165 Works

Data from: Stability of spontaneous, correlated activity in mouse auditory cortex

Richard Betzel, Katherine Wood, Maria Geffen & Danielle Bassett
Neural systems can be modeled as complex networks in which neural elements are represented as nodes linked to one another through structural or functional connections. The resulting network can be analyzed using mathematical tools from network science and graph theory to quantify the system's topological organization and to better understand its function. Here, we used two-photon calcium imaging to record spontaneous activity from the same set of cells in mouse auditory cortex over the course...

Data from: Intranasal administration of dantrolene increased brain concentration and duration

Huafeng Wei, Jintao Wang, Yun Shi, Shuchun Yu, Yan Wang, Qingcheng Meng, Ge Liang & Maryellen F. Eckenhoff
Dantrolene has been demonstrated to be neuroprotective for multiple neurodegenerative diseases. However, dantrolene’s limited penetration into the CNS hampers its effectiveness as a neuroprotective agent. Here, we studied whether the intranasal administration of dantrolene provided better penetration into the brain than the commonly used oral approach. C57BL/6 mice, aged 2-4 months, received a single dose of either intranasal or oral dantrolene (5mg/kg). Inhibition of dantrolene clearance from the brain was examined by co-administration with P-gp/BCRP...

Risk factors for cardiovascular disease (CVD) in adults with type 1 diabetes: findings from prospective real-life T1D exchange registry

Nicole Foster, Viral N Shah, Ryan Bailey, Mengdi Wu, Rodica Pop-Busui, Michelle Katz, Jill Crandall, Fida Bacha, Kristen Nadeau, Ingrid Libman, Paul Hiers, Kara Mizokami-Stout, Linda A DiMeglio, Jennifer Sherr, Richard Pratley, Shivani Agarwal, Janet Snell-Bergeon, Eda Cengiz, Sarit Polsky & Sanjeev N Mehta
Context Cardiovascular disease (CVD) is a major cause of mortality in adults with type 1 diabetes. Objective We prospectively evaluated CVD risk factors in a large, contemporary cohort of adults with type 1 diabetes living in the United States. Design Observational study of CVD and CVD risk factors over a median of 5.3 years. Setting The T1D Exchange clinic network. Patients Adults (age ≥18 years) with type 1 diabetes and without known CVD diagnosed before...

Data from: Locomotory abilities and habitat of the Cretaceous bird Gansus yumenensis inferred from limb length proportions

Robert L. Nudds, Jessie Atterholt, Xia Wang, H. L. You, Gareth J. Dyke & H.-L. You
The relative length proportions of the three bony elements of the pelvic (femur, tibiotarsus and tarsometatarsus) and pectoral (humerus, ulna and manus) limbs of the early Cretaceous bird Gansus yumenensis, a well-represented basal ornithuromorph from China are investigated and compared to those of extant taxa. Ternary plots show that the pectoral limb length proportions of Gansus are most similar to Apodiformes (swifts and hummingbirds), which plot away from all other extant birds. In contrast, the...

Data from: Racial differences in recurrent ischemic stroke risk and recurrent stroke case fatality

Karen C. Albright, Lei Huang, Justin Blackburn, George Howard, Michael Mullen, Vera Bittner, Paul Muntner & Virginia Howard
Objective: To determine black-white differences in 1-year recurrent stroke and 30-day case fatality following a recurrent stroke in older US adults. Methods: We conducted a retrospective cohort study using a 5% random sample of Medicare beneficiaries with fee-for-service health insurance coverage who were hospitalized for ischemic stroke between 1999 and 2013. Hazard ratios (HR) for recurrent ischemic stroke and risk ratios (RR) for 30-day case fatality comparing blacks to whites were calculated with adjustment for...

Data from: The transcriptomic and evolutionary signature of social interactions regulating honey bee caste development

Svjetlana Vojvodic, Brian R. Johnson, Brock A. Harpur, Clement F. Kent, Amro Zayed, Kirk E. Anderson & Timothy A. Linksvayer
The caste fate of developing female honey bee larvae is strictly socially regulated by adult nurse workers. As a result of this social regulation, nurse-expressed genes as well as larval-expressed genes may affect caste expression and evolution. We used a novel transcriptomic approach to identify genes with putative direct and indirect effects on honey bee caste development, and we subsequently studied the relative rates of molecular evolution at these caste-associated genes. We experimentally induced the...

