29 Works

Data from: They are likely to be there: using a family-centered index-testing approach to identify HIV-positive children in Kenya

Jayne Lewis-Kulzer, Nicollate Okoko, Kirsten Ohe, Margaret Mburu, Hellen Muttai, Lisa Abuogi, Elizabeth Bukusi, Craig Cohen & Jeremy Penner
In Kenya, only half of children with an HIV-positive parent have been tested for HIV. The effectiveness of a family-centred index-testing approach to identify children (0-14 years) living with HIV was examined. A retrospective clinical record review was conducted among adult index patients newly enrolled in HIV care between May–July 2015 and family outcomes were followed through May 2016 at 60 high-volume clinics in western Kenya. HIV testing uptake and results, health facility level, enrollment...

On the cross-population generalizability of gene expression prediction models

Kevin L. Keys, Angel C.Y. Mak, Marquitta J. White, Walter L. Eckalbar, Andrew W. Dahl, Joel Mefford, Anna V. Mikhaylova, María G. Contreras, Jennifer R. Elhawary, Celeste Eng, Donglei Hu, Scott Huntsman, Sam S. Oh, Sandra Salazar, Michael A. Lenoir, Jimmie Chun Ye, Timothy A. Thornton, Noah Zaitlen, Esteban G. Burchard & Christopher R. Gignoux
The genetic control of gene expression is a core component of human physiology. For the past several years, transcriptome-wide association studies have leveraged large datasets of linked genotype and RNA sequencing information to create a powerful gene-based test of association that has been used in dozens of studies. While numerous discoveries have been made, the populations in the training data are overwhelmingly of European descent, and little is known about the generalizability of these models...

Data from: Acute cytotoxicity and increased vascular endothelial growth factor after in vitro nitrogen mustard vapor exposure

Matthew McGraw, So‐Young Kim, Carl W. White & Livia A. Veress
RATIONALE: Nitrogen mustard (NM) is a highly toxic alkylating agent. It is classified as chemical threat due to its potential use as a warfare agent. When inhaled, mustard exposure can cause both acute and chronic lung injury. The aims of this study are to develop an in vitro culture system for modeling mustard-induced airway injury and to identify growth factors contributing to airway pathology. METHODS: Primary human bronchial epithelial cells co-cultured with primary human pulmonary...

Data from: A rapidly evolved shift in life history timing during ecological speciation is driven by the transition between developmental phases

Thomas Powell, Andrew Nguyen, Qinwen Xia, Jeffrey Feder, Gregory Ragland & Daniel Hahn
For insect species in temperate environments, seasonal timing is often governed by the regulation of diapause, a complex developmental program that allows insects to weather unfavorable conditions and synchronize their lifecycles with available resources. Diapause development consists of a series of distinct phases including initiation, maintenance, termination, and post-diapause development. The evolution of insect seasonal timing depends in part on how these phases of diapause development and post-diapause development interact to affect variation in phenology....

Data from: Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Eddy J. Dowle, Ryan R. Bracewell, Michael E. Pfrender, Karen E. Mock, Barbara J. Bentz & Gregory J. Ragland
Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and gene flow analyses revealed three distinct...

Data from: Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies

Daren C. Card, Drew R. Schield, Jacobo Reyes-Velasco, Matthew K. Fujita, Audra L. Andrew, Sara J. Oyler-McCance, Jennifer A. Fike, Diana F. Tomback, Robert P. Ruggiero & Todd A. Castoe
As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (~3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species...

Data from: Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae)

Vid Bakovic, Hannes Schuler, Martin Schebeck, Jeffrey L. Feder, Christian Stauffer & Gregory J. Ragland
Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for...

Early angiogenic proteins associated with high risk for bronchopulmonary dysplasia and pulmonary hypertension in preterm infants

Sanne Arjaans, Brandie Wagner, Peter Mourani, Erica Mandell, Brenda Poindexter, Rolf Berger & Steven Abman
Introduction: Early pulmonary vascular disease in preterm infants is associated with the subsequent development of bronchopulmonary dysplasia (BPD) and pulmonary hypertension (PH), however, mechanisms that contribute to or identify infants with increased susceptibility for BPD and/or PH are incompletely understood. Therefore, we tested if changes in circulating angiogenic peptides during the first week of life are associated with the later development of BPD and/or PH. We further sought to determine alternate peptides and related signalling...

