422 Works

Homologous chromosomes undergo sequential quasi-stable interactions during meiotic prophase

Trent Newman
The pairing of homologous chromosomes in meiosis I is essential for sexual reproduction and is mediated, in part, by the formation and repair of Spo11-induced DNA double strand breaks (DSBs). In budding yeast, each cell receives 150-200 DSBs, yet only a fraction go on to form crossover products. How and why the cell initially coordinates so many interactions along each chromosome is not well understood. Using a fluorescent reporter-operator system (FROS), we measure the kinetics...

Should Central Banks Worry About Nonlinearities of their Large-Scale Macroeconomic Models?

Vadym Lepetyuk, Lilia Maliar & Serguei Maliar
How wrong could policymakers be when using linearized solutions to their macroeconomic models instead of nonlinear global solutions? This question became of much practical interest during the Great Recession and the recent zero lower bound crisis. We assess the importance of nonlinearities in a scaled-down version of the Terms of Trade Economic Model (ToTEM), the main projection and policy analysis model of the Bank of Canada. In a meticulously calibrated “baby” ToTEM model with 21...

2014 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

Transient osmotic perturbation causes long-term alteration to the gut microbiota

Carolina Tropini & Justin Sonnenburg
"Osmotic diarrhea is a prevalent condition in humans caused by food intolerance, malabsorption, and widespread laxative use. Here, we assess the resilience of the gut ecosystem to osmotic perturbation at multiple length and time scales using mice as model hosts. Osmotic stress caused reproducible extinction of highly abundant taxa and expansion of less prevalent members in human and mouse microbiotas. Quantitative imaging revealed decimation of the mucus barrier during osmotic perturbation, followed by recovery. The...

Interview data from \"Fishers' solutions for hammerhead shark conservation in Peru\"

Julia Grace Mason
These are the interview protocols and transcripts from 88 semi-structured interviews conducted with small-scale drift gillnet captains or boat owners in northern Peru. The purpose of the study was to elicit fishers' perspectives on the context of juvenile hammerhead fishing in Peru, their qualitative and quantitative ecological knowledge of where and how they catch hammerheads, and their perceptions of a seasonal hammerhead ban implemented in 2016. Interviews were conducted between February 8, 2018 and March...

Quantifying the Prosecutorial Preauthorization Intake System and the Costs of ‘No Action’ Cases

Pablo A. Ormachea, Sasha Davenport, Gabe Haarsma & David M. Eagleman
In most jurisdictions, a police officer arrests and books a defendant, then files the criminal complaint before a judge. The judge sets bail, and if necessary, appoints defense counsel for the accused. Inadequate cases are later dropped – often weeks or months later – by prosecutors. This happens only after extensive investigation and usually not before the accused spent several nights in detention. In 1973, Harris County, Texas developed a solution to this inefficiency: prosecutors...

ddRAD of Hawaiian Ariamnes spiders

Ellie Armstrong, Benoît Perez-Lamarque, Ke Bi, Leontine Becking, Jun Lim, Tyler Linderoth, Rosemary Gillespie & Henrik Krehenwinkel
The diversification of a host organism can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, coupled with a chronologically arranged series of volcanic mountains, to determine the evolutionary history of a host and its associated microbial communities, altogether forming the “holobiont”. Using the stick spider Ariamnes waikula (Araneae, Theridiidae) on the island of Hawaiʻi, and outgroup taxa on older islands, we tested whether...

Redefining Near-Unity Luminescence in Quantum Dots with Photothermal Threshold Quantum Yield

David Hanifi, Noah Bronstein, Brent Koscher, Zach Nett, Joseph Swabeck, Kaori Takano, Adam Schwartzberg, Lorenzo Maserati, Koen Vandewal, Yoeri Van De Burgt, Alberto Salleo & Paul Alivisatos
Herin is the code and example data sets for the publication titled: "Redefining Near-Unity Luminescence in Quantum Dots with Photothermal Threshold Quantum Yield." The abstract of this paper is as follows. A variety of optical applications rely on the absorption and reemission of light. The quantum yield of this process often plays an essential role. When the quantum yield deviates from unity by significantly less than 1%, applications such as luminescent concentrators and optical refrigerators...

