107 Works

Data from: Surface energies of elemental crystals

Richard Tran, Zihan Xu, Balachandran Radhakrishnan, Donald Winston, Wenhao Sun, Kristin A. Persson & Shyue Ping Ong
The surface energy is a fundamental property of the different facets of a crystal that is crucial to the understanding of various phenomena like surface segregation, roughening, catalytic activity, and the crystal’s equilibrium shape. Such surface phenomena are especially important at the nanoscale, where the large surface area to volume ratios leads to properties that are significantly different from the bulk. In this work, we present the largest database of the calculated surface energies of...

Data from: Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus

Nadav Kashtan, Sara E. Roggensack, Sébastien Rodrigue, Jessie W. Thompson, Steven J. Biller, Allison Coe, Huiming Ding, Pekka Marttinen, Rex R. Malmstrom, Roman Stocker, Michael J. Follows, Ramunas Stepanauskas & Sallie W. Chisholm
Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct “genomic backbones,” each backbone consisting of a different set of...

Data from: Processing political misinformation: comprehending the Trump phenomenon

Briony Swire, Adam J. Berinsky, Stephan Lewandowsky & Ullrich K. H. Ecker
This study investigated the cognitive processing of true and false political information. Specifically, it examined the impact of source credibility on the assessment of veracity when information comes from a polarizing source (Experiment 1), and effectiveness of explanations when they come from one's own political party or an opposition party (Experiment 2). These experiments were conducted prior to the 2016 Presidential election. Participants rated their belief in factual and incorrect statements that President Trump made...

Data from: Effects of diet on cranial morphology and biting ability in musteloid mammals

Chris J. Law, Emma Duran, Nancy Hung, Ekai Richards, Isaac Santillan & Rita S. Mehta
Size and shape are often considered important variables that lead to variation in performance. In studies of feeding, size‐corrected metrics of the skull are often used as proxies of biting performance; however, few studies have examined the relationship between cranial shape in its entirety and estimated bite force across species and how dietary ecologies may affect these variables differently. Here, we used geometric morphometric and phylogenetic comparative approaches to examine relationships between cranial morphology and...

Data from: A new giant titanosaur sheds light on body mass evolution among sauropod dinosaurs

Jose L. Carballido, Diego Pol, Alejandro Otero, Ignacio Cerda, Leonardo Salgado, Alberto C. Garrido, Jahandar Ramezani, Nestor R. Cúneo & Javier M. Krause
Titanosauria was the most diverse and successful lineage of sauropod dinosaurs. This clade had its major radiation during the middle Early Cretaceous and survived up to the end of that period. Among sauropods, this lineage has the most disparate values of body mass, including the smallest and largest sauropods known. Although recent findings have improved our knowledge on giant titanosaur anatomy, there are still many unknown aspects about their evolution, especially for the most gigantic...

Data from: Pioneer cells established by the [SWI+] prion can promote dispersal and out-crossing in yeast

Gregory A. Newby & Susan Lindquist
To thrive in an ever-changing environment, microbes must widely distribute their progeny to colonize new territory. Simultaneously, they must evolve and adapt to the stresses of unpredictable surroundings. In both of these regards, diversity is key—if an entire population moved together or responded to the environment in the same way, it could easily go extinct. Here, we show that the epigenetic prion switch [SWI+] establishes a specialized subpopulation with a “pioneer” phenotypic program in Saccharomyces...

Data from: Relation between stability and resilience determines the performance of early warning signals under different environmental drivers

Lei Dai, Kirill S. Korolev & Jeff Gore
Shifting patterns of temporal fluctuations have been found to signal critical transitions in a variety of systems, from ecological communities to human physiology. However, failure of these early warning signals in some systems calls for a better understanding of their limitations. In particular, little is known about the generality of early warning signals in different deteriorating environments. In this study, we characterized how multiple environmental drivers influence the dynamics of laboratory yeast populations, which was...

Data from: Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle

Jacob R. Waldbauer, Sebastien Rodrigue, Maureen L. Coleman & Sallie W. Chisholm
BACKGROUND: Growth of the ocean’s most abundant primary producer, the cyanobacterium Prochlorococcus, is tightly synchronized to the natural 24-hour light-dark cycle. We sought to quantify the relationship between transcriptome and proteome dynamics that underlie this obligate photoautotroph’s highly choreographed response to the daily oscillation in energy supply. METHODOLOGY/PRINCIPAL FINDINGS: Using Illumina RNA-sequencing transcriptomics and mass spectrometry-based quantitative proteomics, we measured timecourses of paired mRNA-protein abundances for 312 genes every 2 hours over a light-dark cycle....

