92 Works

Photoprotective pigment scytonemin evolved in cyanobacteria in response to increased Paleoproterozoic oxygenation

Erik Tamre & Gregory Fournier
Protection from radiation damage is an important adaptation for phototrophic microbes. In the case of cyanobacteria, surface, shallow water, and peritidal environments are especially exposed to long- wavelength ultraviolet (UVA) radiation. Several groups of cyanobacteria within these environments are protected from UVA damage by the production of the pigment scytonemin. Paleontological evidence of cyanobacteria in UVA-exposed environments from the Proterozoic, and possibly as early as the Archaean, suggests a long evolutionary history of radiation protection...

WiDS (Women in Data Science) Datathon 2020: ICU Mortality Prediction

Meredith Lee, Jesse Raffa, Marzyeh Ghassemi, Tom Pollard, Sharada Kalanidhi, Omar Badawi, Karen Matthys & Leo Anthony Celi
WiDS (Women in Data Science) Datathon 2020: ICU Mortality Prediction focuses on patient health through data from MIT’s GOSSIS (Global Open Source Severity of Illness Score) initiative. Brought to you by the Global WiDS team, the West Big Data Innovation Hub, and the WiDS Datathon Committee, this year’s datathon is launching on Kaggle: bit.ly/WiDSdatathon2020kaggle.

Data from: Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

Steven J. Biller, Paul M. Berube, Jessie W. Berta-Thompson, Libusha Kelly, Sara E. Roggensack, Lana Awad, Kathryn H. Roache-Johnson, Huiming Ding, Stephen J. Giovannoni, Lisa R. Moore & Sallie W. Chisholm
The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity—both in the lab and in the field. To...

Data from: Evolutionary history and biogeographical patterns of barnacles endemic to deep-sea hydrothermal vents

Santiago Herrera & Timothy M. Shank
The characterization of evolutionary and biogeographical patterns is of fundamental importance to identify factors driving biodiversity. Due to their widespread but discontinuous distribution, deep-sea hydrothermal vent barnacles represent an excellent model for testing biogeographic hypotheses regarding the origin, dispersal, and diversity of modern vent fauna. Here we characterize the global genetic diversity of vent barnacles to infer their time of radiation, place of origin, mode of dispersal, and diversification. Our approach was to target a...

Data from: Combining role-play with interactive simulation to motivate informed climate action: evidence from the World Climate simulation

Juliette N. Rooney-Varga, John D. Sterman, Eduardo Fracassi, Travis Franck, Florian Kapmeier, Victoria Kurker, Ellie Johnston, Andrew P. Jones & Kenneth Rath
Climate change communication efforts grounded in the information deficit model have largely failed to close the gap between scientific and public understanding of the risks posed by climate change. In response, simulations have been proposed to enable people to learn for themselves about this complex and politically charged topic. Here we assess the impact of a widely-used simulation, World Climate, which combines a socially and emotionally engaging role-play with interactive exploration of climate change science...

Data from: Strength of species interactions determines biodiversity and stability in microbial communities

Christoph Ratzke, Julien Barrere & Jeff Gore
Organisms, especially microbes, tend to live in complex communities. While some of these ecosystems are very bio-diverse, others aren′t, and while some are very stable over time others undergo strong temporal fluctuations. Despite a long history of research and a plethora of data it is not fully understood what sets biodiversity and stability of ecosystems. Theory as well as experiments suggest a connection between species interaction, biodiversity, and stability of ecosystems, where an increase of...

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: 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: Cataract surgery visual outcomes and associated risk factors in secondary level eye care centers of L V Prasad Eye Institute, India

Rohit C. Khanna, Sumathi Matta, Gullapalli Rao, Jiwon Park, Ghanshyam Palamaner Subash Shantha & Gullapalli N. Rao
Purpose: To evaluate cataract surgery visual outcomes and associated risk factors in rural secondary level eye care centers of L V Prasad Eye Institute (LVPEI), India. Methods: The Eye Health pyramid of LVPEI has a network of rural secondary care centres (SCs) and attached vision centres (VCs) that provide high quality comprehensive eye care with permanent infrastructure to the most disadvantaged sections of society. The most common procedure performed at SCs is cataract surgery. We...

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: Paleozoic diversification of terrestrial chitin-degrading bacterial lineages

Danielle S. Gruen, Joanna M. Wolfe & Gregory P. Fournier
Background: Establishing the divergence times of groups of organisms is a major goal of evolutionary biology. This is especially challenging for microbial lineages, due to the near-absence of preserved physical evidence (diagnostic body fossils or geochemical biomarkers). Horizontal gene transfer (HGT), can serve as a temporal scaffold between microbial groups and other fossil-calibrated clades, potentially improving these estimates. Specifically, HGT to or from organisms with fossil-calibrated age estimates can propagate these constraints to additional groups...