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: An inverse latitudinal gradient in speciation rate for marine fishes

Daniel L. Rabosky, Jonathan Chang, Pascal O. Title, Peter F. Cowman, Lauren Sallan, Matt Friedman, Kristin Kaschner, Cristina Garilao, Thomas J. Near, Marta Coll & Michael E. Alfaro
Far more species of organisms are found in the tropics than in temperate and polar regions, but the evolutionary and ecological causes of this pattern remain controversial1,2. Tropical marine fish communities are much more diverse than cold-water fish communities found at higher latitudes3,4, and several explanations for this latitudinal diversity gradient propose that warm reef environments serve as evolutionary ‘hotspots’ for species formation5,6,7,8. Here we test the relationship between latitude, species richness and speciation rate...

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: The effects of skeletal asymmetry on interpreting biological variation and taphonomy in the fossil record

Brandon P. Hedrick, Emma R. Schachner, Gabriel Rivera, Peter Dodson & Stephanie E. Pierce
Biological asymmetry is present in all bilaterally symmetric organisms as a result of normal developmental instability. However, fossilized organisms, which have undergone distortion due to burial, may have additional asymmetry as a result of taphonomic processes. To investigate this issue, we evaluated the magnitude of shape variation resulting from taphonomy on vertebrate bone using a novel application of fluctuating asymmetry. We quantified the amount of total variance attributed to asymmetry in a taphonomically distorted fossil...

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: Placental H3K27me3 establishes female resilience to prenatal insults

Bridget M. Nugent, Carly M. O'Donnell, C. Neill Epperson & Tracy L. Bale
Although sex biases in disease presentation are well documented, the mechanisms mediating vulnerability or resilience to diseases are unknown. In utero insults are more likely to produce detrimental health outcomes for males versus females. In our mouse model of prenatal stress, male offspring experience long-term dysregulation of body weight and hypothalamic pituitary adrenal stress axis dysfunction, endophenotypes of male-biased neurodevelopmental disorders. Placental function is critical for healthy fetal development, and we previously showed that sex...

Data from: A phylogenomic analysis of turtles

Nicholas G. Crawford, James F. Parham, Anna B. Sellas, Brant C. Faircloth, Travis C. Glenn, Theodore J. Papefuss, James B. Henderson, Madison H. Hansen, W. Brian Simison & Theodore J. Papenfuss
Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2,381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust...

Data from: The diversity of population responses to environmental change

Fernando Colchero, Owen R. Jones, Dalia A. Conde, Dave Hodgson, Felix Zajitschek, Benedikt R. Schmidt, Aurelio F. Malo, Susan C. Alberts, Peter H. Becker, Sandra Bouwhuis, Anne M. Bronikowski, Kristel M. De Vleeschouwer, Richard J. Delahay, Stefan Dummermuth, Eduardo Fernández-Duque, John Frisenvænge, Martin Hesselsøe, Sam Larson, Jean-Francois Lemaitre, Jennifer McDonald, David A.W. Miller, Colin O'Donnell, Craig Packer, Becky E. Raboy, Christopher J. Reading … & Chris J. Reading
The current extinction and climate change crises pressure us to predict population dynamics with ever-greater accuracy. Although predictions rest on the well-advanced theory of age-structured populations, two key issues remain poorly-explored. Specifically, how the age-dependency in demographic rates and the year-to-year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations, and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age-specific demographic rates and...

Data from: Population structure of the Chagas disease vector Triatoma infestans in an urban environment

Camilo E. Khatchikian, Erica A. Foley, Corentin M. Barbu, Josephine Hwang, Jenny Ancca-Juárez, Katty Borrini-Mayori, Victor R. Quıspe-Machaca, Cesar Naquira, Dustin Brisson & Michael Z. Levy
Chagas disease is a vector-borne disease endemic in Latin America. Triatoma infestans, a common vector of this disease, has recently expanded its range into rapidly developing cities of Latin America. We aim to identify the environmental features that affect the colonization and dispersal of T. infestans in an urban environment. We amplified 13 commonly used microsatellites from 180 T. infestans samples collected from a sampled transect in the city of Arequipa, Peru, in 2007 and...

Data from: Contrasting dynamics of a mutator allele in asexual populations of differing size

Yevgeniy Raynes, Matthew R. Gazzara & Paul D. Sniegowski
Mutators have been shown to hitchhike in asexual populations when the anticipated beneficial mutation supply rate of the mutator subpopulation, NU_b (for subpopulation of size N and beneficial mutation rate U_b) exceeds that of the wild-type subpopulation. Here, we examine the effect of total population size on mutator dynamics in asexual experimental populations of Saccharomyces cerevisiae. Although mutators quickly hitchhike to fixation in smaller populations, mutator fixation requires more and more time as population size...

