21 Works

Data from: Changeable camouflage: how well can flounder resemble the colour and spatial scale of substrates in their natural habitats?

Derya Akkaynak, Liese Siemann, Alexandra Barbosa & Lydia M. Mäthger
Flounder change colour and pattern for camouflage. We used a spectrometer to measure reflectance spectra and a digital camera to capture body patterns of two flounder species camouflaged on four natural backgrounds of different spatial scale (sand, small gravel, large gravel and rocks). We quantified the degree of spectral match between flounder and background relative to the situation of perfect camouflage in which flounder and background were assumed to have identical spectral distribution. Computations were...

Data from: Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

Dmitry Shungin, Wei Q. Deng, Tibor V. Varga, Jian'an Luan, Evelin Mihailov, Andres Metspalu, Andrew P. Morris, Nita G. Forouhi, Cecilia Lindgren, Patrik K. E. Magnusson, Nancy L. Pedersen, Göran Hallmans, Audrey Y. Chu, Anne E. Justice, Mariaelisa Graff, Thomas W. Winkler, Lynda M. Rose, Claudia Langenberg, L. Adrienne Cupples, Paul M. Ridker, Nicholas J. Wareham, Ken K. Ong, Ruth J. F. Loos, Daniel I. Chasman, Erik Ingelsson … & Paul W. Franks
Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (G·E) or gene-gene interactions. We modeled variance heterogeneity for blood lipids and BMI in up to 44,211 participants and investigated relationships between variance effects (Pv), G·E interaction effects (with smoking and physical activity), and marginal genetic effects (Pm). Correlations between Pv and Pm were stronger for SNPs with established marginal effects (Spearman's ρ=0.401 for triglycerides, and ρ=0.236 for BMI) compared...

Data from: Will a small randomly-assembled community be feasible and stable?

Chuliang Song & Serguei Saavedra
How likely is that few species can randomly assemble into a feasible and stable community? Some studies have answered that as long as the community is feasible, it will nearly always be stable. In contrast, other studies have answered that the likelihood is almost null. Here, we show that the origin of this debate has been the underestimation of the association of the parameter space of intrinsic growth rates with the feasibility and stability properties...

Data from: A structural approach for understanding multispecies coexistence

Serguei Saavedra, Rudolf P. Rohr, Jordi Bascompte, Oscar Godoy, Nathan J.B. Kraft, Jonathan M. Levine & Nathan J. B. Kraft
Although observations of species-rich communities have long served as a primary motivation for research on the coexistence of competitors, the majority of our empirical and theoretical understanding comes from two-species systems. How much of the coexistence observed in species rich communities results from indirect effects among competitors that only emerge in diverse systems remains poorly understood. Resolving this issue requires simple, scalable, and intuitive metrics for quantifying the conditions for coexistence in multispecies systems, and...

Data from: Mapping and analysis of the connectome of sympathetic premotor neurons in the rostral ventrolateral medulla of the rat using a volumetric brain atlas

Bowen Dempsey, Sheng Le, Anita Turner, Phill Bokiniec, Radhika Ramadas, Jan G. Bjaalie, Clement Menuet, Rachael Neve, Andrew Allen, Ann Goodchild, Simon McMullan, Phil Bokiniec, Ann K. Goodchild & Andrew M. Allen
Spinally projecting neurons in the rostral ventrolateral medulla (RVLM) play a critical role in the generation of vasomotor sympathetic tone and are thought to receive convergent input from neurons at every level of the neuraxis; the factors that determine their ongoing activity remain unresolved. In this study we use a genetically restricted viral tracing strategy to definitively map their spatially diffuse connectome. We infected bulbospinal RVLM neurons with recombinant rabies variant that drives reporter expression...

Data from: How temporal patterns in rainfall determine the geomorphology and carbon fluxes of tropical peatlands

Alexander R. Cobb, Alison M. Hoyt, Laure Gandois, Jangarun Eri, René Dommain, Kamariah Abu Salim, Fuu Ming Kai, Nur Salihah Haji Su'ut & Charles F. Harvey
Tropical peatlands now emit hundreds of megatons of carbon dioxide per year because of human disruption of the feedbacks that link peat accumulation and groundwater hydrology. However, no quantitative theory has existed for how patterns of carbon storage and release accompanying growth and subsidence of tropical peatlands are affected by climate and disturbance. Using comprehensive data from a pristine peatland in Brunei Darussalam, we show how rainfall and groundwater flow determine a shape parameter (the...

