167 Works

Data from: Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate

Zena T. Wolf, Harrison A. Brand, John R. Shaffer, Elizabeth J. Leslie, Boaz Arzi, Cali E. Willet, Timothy C. Cox, Toby McHenry, Nicole Narayan, Eleanor Feingold, Xioajing Wang, Saundra Sliskovic, Nili Karmi, Noa Safra, Carla Sanchez, Frederic W. B. Deleyiannis, Jeffrey C. Murray, Claire M. Wade, Mary L. Marazita & Danika L. Bannasch
Cleft lip with or without cleft palate (CL/P) is the most commonly occurring craniofacial birth defect. We provide insight into the genetic etiology of this birth defect by performing genome-wide association studies in two species: dogs and humans. In the dog, a genome-wide association study of 7 CL/P cases and 112 controls from the Nova Scotia Duck Tolling Retriever (NSDTR) breed identified a significantly associated region on canine chromosome 27 (unadjusted p=1.1 x 10-13; adjusted...

Data from: IL-33 mediated iLC2 activation and neutrophil IL-5 production in the lung response after severe trauma: a reverse translation study from a human cohort to a mouse trauma model

Jing Xu, Jesse Guardado, Rosemary Hoffman, Hui Xu, Rami Namas, Yoram Vodovotz, Li Xu, Mostafa Ramadan, Joshua Brown, Heth R. Turnquist & Timothy R. Billiar
Background: The immunosuppression and immune dysregulation that follows severe injury includes type 2 immune responses manifested by elevations in interleukin (IL) 4, IL5, and IL13 early after injury. We hypothesized that IL33, an alarmin released early after tissue injury and a known regulator of type 2 immunity, contributes to the early type 2 immune responses after systemic injury. Methods and findings: Blunt trauma patients admitted to the trauma intensive care unit of a level I...

Data from: Geographic patterns of genetic variation in three genomes of North American diploid strawberries with special reference to Fragaria vesca subsp. bracteata

Lauren Stanley, Nicole J. Forrester, Rajanikanth Govindarajulu, Aaron Liston & Tia-Lynn Ashman
Geographic patterns of genetic variation in wild species reflect the interplay of ecological and evolutionary processes. We assessed genetic variation in three genomes across four North American diploid strawberry taxa, with special emphasis on the gynodioecious Fragaria vesca subsp. bracteata (A.Heller) Staudt. Specifically, we sequenced one chloroplast (rpoC2) and two mitochondrial (atp8 and atp8-orf225) genes along with several nuclear microsatellite markers. In addition, we assessed indicators of breeding system (pollen viability and female frequency) for...

Data from: Leaf litter species identity alters the structure of pond communities

Aaron B. Stoler & Rick A. Relyea
The input of leaf litter resources is a major driver of ecosystem processes in terrestrial and freshwater habitats. Although variation exists in the quantity and composition of litter inputs due to natural and anthropogenic causes, few studies have examined how such variation influences the structure and composition of aquatic food webs. Using outdoor mesocosms, we examined the bottom–up effects of 10 chemically distinct tree litter species on microbial, algal, invertebrate and vertebrate fauna found in...

Data from: Information-theoretic analysis of realistic odor plumes: what cues are useful for determining location?

Sebastian D. Boie, Erin G. Connor, Margaret McHugh, Katherine I. Nagel, G. Bard Ermentrout, John P. Crimaldi & Jonathan D. Victor
Many species rely on olfaction to navigate towards food sources or mates. Olfactory navigation is a challenging task since odor environments are typically turbulent. While time-averaged odor concentration varies smoothly with the distance to the source, instaneous concentrations are intermittent and obtaining stable averages takes longer than the typical intervals between animals’ navigation decisions. How to effectively sample from the odor distribution to determine sampling location is the focus on this article. To investigate which...

Data from: Selection, periodicity and potential function for highly iterative Palindrome-1 (HIP1) in cyanobacterial genomes

Minli Xu, Jeffrey G. Lawrence & Dannie Durand
Highly Iterated Palindrome 1 (HIP1, GCGATCGC) is hyper-abundant in most cyanobacterial genomes. In some cyanobacteria, average HIP1 abundance exceeds one motif per gene. Such high abundance suggests a significant role in cyanobacterial biology. However, 20 years of study have not revealed whether HIP1 has a function, much less what that function might be. We show that HIP1 is 15-300 fold over-represented in genomes analysed. More importantly, HIP1 sites are conserved both within and between open...

