418 Works

Trajectories of body landmarks in videos of cerebral palsy patients and corresponding clinical labels

Łukasz Kidziński, Bryan Yang, Jennifer Hicks, Apoorva Rajagopal, Scott Delp & Michael Schwartz
Cerebral Palsy (CP) is a neurological disorder that is usually caused by mechanical damage to the brain at or around birth. One of the main symptoms of CP is impaired motor control and development of walking skills. In clinical practice in the US child’s gait is often recorded with a camera and the recording can be used by a doctor for assessment. In this dataset we provide body landmarks (such as positions of knees, elbow,...

Monitoring Data from Pilot-Scale Open-Water Unit Process Wetland Treatment of Reverse Osmosis Concentrate from Water Reuse

Rachel Scholes, Jack King, Michael Vega, Josh Sharp, William Mitch & David Sedlak
This workbook provides monitoring data from a pilot-scale ozone/open-water wetland treatment system for reverse osmosis concentrate from the Silicon Valley Advanced Water Purification Center (San Jose, CA). Water quality analyses included common water quality parameters, nutrients, trace metals, and trace organics. These analyses were performed by UC Berkeley, Stanford University, Valley Water's Water Quality Lab, and a contract lab (Eurofins). Functional gene analyses (qPCR) were conducted at Colorado School of Mines for samples of the...

Data for \"Tuning time and energy resolution in time-resolved photoemission spectroscopy with nonlinear crystals\"

Alexandre Gauthier, Jonathan A. Sobota, Nicolas Gauthier, Ke-Jun Xu, Heike Pfau, Costel R. Rotundu, Zhi-Xun Shen & Patrick S. Kirchmann
This archive contains the data that supports the findings of "Tuning time and energy resolution in time-resolved photoemission spectroscopy with nonlinear crystals" authored by A. Gauthier, J. A. Sobota, N. Gauthier, K.-J. Xu, H. Pfau, C. R. Rotundu, Z.-X. Shen, and P. S. Kirchmann. Preprint available at https://arxiv.org/abs/2006.07758.

2012 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...

2017 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...

2018 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...

Data for: Emergent ferromagnetism near three-quarters filling in twisted bilayer graphene

Aaron Sharpe, Eli Fox, Arthur Barnard, Joe Finney, Kenji Watanabe, Takashi Taniguchi, Marc Kastner & David Goldhaber-Gordon
This archive contains the data and Python code generating figures for the article "Emergent ferromagnetism near three-quarters filling in twisted bilayer graphene" by Aaron L. Sharpe, Eli J. Fox, Arthur W. Barnard, Joe Finney, Kenji Watanabe, Takashi Taniguchi, M. A. Kastner, and David Goldhaber-Gordon and available at https://arxiv.org/abs/1901.03520. This archive contains the following: 1) TBG_ferromagnetism_figures.ipynb, a Jupyter notebook loading data and generating figures. The notebook has been tested with Python version 3.6.7 and Jupyter notebook...

A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity

Kevin Leempoel, Elizabeth Hadly & Trevor Hebert
Before environmental DNA (eDNA) can establish itself as a robust tool for biodiversity monitoring, comparison with existing approaches is necessary, yet is lacking for terrestrial mammals. Moreover, much is unknown regarding the nature, spread and persistence of DNA shed by animals into terrestrial environments, or the optimal experimental design for understanding these potential biases. To address some of these challenges, we compared the detection of terrestrial mammals using eDNA analysis of soil samples against confirmed...

Do tradeoffs govern plant species responses to different global change treatments?

J. Adam Langley, Emily Grman, Kevin Wilcox, Meghan Avolio, Kimberly Komatsu, Scott Collins, Sally Koerner, Melinda Smith, Andrew Baldwin, William Bowman, Nona Chiariello, Anu Eskelinen, Harry Harmens, Mark Hovenden, Kari Klanderud, Rebecca McCulley, Vladimir Onipchenko, Clare Robinson & Katharine Suding
Plants are subject to tradeoffs among growth strategies such that adaptations for optimal growth in one condition can preclude optimal growth in another. Thus, we hypothesized that the response of plant species abundance to one global change treatment would relate inversely to the response to a second treatment, particularly for treatment combinations that accentuate distinct traits. To address this hypothesis, we examined plant species abundances in 39 global change experiments manipulating CO2, nitrogen, phosphorus, water,...

Census and phenotype data supporting Drosophila adaptive tracking

Seth Rudman, Paul Schmidt, Subhash Rajpurohit, Sharon Greenblum & Dmitri Petrov
Direct observation of evolution in response to natural environmental change can resolve fundamental questions about adaptation including its pace, temporal dynamics, and underlying phenotypic and genomic architecture. We tracked evolution of fitness-associated phenotypes and allele frequencies genome-wide in ten replicate field populations of Drosophila melanogaster over ten generations from summer to late fall. Adaptation was evident over each sampling interval (1-4 generations) with exceptionally rapid phenotypic adaptation and large allele frequency shifts at many independent...

