341 Works

Data from: Rapid evolution of adaptive niche construction in experimental microbial populations

Benjamin J. Callahan, Tadashi Fukami & Daniel S. Fisher
Many species engage in adaptive niche construction: modification of the local environment that increases the modifying organism's competitive fitness. Adaptive niche construction provides an alternative pathway to higher fitness, shaping the environment rather than conforming to it. Yet, experimental evidence for the evolutionary emergence of adaptive niche construction is lacking, leaving its role in evolution uncertain. Here we report a direct observation of the de novo evolution of adaptive niche construction in populations of the...

Data from: Forensic genomics as a novel tool for identifying the causes of mass mortality events

Pierre De Wit, Laura Rogers-Bennett, Raphael M. Kudela & Stephen R. Palumbi
Toxic spills, hypoxia, disease outbreaks and toxin-producing algal blooms are all possible causes of mass mortality events, but in many cases it can be difficult to pinpoint the cause of death. Here we present a new approach that we name ‘forensic genomics’, combining field surveys, toxin testing and genomic scans. Forensic genomics queries allele frequencies of surviving animals for signatures of agents causing mass mortality and, where genetic diversity is high, is uniquely suited to...

Data from: Constraints on the adult-offspring size relationship in protists

Franklin Caval-Holme, Jonathan L. Payne, Jan M. Skotheim & Jonathan Payne
The relationship between adult and offspring size is an important aspect of reproductive strategy. Although this filial relationship has been extensively examined in plants and animals, we currently lack comparable data for protists, whose strategies may differ due to the distinct ecological and physiological constraints on single-celled organisms. Here, we report measurements of adult and offspring sizes in 3,888 species and subspecies of foraminifera, a class of large marine protists. Foraminifera exhibit a wide range...

Data from: Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast

Aymé Spor, Daniel J. Kvitek, Thibault Nidelet, Juliette Martin, Judith Legrand, Christine Dillmann, Aurélie Bourgais, Dominique De Vienne, Gavin Sherlock & Delphine Sicard
Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence may be caused by genotypic convergence and in addition, constrained by historical contingency. To investigate how convergence may be driven by selection in a particular environment and constrained by history, we analyzed nine life-history traits and four metabolic traits during an experimental evolution of six yeast strains in four different environments. In each of the environments, the...

Presentation Panel on Metadata Standards

Andrea d'Andrea, Christina Harlow, Julie Hardesty & Jon Blundell
Examples of topics of interest- Why do we need metadata standards development? How are standards developed? Given the lack of agreed upon standards for 3D data, what solutions are institutions currently using? What are users’ needs regarding metadata? Who are the targeted users? What constitutes the minimal metadata for inclusion in a repository? How can linked metadata be developed for improved workflows. What would be required for data clean up or migration for previously unstandardized...

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...

The anthropology of mind: Exploring unusual sensations and spiritual experiences across cultures. An interview with Tanya Luhrmann.

Tanya Luhrmann & Martin Fortier
In this interview, Tanya Luhrmann discusses her position within the field of anthropology as well as her methodological commitments. She also addresses her view about the mechanisms governing the shift from experiential unreality (imagination-like mental representations) to experiential reality (perception-like mental representations) as well as the role of personal proclivity (in particular the trait of absorption) within religious practice and experience. Finally, the interview tackles the question of cognitive penetrability: can folk models of the...

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...

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.

Codes, models and synthesized data for paper \"Learning from past respiratory infections to predict COVID-19 Outcomes: A retrospective study\"

Shengtian Sang & Tina Boussard
This repository contains the codes and synthesized data for our paper "Learning from past respiratory infections to predict COVID-19 Outcomes: A retrospective study". In this paper we proposed a framework that used COVID-like cohorts (you can find the description in our paper) to train machine learning models and validated them on the COVID-19 population.If you just want to test the model on synthetic COVID dataset, you could run the predict_COVID.py directly, or if you want...

Ecosystem Scale Measurements of Methyl Halide Fluxes from a Brackish Tidal Marsh Invaded with Perennial Pepperweed (Lepidium latifolium)

Malte Julian Deventer, Yi Jiao, Sarah Knox, Frank Anderson, Matthew Ferner, Jared Lewis & Robert Rhew
Natural methyl chloride (CH3Cl) and methyl bromide (CH3Br) emissions from coastal marsh ecosystems may constitute a significant proportion of stratospheric chlorine and bromine, which catalyze ozone depletion. Current inventories involve substantial uncertainties associated with up-scaling plot-scale footprints (i.e., ≤ 1m2). Here we present net ecosystem flux measurements of methyl halides from a brackish tidal marsh on the west coast of the United States between April 2016 and June 2017 using the relaxed eddy accumulation method....

Software and Calibration for Photothermal Threshold Quantum Yield

David Hanifi
This is code used to process and apply calibrations to photothermal threshold quantum yields taken, with our specific spectrometer. The calibrations included will not work for any other optics path or components, but this serves as a guide to calibrate one built in any other lab. This code is written in Matlab2018b.

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...

Data from: Shark movement strategies influence poaching risk and can guide enforcement decisions in a large, remote Marine Protected Area

David Jacoby, Francesco Ferretti, Robin Freeman, Aaron Carlisle, Taylor Chapple, David Curnick, Jonathan Dale, Robert Schallert, David Tickler & Barbara Block
Large, remote marine protected areas (MPAs) containing both reef and pelagic habitats, have been shown to offer considerable refuge to populations of reef-associated sharks. Many large MPAs are, however, impacted by illegal fishing activity conducted by unlicensed vessels. While enforcement of these reserves is often expensive, it would likely benefit from the integration of ecological data on the mobile animals they are designed to protect. Consequently, shark populations in some protected areas continue to decline,...

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...

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...

Date from: Foundation species promote local adaptation and fine-scale distribution of herbaceous plants

Michael O'Brien, Elisa Carbonell, Gianalberto Losapio, Philipp Schlüter & Christian Schöb
1) Interactions among neighbors can alter demography and traits of commingled species via adaptation or plasticity in phenotypic expression and understanding these two mechanisms in diverse communities is important for determining the ecological and evolutionary consequences of plant–plant interactions. 2) We reciprocally transplanted perennial species (Arenaria armerina and Festuca indigesta) among patches of two foundation shrub species and open ground to assess whether origin microsite (defined as the spatially distinct abiotic and biotic conditions associated...

Data from: Isolation by resistance across a complex coral reef seascape

Luke Thomas, W. Jason Kennington, Michael Stat, Shaun P. Wilkinson, Jonathan T. Kool & Gary A. Kendrick
A detailed understanding of the genetic structure of populations and an accurate interpretation of processes driving contemporary patterns of gene flow are fundamental to successful spatial conservation management. The field of seascape genetics seeks to incorporate environmental variables and processes into analyses of population genetic data to improve our understanding of forces driving genetic divergence in the marine environment. Information about barriers to gene flow (such as ocean currents) is used to define a resistance...

Data from: Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

Jesse A. Port, James L. O'Donnell, Ofelia C. Romero-Maraccini, Paul R. Leary, Steven Y. Litvin, Kerry J. Nickols, Kevan M. Yamahara & Ryan P. Kelly
Preserving biodiversity is a global challenge requiring data on species’ distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species’ distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource-intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by...

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