Hormonal and neural correlates of care in active versus observing poison frog parents

Eva K. Fischer & Lauren A. O'Connell
The occasional reversal of sex-typical behavior suggests that many of the neural circuits underlying behavior are conserved between males and females and can be activated in response to the appropriate social condition or stimulus. Most poison frog species (Family Dendrobatidae) exhibit male uniparental care, but flexible compensation has been observed in some species, where females will take over parental care duties when males disappear. We investigated hormonal and neural correlates of sex-typical and sex-reversed parental...

Genetic Adaptation in New York City Rats

Arbel Harpak, Nandita Garud, Noah Rosenberg, Dmitri Petrov, Pleuni Pennings & Jason Munshi-South
Brown rats (Rattus norvegicus) thrive in urban environments by navigating the anthropocentric environment and taking advantage of human resources and by-products. From the human perspective, rats are a chronic problem that causes billions of dollars in damage to agriculture, health and infrastructure. Did genetic adaptation play a role in the spread of rats in cities? To approach this question, we collected whole-genome sequences from 29 brown rats from New York City (NYC) and scanned for...

Data from: The effects of ground-irregularity-cancelling prosthesis control on balance over uneven surfaces

Vincent Chiu, Alexandra Voloshina & Steven Collins
Over half of individuals with a lower-limb amputation are unable to walk on uneven terrain. Using a prosthesis emulator system, we developed an irregularity-cancelling controller intended to reduce the effect of disturbances resulting from uneven surfaces. This controller functions by changing the neutral angles of two forefoot digits in response to local terrain heights. To isolate the effects of the controller, we also programmed a spring-like controller that maintained fixed neutral angles. Five participants with...

Maps of northern peatland extent, depth, carbon storage and nitrogen storage

Gustaf Hugelius, Julie Loisel, Sarah Chadburn, Robert B. Jackson, Miriam Jones, Glen MacDonald, Maija Marushchak, David Olefeldt, Maara Packalen, Matthias B. Siewert, Claire Treat, Merritt Turestsky, Carolina Voigt & Zicheng Yu
This dataset is grids of peatland extent, peat depth, peatland organic carbon storage, peatland total nitrogen storage and approximate extent of ombrotrophic/minerotrophic peatlands. The grids are geotiff files in 10 km pixel resolution projected in the World Azimuthal Equidistant projection. Note that the peat depth grid shows potential peat depth everywhere,also where there is no peatland cover. For files on peatland organic carbon, total nitrogen extent and extent of ombrotrophic/minerotrophic peatlands, there are separate files...

Data from: Gene expression correlates of social evolution in coral reef butterflyfishes

Jessica Nowicki, Morgan Pratchett, Stefan Walker, Darren Coker & Lauren O'Connell
Animals display remarkable variation in social behavior. However, outside of rodents, little is known about the neural mechanisms of social variation, and whether they are shared across species and sexes, limiting our understanding of how sociality evolves. Using coral reef butterflyfishes, we examined gene expression correlates of social variation (i.e., pair bonding vs. solitary living) within and between species and sexes. In several brain regions, we quantified gene expression of receptors important for social variation...

Bio-optical Database of the Arctic Ocean

Kate Lewis, Gert Van Dijken & Kevin Arrigo
The Arctic bio-optical database assembles a diverse suite of biological and optical data from 34 expeditions throughout the Arctic Ocean. Data combined into a single AO database following the OBPG criteria (Pegau et al. 2003), as was done in the development of the global NASA Bio-optical Marine Algorithm Data Set (NOMAD) (Werdell 2005, Werdell & Bailey 2005). This Arctic database combines coincident in situ observations of IOPs, apparent optical properties (AOPs), Chl a, environmental data...

Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer

Molly Schumer, Daniel Powell & Russell Corbett-Detig
It is now clear that hybridization between species is much more common than previously recognized. As a result, we now know that the genomes of many modern species, including our own, are a patchwork of regions derived from past hybridization events. Increasingly researchers are interested in disentangling which regions of the genome originated from each parental species using local ancestry inference methods. Due to the diverse effects of admixture, this interest is shared across disparate...

Data from: Biodiversity response to natural gradients of multiple stressors on continental margins

Erik A. Sperling, Christina A. Frieder & Lisa A. Levin
Sharp increases in atmospheric CO2 are resulting in ocean warming, acidification and deoxygenation that threaten marine organisms on continental margins and their ecological functions and resulting ecosystem services. The relative influence of these stressors on biodiversity remains unclear though, as well as the threshold levels for change and when secondary stressors become important. One strategy to interpret adaptation potential and predict future faunal change is to examine ecological shifts along natural gradients in the modern...

Data from: Soil fungi underlie a phylogenetic pattern in plant growth responses to nitrogen enrichment

Rachel C. Wooliver, John K. Senior, Brad M. Potts, Michael E. Van Nuland, Joseph K. Bailey & Jennifer A. Schweitzer
1. Under increasing anthropogenic nitrogen (N) deposition, some plant species will thrive while others will not. Previous work has shown that plant phylogeny can predict these responses, and that interactions with mycorrhizal fungi are a mechanism that drives variation in plant responses to N enrichment. Yet, much of this work has ignored the roles of other root-associated fungi and whole soil fungal communities in driving these responses. 2. We tested whether soil fungi mediate responses...

Data from: Tradeoffs between three forest ecosystem services across the state of New Hampshire, USA: timber, carbon, and albedo

David A. Lutz, Elizabeth A. Burakowski, Mackenzie B. Murphy, Mark E. Borsuk, Rebecca M. Niemiec & Richard B. Howarth
Forests are more frequently being managed to store and sequester carbon for the purposes of climate change mitigation. Generally, this practice involves long-term conservation of intact mature forests and/or reductions in the frequency and intensity of timber harvests. However, incorporating the influence of forest surface albedo often suggests that long rotation lengths may not always be optimal in mitigating climate change in forests characterized by frequent snowfall. To address this, we investigated tradeoffs between three...

Data from: Combining fish and benthic communities into multiple regimes reveals complex reef dynamics

Mary K. Donovan, Alan M. Friedlander, Joey Lecky, Jean-Baptiste Jouffray, Gareth J. Williams, Lisa M. Wedding, Larry B. Crowder, Ashley L. Erickson, Nick A. J. Graham, Jamison M. Gove, Carrie V. Kappel, Kendra Karr, John N. Kittinger, Albert V. Norström, Magnus Nyström, Kirsten L. L. Oleson, Kostantinos A. Stamoulis, Crow White, Ivor D. Williams & Kimberly A. Selkoe
Coral reefs worldwide face an uncertain future with many reefs reported to transition from being dominated by corals to macroalgae. However, given the complexity and diversity of the ecosystem, research on how regimes vary spatially and temporally is needed. Reef regimes are most often characterised by their benthic components; however, complex dynamics are associated with losses and gains in both fish and benthic assemblages. To capture this complexity, we synthesised 3,345 surveys from Hawai‘i to...

Data from: Movements of four native Hawaiian birds across a naturally fragmented landscape

Jessie L. Knowlton, David J. Flaspohler, Eben H. Paxton, Tadashi Fukami, Christian P. Giardina, Daniel S. Gruner & Erin E. Wilson Rankin
Animals often increase their fitness by moving across space in response to temporal variation in habitat quality and resource availability, and as a result of intra and inter-specific interactions. The long-term persistence of populations and even whole species depends on the collective patterns of individual movements, yet animal movements have been poorly studied at the landscape level. We quantified movement behavior within four native species of Hawaiian forest birds in a complex lava-fragmented landscape: Hawai‛i...

