47 Works

Data from: Hedging your bets: intermediate movements as optimal behavior in the context of an incomplete decision

Adrian M. Haith, David M. Huberdeau & John W. Krakauer
Existing theories of movement planning suggest that it takes time to select and prepare the actions required to achieve a given goal. These theories often appeal to circumstances where planning apparently goes awry. For instance, if reaction times are forced to be very low, movement trajectories are often directed between two potential targets. These intermediate movements are generally interpreted as errors of movement planning, arising either from planning being incomplete or from parallel movement plans...

Data from: Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans

Ho-Yon Hwang & Jiou Wang
Genetic diversity is maintained by continuing generation and removal of variants. While examining over 800,000 DNA variants in wild isolates of Caenorhabditis elegans, we made a discovery that the proportions of variant types are not constant across the C. elegans genome. The variant proportion is defined as the fraction of a specific variant type (e.g. single nucleotide polymorphism (SNP) or indel) within a broader set of variants (e.g. all variants or all non-SNPs). The proportions...

Data from: Cherry-picking by trialists and meta-analysts can drive conclusions about intervention efficacy

Evan Mayo-Wilson, Tianjing Li, Nicole Fusco, Lorenzo Bertizzolo, Joseph K. Canner, Terrie Cowley, Peter Doshi, Jeffrey Ehmsen, Gillian Gresham, Nan Guo, Jennifer A. Haythornthwaite, James Heyward, Hwanhee Hong, Diana Pham, Jennifer L. Payne, Lori Rosman, Elizabeth A. Stuart, Catalina Suarez-Cuervo, Elizabeth Tolbert, Claire Twose, Swaroop Vedula & Kay Dickersin
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN SUBSEQUENT PUBLICATIONS. PLEASE SEE http://dx.doi.org/10.1016/j.jclinepi.2017.05.007 FOR MORE INFORMATION. Objectives The objective of this study was to determine whether disagreements among multiple data sources affect systematic reviews of randomized clinical trials (RCTs). Study Design and Setting Eligible RCTs examined gabapentin for neuropathic pain and quetiapine for bipolar depression, reported in public (e.g., journal articles) and nonpublic sources (clinical study reports [CSRs] and individual participant data [IPD]). Results...

Data from: Vocal turn-taking in a nonhuman primate is learned during ontogeny

Cecilia P. Chow, Jude F. Mitchell & Cory T. Miller
Conversational turn-taking is an integral part of language development, as it reflects a confluence of social factors that mitigate communication. Humans coordinate the timing of speech based on the behaviour of another speaker, a behaviour that is learned during infancy. While adults in several primate species engage in vocal turn-taking, the degree to which similar learning processes underlie its development in these non-human species or are unique to language is not clear. We recorded the...

Data from: Evolution of early Eocene Palaeosinopa (Mammalia, Pantolestidae) in the Willwood Formation of the Bighorn Basin, Wyoming

Rachel H. Dunn & Kenneth D. Rose
Species-level diversity and evolution of Palaeosinopa from the Willwood Formation of the Bighorn Basin is reassessed based on substantial new material from the Bighorn, Powder River, and Wind River basins. We recognize three species of Palaeosinopa in the Willwood Formation of the Bighorn Basin: P. lutreola, P. incerta, and P. veterrima. The late Wasatchian species P. didelphoides is not present in the Bighorn Basin. The Willwood species can be differentiated based only on size. P....

Social bonds, social status and survival in wild baboons: a tale of two sexes

Fernando Campos, Francisco Villavicencio, Elizabeth Archie, Fernando Colchero & Susan Alberts
People who are more socially integrated or have higher socio-economic status live longer. Recent studies in nonhuman primates show striking convergences with this human pattern: female primates with more social partners, stronger social bonds or higher dominance rank all lead longer lives. However, it remains unclear whether social environments also predict survival in male nonhuman primates, as it does in men. This gap persists because, in most primates, males disperse among social groups, resulting in...

2019 NSF Workshop on Connecting Large Facilities and Cyberinfrastructure

Ewa Deelman, Ilya Baldin, Brian Bockelman, Adam Bolton, Patrick Brady, Tom Cheatham, Laura Christopherson, Rafael Ferreira da Silva, Tom Gulbransen, Kate Keahey, Marina Kogan, Anirban Mandal, Angela Murillo, Jarek Nabrzyski, Valerio Pascucci, Steve Petruzza, Mats Rynge, Susan Sons, Dan Stanzione, Chaudhuri Surajit, Daryl Swensen, Alexander Szalay, Douglas Thain, John Towns, Charles Vardeman … & Jane Wyngaard

Data from: Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish

Stefan Dennenmoser, Fritz J. Sedlazeck, Michael C. Schatz, Janine Altmüller, Matthias Zytnicki & Arne W. Nolte
Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through non-allelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination-based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genome-wide distribution of transposon insertions in a young hybrid lineage (“invasive...

