Data from: Genomic basis of life history evolution in Drosophila melanogasterSilvia C. Remolina, Peter L. Chang, Jeff Leips, Sergey V. Nuzhdin & Kimberly A. Hughes
Natural diversity in aging and other life history patterns is a hallmark of organismal variation. Related species, populations, and individuals within populations show genetically based variation in life span and other aspects of age-related performance. Population differences are especially informative because these differences can be large relative to within-population variation and because they occur in organisms with otherwise similar genomes. We used experimental evolution to produce populations divergent for life span and late-age fertility and...
Data from: Disentangling the effects of geographic and ecological isolation on genetic differentiationGideon S. Bradburd, Peter L. Ralph & Graham M. Coop
Populations can be genetically isolated by both geographic distance and by differences in their ecology or environment that decrease the rate of successful migration. Empirical studies often seek to investigate the relationship between genetic differentiation and some ecological variable(s) while accounting for geographic distance, but common approaches to this problem (such as the partial Mantel test) have a number of drawbacks. In this article, we present a Bayesian method that enables users to quantify the...
Data from: Westermann Morphospace displays ammonoid shell shape and hypothetical paleoecologyKathleen A. Ritterbush & David J. Bottjer
PLEASE NOTE: R scripts will be added to this data package as soon as possible. Abstract: The Westermann Morphospace method displays fundamental morphotypes and hypothesized life modes of measured ammonoid fossils in a ternary diagram. It quantitatively describes shell shape, without assumption of theoretical coiling laws, in a single, easy-to-read diagram. This allows direct comparison between data sets presented in Westermann Morphospace, making it an ideal tool to communicate morphology. By linking measured shells to...
Data from: Sex without sex chromosomes: genetic architecture of multiple loci independently segregating to determine sex ratios in the copepod Tigriopus californicusHeather J. Alexander, Jean M. L. Richardson, Suzanne Edmands & Bradley R. Anholt
Sex determining systems are remarkably diverse and may evolve rapidly. Polygenic sex determination systems are predicted to be transient and evolutionarily unstable yet examples have been reported across a range of taxa. Here we provide the first direct evidence of polygenic sex determination in Tigriopus californicus, a harpacticoid copepod with no heteromorphic sex chromosomes. Using genetically distinct inbred lines selected for male- and female-biased clutches, we generated a genetic map with 39 SNPs across 12...
Data from: A tradeoff between precopulatory and postcopulatory trait investment in male cetaceansJames P. Dines, Sarah L. Mesnick, Katherine Ralls, Laura J. May Collado, Ingi Agnarsson, Matthew D. Dean & Laura May-Collado
Mating with multiple partners is common across species, and understanding how individual males secure fertilization in the face of competition remains a fundamental goal of evolutionary biology. Game theory stipulates that males have a fixed budget for reproduction that can lead to a trade-off between investment in precopulatory traits like body size, armaments, and ornaments, and postcopulatory traits such as testis size and spermatogenic efficiency. Recent theoretical and empirical studies have shown that if males...
Data from: Sexual selection targets cetacean pelvic bonesJames P. Dines, Erik Otárola-Castillo, Peter Ralph, Jesse Alas, Timothy Daley, Andrew D. Smith & Matthew D. Dean
Male genitalia evolve rapidly, probably as a result of sexual selection. Whether this pattern extends to the internal infrastructure that influences genital movements remains unknown. Cetaceans (whales and dolphins) offer a unique opportunity to test this hypothesis: since evolving from land-dwelling ancestors, they lost external hind limbs and evolved a highly reduced pelvis which seems to serve no other function except to anchor muscles that maneuver the penis. Here we create a novel morphometric pipeline...
Data from: Quantitative analysis of the ecological dominance of benthic disaster taxa in the aftermath of the end-Permian mass extinctionElizabeth Petsios & David J. Bottjer
The end-Permian mass extinction, the largest extinction of the Phanerozoic, led to a severe reduction in both taxonomic richness and ecological complexity of marine communities in its aftermath, eventually culminating in a dramatic ecological restructuring of communities. During the Early Triassic recovery interval, disaster taxa proliferated and numerically dominated many marine benthic invertebrate assemblages. These disaster taxa include the bivalve genera Claraia, Unionites, Eumorphotis and Promyalina, and the inarticulate brachiopod Lingularia. The exact nature and...
Data from: Effects of ultraviolet radiation on photosynthetic performance and N2 fixation in Trichodesmium erythraeum IMS 101Xiaoni Cai, David A. Hutchins, Feixue Fu & Kunshan Gao
Biological effects of ultraviolet radiation (UVR; 280–400 nm) on marine primary producers are of general concern, as oceanic carbon fixers that contribute to the marine biological CO2 pump are being exposed to increasing UV irradiance due to global change and ozone depletion. We investigated the effects of UV-B (280–320 nm) and UV-A (320–400 nm) on the biogeochemically critical filamentous marine N2-fixing cyanobacterium Trichodesmium (strain IMS101) using a solar simulator as well as under natural solar...
