396 Works

2010 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...

2015 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...

2016 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...

Complex landscapes stabilize farm bird communities and their expected ecosystem services

Olivia Smith, Christina M. Kennedy, Alejandra Echeverri, Daniel Karp, Christopher Latimer, Joseph Taylor, Erin Wilson-Rankin, Jeb Owen & William Snyder
1. Birds play many roles within agroecosystems including as consumers of crops and pests, carriers of pathogens, and beloved icons. Birds are also rapidly declining across North America, in part due to agricultural intensification. Thus, it is imperative to identify how to manage agroecosystems to best support birds for multi-functional outcomes (e.g., crop production and conservation). Both the average amounts of services/disservices provided and their temporal stability are important for effective farm planning. 2. Here,...

Data from: Rapid evolution rescues hosts from competition and disease but—despite a dilution effect—increases the density of infected hosts

Alexander T. Strauss, Jessica L. Hite, Marta S. Shocket, Carla E. Cáceres, Meghan A. Duffy & Spencer R. Hall
Virulent parasites can depress the densities of their hosts. Taxa that reduce disease via dilution effects might alleviate this burden. However, ‘diluter’ taxa can also depress host densities through competition for shared resources. The combination of disease and interspecific competition could even drive hosts extinct. Then again, genetically variable host populations can evolve in response to both competitors and parasites. Can rapid evolution rescue host density from the harm caused by these ecological enemies? How...

Data from: Priority effects are interactively regulated by top-down and bottom-up forces: evidence from wood decomposer communities

Devin R. Leopold, J. Paula Wilkie, Ian A. Dickie, Robert B. Allen, Peter K. Buchanan & Tadashi Fukami
Both top-down (grazing) and bottom-up (resource availability) forces can determine the strength of priority effects, or the effects of species arrival history on the structure and function of ecological communities, but their combined influences remain unresolved. To test for such influences, we assembled experimental communities of wood-decomposing fungi using a factorial manipulation of fungivore (Folsomia candida) presence, nitrogen availability, and fungal assembly history. We found interactive effects of all three factors on fungal species composition...

Data from: Utilization of health services in a resource-limited rural area in Kenya: prevalence and associated household-level factors

Anthony K. Ngugi, Felix Agoi, Megan R. Mahoney, Amyn Lakhani, David Mang’ong’o, Esther Nderitu, Robert Armstrong & Sarah Macfarlane
Introduction Knowledge of utilization of health services and associated factors is important in planning and delivery of interventions to improve health services coverage. We determined the prevalence and factors associated with health services utilization in a rural area of Kenya. Our findings inform the local health management in development of appropriately targeted interventions. Methods and Results We used a cluster sample survey design and interviewed household key informants on history of illness for household members...

Data from: Characterizing driver-response relationships in marine pelagic ecosystems for improved ocean management

Mary E. Hunsicker, Carrie V. Kappel, Kimberly A. Selkoe, Benjamin S. Halpern, Courtney Scarborough, Lindley Mease & Alisan Amrhein
Scientists and resources managers often use methods and tools that assume ecosystem components respond linearly to environmental drivers and human stressor. However, a growing body of literature demonstrates that many relationships are non-linear, where small changes in a driver prompt a disproportionately large ecological response. Here we aim to provide a comprehensive assessment of the relationships between drivers and ecosystem components to identify where and when non-linearities are likely to occur. We focus our analyses...

Data from: Does gene tree discordance explain the mismatch between macroevolutionary models and empirical patterns of tree shape and branching times?

Tanja Stadler, James H. Degnan & Noah A. Rosenberg
Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because...

Data from: Large wildlife removal drives immune defense increases in rodents

Hillary S. Young, Rodolfo Dirzo, Kristofer M. Helgen, Douglas J. McCauley, Charles L. Nunn, Paul Snyder, Kari E. Veblen, Serena Zhao & Vanessa O. Ezenwa
Anthropogenic disturbances involving land use change, climate disruption, pollution, and invasive species have been shown to impact immune function of wild animals. These immune changes have direct impacts on the fitness of impacted animals and, also, potentially indirect effects on other species and on ecological processes, notably involving the spread of infectious disease. Here, we investigate whether the selective loss of large wildlife can also drive changes in immune function of other consumer species. Using...

Data from: Exams disadvantage women in introductory biology

Sehoya Cotner, Shima Salehi & Cissy J. Ballen
The gender gap in STEM fields has prompted a great deal of discussion, but what factors underlie performance deficits remain poorly understood. We show that female students underperformed on exams compared to their male counterparts across ten large introductory biology course sections in fall 2016 (N > 1500 students). Females also reported higher levels of test anxiety and course-relevant science interest. Results from mediation analyses revealed an intriguing pattern: for female students only, and regardless...

Data from: Gene duplication in an African cichlid adaptive radiation

Heather E. Machado, Ginger Jui, Domino A. Joyce, Christian R. L. Reilly, David H. Lunt & Suzy C. P. Renn
Background: Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; however, the relative importance of this process remains to be determined. The explosive divergence of the African cichlid adaptive radiations provides both a model for studying the general role of gene duplication in the divergence of lineages and also an exciting foray into the identification of genomic features that underlie the dramatic phenotypic and ecological diversification in this...