RNA sequencing of nuclease dead PET127 conditions

Daniel Corbi & Angelika Amon
PET127, is thought to be a mitochondrial RNA exonuclease and loss of PET127 is thought to cause accumulation of untrimmed RNA in the mitochondria. Here we show RNA sequencing of Saccharomyces cerevisiae in four PET127 conditions: PET127 wild-type, pet127∆, pet127-nd (nuclease dead)/pet127∆, and pet127-nd/PET127. The resulting sequences show that regions of mitochondrial RNA accumulate in the pet127∆ background, and the RNA sequencing profile of PET127 containing disruptive mutations in the conserved exonuclease active site mimics...

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.

Neural representations of space in the hippocampus of a food-caching bird

Hannah Payne, Galen Lynch & Dmitriy Aronov
Spatial memory in vertebrates requires brain regions homologous to the mammalian hippocampus. Between vertebrate clades, however, these regions are anatomically distinct and appear to produce different spatial patterns of neural activity. We asked whether hippocampal activity is fundamentally different even between distant vertebrates that share a strong dependence on spatial memory. We studied tufted titmice, food-caching birds capable of remembering many concealed food locations. We found mammalian-like neural activity in the titmouse hippocampus, including sharp-wave...

Archival data and code in support of uncertainty quantification of climate system properties using the MIT Earth System Model (MESM)

Chris Forest, Alex Libardoni, Andrei P. Sokolov & Erwan Monier
This archive provides the climate model outputs, observational data, and analysis codes that were used to quantify uncertainty in the climate system response properties of the MIT Earth System Model (MESM). Three papers (Libardoni et al. 2018a, 2018b, 2019) include results using these data and codes to provide conditional probability distributions of equilibrium climate sensitivity (ECS), the transient climate response (TCR), and the net radiative forcing by aerosols. The analysis codes are either written in...

Signature of a pair of Majorana zero modes in superconducting gold surface states

Peng Wei, Sujit Manna, Yingming Xie, Kam Tuen Law, Patrick Lee & Jagadeesh Moodera
Under certain conditions, a fermion in a superconductor can separate in space into two parts known as Majorana zero modes, which are immune to decoherence from local noise sources and are attractive building blocks for quantum computers. Promising experimental progress has been made to demonstrate Majorana zero modes in materials with strong spin-orbit coupling proximity coupled to superconductors. Here we show direct evidence of the split Majorana pair in a new material platform utilizing the...

Acceleration time histories and road elevation profiles

Arghavan Louhghalam, Meshkat Botshekan, Erfan Asaadi, Jacob Roxon, Franz-Josef Ulm & Mazdak Tootkaboni
Low-cost smartphone-based sensing approaches have recently emerged as an alternative to the traditional and oftentimes expensive or laborious road surface monitoring technologies. We develop an approach, resting on a rigorously derived mechanistic and stochastic model in spectral domain, that relates the vertical acceleration signal measured by a smartphone positioned in a moving car to road surface roughness metrics. We illustrate that the inferred roughness metrics from the acceleration data sets, acquired with different smartphones and...

Data from: European sea bass show behavioural resilience to near-future ocean acidification

Mathieu Duteil, Edward C. Pope, Alfonso Perez-Escudero, Gonzalo G. De Polavieja, Ines Fürtbauer, M. R. Brown & Andrew J. King
Ocean acidification (OA)—caused by rising concentrations of carbon dioxide (CO2)—is thought to be a major threat to marine ecosystems and has been shown to induce behavioural alterations in fish. Here we show behavioural resilience to near-future OA in a commercially important and migratory marine finfish, the Sea bass (Dicentrarchus labrax). Sea bass were raised from eggs at 19°C in ambient or near-future OA (1000 µatm pCO2) conditions and n = 270 fish were observed 59–68...

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: Genetic evidence for landscape effects on dispersal in the army ant Eciton burchellii

Thomas W. Soare, Anjali Kumar, Kerry A. Naish & Sean O'Donnell
Inhibited dispersal, leading to reduced gene flow, threatens populations with inbreeding depression and local extinction. Fragmentation may be especially detrimental to social insects because inhibited gene flow has important consequences for cooperation and competition within and among colonies. Army ants have winged males and permanently wingless queens; these traits imply male-biased dispersal. However, army ant colonies are obligately nomadic and have the potential to traverse landscapes. Eciton burchellii, the most regularly nomadic army ant, is...

Data from: Migration strategy affects avian influenza dynamics in mallards (Anas platyrhynchos)

Nichola J. Hill, John Y. Takekawa, Joshua T. Ackerman, Keith A. Hobson, Garth Herring, Carol J. Cardona, Jonathan A. Runstadler & Walter M. Boyce
Studies of pathogen transmission typically overlook that wildlife hosts can include both migrant and resident populations when attempting to model circulation. Through the application of stable isotopes in flight feathers, we estimated the migration strategy of mallards (Anas platyrhynchos) - resident, intermediate-distance migrant or long-distance migrant, occurring on California wintering grounds. Our study demonstrates that mallards, a principal host of avian influenza virus (AIV) in nature, contribute differently to virus gene flow depending on migration...

Data from: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

Mary Gehring, Daniela Pignatta, Robert M. Erdmann, George W. Bell, Elias Scheer & Colette L Picard
Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However,...

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...

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....

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