Data from: A 2.6‐g sound and movement tag for studying the acoustic scene and kinematics of echolocating bats

Laura Stidsholt, Mark Johnson, Kristian Beedholm, Lasse Jakobsen, Kathrin Kugler, Signe Brinkløv, Angeles Salles, Cynthia F. Moss & Peter Teglberg Madsen
1. To study sensorimotor behaviour in wild animals, it is necessary to synchronously record the sensory inputs available to the animal, and its movements. To do this, we have developed a biologging device that can record the primary sensory information and the associated movements during foraging and navigating in echolocating bats. 2. This 2.6 -gram tag records the sonar calls and echoes from an ultrasonic microphone, while simultaneously sampling fine-scale movement in three dimensions from...

Data from: Clinical study reports of randomised controlled trials: an exploratory review of previously confidential industry reports

Peter Doshi & Tom Jefferson
Objective: To explore the structure and content of a non-random sample of clinical study reports (CSRs) to guide clinicians and systematic reviewers. Search strategy: We searched public sources and lodged Freedom of Information requests for previously confidential CSRs primarily written by industry for regulators. Selection criteria: CSR reporting sufficient information for extraction (“adequate”). Primary outcome measures: Presence and length of essential elements of trial design and reporting and compression factor (ratio of page length for...

Data from: Fisher’s geometric model predicts the effects of random mutations when tested in the wild

Frank W. Stearns & Charles B. Fenster
Fisher's Geometric Model of Adaptation (FGM) has been the conceptual foundation for studies investigating the genetic basis of adaptation since the onset of the neo Darwinian synthesis. FGM describes adaptation as the movement of a genotype toward a fitness optimum due to beneficial mutations. To date, one prediction of FGM, the probability of improvement is related to the distance from the optimum, has only been tested in microorganisms under laboratory conditions. There is reason to...

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas Buckley, Brett Calcott, Junqing Chen … & Xin Zhou
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight...

Data from: Protein synthesis inhibition in the peri-infarct cortex slows motor recovery in rats

Maximilian Schubring-Giese, Susan Leemburg, Andreas Rüdiger Luft & Jonas Aurel Hosp
Neuroplasticity and reorganization of brain motor networks are thought to enable recovery of motor function after ischemic stroke. Especially in the cortex surrounding the ischemic scar (i.e., peri-infarct cortex), evidence for lasting reorganization has been found at the level of neurons and networks. This reorganization depends on expression of specific genes and subsequent protein synthesis. To test the functional relevance of the peri-infarct cortex for recovery we assessed the effect of protein synthesis inhibition within...

Data from: Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

Anand Ranjan, Vu Q. Nguyen, Sheng Liu, Jan Wisniewski, Kim Jee Min, Xiaona Tang, Gaku Mizuguchi, Vivian Jou, Timothy J. Nickels, Brian P. English, Qinsi Zheng, Ed Luk, Timothee Lionnet, Luke D. Lavis, Carl Wu & Ejlal Elalaoui
The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit...

Microfluidic droplet application for bacterial surveillance in fresh-cut produce wash waters

J. B. Harmon, H. K. Gray, C. Young & K. J. Schwab
Foodborne contamination and associated illness in the United States is responsible for an estimated 48 million cases per year. Increased food demand, global commerce of perishable foods, and the growing threat of antibiotic resistance are driving factors elevating concern for food safety. Foodborne illness is often associated with fresh-cut, ready-to-eat produce commodities due to the perishable nature of the product and relatively minimal processing from farm to the consumer. The research presented here optimizes and...

Data from: Cardiac and skeletal muscle effects in the randomized HOPE-Duchenne trial

Michael Taylor, John Jefferies, Barry Byrne, Joao Lima, Bharath Ambale-Venkatesh, Mohammad R. Ostovaneh, Raj Makkar, Bryan Goldstein, Rachel Ruckdeschel Smith, James Fudge, Konstantinos Malliaras, Brian Fedor, Jeff Rudy, Janice M. Pogoda, Linda Marbán, Deborah D. Ascheim, Eduardo Marbán & Ronald G. Victor
Objective: To assess the feasibility, safety, and efficacy of intracoronary allogeneic cardiosphere-derived cells (CAP-1002) in patients with Duchenne muscular dystrophy (DMD). Methods: The Halt Cardiomyopathy Progression (HOPE)-Duchenne trial is a phase I/II, randomized, controlled, open-label trial (NCT02485938). Patients with DMD >12 years old, with substantial myocardial fibrosis, were randomized (1:1) to usual care (control) or global intracoronary infusion of CAP-1002 (75 million cells). Participants were enrolled at 3 US medical centers between January and August...