Data from: GloPL, a global data base on pollen limitation of plant reproduction

Joanne. M. Bennett, Janette. A. Steets, Jean. H. Burns, Walter Durka, Jana. C. Vamosi, Gerardo Arceo-Gómez, Martin Burd, Laura. A. Burkle, Allan. G Ellis, Leandro Freitas, Junmin Li, James. G. Rodger, Marina Wolowski, Jing Xia, Tia-Lynn Ashman & Tiffany. M. Knight
Plant reproduction relies on transfer of pollen from anthers to stigmas, and the majority of flowering plants depend on biotic or abiotic agents for this transfer. A key metric for characterizing if pollen receipt is insufficient for reproduction is pollen limitation, which is assessed by pollen supplementation experiments. In a pollen supplementation experiment, fruit or seed production by flowers exposed to natural pollination is compared to that following hand pollination either by pollen supplementation (i.e....

Data from: Social interactions shape individual and collective personality in social spiders

Edmund R. Hunt, Brian Mi, Camila Fernandez, Brandyn M. Wong, Jonathan N. Pruitt & Noa Pinter-Wollman
The behavioural composition of a group and the dynamics of social interactions can both influence how social animals work collectively. For example, individuals exhibiting certain behavioural tendencies may have a disproportionately large impact on the group, and so are referred to as keystone individuals, while interactions between individuals can facilitate information transmission about resources. Despite the potential impact of both behavioural composition and interactions on collective behaviour, the relationship between consistent behaviours, also known as...

Data from: Cross-scale interactions and the distribution-abundance relationship

Earl E. Werner, Christopher Davis, David K. Skelly, Rick A. Relyea, Michael F. Benard, Shannon J. McCauley & Christopher J. Davis
Positive interspecific relationships between local abundance and extent of regional distribution are among the most ubiquitous patterns in ecology. Although multiple hypotheses have been proposed, the mechanisms underlying distribution-abundance (d-a) relationships remain poorly understood. We examined the intra- and interspecific distribution-abundance relationships for a metacommunity of 13 amphibian species sampled for 15 consecutive years. Mean density of larvae in occupied ponds was positively related to number of ponds occupied by species; employing the fraction of...

Data from: Genetic and phenotypic influences on copulatory plug survival in mice

Rachel Mangels, Brent Young, Sara Keeble, Reza Ardekani, Camille Meslin, Zelia Ferreira, Nathan L. Clark, Jeffrey M. Good & Matthew D. Dean
Across a diversity of animals, male seminal fluid coagulates upon ejaculation to form a hardened structure known as a copulatory plug. Previous studies suggest that copulatory plugs evolved as a mechanism for males to impede remating by females, but detailed investigations into the time course over which plugs survive in the female’s reproductive tract are lacking. Here, we cross males from eight inbred strains to females from two inbred strains of house mice (Mus musculus...

Data from: Phosphorescence monitoring of hypoxic microenvironment in solid-tumors to evaluate chemotherapeutic effects using the hypoxia-sensitive iridium (III) coordination compound

Yun Zeng, Yang Liu, Jin Shang, Jingwen Ma, Rong Wang, Lei Deng, Youmin Guo, Fan Zhong, Mingfeng Bai, Shaojuan Zhang & Daocheng Wu
Objectives: To utilize phosphorescence to monitor hypoxic microenvironment in solid-tumors and investigate cancer chemotherapeutic effects in vivo. Methods: A hypoxia-sensitive probe named BTP was used to monitor hypoxic microenvironment in solid-tumors. The low-dose metronomic treatment with cisplatin was used in anti-angiogenetic chemotherapeutic programs. The phosphorescence properties of BTP were detected by a spectrofluorometer. BTP cytotoxicity utilized cell necrosis and apoptosis, which were evaluated by trypan blue dye exclusion and Hoechst33342 plus propidium iodide assays. Tumor-bearing...

Data from: Developmental instability is genetically correlated with phenotypic plasticity, constraining heritability, and fitness

Stephen J. Tonsor, Tarek W. Elnaccash & Samuel M. Scheiner
Although adaptive plasticity would seem always to be favored by selection, it occurs less often than expected. This lack of ubiquity suggests that there must be trade-offs, costs, or limitations associated with plasticity. Yet, few costs have been found. We explore one type of limitation, a correlation between plasticity and developmental instability, and use quantitative genetic theory to show why one should expect a genetic correlation. We test that hypothesis using the Landsberg erecta ×...