Data from: A migratory divide spanning two continents is associated with genomic and ecological divergence

Sheela Turbek, Drew Schield, Elizabeth Scordato, Andrea Contina, Xin-Wei Da, Yang Liu, Yu Liu, Emilio Pagani-Núñez, Qing-Miao Ren, Chris Smith, Craig Stricker, Michael Wunder, David Zonana & Rebecca Safran
Migratory divides are contact zones between breeding populations with divergent migratory strategies during the non-breeding season. These locations provide an opportunity to evaluate the role of seasonal migration in the maintenance of reproductive isolation, particularly the relationship between population structure and features associated with distinct migratory strategies. We combine light-level geolocators, genomic sequencing, and stable isotopes to investigate the timing of migration and migratory routes of individuals breeding on either side of a migratory divide...

Genomic evidence for correlated trait combinations and antagonistic selection contributing to counterintuitive genetic patterns of adaptive diapause divergence in Rhagoletis flies

McCall Calvert, Meredith Doellman, Jeffrey Feder, Glenn Hood, Peter Meyers, Scott Egan, Thomas Powell, Mary Glover, Cheyenne Tait, Hannes Schuler, Stewart Berlocher, James Smith, Patrik Nosil, Dan Hahn & Gregory Ragland
Adaptation to novel environments often results in unanticipated genomic responses to selection. Here, we illustrate how multifarious, correlational selection helps explain a counterintuitive pattern of genetic divergence between the recently derived apple- and ancestral hawthorn-infesting host races of Rhagoletis pomonella (Diptera: Tephritidae). The Apple host race terminate diapause and emerge as adults earlier in the season than the hawthorn host race to coincide with the earlier fruiting phenology of their apple hosts. However, alleles at...

Dataset associated with “Understanding the Physics of the Auxetic Response in a Liquid Crystal Elastomer”.

Thomas Raistrick, Devesh Mistry, Zhaopeng Zhang, Johan Mattsson & Helen Gleeson
Contains polarised Raman spectroscopy of a liquid crystal elastomer known to display an auxetic response and a mechanical Fréedericksz transition as a function of strain. Files include full evolution of the uniaxial and biaxial order parameters as a function of strain parallel and perpindicular to the director. Depolarization data is provided for various bond vibrations to determine the director behaviour as a function of strain.

Data from: New Guinea bone daggers were engineered to preserve social prestige

Nathaniel J. Dominy, Samuel T. Mills, Christopher M. Yakacki, Paul B. Roscoe & R. Dana Carpenter
Bone daggers were once widespread in New Guinea. Their purpose was both symbolic and utilitarian; they functioned as objects of artistic expression with the primary function of stabbing and killing people at close quarters. Most daggers were shaped from the tibiotarsus of cassowaries, but daggers shaped from the femora of respected men carried greater social prestige. The greater cross-sectional curvature of human bone daggers indicates superior strength, but the material properties of cassowary bone are...

OpenSense: Validation of IMU-based estimates of kinematics over long durations

Johanna O'Day, Scott Delp, Mazen Al Borno, Vanessa Ibarra, James Dunne, Ajay Seth, Ayman Habib, Carmichael Ong, Jennifer Hicks & Scott Uhlrich
Here we provide the dataset for validation of OpenSense, an open-source toolbox for Inertial-Measurement-Unit-based measurement of lower extremity kinematics over long durations (10 minutes). We computed IMU-based estimates of kinematics using sensor fusion and an inverse kinematics approach with a constrained biomechanical model. We measured kinematics for 11 subjects as they performed two 10-minute trials: (1) walking and turning, and (2) a repeated sequence of varied lower-extremity movements (sitting, standing, stair-climbing, side-stepping, walking, running). Subjects...

