43 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...

The human origin recognition complex (ORC) is essential for pre-RC assembly, mitosis and maintenance of nuclear structure

Hsiang-Chen Chou, Kuhulika Bhalla, Osama-El Demerdesh, Olaf Klingbeil, Kaarina Hanington, Sergey Aganezov, Peter Andrews, Habeeb Alsudani, Kenneth Chang, Christopher R. Vakoc, Michael C. Schatz, Richard W. McCombie & Bruce Stillman
The origin recognition complex (ORC) cooperates with CDC6, MCM2-7, and CDT1 to form pre-RC complexes at origins of DNA replication. Here, using tiling-sgRNA CRISPR screens, we report that each subunit of ORC and CDC6 is essential in human cells. Using an auxin-inducible degradation system, we created stable cell lines capable of ablating ORC2 rapidly, revealing multiple cell division cycle phenotypes. The primary defects in the absence of ORC2 were cells encountering difficulty in initiating DNA...

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: Integration of genomics and transcriptomics predicts diabetic retinopathy susceptibility genes

Andrew Skol, Segun Jung, Ana Marija Sokovic, Siquan Chen, Sarah Fazal, Olukayode Sosina, Poulami Borkar, Amy Lin, Maria Sverdlov, Dingcai Cao, Anand Swaroop, Ionut Bebu, Barbara Stranger & Michael Grassi
We determined differential gene expression in response to high glucose in lymphoblastoid cell lines derived from matched individuals with type 1 diabetes with and without retinopathy. Those genes exhibiting the largest difference in glucose response were assessed for association to diabetic retinopathy in a genome-wide association study meta-analysis. Expression Quantitative Trait Loci (eQTLs) of the glucose response genes were tested for association with diabetic retinopathy. We detected an enrichment of the eQTLs from the glucose...

Mass ratio effects underlie ecosystem responses to environmental change

Melinda Smith, Sally Koerner, Alan Knapp, Meghan Avolio, Francis Chaves, Elsie Denton, John Dietrich, David Gibson, Jesse Gray, Ava Hoffman, David Hoover, Kimberly Komatsu, Andrea Silletti, Kevin Wilcox, Qiang Yu & John Blair
1. Random species loss has been shown experimentally to reduce ecosystem function, sometimes more than other anthropogenic environmental changes. Yet, controversy surrounds the importance of this finding for natural systems where species loss is non-random. 2. We compiled data from 16 multi-year experiments located at a single site in native tallgrass prairie. These experiments included responses to 11 anthropogenic environmental changes, as well as non-random biodiversity loss - either the removal of uncommon/rare plant species...

Data from: Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance

Michael D. Martin, Elizabeth A. Zimmer, Morten T. Olsen, Andrew D. Foote, M. Thomas P. Gilbert & Grace S. Brush
Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre-dating introduction can be important determinants of later success, large-scale investigations of historical genetic structure have not been feasible. Common ragweed (Ambrosia artemisiifolia L.) is an invasive weed native to North America that is known for its allergenic pollen. Palynological records from sediment cores indicate that this species was uncommon before European colonization of North...

Data from: EDAPHOLOG monitoring system: automatic, real-time detection of soil microarthropods

Miklós Dombos, Oxána Bánszegi, Katalin Szlávecz & Andrés Kosztolányi
Soil microarthropods as organic matter decomposers play an important role in soil functioning thus providing ecosystem services. However, ecosystem scale investigations on their abundance and dynamics are scarce because their high spatio-temporal heterogeneity requires huge sample size. Processing and identifying large number of individuals are extremely labour-intensive. We prototyped a device called EDAPHOLOG monitoring system that consists of (1) a probe that catches and detects microarthropods and estimates their body size; (2) a data logger...

Data from: Phylogenetic, ecological, and allometric correlates of cranial shape in Malagasy lemuriforms

Karen L. Baab, Jonathan M. G. Perry, F. James Rohlf & William L. Jungers
Adaptive radiations provide important insights into many aspects of evolution, including the relationship between ecology and morphological diversification as well as between ecology and speciation. Many such radiations include divergence along a dietary axis, although other ecological variables may also drive diversification, including differences in diel activity patterns. This study examines the role of two key ecological variables, diet and activity patterns, in shaping the radiation of a diverse clade of primates, the Malagasy lemurs....

Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

Gerard A. Silvestri, Nichole T. Tanner, Paul Kearney, Anil Vachani, Pierre P. Massion, Alexander Porter, Steven C. Springmeyer, Kenneth C. Fang, David Midthun, Peter J. Mazzone, D. Madtes, J. Landis, A. Levesque, K. Rothe, M. Balaan, B. Dimitt, B. Fortin, N. Ettinger, A. Pierre, L. Yarmus, K. Oakjones-Burgess, N. Desai, Z. Hammoud, A. Sorenson, R. Murali … & F. Allison
Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two...

Data from: Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

Oliver Ratmann, M. Kate Grabowski, Matthew Hall, Tanya Golubchik, Chris Wymant, Lucie Abeler-Dörner, David Bonsall, Anne Hoppe, Andrew Leigh Brown, Tulio De Oliveira, Astrid Gall, Paul Kellam, Deenan Pillay, Joseph Kagaayi, Godfrey Kigozi, Thomas C. Quinn, Maria J. Wawer, Oliver Laeyendecker, David Serwadda, Ronald H. Gray, Christophe Fraser, &
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from...

Data from: Neural correlates of domain-specific cognitive decline: the ARIC-NCS study

Andrea Lauren Christman Schneider, Matthew L Senjem, Aozhou Wu, Alden Gross, David S. Knopman, Jeffrey L Gunter, Christopher G Schwarz, Tom H. Mosley, Rebecca F. Gottesman, A. Richey Sharrett & Clifford R. Jack
Objective: To evaluate the association of cognitive declines in the domains of memory, language, and executive function with brain gray matter (GM) volume in old age. Methods: Prospective study of 1,846 participants in the Atherosclerosis Risk in Communities (ARIC) study who underwent 3T brain MRI scans in 2011-2013. Participants were categorized by cognitive domain performance trajectory over the prior 20 years (cut-point to define decline: 20th percentile). Associations between GM volume and cognitive declines were...

Data from: Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies

Meredith M. Doellman, Scott P. Egan, Gregory J. Ragland, Peter J. Meyers, Glen R. Hood, Thomas H.Q. Powell, Peter Lazorchak, Daniel A. Hahn, Stewart H. Berlocher, Patrik Nosil, Jeff L. Feder, Jeffrey L. Feder & Thomas H. Q. Powell
Taxa harboring high levels of standing variation may be more likely to adapt to rapid environmental shifts and experience ecological speciation. Here, we characterize geographic and host-related differentiation for 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies to infer if standing genetic variation in adult eclosion time in the ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new mutations, contributed substantially to its recent shift to earlier fruiting apple (Malus domestica). Allele frequency...

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