Clinical Trial Transparency and Data-Sharing Among Bio-Pharmaceutical Companies and the Role of Company Size, Location, and Product Type: A Cross-Sectional Descriptive Analysis

Sydney Axson, Michelle Mello, Deborah Lincow, Catherine Yang, Cary Gross, Joseph Ross & Jennifer Miller
Objective: To examine company characteristics associated with better transparency and to apply a tool used to measure and improve clinical trial transparency among large companies and drugs, to smaller companies and biologics. Design: Cross-sectional descriptive analysis. Setting and participants. Novel drugs and biologics FDA approved in 2016 and 2017, and their company sponsors. Using established Good Pharma Scorecard (GPS) measures, companies and products were evaluated on their clinical trial registration, results dissemination, and FDA Amendments...

Flash sequence duration

Jamie Zeitzer, Daniel Joyce & Manuel Spitschan
Unlike light input for forming images, non-image forming retinal pathways are optimized to convey information about the total light environment, integrating over time and space. It has been demonstrated in a variety of species that the retinohypothalamic pathway underlying circadian entrainment can effectively integrate the impact of individual flashes over time and convey this information as if continuous light exposure had occurred. In this study, we examine the extent to which this temporal integration can...

Resilient consumers accelerate the plant decomposition in a naturally acidified seagrass ecosystem

Juhyung Lee, Maria Cristina Gambi, Kristy Kroeker, Marco Munari, Kabir Peay & Fiorenza Micheli
Anthropogenic stressors are predicted to alter biodiversity and ecosystem functioning worldwide. However, scaling up from species to ecosystem responses poses a challenge, as species and functional groups can exhibit different capacities to adapt, acclimate, and compensate under changing environments. We used a naturally acidified seagrass ecosystem (the endemic Mediterranean Posidonia oceanica) as a model system to examine how ocean acidification (OA) modifies the community structure and functioning of plant detritivores, which play vital roles in...

A peripheral immune signature of labor induction

Kazuo Ando, Julien Hédou, Brendan Carvalho, Ina Stelzer & Brice Gaudilliere
Approximately 1 in 4 pregnant women in the United States undergo labor induction. The onset and establishment of labor, particularly induced labor, is a complex and dynamic process influenced by multiple endocrine, inflammatory, and mechanical factors as well as obstetric and pharmacological interventions. The duration from labor induction to the onset of active labor remains unpredictable. Moreover, prolonged labor is associated with severe complications for the mother and her offspring, most importantly chorioamnionitis, uterine atony,...

Body size, sampling completeness, and extinction risk in the marine fossil record

Jonathan Payne & Noel Heim
Larger body size has long been assumed to correlate with greater risk of extinction, helping to shape body size distributions across the tree of life, but lack of comprehensive size data for fossil taxa have left this hypothesis untested for most higher taxa across the vast majority of evolutionary time. Here we assess the relationship between body size and extinction using a dataset comprising the body sizes, stratigraphic ranges, and occurrence patterns of 9,408 genera...

Data from: The future of food from the sea

Tracey Mangin, Christopher Costello, Ling Cao, Stefan Gelcich, Miguel A. Cisneros-Mata, Christopher M. Free, Halley E. Froehlich, Christopher D. Golden, Gakushi Ishimura, Jason Maier, Ilan Macadam-Somer, Michael C. Melnychuk, Masanori Miyahara, Carryn L. De Moor, Rosamond Naylor, Linda Nøstbakken, Elena Ojea, Erin O’Reilly, Ana M. Parma, Andrew J. Plantinga, Shakuntala H. Thilsted & Jane Lubchenco
Global food demand is on the rise and serious questions remain about whether supply can increase sustainably. Land-based expansion is possible, but may exacerbate climate change and biodiversity loss and compromise the delivery of other ecosystem services. As food from the sea represents only 17% of current edible meat production, we ask: How much food can we expect the ocean to sustainably produce by 2050? We examine the main food-producing sectors in the ocean—wild fisheries,...

Interspecific variation and elevated CO2 influence the relationship between plant chemical resistance and regrowth tolerance

Leslie Decker & Mark D. Hunter
To understand how comprehensive plant defense phenotypes will respond to global change, we investigated the legacy effects of elevated CO2 on the relationships between chemical resistance (constitutive and induced via mechanical damage) and regrowth tolerance in four milkweed species (Asclepias). We quantified potential resistance and tolerance tradeoffs at the physiological level following simulated clipping/mowing, which are relevant to milkweed ecology and conservation. We examined the legacy effects of elevated CO2 on four hypothesized tradeoffs between:...

