147 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: 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: 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...

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: 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: 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...

Taking Action to Reduce Waste: Quantifying Impacts of Model Use in a Multiorganizational Sustainability Negotiation

Ellen Czaika & Noelle Selin

Every ambiguity isn't syntactic in nature: Testing the Rational Speech Act model of scope ambiguity

Sherry Yong Chen & Bob van Tiel

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: 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,...

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...

Synergistic phase separation of two pathways promotes integrin clustering and nascent adhesion formation

Lindsay Case & Michael Rosen
Integrin adhesion complexes (IACs) are integrin-based plasma membrane-associated compartments where cells sense environmental cues. The physical mechanisms and molecular interactions that mediate initial IAC formation are unclear. We found that both p130Cas (“Cas”) and Focal adhesion kinase (“FAK”) undergo liquid-liquid phase separation in vitrounder physiologic conditions. Cas- and FAK- driven phase separation is sufficient to reconstitute kindlin-dependent integrin clustering in vitro with recombinant mammalian proteins. In vitro condensates and IACs in mouse embryonic fibroblasts (MEFs)...

Data from: A new lineage of Galapagos giant tortoises identified from museum samples

Evelyn L. Jensen, Maud C. Quinzin, Joshua M. Miller, Michael A. Russello, Ryan Garrick, Danielle L. Edwards, Scott Glaberman, Ylenia Chiari, Nikos Poulakakis, Washington Tapia, James P. Gibbs & Adalgisa Caccone
The Galapagos Archipelago is recognized as a natural laboratory for studying evolutionary processes. San Cristóbal was one of the first islands colonized by tortoises, which radiated from there across the archipelago to inhabit 10 islands. Here, we sequenced the mitochondrial control region from six historical giant tortoises from San Cristóbal (five long deceased individuals found in a cave and one found alive during an expedition in 1906) and discovered that the five from the cave...

Label-free three-photon imaging of intact human cerebral organoids: Tracking early events in brain development and deficits in Rett Syndrome

Murat Yildirim, Chloe Delepine, Danielle Feldman, Vincent Pham, Stephanie Chou, Jacque Ip, Alexi Nott, Li-Huei Tsai, Guo-Li Ming, Peter So & Mriganka Sur
Human cerebral organoids are unique in their development of progenitor-rich zones akin to ventricular zones from which neuronal progenitors differentiate and migrate radially. Analyses of cerebral organoids thus far have been performed in sectioned tissue or in superficial layers due to their high scattering properties. Here, we demonstrate label-free three-photon imaging of whole, uncleared intact organoids (~2 mm depth) to assess early events of early human brain development. Optimizing a custom-made three-photon microscope to image...

AI3SD Video: Audacity of huge: Machine Learning for the discovery of transition metal catalysts and materials

Heather Kulik & Jeremy G. Frey
I will discuss our efforts to use machine learning (ML) to accelerate the computational tailoring and design of transition metal complexes and metal-organic framework (MOF) materials. One limitation in a challenging materials space such as open shell, 3d transition metal chemistry is that ML models and ML-accelerated high-throughput screening traditionally rely on density functional theory (DFT) for data generation, but DFT is both computationally demanding and prone to errors that limit its accuracy in predicting...

Inferred ancestry of scytonemin biosynthesis proteins in cyanobacteria indicates a response to Paleoproterozoic oxygenation

Erik Tamre & Gregory P. 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...

Game Design Considerations for Screening, Interim, and Diagnostic Educational Assessments

David Dockterman, Yaacov Petscher, Alison McAfee, Eric Klopfer, Scot Osterweil & Cody Diefenthaler
To inform instruction, screening and diagnostic assessments must collect accurate data about the current state of the learner. Unfortunately, students may find assessments unengaging, intimidating, or irrelevant, undermining the quality of their effort and the quality of the data. The application of gaming to assessments may provide a way to boost and sustain effortful test-taker engagement, an integration that has thus far yielded mixed results, at best. Our interdisciplinary team reviewed and evaluated existing gamification...

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.

Phylogenomic analysis of chitinase

Giovanna Capovilla, Rogier Braakman, Gregory Fournier, Thomas Hackl, Julia A. Schwartzman, Xinda Lu, Alexis Yelton, Krista Longnecker, Melissa K. Soule, Elaina Thomas, Gretchen Swarr, Alessandro Mongera, Jack Payette, Jacob Waldbauer, Elizabeth B. Kujawinski, Otto X. Cordero & Sallie W. Chisholm
Supplemental Information: Phylogenomic analysis of chitinase Picocyanobacterial sequences for genes involved in chitin degradation and peptidoglycan recycling pathways were found nested within branches of cyanobacterial genes, indicating vertical inheritance of peptidoglycan recycling. Picocyanobacterial sequences for chitinase (ChiA and ChiA-like) and N-acetylglucosamine kinase (NagK) were nested within non-cyanobacterial taxa, indicating Horizontal Gene Transfer (HGT) to picocyanobacteria after their divergence from other cyanobacteria. To contextualize the HGT of chitinase genes into ancestors of marine SynPro, we examined...

Inferring Minimalist Grammars with an SMT-Solver

Sagar Indurkhya

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...

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: 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...

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