Data from: Effect of IV glyburide on adjudicated edema endpoints in the GAMES-RP Trial

W. Taylor Kimberly, Matthew B. Bevers, Rüdiger Von Kummer, Andrew M. Demchuk, Javier M. Romero, Jordan J. Elm, Holly E. Hinson, Bradley J. Molyneaux, J. Marc Simard & Kevin Navin Sheth
Objective: In this secondary analysis of the GAMES-RP trial, we report the effect of IV glyburide on adjudicated, edema-related endpoints. Methods: Blinded adjudicators assigned designations for hemorrhagic transformation, neurological deterioration, malignant edema and edema-related death to patients from the GAMES-RP Phase II randomized controlled trial of IV glyburide for large hemispheric infarct. Rates of these endpoints were compared between treatment arms in the per-protocol sample. In those participants with malignant edema, the effects of treatment...

Data from: Genetic architecture of sexual dimorphism in a subdioecious plant with a proto-sex chromosome

Rachel B. Spigler, Kim S. Lewers & Tia-Lynn Ashman
The rise of sexual dimorphism is thought to coincide with the evolution of sex chromosomes. Yet because sex chromosomes in many species are ancient, we lack empirical evidence of the earliest stages of this transition. We use QTL analysis to examine the genetic architecture of sexual dimorphism in subdioecious octoploid Fragaria virginiana. We demonstrate that the region housing the male-function locus controls the majority of quantitative variation in proportion fruit set, confirming the existence of...

Data from: Monoamine abnormalities in the SAPAP3 knockout model of obsessive-compulsive disorder-related behaviour

Jesse Wood, Zoe LaPalombara & Susanne E. Ahmari
Obsessive-compulsive disorder (OCD) is a leading cause of illness-related disability, but the neuralmechanisms underlying OCDsymptoms are unclear. One potential mechanism of OCD pathology is monoamine dysregulation. Because of the difficulty of studying monoamine signalling in patients, animal models offer a viable alternative to understanding this aspect of OCD pathophysiology. We used HPLC to characterize post-mortem monoamine levels in lateral orbitofrontal cortex (OFC), medial OFC, medial prefrontal cortex and dorsal and ventral striatum of SAPAP-3 knockout...

Data from: Revisiting protein aggregation as pathogenic in sporadic Parkinson’s and Alzheimer’s diseases

Alberto J. Espay, Joaquin A. Vizcarra, Luca Marsili, Anthony E. Lang, David K. Simon, Aristide Merola, Keith A. Josephs, Alfonso Fasano, Francesca Morgante, Rodolfo Savica, J. Timothy Greenamyre, Franca Cambi, Tritia R. Yamasaki, Caroline M. Tanner, Ziv Gan-Or, Irene Litvan, Ignacio F. Mata, Cyrus P. Zabetian, Patrik Brundin, Hubert H. Fernandez, David G. Standaert, Marcelo A. Kauffman, Michael A. Schwarzschild, S. Pablo Sardi, Todd Sherer … & James B. Leverenz
The gold standard for a definitive diagnosis of Parkinson’s disease (PD) is the pathologic finding of aggregated alpha-synuclein into Lewy bodies and for Alzheimer’s disease (AD) aggregated amyloid into plaques and hyperphosphorylated tau into tangles. Implicit in this clinico-pathologic-based nosology is the assumption that pathological protein aggregation at autopsy reflect pathogenesis at disease onset. While these aggregates may in exceptional cases be on a causal pathway in humans (e.g., aggregated alpha-synuclein in SNCA gene multiplication...

Data from: Selection for collective aggressiveness favors social susceptibility in social spiders

Jonathan N. Pruitt, Colin M. Wright, James L. L. Lichtenstein, Gregory T. Chism, Brendan L. McEwen, Ambika Kamath & Noa Pinter-Wollman
Particularly socially influential individuals are present in many groups, but it is unclear whether their emergence is determined by their social influence versus the social susceptibility of others. The social spider Stegodyphus dumicola shows regional variation in apparent leader-follower dynamics. We use this variation to evaluate the relative contributions of leader social influence versus follower social susceptibility in driving this social order. Using chimeric colonies that combine potential leaders and followers, we discover that leader-follower...

