56 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...

Robust and distributed neural representation of action values

Eunju Shin, YunSil Jang, Soyoun Kim, Hoseok Kim, Xinying Cai, Hyunjung Lee, Jung Hoon Sul, Sung-Hyun Lee, Yeonseung Chung, Daeyeol Lee & Min Whan Jung
Studies in rats, monkeys, and humans have found action-value signals in multiple regions of the brain. These findings suggest that action-value signals encoded in these brain structures bias choices toward higher expected rewards. However, previous estimates of action-value signals might have been inflated by serial correlations in neural activity and also by activity related to other decision variables. Here, we applied several statistical tests based on permutation and surrogate data to analyze neural activity recorded...

Quantitative assessment of agricultural sustainability reveals divergent priorities among nations

Guolin Yao, Xin Zhang, Srishti Vishwakarma, Carole Dalin, Adam Komarek, David Kanter, Kyle Davis, Kimberly Pfeifer, Jing Zhao, Tan Zou, Paolo D'Odorico, Christian Folberth, Fernando Galeana Rodriguez, Jessica Fanzo, Lorenzo Rosa, William Dennison, Mark Musumba, Amy Heyman & Eric Davidson
Agriculture is fundamental to all three pillars of sustainability, environment, society, and economy. However, the definition of sustainable agriculture and capacities to measure it remain elusive. Independent and transparent measurements of national sustainability are needed to gauge progress, encourage accountability, and inform policy. Here, we developed a Sustainable Agriculture Matrix (SAM) to quantify national performance indicators in agriculture and to investigate the tradeoffs and synergies based on historical data for most countries of the world....

Left ventricular MRI segmentations

Ryan O'Hara
Hypertrophic cardiomyopathy (HCM) causes sudden cardiac death (SCD) due to ventricular arrhythmias (VA) manifesting from myocardial fibrosis proliferation. Current clinical risk stratification criteria inadequately identify at-risk patients in need of primary prevention of VA. Here, we use mechanistic computational modeling of the heart to analyze how HCM-specific remodeling of the heart promotes arrhythmogenesis and to develop a personalized strategy to forecast risk of VAs in these patients. We combine contrast-enhanced cardiac magnetic-resonance (CMR) imaging and...

Improved household living standards can restore dry tropical forests

Ruth DeFries, Meghna Agarwala, Sandra Baquie, Pooja Choksi, Sarika Khanwilkar, Pinki Mondal, Harini Nagendra & Johannes Uperlainen.
Despite multiple approaches over the last several decades to harmonize conservation and development goals in the tropics, forest-depende­­­­­­nt households remain the poorest in the world. Durable housing and alternatives to fuelwood for cooking are critical needs to reduce multi-dimensional poverty. These improvements also potentially reduce pressure on forests and alleviate forest degradation. We test this possibility in dry tropical forests of the Central Indian Highlands where tribal and other marginalized populations rely on forests for...

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...

Multiple cropping alone does not improve year-round food security among smallholders in rural India

Pinki Mondal, Ruth DeFries, Jessica Clark, Nicole Flowerhill, , Aurélie Harou, Shauna Downs & Jessica Fanzo
Achieving and maintaining food and nutrition security is an important Sustainable Development Goal (SDG), especially in countries with largely vulnerable population with high occurrence of hunger and malnutrition. By studying a small-scale agricultural system in India, we aim to understand the current state of dietary diversity and food insecurity among the farmer communities. The study landscape has witnessed a steady rise in multiple cropping along with irrigation over the last two decades. Whether this multiple...

Data from: Cholera outbreaks (2012) in three districts of Nepal reveal clonal transmission of multi-drug resistant Vibrio cholerae O1

Sameer M. Dixit, Fatema-Tuz Johura, Sulochana Manandhar, Abdus Sadique, Rajesh M. Rajbhandari, Shahnewaj B. Mannan, Mahamud-Ur Rashid, Saiful Islam, Dibesh Karmacharya, Haruo Watanabe, R. Bradley Sack, Alejandro Cravioto & Munirul Alam
Background: Although endemic cholera causes significant morbidity and mortality each year in Nepal, lack of information about the causal bacterium often hinders cholera intervention and prevention. In 2012, diarrheal outbreaks affected three districts of Nepal with confirmed cases of mortality. This study was designed to understand the drug response patterns, source, and transmission of Vibrio cholerae associated with 2012 cholera outbreaks in Nepal. Methods: V. cholerae (n = 28) isolated from 2012 diarrhea outbreaks {n...

Data from: Methods to identify and prioritize patient-centered outcomes for use in comparative effectiveness research

Evan Mayo-Wilson, Asieh Golozar, Terrie Cowley, Nicole Fusco, Gillian Gresham, Jennifer Haythornthwaite, Elizabeth Tolbert, Jennifer L. Payne, Lori Rosman, Susan Hutfless, Joseph K. Canner & Kay Dickersin
Background: We used various methods for identifying and prioritizing patient-centered outcomes (PCOs) for comparative effectiveness research (CER). Methods: We considered potential PCOs (“benefits” and “harms”) related to (1) gabapentin for neuropathic pain and (2) quetiapine for bipolar depression. Part 1 (April 2014 to March 2015): we searched for PCO research and core outcome sets (COSs). We conducted electronic searches of bibliographic databases and key websites and examined FDA prescribing information and reports of clinical trials...

Preservation of erniettomorph fossils in clay-rich siliciclastic deposits from the Ediacaran Wood Canyon Formation, Nevada

James Hall, Emmy Smith, Nobumichi Tamura, Sirine Fakra & Tanja Bosak
Three-dimensionally preserved Ediacaran fossils occur globally within sandstone beds. Sandy siliciclastic deposits of the Ediacaran Wood Canyon Formation (WCF) in the Montgomery Mountains, Nevada, contain two taphomorphs of erniettomorphs, soft-bodied organisms with uncertain taxonomic affinities. One taphomorph exhibits mm-scale ridges and a distinct lower boundary, the other is devoid of these diagnostic features but is similar in size and shape. We explore the cast-and-mould preservation of both taphomorphs by petrography, Raman spectroscopy, X-ray fluorescence microprobe,...

Data from: Suppression and facilitation of human neural responses

Michael-Paul Schallmo, Alexander M. Kale, Rachel Millin, Anastasia V. Flevaris, Zoran Brkanac, Richard A.E. Edden, Raphael A. Bernier, Scott Murray, Scott O Murray & Richard AE Edden
Efficient neural processing depends on regulating responses through suppression and facilitation of neural activity. Utilizing a well-known visual motion paradigm that evokes behavioral suppression and facilitation, and combining 5 different methodologies (behavioral psychophysics, computational modeling, functional MRI, pharmacology, and magnetic resonance spectroscopy), we provide evidence that challenges commonly held assumptions about the neural processes underlying suppression and facilitation. We show that: 1) both suppression and facilitation can emerge from a single, computational principle - divisive...

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  • Johns Hopkins University
  • University of Washington
  • University of Delaware
  • New York University
  • McGill University
  • Imperial College London
  • Howard Hughes Medical Institute
  • Rice University
  • Sao Paulo State University
  • Columbia University