Data from: Historical DNA documents long distance natal homing in marine fish

Sara Bonanomi, Nina Overgaard Therkildsen, Anja Retzel, Rasmus Berg Hedeholm, Martin Wæver Wæver Pedersen, Dorte Meldrup, Christophe Pampoulie, Jakob Hemmer-Hansen, Peter Grønkjær & Einar Nielsen
The occurrence of natal homing in marine fish remains a fundamental question in fish ecology as its unequivocal demonstration requires tracking of individuals from fertilization to reproduction. Here, we provide evidence of long distance natal homing (> 1000 km) over more than sixty years in Atlantic cod (Gadus morhua), through genetic analysis of archived samples from marked and recaptured individuals. Using a high differentiation Single Nucleotide Polymorphism assay we demonstrate that the vast majority of...

Data from: A highly pleiotropic amino acid polymorphism in the Drosophila insulin receptor contributes to life history adaptation

Annalise B. Paaby, Alan O. Bergland, Emily L. Behrman & Paul S. Schmidt
Finding the specific nucleotides that underlie adaptive variation is a major goal in evolutionary biology, but polygenic traits pose a challenge because the complex genotype-phenotype relationship can obscure the effects of individual alleles. However, natural selection working in large wild populations can shift allele frequencies and indicate functional regions of the genome. Previously, we showed that the two most common alleles of a complex amino acid insertion-deletion polymorphism in the Drosophila insulin receptor show independent,...

Data from: Temperature explains broad patterns of Ross River virus transmission

Marta Shocket, Sadie Ryan, Erin Mordecai, Marta Strecker Shocket, Erin A Mordecai & Sadie J Ryan
Thermal biology predicts that vector-borne disease transmission peaks at intermediate temperatures and declines at high and low temperatures. However, thermal optima and limits remain unknown for most vector-borne pathogens. We built a mechanistic model for the thermal response of Ross River virus, an important mosquito-borne pathogen in Australia, Pacific Islands, and potentially at risk of emerging worldwide. Transmission peaks at moderate temperatures (26.4{degree sign}C) and declines to zero at thermal limits (17.0{degree sign}C and 31.5{degree...

Data from: Rapid divergence of mussel populations despite incomplete barriers to dispersal

Diede L. Maas, Stefan Prost, Ke Bi, Lydia L. Smith, Ellie E. Armstrong, Ludi P. Aji, Abdul H.A. Toha, Rosemary G. Gillespie & Leontine E. Becking
Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment, and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to...

Data from: Genome-wide evidence for speciation with gene flow in Heliconius butterflies

Simon H. Martin, Kanchon K. Dasmahapatra, Nicola J. Nadeau, Camilo Salazar, James R. Walters, Fraser Simpson, Mark Blaxter, Andrea Manica, James Mallet & Chris D. Jiggins
Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. Documenting the extent and timing of admixture between diverging species can clarify the role of geographic isolation in speciation. Here we use new methodology to quantify admixture at different stages of divergence in Heliconius butterflies, based on whole genome sequences of 31 individuals. Comparisons between...

Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission

Chelsea Wood, Susanne Sokolow, Isabel Jones, Andrew Chamberlin, Kevin Lafferty, Armand Kuris, Merlijn Jocque, Skylar Hopkins, Grant Adams, Julia Buck, Andrea Lund, Ana Garcia-Vedrenne, Evan Fiorenza, Jason Rohr, Fiona Allan, Bonnie Webster, Muriel Rabone, Joanne Webster, Lydie Bandagny, Raphael Ndione, Simon Senghor, Anne-Marie Schacht, Nicolas Jouanard, Gilles Riveau & Giulio De Leo
Recently, the World Health Organization recognized that efforts to interrupt schistosomiasis transmission through mass drug administration have been ineffective in some regions; one of their new recommended strategies for global schistosomiasis control emphasizes targeting the freshwater snails that transmit schistosome parasites. We sought to identify robust indicators that would enable precision targeting of these snails. At the site of the world’s largest recorded schistosomiasis epidemic—the Lower Senegal River Basin in Senegal—intensive sampling revealed positive relationships...

Respiratory medium and circulatory anatomy constrain size evolution in marine macrofauna

Noel Heim, Saket Bakshi, Loc Buu, Stephanie Chen, Shannon Heh, Ashli Jain, Christopher Noll, Ameya Patkar, Noah Rizk, Sriram Sundararajan, Isabella Villante, Matthew Knope & Jonathan Payne
The typical marine animal has increased in biovolume by more than two orders of magnitude since the beginning of the Cambrian, but the causes of this trend remain unknown. We test the hypothesis that the efficiency of intra-organism oxygen delivery is a major constraint on body size evolution in marine animals. To test this hypothesis, we compiled a dataset comprising 13,723 marine animal genera spanning the Phanerozoic. We coded each genus according to its respiratory...