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...

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: 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: 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: 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: 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: 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: 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: 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...

The eICU Collaborative Research Database

Tom Joseph Pollard, Alistair Edward William Johnson, Jesse Raffa & Omar Badawi
The eICU Collaborative Research Database is a multi-center database comprising deidentified health data associated with over 200,000 admissions to ICUs across the United States between 2014-2015. The database includes vital sign measurements, care plan documentation, severity of illness measures, diagnosis information, and treatment information. Data is collected through the Philips eICU program, a critical care telehealth program that delivers information to caregivers at the bedside.

Data from: Aneuploidy causes non-genetic individuality

Rebecca R. Beach, Chiara Ricci-Tam, Christopher M. Brennan, Christine A. Moomau, Pei-Hsin Hsu, Bo Hua, Rebecca E. Silberman, Michael Springer & Angelika Amon
Phenotypic variability is a hallmark of diseases involving chromosome gains and losses, such as Down syndrome and cancer. Allelic variances have been thought to be the sole cause of this heterogeneity. Here, we systematically examine the consequences of gaining and losing single or multiple chromosomes to show that the aneuploid state causes non-genetic phenotypic variability. Yeast cell populations harboring the same defined aneuploidy exhibit heterogeneity in cell-cycle progression and response to environmental perturbations. Variability increases...

Data from: Preservation of uropygial gland lipids in a 48-million-year-old bird

Shane O'Reilly, Roger Summons, Gerald Mayr & Jakob Vinther
Although various kinds of organic molecules are known to occur in fossils and rocks, most soft tissue preservation in animals is attributed to melanin or porphyrins. Lipids are particularly stable over time—as diagenetically altered ‘geolipids’ or as major molecular constituents of kerogen or fossil ‘geopolymers’—and may be expected to be preserved in certain vertebrate tissues. Here we analysed lipid residues from the uropygial gland of an early Eocene bird using pyrolysis gas chromatography mass spectroscopy....

Data from: Genome-wide sensitivity analysis of the microsymbiont Sinorhizobium meliloti to symbiotically important, defensin-like host peptides

Markus F. F. Arnold, Mohammed Shabab, Jon Penterman, Kevin L. Boehme, Joel S. Griffitts & Graham C. Walker
The model legume species Medicago truncatula expresses more than 700 nodule-specific cysteine-rich (NCR) signaling peptides that mediate the differentiation of Sinorhizobium meliloti bacteria into nitrogen-fixing bacteroids. NCR peptides are essential for a successful symbiosis in legume plants of the inverted-repeat-lacking clade (IRLC) and show similarity to mammalian defensins. In addition to signaling functions, many NCR peptides exhibit antimicrobial activity in vitro and in vivo. Bacterial resistance to these antimicrobial activities is likely to be important...

Data from: Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells

Minseung Choi, Diane P. Genereux, Jamie Goodson, Haneen Al-Azzawi, Shannon Q. Allain, Noah Simon, Stan Palasek, Carol B. Ware, Chris Cavanaugh, Daniel G. Miller, Winslow C. Johnson, Kevin D. Sinclair, Reinhard Stöger & Charles D. Laird
In storing and transmitting epigenetic information, organisms must balance the need to maintain information about past conditions with the capacity to respond to information in their current and future environments. Some of this information is encoded by DNA methylation, which can be transmitted with variable fidelity from parent to daughter strand. High fidelity confers strong pattern matching between the strands of individual DNA molecules and thus pattern stability over rounds of DNA replication; lower fidelity...

Registration Year

  • 2017
    21

Resource Types

  • Dataset
    21

Affiliations

  • Massachusetts Institute of Technology
    21
  • Harvard University
    3
  • University of Bristol
    3
  • Broad Institute
    3
  • University of Western Australia
    2
  • Uppsala University
    2
  • Carnegie Mellon University
    2
  • Howard Hughes Medical Institute
    1
  • University of Washington
    1
  • National Museum of Natural History
    1