Repeated fire shifts carbon and nitrogen cycling by changing plant inputs and soil decomposition across ecosystems

Adam Francis Pellegrini, Sarah Hobbie, Peter Reich, Ari Jumpponen, Jack Brookshire, Anthony Caprio, Corli Coetsee & Robert Jackson
Fires shape the biogeochemistry and functioning of many ecosystems, and fire frequencies are changing across much of the globe. Frequent fires can change soil carbon (C) and nitrogen (N) storage by altering the quantity and chemistry of plant inputs through changes in plant biomass and composition as well as altering decomposition of soil organic matter. How decomposition rates change with shifting inputs remains uncertain because most studies focus on the effects of single fires, where...

Data from: Seasonal changes in diet and toxicity in the Climbing Mantella frog (Mantella laevigata)

Nora A. Moskowitz, Alexandre B. Roland, Eva K. Fischer, Ndimbintsoa Ranaivorazo, Charles Vidoudez, Marianne T. Aguilar, Sophia M. Caldera, Jackie Chea, Miruna G. Cristus, Jett P. Crowdis, Bluyé DeMessie, Caroline R. Desjardins-Park, Audrey H. Effenberger, Felipe Flores, Michael Giles, Emma Y. He, Nike S. Izmaylov, ChangWon C. Lee, Nicholas A. Pagel, Krystal K. Phu, Leah U. Rosen, Danielle A. Seda, Yong Shen, Santiago Vargas, Hadley S. Weiss … & Lauren A. O’Connell
Poison frogs acquire chemical defenses from the environment for protection against potential predators. These defensive chemicals are lipophilic alkaloid toxins that are sequestered by poison frogs from dietary arthropods and stored in skin glands. Despite decades of research focusing on identifying poison frog toxins, we know relatively little about how environmental variation and subsequent arthropod availability impacts toxicity in poison frogs. We investigated how seasonal environmental variation influences poison frog toxin profiles through changes in...

Parallel molecular mechanisms for enzyme temperature adaptation

Margaux M. Pinney, Daniel A. Mokhtari, Eyal Akiva, Filip Yabukarski, David M. Sanchez, Ruibin Liang, Tzanko Doukov, Todd J. Martinez, Patricia C. Babbitt & Daniel Herschlag
The mechanisms that underly the adaptation enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Herein, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis and we establish the underlying physical mechanisms. This...

Current status and future strategies for mentoring women in neurology

Christa San Luis Nobleza, Amtul Farheen, Ilena George, Divya Singhal, Regina Troxell, Jyoti Pillai, Logan Schneider, Catherine Lomen-Hoerth, Jennifer Graves & Stefano Sandrone
The American Academy of Neurology's (AAN) 2017 Gender Disparity Report identified improving mentorship as a key intervention to fill the leadership and pay gaps for women in neurology. Here we summarize the literature on mentoring women, provide an outline of ideal components of programs geared toward closing gender gaps, and present a mentoring program for AAN members. The strategies discussed share similarities with those for closing gaps related to race, ethnicity and religion. Developing effective...

Three-dimensional biofilm growth supports a mutualism involving matrix and nutrient sharing - related scripts and data

Heidi Arjes
This dataset contains the supporting scripts and data used to analyze co-culture fluorescent colony images in high-throughput. It contains some example images that can be used in the scripts. It also contains the script used to plot and determine the maximum growth rates of growth curves of some of the mutants and the script used to stitch overlapping microscope images.

Data: Experimental evidence of warming-induced disease emergence and its prediction by a trait-based mechanistic model

Devin Kirk, Pepijn Luijckx, Natalie Jones, Leila Krichel, Clara Pencer, Peter Molnár & Martin Krkosek
Predicting the effects of seasonality and climate change on the emergence and spread of infectious disease remains difficult, in part because of poorly understood connections between warming and the mechanisms driving disease. Trait-based mechanistic models combined with thermal performance curves arising from the Metabolic Theory of Ecology (MTE) have been highlighted as a promising approach going forward; however, this framework has not been tested under controlled experimental conditions that isolate the role of gradual temporal...

Resources for gasAcu1-4, a new stickleback reference genome

Garrett Roberts Kingman, Heidi Chen, David Kingsley, Deven Vyas, Krishna Veeramah, Felicity Jones & Mike Bell
gasAcu1-4 is a new version of the stickleback reference genome. It only minorly differs from the 2017 Hi-C guided assembly by Peichel, Sullivan, Liachko, and White (https://doi.org/10.1093/jhered/esx058) to improve the subtelomeric Pitx1 locus and the mitochondrial genome. We here present basic resources for utilizing this version of the reference genome: the fasta sequence of the assembly and liftOver chains for converting coordinates between this reference version and the original (Broad S1) gasAcu1 assembly (https://www.nature.com/articles/nature10944). This...

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