Data from: International collaboration and spatial dynamics of US patenting in Central and Eastern Europe 1981-2010

Mariann Leskó & Balázs Lengyel
How did post-socialist transition and a parallel shift in international labor division restructure regional innovation systems in Central and Eastern Europe? This question is increasingly important, because current EU innovation policy is combined with regional development in Smart Specialization Strategies; however, spatial trends of innovation in Central and Eastern Europe are not fully understood which might lead to less than perfectly efficient policy. In this paper we describe the spatial dynamics of inventor activity in...

Data from: Metamorphosis is ancestral for crown euarthropods, and evolved in the Cambrian or earlier

Joanna M. Wolfe
Macroevolutionary developmental biology employs fossilized ontogenetic data and phylogenetic comparative methods to probe the evolution of development at ancient nodes. Despite the prevalence of ecologically differentiated larval forms in marine invertebrates, it has been frequently presumed that the ancestors of arthropods were direct developers, and that metamorphosis may not have evolved until the Ordovician or later. Using fossils and new dated phylogenies, I infer that metamorphosis was likely ancestral for crown arthropods, contradicting this assumption....

Data from: Horizontal gene transfer constrains the timing of methanogen evolution

Joanna M. Wolfe & Gregory P. Fournier
Microbial methanogenesis may have been a major component of Earth’s carbon cycle during the Archaean eon, generating a methane greenhouse that increased global temperatures enough for a liquid hydrosphere, despite the Sun’s lower luminosity at the time. Evaluation of potential solutions to the ‘faint young Sun’ hypothesis by determining the age of microbial methanogenesis has been limited by ambiguous geochemical evidence and the absence of a diagnostic fossil record. To overcome these challenges, we use...

Data from: Seasonal variation in life history traits in two Drosophila species

Emily L. Behrman, Samuel S. Watson, Katherine R. O'Brien, Shane M. Heschel & Paul S. Schmidt
Seasonal environmental heterogeneity is cyclic, persistent and geographically widespread. In species that reproduce multiple times annually, environmental changes across seasonal time may create different selection regimes that may shape the population ecology and life history adaptation in these species. Here, we investigate how two closely related species of Drosophila in a temperate orchard respond to environmental changes across seasonal time. Natural populations of Drosophila melanogaster and D. simulans were sampled at four timepoints from June...

Physiologic Response to Changes in Posture

Thomas Heldt
A collection of physiological signals in ten healthy subjects in response to a slow tilt, a fast tilt, and a standing-up maneuver.

Tidal dispersion in short estuaries

Adrian Mikhail P. Garcia & W. Rockwell Geyer
The salinity distribution of an estuary depends on the balance between the river outflow, which is seaward, and a dispersive salt flux, which is landward. The dispersive salt flux at a fixed cross-section can be divided into shear dispersion, which is caused by spatial correlations of the cross-sectionally varying velocity and salinity, and the tidal oscillatory salt flux, which results from the tidal correlation between the cross-section averaged, tidally varying components of velocity and salinity....

Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids

Rubén Sancho, Luis Ángel Inda, Antonio Díaz-Pérez, David L Des Marais, Sean Gordon, John Vogel, Joanna Lusinska, Robert Hasterok, Bruno Contreras-Moreira & Pilar Catalán
Unraveling the evolution of plant polyploids is a challenge when their diploid progenitor species are extinct or unknown or when genome sequences of known progenitors are unavailable. Existing subgenome identification methods cannot adequately infer the homeologous genomes that are present in the allopolyploids if they do not take into account the potential existence of unknown progenitors. We addressed this challenge in the widely distributed dysploid grass genus Brachypodium, which is a model genus for temperate...

Data from: Deep learning unlocks X‐ray microtomography segmentation of multiclass microdamage in heterogeneous materials

Reed Kopp, Joshua Joseph, Xinchen Ni, Nicholas Roy & Brian L. Wardle
Four-dimensional quantitative characterization of heterogeneous materials using in situ synchrotron radiation computed tomography can reveal 3D sub-micron features, particularly damage, evolving under load, leading to improved materials. However, dataset size and complexity increasingly require time-intensive and subjective semi-automatic segmentations. Here, we present the first deep learning (DL) convolutional neural network (CNN) segmentation of multiclass microscale damage in heterogeneous bulk materials, teaching on advanced aerospace-grade composite damage using ≈65,000 (trained) human-segmented tomograms. The trained CNN machine...

Data from: Automated deep-phenotyping of the vertebrate brain

Amin Allalou, Yuelong Wu, Mostafa Ghannad-Rezaie, Peter M. Eimon, Mehmet Faith Yanik & Mehmet Fatih Yanik
Here we describe an automated platform suitable for large-scale deep-phenotyping of zebrafish mutant lines, which uses optical projection tomography to rapidly image brain-specific gene expression patterns in 3D at cellular resolution. Registration algorithms and correlation analysis are then used to compare 3D expression patterns, to automatically detect all statistically significant alterations in mutants, and to map them onto a brain atlas. Automated deep-phenotyping of a mutation in the master transcriptional regulator fezf2 not only detects...