Data from: Genetic structure in village dogs reveals a Central Asian domestication origin

Laura M. Shannon, Ryan H. Boyko, Marta Castelhano, Elizabeth Corey, Jessica J. Hayward, Corin McLean, Michelle E. White, Mounir Abi Said, Baddley A. Anita, Nono Bondjengo Ikombe, Jorge Calero, Ana Galov, Marius Hedimbi, Bulu Imam, Rajashree Khalap, Douglas Lally, Andrew Masta, Kyle C. Oliveira, Lucía Pérez, Julia Randall, Nguyen Minh Tam, Francisco J. Trujillo-Cornejo, Carlos Valeriano, Nathan B. Sutter, Rory J. Todhunter … & Adam R. Boyko
Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we...

Data from: Cell signaling-based classifier predicts response to induction therapy in elderly patients with acute myeloid leukemia

Alessandra Cesano, Cheryl L. Willman, Kenneth J. Kopecky, Urte Gayko, Santosh Putta, Brent Louie, Matt Westfall, Norman Purvis, David C. Spellmeyer, Carol Marimpietri, Aileen C. Cohen, James Hackett, Jing Shi, Michael G. Walker, Zhuoxin Sun, Elisabeth Paietta, Martin S. Tallman, Larry D. Cripe, Susan Atwater, Frederick R. Appelbaum & Jerald P. Radich
Single-cell network profiling (SCNP) data generated from multi-parametric flow cytometry analysis of bone marrow (BM) and peripheral blood (PB) samples collected from patients >55 years old with non-M3 AML were used to train and validate a diagnostic classifier (DXSCNP) for predicting response to standard induction chemotherapy (complete response [CR] or CR with incomplete hematologic recovery [CRi] versus resistant disease [RD]). SCNP-evaluable patients from four SWOG AML trials were randomized between Training (N = 74 patients...

Data from: Genomic diversity of a nectar yeast clusters into metabolically, but not geographically, distinct lineages

Manpreet K. Dhami, Thomas Hartwig, Andrew D. Letten, Michael Banf & Tadashi Fukami
Both dispersal limitation and environmental sorting can affect genetic variation in populations, but their contribution remains unclear, particularly in microbes. We sought to determine the contribution of geographic distance (as a proxy for dispersal limitation) and phenotypic traits (as a proxy for environmental sorting), including morphology, metabolic ability, and interspecific competitiveness, to the genotypic diversity in a nectar yeast species, Metschnikowia reukaufii. To measure genotypic diversity, we sequenced the genomes of 102 strains of M....

Data from: Biodiversity monitoring, earth observations, and the ecology of scale

Christopher B. Anderson
Human activity and land use change are dramatically altering the sizes, geographic distributions, and functioning of biological populations worldwide, with tremendous consequences for human well-being. Yet our ability to measure, monitor, and forecast biodiversity change – crucial to addressing it – remains limited. Biodiversity monitoring systems are being developed to improve this capacity by deriving metrics of change from an array of in situ data (e.g., field plots or species occurrence records) and Earth observations...

Data from: Validation of an algorithm for identifying MS cases in administrative health claims datasets

William J. Culpepper, Ruth Anne Marrie, Annette Langer-Gould, Mitchell T. Wallin, Jonathan D. Campbell, Lorene M. Nelson, Wendy E. Kaye, Laurie Wagner, Helen Tremlett, Lie H. Chen, Stella Leung, Charity Evans, Shenzhen Yao & Nicholas G. LaRocca
Objective: To develop a valid algorithm for identifying multiple sclerosis (MS) cases in administrative health claims (AHC) datasets. Methods: We used 4 AHC datasets from the Veterans Administration (VA), Kaiser Permanente Southern California (KPSC), Manitoba (Canada), and Saskatchewan (Canada). In the VA, KPSC, and Manitoba, we tested the performance of candidate algorithms based on inpatient, outpatient, and disease-modifying therapy (DMT) claims compared to medical records review using sensitivity, specificity, positive and negative predictive values, and...

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