress, Stephanie Copeland, Bartholomew DiFiore, Elizabeth Forbes, Maggie Klope, Carina Motta, Devyn Orr, Katherine Plummer, Daniel Preston & Hillary Young
Predator-prey interactions shape ecosystem stability and are influenced by changes in ecosystem productivity. However, because multiple biotic and abiotic drivers shape the trophic responses of predators to productivity, we often observe patterns, but not mechanisms, by which productivity drives food web structure. One way to capture mechanisms shaping trophic response is to quantify trophic interactions among multiple trophic groups and by using complementary metrics of trophic ecology. In this study, we combine two diet-tracing methods:...

Experimental study on the seismic behavior of RC columns improved with central large-diameter butted steel rods

Hanming Zhang, Jie Luo, Jianchun Xiao, Jing Chen, Zhuoqun Liu, Yi Zhang, Zongli Luo & Hong Zhang
Abstract A reinforced concrete (RC) column improved with central large-diameter butted steel rods (CLBSR column) has been proposed to increase the limit value of the axial compression ratio. This paper presents the seismic behavior analysis of CLBSR columns subjected to low-cycle reciprocating loading. The CLBSR columns were also compared with the RC column improved with central large-diameter steel rods (CLSR column) and the RC column improved with central reinforcement bars (CRB column) under the same...

Experimental study on the seismic behavior of RC columns improved with central large-diameter butted steel rods

Hanming Zhang, Jie Luo, Jianchun Xiao, Jing Chen, Zhuoqun Liu, Yi Zhang, Zongli Luo & Hong Zhang
Abstract A reinforced concrete (RC) column improved with central large-diameter butted steel rods (CLBSR column) has been proposed to increase the limit value of the axial compression ratio. This paper presents the seismic behavior analysis of CLBSR columns subjected to low-cycle reciprocating loading. The CLBSR columns were also compared with the RC column improved with central large-diameter steel rods (CLSR column) and the RC column improved with central reinforcement bars (CRB column) under the same...

Additional file 2 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 2. Table S2: Adjuvant treatment information.

Additional file 4 of Small molecule modulation of microbiota: a systems pharmacology perspective

Qiao Liu, Bohyun Lee & Lei Xie
Additional file 4. Table S3. The Microbes with unknown effects in literature reviews and their SRWR inferred microbe effects.

Additional file 3 of Small molecule modulation of microbiota: a systems pharmacology perspective

Qiao Liu, Bohyun Lee & Lei Xie
Additional file 3. Table S2. Microbes with commensal effects on human health by manually literature review.

Additional file 8 of Circulating N-formylmethionine and metabolic shift in critical illness: a multicohort metabolomics study

Martin Ingi Sigurdsson, Hirotada Kobayashi, Karin Amrein, Kiichi Nakahira, Angela J. Rogers, Mayra Pinilla-Vera, Rebecca M. Baron, Laura E. Fredenburgh, Jessica A. Lasky-Su & Kenneth B. Christopher
Additional file 8. Additional metabolomics results from VITdAL-ICU and RoCI Cohorts. Nine individual worksheets include Linear regression results of Day 0 data from the VITdAL-ICU cohort adjusted for age, sex, baseline 25(OH)D, SAPS II, admission diagnosis, with additional adjustment for total bilirubin, creatinine, sepsis or propofol exposure. Day 0 data from the VITdAL-ICU cohort is also shown adjusted for age, sex, baseline 25(OH)D, and admission diagnosis but without SAPS II. Linear regression results of Day...

EIF3D promoted cervical carcinoma through Warburg effect by interacting with GRP78

Qing Liu, Jing Liu, Dan Zheng, Ranxi Zhang, Yan Xiang, Fei Xu, Xiaochan Zhou & Juan Qin
The incidence of cervical cancer ranks third among all female tumours globally and second in developing countries. However, the role of eukaryotic translation initiation factor 3 subunit D (EIF3D) in cervical carcinoma is unknown. This study investigated the effects of EIF3D on cell progression of cervical carcinoma and its underlying mechanism in vivo and vitro models. There were increases of EIF3D expression mRNA and protein expression levels in patients with cervical carcinoma. Disease-free survival (DFS)...

EIF3D promoted cervical carcinoma through Warburg effect by interacting with GRP78

Qing Liu, Jing Liu, Dan Zheng, Ranxi Zhang, Yan Xiang, Fei Xu, Xiaochan Zhou & Juan Qin
The incidence of cervical cancer ranks third among all female tumours globally and second in developing countries. However, the role of eukaryotic translation initiation factor 3 subunit D (EIF3D) in cervical carcinoma is unknown. This study investigated the effects of EIF3D on cell progression of cervical carcinoma and its underlying mechanism in vivo and vitro models. There were increases of EIF3D expression mRNA and protein expression levels in patients with cervical carcinoma. Disease-free survival (DFS)...

