18 Works

Data from: Cardiovascular disease risk factors in Ghana during the rural-to-urban transition: a cross-sectional study

Nuri Kodaman, Melinda C. Aldrich, Rafal Sobota, Folkert Asselbergs, Kwabena Poku, Nancy J. Brown, Jason H. Moore, Scott M. Williams, Folkert W. Asselbergs & Kwabena A. Poku
Populations in sub-Saharan Africa are shifting from rural to increasingly urban. Although the burden of cardiovascular disease is expected to increase with this changing landscape, few large studies have assessed a wide range of risk factors in urban and rural populations, particularly in West Africa. We conducted a cross-sectional, population-based survey of 3317 participants from Ghana (≥18 years old), of whom 2265 (57% female) were from a mid-sized city (Sunyani, population ~250,000) and 1052 (55%...

Data from: A stochastic neuronal model predicts random search behaviors at multiple spatial scales in C. elegans

William M. Roberts, Steven B. Augustine, Kristy J. Lawton, Theodore H. Lindsay, Tod R. Thiele, Eduardo J. Izquierdo, Serge Faumont, Rebecca A. Lindsay, Matthew Cale Britton, Navin Pokala, Cornelia I. Bargmann & Shawn R. Lockery
Random search is a behavioral strategy used by organisms from bacteria to humans to locate food that is randomly distributed and undetectable at a distance. We investigated this behavior in the nematode Caenorhabditis elegans, an organism with a small, well-described nervous system. Here we formulate a mathematical model of random search abstracted from the C. elegans connectome and fit to a large-scale kinematic analysis of C. elegans behavior at submicron resolution. The model predicts behavioral...

Data from: Artificial selection on ant female caste ratio uncovers a link between female-biased sex ratios and infection by Wolbachia endosymbionts

Luigi Pontieri, Anna M. Schmidt, Rohini Singh, Jes Søe Pedersen & Timothy A. Linksvayer
Social insect sex and caste ratios are well-studied targets of evolutionary conflicts, but the heritable factors affecting these traits remain unknown. To elucidate these factors, we carried out a short-term artificial selection study on female caste ratio in the ant Monomorium pharaonis. Across three generations of bidirectional selection, we observed no response for caste ratio, but sex ratios rapidly became more female-biased in the two replicate high selection lines and less female-biased in the two...

Data from: Dietary regulation of the gut microbiota engineered by a minimal defined bacterial consortium

Gary D. Wu, Evelyn Hsu, Ting-Chin Shen, Christel Chehoud, Aubrey Bailey, Josephine Ni, Ying-Yu Chen, Frederic D. Bushman, Alice Laughlin, Kyle Bittinger & Ting-Chin David Shen
We have recently reported that Altered Schaedler Flora (ASF) can be used to durably engineer the gut microbiota to reduce ammonia production as an effective modality to reduce morbidity and mortality in the setting of liver injury. Here we investigated the effects of a low protein diet on ASF colonization and its ability to engineer the microbiota. Initially, ASF inoculation was similar between mice fed a normal protein diet or low protein diet, but the...

Data from: Clinical factors associated with long-term complete remission versus poor response to chemotherapy in HIV-infected children and adolescents with Kaposi sarcoma receiving bleomycin and vincristine: a retrospective observational study

Nader Kim El-Mallawany, William Kamiyango, Jeremy S. Slone, Jimmy Villiera, Carrie L. Kovarik, Carrie M. Cox, Dirk P. Dittmer, Saeed Ahmed, Gordon E. Schutze, Michael E. Scheurer, Peter N. Kazembe & Parth S. Mehta
Kaposi sarcoma (KS) is the most common HIV-associated malignancy in children and adolescents in Africa. Pediatric KS is distinct from adult disease. We evaluated the clinical characteristics associated with long-term outcomes. We performed a retrospective observational analysis of 70 HIV-infected children and adolescents with KS less than 18 years of age diagnosed between 8/2010 and 6/2013 in Lilongwe, Malawi. Local first-line treatment included bleomycin and vincristine plus nevirapine-based highly active anti-retroviral therapy (HAART). Median age...