Efficacy and safety of semaglutide for type 2 diabetes by race and ethnicity: a post hoc analysis of the SUSTAIN trials

Cyrus Desouza, Bertrand Cariou, Satish Garg, Nanna Lausvig, Andrea Navarria & Vivian Fonseca
Context: Variations in the prevalence and aetiology of type 2 diabetes (T2D) across race and ethnicity may affect treatment responses. Semaglutide is a glucagon-like peptide-1 (GLP-1) analog approved for once–weekly, subcutaneous (s.c.) treatment of T2D. Objective: To compare semaglutide efficacy and safety in race and ethnicity subgroups across the SUSTAIN trials. Design: Post hoc analysis of data from phase 3 randomized SUSTAIN 1–5 and 7 (pooled) and SUSTAIN 6 trials. Participants: 3,074 subjects (SUSTAIN 1–5...

Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis

Meredith M. Doellman, Peter J. Meyers, Gregory J. Ragland, Glen R. Hood, Scott P. Egan, Thomas H. Q. Powell, Patrik Nosil & Jeffrey L. Feder
Studies assessing the predictability of evolution typically focus on short-term adaptation within populations or the repeatability of change among lineages. A missing consideration in speciation research is to determine whether natural selection predictably transforms standing genetic variation within populations into differences between species. Here, we test whether host-related selection on diapause timing anticipates genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of Rhagoletis pomonella to their sibling species...

Data from: Looking up: a dozen years of evolution of neurology clerkships in the United States

Joseph E. Safdieh, Adam D. Quick, Pearce J. Korb, Diego R. Torres-Russotto, Karissa L. Gable, Maggie M. Rock, Carolyn M. Cahill & Madhu Soni
Objective: To report a 2017 survey of all US medical school neurology clerkship directors (CDs) and to compare the results to similar surveys conducted in 2005 and 2012. Methods: An American Academy of Neurology (AAN) Consortium of Neurology Clerkship Directors (CNCD) workgroup developed the survey that was sent to all neurology CDs listed in the AAN CNCD database. Comparisons were made to similar 2005 and 2012 surveys. Results: The response rate was 92 of 146...

Data from: Context-dependent expression of the foraging gene in field colonies of ants: the interacting roles of age, environment and task

Krista K. Ingram, Deborah M. Gordon, Daniel A. Friedman, Michael Greene, John Kahler & Swetha Peteru
Task allocation among social insect workers is an ideal framework for studying the molecular mechanisms underlying behavioural plasticity because workers of similar genotype adopt different behavioural phenotypes. Elegant laboratory studies have pioneered this effort, but field studies involving the genetic regulation of task allocation are rare. Here, we investigate the expression of the foraging gene in harvester ant workers from five age- and task-related groups in a natural population, and we experimentally test how exposure...

Data from: A new way to estimate neurologic disease prevalence in the United States

Lorene M. Nelson, Mitchell T. Wallin, Ruth Ann Marrie, W.J. Culpepper, Annette Langer-Gould, Jon Campbell, Stephen Buka, Helen Tremlett, Gary Cutter, Wendy Kaye, Laurie Wagner & Nicholas G. Larocca
Objective: Considerable gaps exist in knowledge regarding the prevalence of neurologic diseases, such as multiple sclerosis (MS), in the United States. Therefore, the MS Prevalence Working Group sought to review and evaluate alternative methods for obtaining a scientifically valid estimate of national MS prevalence in the current health care era. Methods: We carried out a strengths, weaknesses, opportunities, and threats (SWOT) analysis for 3 approaches to estimate MS prevalence: population-based MS registries, national probability health...

Data from: Divergent diapause life history timing drives both allochronic speciation and reticulate hybridization in an adaptive radiation of Rhagoletis flies

Meredith Doellman, Katherine Inskeep, Thomas Powell, Stewart Berlocher, Nicholas Seifert, Glen Hood, Gregory Ragland, Peter Meyers & Jeff Feder
Divergent adaptation to new ecological opportunities can be an important factor initiating speciation. However, as niches are filled during adaptive radiations, trait divergence driving reproductive isolation between sister taxa may also result in trait convergence with more distantly related taxa, increasing the potential for reticulated gene flow across the radiation. Here, we demonstrate such a scenario in a recent adaptive radiation of Rhagoletis fruit flies, specialized on different host plants. Throughout this radiation, shifts to...