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: DNA recovery from wild chimpanzee tools

Fiona A. Stewart, Alexander K. Piel, Lydia Luncz, Joanna Osborne, Yingying Li, Beatrice H. Hahn, Michael Haslam & Joanna Osborn
Most of our knowledge of wild chimpanzee behaviour stems from fewer than 10 long-term field sites. This bias limits studies to a potentially unrepresentative set of communities known to show great behavioural diversity on small geographic scales. Here, we introduce a new genetic approach to bridge the gap between behavioural material evidence in unhabituated chimpanzees and genetic advances in the field of primatology. The use of DNA analyses has revolutionised archaeological and primatological fields, whereby...

Data from: Predicting optimal outcomes in cognitive therapy or interpersonal psychotherapy for depressed individuals using the Personalized Advantage Index approach

Marcus J. H. Huibers, Zachary D. Cohen, Lotte H. J. M. Lemmens, Arnoud Arntz, Frenk P. M. L. Peeters, Pim Cuijpers & Robert J. DeRubeis
Introduction: Although psychotherapies for depression produce equivalent outcomes, individual patients respond differently to different therapies. Predictors of outcome have been identified in the context of randomized trials, but this information has not been used to predict which treatment works best for the depressed individual. In this paper, we aim to replicate a recently developed treatment selection method, using data from an RCT comparing the effects of cognitive therapy (CT) and interpersonal psychotherapy (IPT). Methods: 134...

Data from: Influenza hemagglutination-inhibition antibody titer as a mediator of vaccine-induced protection for influenza B

Benjamin J. Cowling, Wey Wen Lim, Ranawaka A.P.M. Perera, Vicky J. Fang, Gabriel M. Leung, J.S. Malik Peiris, Eric J. Tchetgen Tchetgen, Ranawaka A P M Perera & J S Malik Peiris
Background: The hemagglutination inhibition (HAI) assay is an established correlate of protection for the inactivated influenza vaccine, but the proportion of vaccine-induced protection that is mediated by the post-vaccination HAI titer has not been assessed. Methods: We used data from a randomized placebo-controlled trial of a split-virion inactivated influenza vaccine in children 6-17 years of age. Sera were collected before and 30 days after receipt of vaccination or placebo, and tested by the HAI assay...

Data from: Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

Shadi Shokralla, Joel F. Gibson, Hamid Nikbakht, Daniel H. Janzen, Winnie Hallwachs & Mehrdad Hajibabaei
DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need...

Phenotypic data for clinal populations, foxo genotypes

Paul Schmidt
The insulin/insulin-like growth factor signaling pathway has been hypothesized as a major determinant of life-history profiles that vary adaptively in natural populations. In Drosophila melanogaster, multiple components of this pathway vary predictably with latitude; this includes foxo, a conserved gene that regulates insulin signaling and has pleiotropic effects on a variety of fitness-associated traits. We hypothesized that allelic variation at foxo contributes to genetic variance for size-related traits that vary adaptively with latitude. We first...

Data From: Fear conditioning potentiates the Hippocampal CA1 commissural pathway In vivo and increases awake phase sleep

Manivannan Subramaniyan, Sumithrra Manivannan, Vikas Chelur, Theodoros Tsetsenis, Evan Jiang & John Dani
The hippocampus is essential for spatial learning and memory. To assess learning we used contextual fear conditioning (cFC), where animals learn to associate a place with aversive events like foot-shocks. Candidate memory mechanisms for cFC are long-term potentiation and long-term depression, but there is little direct evidence of them operating in the hippocampus in vivo following cFC. Also, little is known about the behavioral state changes induced by cFC. To address these issues, we recorded...

Harvestmen locomotion kinematics

Ignacio Escalante, Marc Badger & Damian Elias
Dataset is the experimental test of changes in biomechanics of Neotropical harvestmen after leg loss. Data includes locomotor performance, as well as postural and stride kinematic variables. Please see the associated manuscript for more details and information (Escalante, I., Badger, M.A. & Elias, D.O. Rapid recovery of locomotor performance after leg loss in harvestmen. Sci Rep 10, 13747 (2020). https://doi.org/10.1038/s41598-020-70557-2).

Data from: A generalist nematode destabilizes plant competition: no evidence for direct effects, but strong evidence for indirect effects on rhizobia abundance

Samantha Catella, Castilleja Olmsted, Shaniya Markalanda, Connor McFadden, Corlett Wood & Sara Kuebbing
1. Difficulties quantifying pathogen load and mutualist abundance limit our ability to connect disease dynamics to host community ecology. For example, specific predictions about how differential pathogen load is hypothesized to drive host competitive outcomes are rarely tested. Additionally, although infection is known to affect mutualists, we rarely measure the magnitude of pathogen effects on mutualist abundance across host competitive contexts. We tested for both mechanisms in a plant-rhizobia-nematode system. 2. We paired the legume...

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