Data from: Chimpanzees breed with genetically dissimilar mates

Kara K. Walker, Rebecca S. Rudicell, Yingying Li, Beatrice H. Hahn, Emily Wroblewski & Anne E. Pusey
Inbreeding adversely affects fitness, whereas heterozygosity often augments it. Therefore, mechanisms to avoid inbreeding and increase genetic distance between mates should be advantageous in species where adult relatives reside together. Here we investigate mate choice for genetic dissimilarity in chimpanzees, a species in which many females avoid inbreeding through dispersal, but where promiscuous mating and sexual coercion can limit choice when related adults reside together. We take advantage of incomplete female dispersal in Gombe National...

Data from: Biophysically inspired model for functionalized nanocarrier adhesion to cell surface: roles of protein expression and mechanical factors

N. Ramakrishnan, Richard W. Tourdot, David M. Eckmann, Portonovo S. Ayyaswamy, Vladimir M. Muzykantov & Ravi Radhakrishnan
In order to achieve selective targeting of affinity–ligand coated nanoparticles to the target tissue, it is essential to understand the key mechanisms that govern their capture by the target cell. Next-generation pharmacokinetic (PK) models that systematically account for proteomic and mechanical factors can accelerate the design, validation and translation of targeted nanocarriers (NCs) in the clinic. Towards this objective, we have developed a computational model to delineate the roles played by target protein expression and...

Data from: Strategic use of affiliative vocalizations by wild female baboons

Joan B. Silk, Robert M. Seyfarth & Dorothy L. Cheney
Although vocal production in non-human primates is highly constrained, individuals appear to have some control over whether to call or remain silent. We investigated how contextual factors affect the production of grunts given by wild female chacma baboons, Papio ursinus, during social interactions. Females grunted as they approached other adult females 28% of the time. Supporting previous research, females were much more likely to grunt to mothers with young infants than to females without infants....

Data from: Stimulation-based control of dynamic brain networks

Sarah Feldt Muldoon, Fabio Pasqualetti, Shi Gu, Matthew Cieslak, Scott T. Grafton, Jean M. Vettel & Danielle S. Bassett
The ability to modulate brain states using targeted stimulation is increasingly being employed to treat neurological disorders and to enhance human performance. Despite the growing interest in brain stimulation as a form of neuromodulation, much remains unknown about the network-level impact of these focal perturbations. To study the system wide impact of regional stimulation, we employ a data-driven computational model of nonlinear brain dynamics to systematically explore the effects of targeted stimulation. Validating predictions from...

Data from: ASSET: analysis of sequences of synchronous events in massively parallel spike trains

Emiliano Torre, Carlos Canova, Michael Denker, Goerge Gerstein, Moritz Helias, Sonja Grün & George Gerstein
With the ability to observe the activity from large numbers of neurons simultaneously using modern recording technologies, the chance to identify sub-networks involved in coordinated processing increases. Sequences of synchronous spike events (SSEs) constitute one type of such coordinated spiking that propagates activity in a temporally precise manner. The synfire chain was proposed as one potential model for such network processing. Previous work introduced a method for visualization of SSEs in massively parallel spike trains,...

Data from: Adaptive patterns of phenotypic plasticity in laboratory and field environments in Drosophila melanogaster

Vinayak Mathur & Paul S. Schmidt
Identifying mechanisms of adaptation to variable environments is essential in developing a comprehensive understanding of evolutionary dynamics in natural populations. Phenotypic plasticity allows for phenotypic change in response to changes in the environment, and as such may play a major role in adaptation to environmental heterogeneity. Here, the plasticity of stress response in D. melanogaster originating from two distinct geographic regions and ecological habitats was examined. Adults were given a short-term, 5-day exposure to combinations...

Data from: Rhesus monkeys show human-like changes in gaze following across the lifespan

Alexandra G. Rosati, Alyssa M. Arre, Michael L. Platt & Laurie R. Santos
Gaze following, or co-orienting with others, is a foundational skill for human social behavior. The emergence of this capacity scaffolds critical human-specific abilities such as theory of mind and language. Nonhuman primates also follow others’ gaze, but less is known about how the cognitive mechanisms supporting this behavior develop over the lifespan. Here we experimentally tested gaze following in 481 semi-free-ranging rhesus macaques (Macaca mulatta) ranging from infancy to old age. We found that monkeys...