Additional file 4 of ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq

Elisabeth Meyer, Kaitlin Chaung, Roozbeh Dehghannasiri & Julia Salzman
Additional file 4: Table S3. This table contains the cases of regulated RNA processing detected in human and mouse spermatogenesis.

Additional file 6 of CCHCR1-astrin interaction promotes centriole duplication through recruitment of CEP72

Zhenguang Ying, Kaifang Wang, Junfeng Wu, Mingyu Wang, Jing Yang, Xia Wang, Guowei Zhou, Haibin Chen, Hongwu Xu, Stephen Cho Wing Sze, Feng Gao, Chunman Li & Ou Sha
Additional file 6. Individual data values. Raw data of Fig. 3A,B,F,G,7C and 7I.

The evolutionary trajectory of drosophilid walking

Ryan York, Luke E. Brezovec, Jenn Coughlan, Steven Herbst, Avery Krieger, Su-Yee Lee, Brandon Pratt, Ashley D. Smart, Eugene Song, Anton Suvorov, Daniel R. Matute, John C. Tuthill & Thomas R. Clandinin
Neural circuits must both execute the behavioral repertoire of individuals and account for behavioral variation across species. Understanding how this variation emerges over evolutionary time requires large-scale phylogenetic comparisons of behavioral repertoires. Here, we describe the evolution of walking in fruit flies by capturing high-resolution, unconstrained movement from 13 species and 15 strains of drosophilids. We find that walking can be captured in a universal behavior space, the structure of which is evolutionarily conserved. However,...

Supplementary Information

Jingyu Lin, Brett Bryan, Xudong Zhou, Peirong Lin, Hong Xuan Do, Lei Gao, Xinchen Gu, Zhifeng Liu, Luwen Wang, Shanlin Tong, Jiacong Huang, Qian Wang, Yuan Zhang, Hongkai Gao, Zilong Chen, Weili Duan, Zheyu Xie, Tong Cui, Junzhi Liu, Mingqian Li, Xiaodong Li, Zhenwu Xu, Fei Guo, Lele Shu, Bin Li … & Zhifeng Yang
This is the Supplementary Information for the paper

Word file S1

Jingyu Lin, Brett Bryan, Xudong Zhou, Peirong Lin, Hong Xuan Do, Lei Gao, Xinchen Gu, Zhifeng Liu, Luwen Wang, Shanlin Tong, Jiacong Huang, Qian Wang, Yuan Zhang, Hongkai Gao, Zilong Chen, Weili Duan, Zheyu Xie, Tong Cui, Junzhi Liu, Mingqian Li, Xiaodong Li, Zhenwu Xu, Fei Guo, Lele Shu, Bin Li … & Zhifeng Yang
Specific content of the survey

Additional file 3 of Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative

Ruth Johnson, Yi Ding, Vidhya Venkateswaran, Arjun Bhattacharya, Kristin Boulier, Alec Chiu, Sergey Knyazev, Tommer Schwarz, Malika Freund, Lingyu Zhan, Kathryn S. Burch, Christa Caggiano, Brian Hill, Nadav Rakocz, Brunilda Balliu, Christopher T. Denny, Jae Hoon Sul, Noah Zaitlen, Valerie A. Arboleda, Eran Halperin, Sriram Sankararaman, Manish J. Butte, Clara Lajonchere, Daniel H. Geschwind & Bogdan Pasaniuc
Additional file 3: Table S7. Associations between genetically inferred ancestry and phecodes within ATLAS.

Additional file 6 of Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative

Ruth Johnson, Yi Ding, Vidhya Venkateswaran, Arjun Bhattacharya, Kristin Boulier, Alec Chiu, Sergey Knyazev, Tommer Schwarz, Malika Freund, Lingyu Zhan, Kathryn S. Burch, Christa Caggiano, Brian Hill, Nadav Rakocz, Brunilda Balliu, Christopher T. Denny, Jae Hoon Sul, Noah Zaitlen, Valerie A. Arboleda, Eran Halperin, Sriram Sankararaman, Manish J. Butte, Clara Lajonchere, Daniel H. Geschwind & Bogdan Pasaniuc
Additional file 6: Table S10. Summary of GWAS analyses in ATLAS.

Registration Year

  • 2022
    233

Resource Types

  • Dataset
    233

Affiliations

  • Stanford University
    233
  • Sichuan University
    117
  • West China Hospital of Sichuan University
    83
  • Zhejiang University
    80
  • University of Chinese Academy of Sciences
    74
  • Shanghai Jiao Tong University
    73
  • Peking University
    72
  • Capital Medical University
    70
  • Huazhong Agricultural University
    63
  • Chinese Academy of Sciences
    63