10 Works

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: 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...

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....

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...

Geographic Variation in the Structure of Kentucky’s Population Health Systems

Rachel Hogg-Graham, Angela Carman, Glen P. Mays & Pierre Martin Dominique Zephyr
Introduction: Research examining geographic variation in the structure of population health systems is continuing to emerge, and most of the evidence that currently exists divides systems by urban and rural designation. Very little is understood about how being rural and Appalachian impacts population health system structure and strength. Purpose: This study examines geographic differences in key characteristics of population health systems in urban, rural non-Appalachian, and rural Appalachian regions of Kentucky. Methods: Data from a...

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...

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...

Dunlin subspecies exhibit regional segregation and high site fidelity along the East Asian−Australasian Flyway

Benjamin Lagassé, Richard Lanctot, Mark Barter, Stephen Brown, Chung-Yu Chiang, Chi-Yeung Choi, Yuri Gerasimov, Steve Kendall, Joseph Liebezeit, Konstantin Maslovsky, Alexander Matsyna, Ekaterina Matsyna, David Payer, Sarah Saalfeld, Yoshimitsu Shigeta, Ivan Tiunov, Pavel Tomkovich, Olga Valchuk & Michael Wunder
The degree that individuals migrate among particular breeding, migration, and wintering sites can have important implications for prioritizing conservation efforts. Four subspecies of Dunlin (Calidris alpina) migrate along the East Asian−Australasian Flyway (EAAF). Each subspecies has a distinct and well-defined breeding range, but their migration and winter ranges are poorly defined or unknown. We assessed the migratory connectivity of 3 of these subspecies by evaluating a dataset that encompasses 57 years (1960–2017), and comprises more...

Lack of head sparing following third-trimester caloric restriction among Tanzanian Maasai

Paula Gonzalez, Christopher Powell, Warren Wilson, Godwin Olesaningo, Mange Manyama, Heather Jamniczky, Richard Spritz, James Cross, Keneth Lukowiak & Benedikt Hallgrimsson
The reduction of food intake during pregnancy is part of many cultural and religious traditions around the world. The impact of such practices on fetal growth and development are poorly understood. Here, we examined the patterns of diet intake among Maasai pregnant women and assessed their effect on newborn morphometrics. We recruited 141 mother-infant pairs from Ngorongoro Conservation Area (NCA) in Northern Tanzania and quantified dietary intake and changes in maternal diet during pregnancy. We...

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