Data from: Adaptive dynamics of cuticular hydrocarbons in Drosophila

Subhash Rajpurohit, Robert Hanus, Vladimir Vrkoslav, Emily L. Behrman, Alan O. Bergland, Dmitri Petrov, Josef Cvacka & Paul S. Schmidt
Cuticular hydrocarbons (CHCs) are hydrophobic compounds deposited on the arthropod cuticle that are of functional significance with respect to stress tolerance, social interactions, and mating dynamics. We characterized CHC profiles in natural populations of Drosophila melanogaster at five levels: across a latitudinal transect in the eastern U.S., as a function of developmental temperature during culture, across seasonal time in replicate years, and as a function of rapid evolution in experimental mesocosms in the field. Furthermore,...

Data from: Pigmentation and fitness trade-offs through the lens of artificial selection

Subhash Rajpurohit, Rani Richardson, John Dean, Raul Vazquez, Grace Wong & Paul S. Schmidt
Pigmentation is a classic phenotype that varies widely and adaptively in nature both within and among taxa. Genes underlying pigmentation phenotype are highly pleiotropic, creating the potential for functional trade-offs. However, the basic tenets of this trade-off hypothesis with respect to life-history traits have not been directly addressed. In natural populations of Drosophila melanogaster, the degree of melanin pigmentation covaries with fecundity and several other fitness traits. To examine correlations and potential trade-offs associated with...

Data from: Choosing wavelet methods, filters, and lengths for functional brain network construction

Zitong Zhang, Qawi K. Telesford, Chad Giusti, Kelvin O. Lim & Danielle S. Bassett
Wavelet methods are widely used to decompose fMRI, EEG, or MEG signals into time series representing neurophysiological activity in fixed frequency bands. Using these time series, one can estimate frequency-band specific functional connectivity between sensors or regions of interest, and thereby construct functional brain networks that can be examined from a graph theoretic perspective. Despite their common use, however, practical guidelines for the choice of wavelet method, filter, and length have remained largely undelineated. Here,...

Data from: Akt-mTORC1 signaling regulates Acly to integrate metabolic input to control of macrophage activation

Anthony J. Covarrubias, Halil Ibrahim Aksoylar, Jiujiu Yu, Nathaniel W. Snyder, Andrew J. Worth, Shankar S. Iyer, Jiawei Wang, Issam Ben-Sahra, Vanessa Byles, Tiffany Polynne-Stapornkul, Erika C. Espinosa, Dudley Lamming, Brendan D. Manning, Yijing Zhang, Ian A. Blair & Tiffany Horng
Macrophage activation/polarization to distinct functional states is critically supported by metabolic shifts. How polarizing signals coordinate metabolic and functional reprogramming, and the potential implications for control of macrophage activation, remains poorly understood. Here we show that IL-4 signaling co-opts the Akt-mTORC1 pathway to regulate Acly, a key enzyme in Ac-CoA synthesis, leading to increased histone acetylation and M2 gene induction. Only a subset of M2 genes is controlled in this way, including those regulating cellular...

Data from: Parallel effects of the inversion In(3R)Payne on body size across the North American and Australian clines in Drosophila melanogaster

Martin Kapun, Chloe Schmidt, Esra Durmaz, Paul S. Schmidt & Thomas Flatt
Chromosomal inversions are thought to play a major role in climatic adaptation. In D. melanogaster, the cosmopolitan inversion In(3R)Payne exhibits latitudinal clines on multiple continents. Since many fitness traits show similar clines, it is tempting to hypothesize that In(3R)P underlies observed clinal patterns for some of these traits. In support of this idea, previous work in Australian populations has demonstrated that In(3R)P affects body size but not development time or cold resistance. However, similar data...

Data from: TipDatingBeast: an R package to assist the implementation of phylogenetic tip-dating tests using BEAST

Adrien Rieux & Camilo E. Khatchikian
Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. In this context, BEAST, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce TipDatingBeast, an R package built to assist the implementation of various phylogenetic tip-dating tests using BEAST. TipDatingBeast currently contains two main functions....

Registration Year

  • 2016

Resource Types

  • Dataset


  • University of Pennsylvania
  • University of Minnesota
  • Reed College
  • Stanford University
  • University of California System
  • Duke University
  • Stanford University School of Medicine
  • University of North Carolina
  • University of Virginia
  • University of Lausanne