Data from: Phylogeny meets ecotoxicology: evolutionary patterns of sensitivity to a common insecticide

John I. Hammond, Devin K. Jones, Patrick R. Stephens & Rick A. Relyea
Pesticides commonly occur in aquatic systems and pose a substantial challenge to the conservation of many taxa. Ecotoxicology has traditionally met this challenge by focusing on short-term, single-species tests and conducting risk assessments based on the most sensitive species tested. Rarely have ecotoxicology data been examined from an evolutionary perspective and to our knowledge there has never been a phylogenetic analysis of sensitivity, despite the fact that doing so would provide insights into patterns of...

Data from: Animal personality in a foundation species drives community divergence and collapse in the wild

Jonathan N. Pruitt & Andreas P. Modlmeier
1. Despite thousands of papers on the topic, precious few of the studies on animal personality have considered the role of personality in shaping community-level processes. Here, we test the effect of individual variation on the long-term trajectories of biological communities, from initiation to their demise. The spider Anelosimus studiosus builds webs that serve as habitat for >50 species of spider, which together construct a species-rich silken reef. This species also exhibits a temporally consistent...

Data from: Clinal variation in seed traits influencing life cycle timing in Arabidopsis thaliana.

Alicia Montesinos-Navarro, F. Xavier Picó & Stephen J. Tonsor
Early life history transitions are crucial determining lifetime survival and fecundity. Adaptive evolution in early life history traits involves a complex interplay between the developing plant and its current and future environments. We examined the plant’s earliest life history traits, dissecting an integrated suite of pre-germination processes: primary dormancy, thermal induction of secondary dormancy, and seasonal germination response. We examined genetic variation in the three processes, genetic correlations among the processes, and the scaling of...

Data from: Associative learning of flowers by generalist bumble bees can be mediated by microbes on the petals

Avery L. Russell & Tia-Lynn Ashman
Communication is often vital to the maintenance of mutualisms. In plant-pollinator mutualisms, plants signal pollinators via floral displays, composed of olfactory, visual, and other plant-derived cues. While plants are understood to be associated with microbes, only recently has the role of microbial (yeast and bacteria) inhabitants of flowers as intermediaries of plant-pollinator communication been recognized. Animals frequently use microbial cues to find resources, yet no study has examined whether microbes directly mediate learned and innate...

Data from: Using a continuum model to decipher the mechanics of embryonic tissue spreading from time-lapse image sequences: an approximate Bayesian computation approach

Tracy L. Stepien, Holley E. Lynch, Shirley X. Yancey, Laura Dempsey & Lance A. Davidson
Advanced imaging techniques generate large datasets that are capable of describing the structure and kinematics of tissue spreading in embryonic development, wound healing, and the progression of many diseases. Information in these datasets can be integrated with mathematical models to infer important biomechanical properties of the system. Standard computational tools for estimating relevant parameters rely on methods such as gradient descent and typically identify a single set of optimal parameters for a single experiment. These...

Data from: Who shares? Who doesn’t? Factors associated with openly archiving raw research data

Heather A. Piwowar
Many initiatives encourage investigators to share their raw datasets in hopes of increasing research efficiency and quality. Despite these investments of time and money, we do not have a firm grasp of who openly shares raw research data, who doesn’t, and which initiatives are correlated with high rates of data sharing. In this analysis I use bibliometric methods to identify patterns in the frequency with which investigators openly archive their raw gene expression microarray datasets...

Data from: Eutrophication and predation risk interact to affect sexual trait expression and mating success

Rickey Duane Cothran, Andy R Stiff, Punidan D Jeyasingh & Rick A Relyea
Sexual traits are especially sensitive to low food resources. Other environmental parameters (e.g., predation) should also affect sexual trait expression by favoring investment in viability traits rather than sexual traits. We know surprisingly little about how predators alter investment in sexual traits, or how predator and resource environments interact to affect sexual trait investment. We explored how increasing phosphorous (P) availability, at a level mimicking cultural eutrophication, affects the development of sexual, non-sexual, and viability...

Competition for pollination and isolation from mates differentially impact four stages of pollination in a model grassland perennial

Lea K. Richardson, M. Kate Gallagher, Tracie E. Hayes, Amanda S. Gallinat, Gretel Kiefer, Kristen Manion, Miriam Jenkins, Greg Diersen & Stuart Wagenius
1. Species that persist in small populations isolated by habitat destruction may experience reproductive failure. Self-incompatible plants face dual threats of mate-limitation and competition with co-flowering plants for pollination services. Such competition may lower pollinator visitation, increase heterospecific pollen transfer, and reduce the likelihood that a visit results in successful pollination. 2. To understand how isolation from mates and competition with co-flowering species contribute to reproductive failure in fragmented habitat, we conducted an observational study...

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