Parthenogenesis doubles the rate of amino acid substitution in Whiptail mitochondria

Jose Maldonado, , Alexander Hall & Matthew Fujita
Sexual reproduction is ubiquitous in the natural world, suggesting that sex must have extensive benefits to overcome the cost of males compared to asexual reproduction. One hypothesized advantage of sex with strong theoretical support is that sex plays a role in removing deleterious mutations from the genome. Theory predicts that transitions to asexuality should lead to the suppression of recombination and segregation and, in turn, weakened natural selection, allowing for the accumulation of slightly deleterious...

Data from: Opioid use and storage patterns in patients after hospital discharge following surgery

Karsten Bartels, Lena M. Mayes, Colleen Dingmann, Kenneth J. Bullard, Christian J. Hopfer & Ingrid A. Binswanger
Introduction: Opioid-based analgesic therapy represents a cornerstone of pain management after surgery. The recent rise in opioid sales and opioid overdoses suggests it is important to maximize the safety of opioid prescribing after surgery. Given that patients may live with other family members in the home, safe storage and appropriate disposal of excess opioids after hospital discharge are necessary to prevent unintended secondary exposures. Identifying characteristics of patients who are likely to be prescribed excess...

A mathematical model of flow-mediated coagulation identifies factor V as a modifier of thrombin generation in hemophilia A

Michael Stobb, Kathryn Link, Matthew Sorrells, Maria Bortot, Katherine Ruegg, Marilyn Manco-Johnson, Jorge DiPaola, Suzanne Sindi, Aaron Fogelson, Karin Leiderman & Keith Neeves
Hemophilia A is a bleeding disorder categorized as severe, mild, and moderate deficiencies in factor VIII (FVIII). Within these categories the variance in bleeding severity is significant and the origins unknown. The number of parameters that could modify bleeding are so numerous that experimental approaches are not feasible for considering all possible combinations. Consequently, we turn to a mathematical model of coagulation under flow to act as a screening tool to identify parameters that are...

Data from: Stage-specific genotype-by-environment interactions for cold and heat hardiness in Drosophila melanogaster.

Philip J. Freda, Zainab M. Ali, Nicholas Heter, Gregory J. Ragland & Theodore J. Morgan
Environments often vary across a life cycle, imposing fluctuating natural selection across development. Such fluctuating selection can drive evolutionary responses specific to distinct life-history stages. However, selection and genetic variation, phenotypic plasticity, and their interaction (GxE), as well as genetic correlation across development dictate stage-specific evolution. Thus, quantifying genetic covariance of fitness-related traits and plasticity across development is vital to determine whether stage-specific adaptation occurs in nature. Additionally, the interaction of genetic variation and environmental...

Data from: Fire-regime complacency and sensitivity to centennial- through millennial-scale climate change in Rocky Mountain subalpine forests, Colorado, U.S.A.

Philip E. Higuera, Christy E. Briles & Cathy Whitlock
1. Key uncertainties in anticipating future fire regimes are their sensitivity to climate change, and the degree to which climate will impact fire regimes directly, through increasing the probability of fire, versus indirectly, through changes in vegetation and landscape flammability. 2. We studied the sensitivity of subalpine forest fire regimes (i.e., fire frequency, fire severity) to previously documented climate variability over the past 6000 years, utilizing pollen and macroscopic charcoal from high-resolution lake-sediment records in...

Migratory divides coincide with reproductive barriers across replicated avian hybrid zones above the Tibetan Plateau

Elizabeth Scordato, Chris C. R. Smith, Georgy A. Semenov, Yu Liu, Matthew R. Wilkins, Wei Liang, Alexander Rubtsov, Gomboobaatar Sundev, Kazuo Koyama, Sheela P. Turbek, Michael B. Wunder, Craig A. Stricker & Rebecca Safran
Migratory divides are proposed to be catalysts for speciation across a diversity of taxa. However, it is difficult to test the relative contributions of migratory behavior vs. other divergent traits to reproductive isolation. Comparing hybrid zones with and without migratory divides offers a rare opportunity to directly examine the contribution of divergent migratory behavior to reproductive barriers. We show that across replicate sampling transects of two pairs of barn swallow (Hirundo rustica) subspecies, strong reproductive...

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