Data from: Congestion reduction through efficient container movement under stochastic demandMaged Dessouky
In today’s world, there is a significant amount of investigation regarding how to efficiently distribute loaded containers from the ports to the consignees. However, to fully maximize the process and become more environmentally friendly, one should also study how to allocate the empty containers created by these consignees. This is an essential part in the study of container movement since it balances out the load flow at each location. The problem of coordinating the container...
Least-cost habitat linkages for American black bear, Rafinesque's big-eared bat, and timber rattlesnake.Jennifer Costanza, James Watling, Ron Sutherland, Curtis Belyea, Bistra Dilkina, Heather Cayton, David Bucklin, Stephanie Romañach & Nicholas Haddad
This data set contains 3 shapefiles and associated files that map linkages, which are least-cost paths between adjacent habitat cores for three wildlife species in the Southeastern U.S. The species are: the American black bear (Ursus americanus), Rafinesque's big-eared bat (Corynorhinus rafinesquii), and Timber rattlesnake (Crotalus horridus). We mapped habitat cores based on c. 2006 land cover, then used LinkageMapper software to identify least-cost paths between them, and buffered the least-cost paths by 2.5 km...
Data from: Development of an intravascular ultrasound elastography based on a dual-element transducerCho-Chiang Shih, Pei-Yu Chen, Teng Ma, Qifa Zhou, K. Kirk Shung & Chih-Chung Huang
The ability to measure the elastic properties of plaques and vessels would be useful in clinical diagnoses, particularly for detecting a vulnerable plaque. This study demonstrates the feasibility of combination of intravascular ultrasound (IVUS) and acoustic radiation force (ARF) elasticity imaging for detecting the distribution of stiffness within atherosclerotic arteries ex vivo. A dual-frequency IVUS transducer with two elements was used to induce the propagation of shear wave (by the 8.5-MHz pushing element) which could...
Data from: Longitudinal cognitive and biomarker changes in dominantly inherited Alzheimer diseaseEric McDade, Guoqiao Wang, Brian Andrew Gordon, Jason Hassenstab, Tammie L.S. Benzinger, Virginia Buckles, Anne M. Fagan, David M. Holtzman, Nigel J. Cairns, Alison M. Goate, Daniel S. Marcus, John C. Morris, Katrina Paumier, Chengjie Xiong, Ricardo Allegri, Sarah B. Berman, William Klunk, James Nobel, John Ringman, Bernardino Ghetti, Martin Farlow, Reisa Anne Sperling, Jasmeer Chhatwal, Stephen Salloway, Neil R. Graff-Radford … & Randall J. Bateman
Objective: To assess the onset, sequence and rate of progression of comprehensive biomarker and clinical measures across the spectrum of Alzheimer disease using the Dominantly Inherited Alzheimer Network (DIAN) study and compare these to cross-sectional estimates. Methods: We conducted longitudinal clinical, cognitive, cerebrospinal fluid (CSF) and neuroimaging assessments (mean of 2.7 (+/- 1.1) visits) in 217 DIAN participants. Linear mixed effects models were used to assess changes in each measure relative to individuals’ estimated years...
YAP and TAZ maintain PROX1 expression in the developing lymphatic and lymphovenous valves in response to VEGF-C signalingBoksik Cha, Yen-Chun Ho, Xin Geng, , Lijuan Chen, Yeunhee Kim, Dongwon Choi, Tae Hoon Kim, Gwendalyn Randolph, Xinwei Cao, Hong Chen & R. Sathish Srinivasan
Lymphatic vasculature is an integral part of digestive, immune and circulatory systems. The homeobox transcription factor PROX1 is necessary for the development of lymphatic vessels, lymphatic valves (LVs) and lymphovenous valves (LVVs). We and others previously reported a feedback loop between PROX1 and Vascular Endothelial Growth Factor-C (VEGF-C) signaling. PROX1 promotes the expression of the VEGF-C receptor VEGFR3 in lymphatic endothelial cells (LECs). In turn, VEGF-C signaling maintains PROX1 expression in LECs. However, the mechanisms...
Comparing single-species and mixed-species groups in fruit flies: differences in group dynamics but not group formationJulia Saltz, Anna Girardeau & Brad Foley
Mixed-species groups describe active associations among individuals of two or more species at the same trophic level. Mixed-species groups are important to key ecological and evolutionary processes such as competition and predation; and ignoring the presence of other species risks ignoring a key aspect of the environment in which social behavior is expressed and selected. Despite the defining emphasis of active formation for mixed-species groups, surprisingly little is known about the mechanisms by which mixed-species...
2-back task in split-belt adaptationCristina Rossi, Ryan Roemmich, Nicolas Schweighofer, Amy Bastian & Kristan Leech
We studied split-belt treadmill adaptation and savings in young (21±2 y/o) and older (56±6 y/o) adults with or without a secondary 2-back task during adaptation. We here provide here kinematic data for split-belt treadmill walking - specifically, step length asymmetry, double support asymmetry, and limb excursion asymmetry measure. We provide raw response data (button presses and reaction time) for performance in the 2-back cognitive task. We also provide scripts that can be used to analyse...