Data from: The decay of motor adaptation to novel movement dynamics reveals an asymmetry in the stability of motion state-dependent learning

Eghbal A. Hosseini, Katrina P. Nguyen & Wilsaan M. Joiner
Motor adaptation paradigms provide a quantitative method to study short-term modification of motor commands. Despite the growing understanding of the role motion states (e.g., velocity) play in this form of motor learning, there is little information on the relative stability of memories based on these movement characteristics, especially in comparison to the initial adaptation. Here, we trained subjects to make reaching movements perturbed by force patterns dependent upon either limb position or velocity. Following training,...

Data from: Evidence for a time-invariant phase variable in human ankle control

Robert D. Gregg, Elliott J. Rouse, Levi J. Hargrove & Jonathon W. Sensinger
Human locomotion is a rhythmic task in which patterns of muscle activity are modulated by state-dependent feedback to accommodate perturbations. Two popular theories have been proposed for the underlying embodiment of phase in the human pattern generator: a time-dependent internal representation or a time-invariant feedback representation (i.e., reflex mechanisms). In either case the neuromuscular system must update or represent the phase of locomotor patterns based on the system state, which can include measurements of hundreds...

Data from: Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress-response and developmental genes when exposed to a biologically realistic heat stress

Blair P. Bentley, Brian J. Haas, Jamie N. Tedeschi & Oliver Berry
Oviparous reptile embryos are expected to breach their critical thermal maxima if temperatures reach those predicted under current climate change models due to the lack the maternal buffering processes and parental care. Heat shock proteins (HSPs) are integral in the molecular response to thermal stress, and their expression is heritable, but the roles of other candidate families such as the heat shock factors (HSFs) have not been determined in reptiles. Here we subject embryonic sea...

Data from: Generic indicators for loss of resilience before a tipping point leading to population collapse

Lei Dai, Daan Vorselen, Kirill S. Korolev & Jeff Gore
Theory predicts that the approach of catastrophic thresholds in natural systems (e.g., ecosystems, the climate) may result in an increasingly slow recovery from small perturbations, a phenomenon called critical slowing down. We used replicate laboratory populations of the budding yeast Saccharomyces cerevisiae for direct observation of critical slowing down before population collapse. We mapped the bifurcation diagram experimentally and found that the populations became more vulnerable to disturbance closer to the tipping point. Fluctuations of...

Data from: tableone: An open source Python package for producing summary statistics for research papers

Tom J. Pollard, Alistair E. W. Johnson, Jesse D. Raffa & Roger G. Mark
Objectives: In quantitative research, understanding basic parameters of the study population is key for interpretation of the results. As a result, it is typical for the first table (“Table 1”) of a research paper to include summary statistics for the study data. Our objectives are 2-fold. First, we seek to provide a simple, reproducible method for providing summary statistics for research papers in the Python programming language. Second, we seek to use the package to...

Data from: Distinct roles of visual, parietal, and frontal motor cortices in memory-guided sensorimotor decisions

Michael J. Goard, Gerald N. Pho, Jonathan Woodson & Mriganka Sur
Mapping specific sensory features to future motor actions is a crucial capability of mammalian nervous systems. We investigated the role of visual (V1), posterior parietal (PPC), and frontal motor (fMC) cortices for sensorimotor mapping in mice during performance of a memory-guided visual discrimination task. Large-scale calcium imaging revealed that V1, PPC, and fMC neurons exhibited heterogeneous responses spanning all task epochs (stimulus, delay, response). Population analyses demonstrated unique encoding of stimulus identity and behavioral choice...

Data from: Low fossilization potential of keratin protein revealed by experimental taphonomy

Evan T. Saitta, Chris Rogers, Richard A. Brooker, Geoffrey D. Abbott, Sumit Kumar, Shane S. O'Reilly, Paul Donohoe, Suryendu Dutta, Roger E. Summons & Jakob Vinther
Recent studies have suggested the presence of keratin in fossils dating back to the Mesozoic. However, ultrastructural studies revealing exposed melanosomes in many fossil keratinous tissues suggest that keratin should rarely, if ever, be preserved. In this study, keratin's stability through diagenesis was tested using microbial decay and maturation experiments on various keratinous structures. The residues were analysed using pyrolysis-gas chromatography-mass spectrometry and compared to unpublished feather and hair fossils and published fresh and fossil...

Data from: Prediction limits of mobile phone activity modelling

Daniel Kondor, Sebastian Grauwin, Zsófia Kallus, István Gódor, Stanislav Sobolevsky & Carlo Ratti
Thanks to their widespread usage, mobile devices have become one of the main sensors of human behaviour and digital traces left behind can be used as a proxy to study urban environments. Exploring the nature of the spatio-temporal patterns of mobile phone activity could thus be a crucial step towards understanding the full spectrum of human activities. Using 10 months of mobile phone records from Greater London resolved in both space and time, we investigate...

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