Lymph node metastases develop through a wider evolutionary bottleneck than distant metastases

Johannes Reiter, Wei-Ting Hung, I-Hsiu Lee, Shriya Nagpal, Peter Giunta, Sebastian Degner, Gang Liu, Emma Wassenaar, William Jeck, Martin Taylor, Alexander Farahani, Hetal Marble, Simon Knott, Onno Kranenburg, Jochen Lennerz & Kamila Naxerova
Genetic diversity among metastases is poorly understood but contains important information about disease evolution at secondary sites. Here we investigate inter- and intra-lesion heterogeneity for two types of metastases that associate with different clinical outcomes: lymph node and distant organ metastases in human colorectal cancer. We develop a rigorous mathematical framework for quantifying metastatic phylogenetic diversity. Distant metastases are typically monophyletic and genetically similar to each other. Lymph node metastases, in contrast, display high levels...

Rethinking megafauna

Marcos Moleón, José Sánchez-Zapata, José Donázar, Eloy Revilla, Berta Martín-López, Cayetano Gutiérrez-Cánovas, Wayne Getz, Zebensui Morales-Reyes, Ahimsa Campos-Arceiz, Larry Crowder, Mauro Galetti, Manuela González-Suárez, Fengzhi He, Pedro Jordano, Rebecca Lewison, Robin Naidoo, Norman Owen-Smith, Nuria Selva, Jens-Christian Svenning, José Tella, Christiane Zarfl, Sonja Jähnig, Matt Hayward, Søren Faurby, Nuria García … & Klement Tochner
Concern for megafauna is increasing among scientists and non-scientists. Many studies have emphasized that megafauna play prominent ecological roles and provide important ecosystem services to humanity. But, what precisely are “megafauna”? Here we critically assess the concept of megafauna and propose a goal-oriented framework for megafaunal research. First, we review definitions of megafauna and analyze associated terminology in the scientific literature. Second, we conduct a survey among ecologists and paleontologists to assess the species traits...

A human IgSF cell-surface interactome reveals a complex network of protein-protein interactions

Woj Wojtowicz, Jost Vielmetter, Ricardo Fernandes, Dirk Siepe, Catharine Eastman, Gregory Chisholm, Sarah Cox, Heath Klock, Paul Anderson, Sarah Rue, Jessica Miller, Scott Glaser, Melisa Bragstad, Julie Vance, Annie Lam, Scott Lesley, Kai Zinn & Christopher Garcia
Cell-surface protein-protein interactions (PPIs) mediate cell-cell communication, recognition and responses. We executed an interactome screen of 564 human cell-surface and secreted proteins, most of which are immunoglobulin superfamily (IgSF) proteins, using a high-throughput, automated ELISA-based screening platform employing a pooled-protein strategy to test all 318,096 PPI combinations. Screen results, augmented by phylogenetic homology analysis, revealed ~380 previously unreported PPIs. We validated a subset using surface plasmon resonance and cell binding assays. Observed PPIs reveal a...

Data from: Solute Production and Transport Processes in Chinese Monsoonal Rivers: Implications for Global Climate Change

Jun Zhong, Si-Liang Li, Daniel E. Ibarra, Hu Ding & Cong-Qiang Liu
Concentration-discharge (C-Q) relationships provide new insights into solute production processes. Temporal sampling and analyses are needed to investigate the chemical weathering behaviors and reduce the estimation errors of fluxes. But few studies have been done in Asian monsoonal rivers, which play an important role in global carbon cycle. We analyzed the dissolved solutes of Three largest rivers in China. Datong and Qingxi in Changjiang River were selected to represent the midterm and outlet of the...

Land use impacts poison frog chemical defenses through changes in leaf litter ant communities

Nora Moskowitz, Lauren O'Connell, David Donoso, Luis Coloma, Sunia Trauger, Eva Fischer, , , Charles Vidoudez, Olivia Nieves, Tammy Fay & Barbara Dorritie
Much of the world’s biodiversity is held within tropical rainforests, which are increasingly fragmented by agricultural practices. In these threatened landscapes, there are many organisms that acquire chemical defenses from their diet and are therefore intimately connected with their local food webs. Poison frogs (Family Dendrobatidae) are one such example, as they acquire alkaloid-based chemical defenses from their diet of leaf litter ants and mites. It is currently unknown how habitat fragmentation impacts chemical defense...

Estimating the Net Value of Treating Hepatitis C Virus Using Newly Available Direct-Acting Antivirals in India (Supporting Datasets)

David Bloom, Alex Khoury & V. Srinivasan
Recently developed direct-acting antiviral (DAA) treatments for hepatitis C virus (HCV) have been groundbreaking for their high efficacy across disease genotypes and lack of severe side effects. This study uses a cost-of-illness (COI) approach to estimate the net value conferred by this class of drugs using the cost and efficacy of one of these novel drug combinations, sofosbuvir and velpatasvir (SOF/VEL), recently licensed for generic manufacture in India. This study considers COI of lifetime earnings...

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