Data from: Reprogramming the antigen specificity of B cells using genome-editing technologiesJames E. Voss, Alicia Gonzalez-Martin, Raiees Andrabi, Roberta P. Fuller, Ben Murrell, Laura E. McCoy, Katelyn Porter, Deli Huang, Wenjuan Li, Devin Sok, Khoa Le, Bryan Briney, Morgan Chateau, Geoffrey Rogers, Lars Hangartner, Ann J. Feeney, David Nemazee, Paula Cannon & Dennis R. Burton
We have developed a method to introduce novel paratopes into the human antibody repertoire by modifying the immunoglobulin (Ig) genes of mature B cells directly using genome editing technologies. We used CRISPR-Cas9 in a homology directed repair strategy, to replace the heavy chain (HC) variable region in B cell lines with that from an HIV broadly neutralizing antibody, PG9. Our strategy is designed to function in cells that have undergone VDJ recombination using any combination...
A deglacial hazard cascade exemplified by the landslide, tsunami and outburst flood at Elliot Creek, Southern Coast Mountains, British Columbia, CanadaMarten Geertsema, Brian Menounos, Gemma Bullard, Jonathan Carrivick, John Clague, Chunli Dai, Davide Donati, Goran Ekstrom, Jennifer Jackson, Patrick Lynett, Manuele Pichierri, Andy Pon, Dan Shugar, Doug Stead, Justin Del Bel Belluz, Pierre Friele, Ian Giesbrecht, Derek Heathfield, Tom Millard, Sasha Nasonova, Andrew Schaeffer, Brent Ward, Darren Blaney, Erik Blaney, Camille Brillon … & Meghan Sharp
We describe and model the evolution of a recent landslide and outburst flood in the southern Coast Mountains, British Columbia, Canada. About 18 Mm3 of rock descended 1000 m from a steep valley wall and traveled across the toe of a glacier before entering a 0.6 km2 glacier lake and producing a >100-m high wave. Water overtopped the lake outlet and scoured a 10-km long channel before depositing debris on a 2 km2 fan below...
Urinary metals and maternal circulating extracellular vesicle microRNA in the MADRES pregnancy cohortCaitlin G. Howe, Helen B. Foley, Shohreh F. Farzan, Thomas A. Chavez, Mark Johnson, John D. Meeker, Theresa M. Bastain, Carmen J. Marsit & Carrie V. Breton
Exposure to metals increases risk for pregnancy complications. Extracellular vesicle (EV) miRNA contribute to maternal-foetal communication and are dysregulated in pregnancy complications. However, metal impacts on maternal circulating EV miRNA during pregnancy are unknown. Our objective was to investigate the impact of multiple metal exposures on EV miRNA in maternal circulation during pregnancy in the MADRES Study. Associations between urinary concentrations of nine metals and 106 EV miRNA in maternal plasma during pregnancy were investigated...
In silico package models for deriving values of solute parameters in linear solvation energy relationshipsZ.J. Xiao, J.W. Chen, Y. Wang & Z.Y. Wang
Environmental partitioning influences fate, exposure and ecological risks of chemicals. Linear solvation energy relationship (LSER) models may serve as efficient tools for estimating environmental partitioning parameter values that are commonly deficient for many chemicals. Nonetheless, scarcities of empirical solute parameter values of LSER models restricted the application. This study developed and evaluated in silico methods and models to derive the values, in which excess molar refraction, molar volume and logarithm of hexadecane/air partition coefficient were...
Blackburn Nodal Array, , &
181 Fairfield 3-Component Nodes were deployed at Blackburn Saddle in the Clark section of the San Jacinto Fault Zone
Additional file 1 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancerSiwei 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 1. Table S1: Patient demography.
Additional file 2 of A blood DNA methylation biomarker for predicting short-term risk of cardiovascular eventsAndrea Cappozzo, Cathal McCrory, Oliver Robinson, Anna Freni Sterrantino, Carlotta Sacerdote, Vittorio Krogh, Salvatore Panico, Rosario Tumino, Licia Iacoviello, Fulvio Ricceri, Sabina Sieri, Paolo Chiodini, Gareth J. McKay, Amy Jayne McKnight, Frank Kee, Ian S. Young, Bernadette McGuinness, Eileen M. Crimmins, Thalida Em Arpawong, Rose Anne Kenny, Aisling O’Halloran, Silvia Polidoro, Giuliana Solinas, Paolo Vineis, Francesca Ieva … & Giovanni Fiorito
Additional file 2. Supplementary Tables S1, S2, and S3.
Harmonized SHARE COVID, Version ACodi Young, Jenny Wilkens, Hunter Green & Jinkook Lee
Additional file 9 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 9: Table S2: Acetylated proteins and acetylated peptides identified in this study.
Additional file 2 of PredictCBC-2.0: a contralateral breast cancer risk prediction model developed and validated in ~ 200,000 patientsDaniele 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.
University of Southern California208
Chinese Academy of Sciences32
Sun Yat-sen University25
Chinese Academy of Medical Sciences & Peking Union Medical College24
China Agricultural University24
Shanghai Jiao Tong University22
Tianjin University of Traditional Chinese Medicine22
University of Michigan–Ann Arbor20