Data from: Competition and constraint drove Cope's rule in the evolution of giant flying reptiles

Roger B. J. Benson, Rachel A. Frigot, Anjali Goswami, Brian Andres & Richard J. Butler
The pterosaurs, Mesozoic flying reptiles, attained wingspans of more than 10 m that greatly exceed the largest birds and challenge our understanding of size limits in flying animals. Pterosaurs have been used to illustrate Cope’s rule, the influential generalization that evolutionary lineages trend to increasingly large body sizes. However, unambiguous examples of Cope’s rule operating on extended timescales in large clades remain elusive, and the phylogenetic pattern and possible drivers of pterosaur gigantism are uncertain....

Extending adaptor grammars to learn phonological alternations

Canaan Breiss & Colin Wilson

Data from: Validation of serum neurofilaments as prognostic & potential pharmacodynamic biomarkers for ALS

Michael Benatar, Lanyu Zhang, Lily Wang, Volkan Granit, Jeffrey Statland, Richard Barohn, Andrea Swenson, John Ravitz, Carlayne Jackson, Ted Burns, Jaya Trivedi, Erik Pioro, James Caress, Jonathan Katz, Jacob McCauley, Rosa Rademakers, Andrea Malaspina, Lyle Ostrow & Joanne Wuu
Objective. Identify preferred neurofilament assays, and clinically validate serum NfL and pNfH as prognostic and potential pharmacodynamic biomarkers relevant to ALS therapy development. Methods. Prospective, multi-center, longitudinal observational study of patients with ALS (n=229), primary lateral sclerosis (PLS, n=20) and progressive muscular atrophy (PMA, n=11). Biological specimens were collected, processed and stored according to strict standard operating procedures (SOPs) 1. Neurofilament assays were performed in a blinded manner by independent contract research organizations (CROs). Results....

Data from: A prospective study of serum metabolites and risk of ischemic stroke

Daokun Sun, Steffen Tiedt, Bing Yu, Xueqiu Jian, Rebecca F. Gottesman, Tom H. Mosley, Eric Boerwinkle, Martin Dichgans & Myriam Fornage
Objective: To identify promising blood-based biomarkers and novel etiological pathways of disease risk, we applied an untargeted serum metabolomics profiling in a community-based prospective study of ischemic stroke (IS). Methods: In 3,904 men and women from the Atherosclerosis Risk In Communities (ARIC) study, Cox proportional hazard models were used to estimate the association of incident IS with the standardized level of 245 fasting serum metabolites individually, adjusting for age, sex, race, field center, batch, diabetes,...

Data from: Lower carotid revascularization rates after stroke in ethnic minority-serving US hospitals

Roland Faigle, Lisa A. Cooper & Rebecca F. Gottesman
Objective: We sought to determine whether the use of carotid revascularization procedures after stroke due to carotid stenosis differs between minority-serving hospitals and hospitals serving predominantly white patients. Methods: We identified ischemic stroke cases due to carotid disease, identified by ICD9-CM codes, from 2007-2011 in the Nationwide Inpatient Sample. The use of carotid endarterectomy (CEA) and carotid artery stenting (CAS) was recorded. Hospitals with ≥40% ethnic minority patients (minority-serving hospitals) were compared to hospitals with...

Data from: Ethanol abolishes vigilance-dependent astroglia network activation in mice by inhibiting norepinephrine release

Martin Paukert, Liang Ye, Murat Orynbayev, Xiangyu Zhu, Eunice Lim, Ram Dereddi, Amit Agarwal, Dwight Bergles & Manzoor Bhat
This collection of data sets was obtained during a study of the effect of acute ethanol intoxication on vigilance-dependent astroglia network activation in mice. The main findings have been that ethanol inhibits astroglia activation by inhibiting vigilance-dependent norepinephrine release. This leads to a failure of activation of alpha1A-adrenergic receptors on astroglia. Further, this study has revealed that ethanol inhibition of cerebellar Bergmann glia Ca2+ activation does not account for ataxic motor behavior, but may rather...

Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella

Meredith M. Doellman, Gregory J. Ragland, Glen R. Hood, Peter J. Meyers, Scott P. Egan, Thomas H.Q. Powell, Peter Lazorchak, Mary M. Glover, Cheyenne Tait, Hannes Schuler, Daniel A. Hahn, Stewart H. Berlocher, James J. Smith, Patrik Nosil, Jeffrey L. Feder, Daniel Hahn, Stewart Berlocher, Peter Meyers, Scott Egan, Jeffrey Feder, Glen Hood, Thomas Powell & Gregory Ragland
A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: Substance P signalling in primary motor cortex facilitates motor learning in rats

Benjamin Hertler, Jonas Aurel Hosp, Manuel Buitrago Blanco & Andreas Rüdiger Luft
Among the genes that are up-regulated in response to a reaching training in rats, Tachykinin 1 (Tac1) - a gene that encodes the neuropeptide Substance P (Sub P) - shows an especially strong expression. Using Real-Time RT-PCR, a detailed time-course of Tac1 expression could be defined: a significant peak occurs 7 hours after training ended at the first and second training session, whereas no up-regulation could be detected at a later time-point (sixth training session)....

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