84 Works

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,...

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...

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...

Data from: Long-term mechanistic hindcasts predict the structure of experimentally-warmed intertidal communities

Diana LaScala-Gruenewald & Mark Denny
Increases in global temperatures are expected to have dramatic effects on the abundance and distribution of species in the coming years. Intertidal organisms, which already experience temperatures at or beyond their thermal limits, provide a model system in which to investigate these effects. We took advantage of a previous study in which experimental plates were deployed in the intertidal zone and passively warmed for 12 years to a daily maximum temperature on average 2.7°C higher...

Impacts of rodent eradication on seed predation and plant community biomass on a tropical atoll

Ana Miller-Ter Kuile, Devyn Orr, An Bui, Rodolfo Dirzo, Maggie Klope, Douglas McCauley, Carina Motta & Hillary Young
Invasive rodent eradications are frequently undertaken to curb island biodiversity loss. However, the breadth of rodents’ ecological impact, even after eradication, is not always fully recognized. For example, the most widespread invasive rodent, the black rat (Rattus rattus), while omnivorous, eats predominantly seeds and fruit. Yet, the effects of seed predation release after eradication on plant communities and ecological functions are not well understood, posing a gap for island restoration. We examined the role of...

A kaleidoscopic view of ovarian genes associated with infertility, subfertility and senescence

Aaron Hsueh
Ovarian infertility and subfertility presenting with premature ovarian insufficiency (POI) and diminished ovarian reserve are major issues facing in the developed world due to the trend of delaying child birth. Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disorder affecting 6-10% of women in reproductive age. Based on advances in whole exome sequencing, evaluation of gene copy variants, together with family-based and genome-wide association studies (GWAS), we discussed genes responsible for the POI,...

Data from: Nonlinearities between inhibition and T-type calcium channel activity bidirectionally regulate thalamic oscillations

Adam Lu, Christine Lee, Max Kleiman-Weiner, Brian Truong, Megan Wang, John Huguenard & Mark Beenhakker
Absence seizures result from 3-5 Hz generalized thalamocortical oscillations that depend on highly regulated inhibitory neurotransmission in the thalamus. Efficient reuptake of the inhibitory neurotransmitter GABA is essential, and reuptake failure worsens seizures. Here, we show that blocking GABA transporters (GATs) in acute brain slices containing key parts of the thalamocortical seizure network modulates epileptiform activity. As expected, we found that blocking either GAT1 or GAT3 prolonged oscillations. However, blocking both GATs unexpectedly suppressed oscillations....

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...

Magnitude and predictability of pH fluctuations shape plastic responses to ocean acidification

Mark Bitter, Lydia Kapsenberg, Katherine Silliman, Jean-Pierre Gattuso & Catherine Pfister
Phenotypic plasticity is expected to facilitate the persistence of natural populations as global change progresses. The attributes of fluctuating environments that favor the evolution of plasticity have received extensive theoretical investigation, yet empirical validation of these findings is still in its infancy. Here, we combine high-resolution environmental data with a laboratory-based experiment to explore the influence of habitat pH fluctuation dynamics on the plasticity of gene expression in two populations of the Mediterranean mussel, Mytilus...

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...

Data 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...

Frequent burning causes large losses of carbon from deep soil layers in a temperate savanna

Adam Francis Pellegrini, Kendra K. McLauchlan, Sarah E. Hobbie, Michelle C. Mack, Abbey L. Marcotte, David M. Nelson, Steven Perakis, Peter B. Reich & Kyle Whittinghill
1. Fire activity is changing dramatically across the globe, with uncertain effects on ecosystem processes, especially belowground. Fire‐driven losses of soil carbon (C) are often assumed to occur primarily in the upper soil layers because the repeated combustion of aboveground biomass limits organic matter inputs into surface soil. However, C losses from deeper soil may occur if frequent burning reduces root biomass inputs of C into deep soil layers or stimulates losses of C via...

Data set for 'Lunge filter feeding biomechanics constrain rorqual foraging ecology across scale'...

Shirel Rachel Kahane-Rapport
Fundamental scaling relationships influence the physiology of vital rates, which in turn shape the ecology and evolution of organisms. For diving mammals, benefits conferred by large body size include reduced transport costs and enhanced breath-holding capacity, thereby increasing overall foraging efficiency. Rorqual whales feed by engulfing a large mass of prey-laden water at high speed and filter it through baleen plates. However, as engulfment capacity increases with body length across species (Engulfment Volume ∝ Body...

Data from: Integrative genomic analysis in African American children with asthma finds 3 novel loci associated with lung function

Pagé Goddard, Kevin Keys, Angel Mak, Eunice Lee, Amy Liu, Lesly-Anne Samedy-Bates, Oona Risse-Adams, Maria Contreras, Jennifer Elhawary, Donglei Hu, Sam Oh, Sandra Salazar, Celeste Eng, Blanca Himes, Marquitta White & Esteban Burchard
Bronchodilator drugs are commonly prescribed for treatment and management of obstructive lung function present with diseases such as asthma. Administration of bronchodilator medication can partially or fully restore lung function as measured by pulmonary function tests. The genetics of baseline lung function measures taken prior to bronchodilator medication has been extensively studied, and the genetics of the bronchodilator response itself has received some attention. However, few studies have focused on the genetics of post-bronchodilator lung...

Data from: Increased diversity and concordant shifts in community structure of coral-associated Symbiodiniaceae and bacteria subjected to chronic human disturbance

Danielle Claar, Jamie McDevitt-Irwin, Melissa Garren, Rebecca Vega Thurber, Ruth Gates & Julia Baum
Coral-associated bacteria and endosymbiotic algae (Symbiodiniaceae spp.) are both vitally important for the biological function of corals. Yet little is known about their co-occurrence within corals, how their diversity varies across coral species, or how they are impacted by anthropogenic disturbances. Here, we sampled coral colonies (n = 472) from seven species, encompassing a range of life history traits, across a gradient of chronic human disturbance (n = 11 sites on Kiritimati (Christmas) atoll) in...

Data from: ClinicNet: machine learning for personalized order set recommendations

Jonathan Wang, Delaney Sullivan, Alex Wells & Jonathan Chen
Objective This study assesses whether neural networks trained on electronic health record (EHR) data can anticipate what individual clinical orders and existing institutional order set templates clinicians will use more accurately than existing decision support tools. Materials and Methods We process 57,624 patients-worth of clinical event EHR data from 2008-2014. We train a feed-forward neural network (ClinicNet) and logistic regression applied to the traditional problem structure of predicting individual clinical items as well as our...

Wandering along the spectrum of spontaneous thinking: dreaming, meditation, mind-wandering, and well-being. An interview with Kieran Fox.

Kieran Fox & Matthieu Koroma
About half of our conscious activity is not related to our direct sensory environment. Such spontaneous thinking has nevertheless long been neglected due to the difficulty to tackle it experimentally. Neuroscientific Kieran Fox discusses recent efforts to understand and conceptualize the diversity of spontaneous activity within a single framework. The relation of mind-wandering to other phenomena such as dreaming and mediation is highlighted. Far from being a distracting nuisance, the role of spontaneous thoughts in...

Data for \"Quantum well states in fractured crystals of the heavy fermion material CeCoIn5\"

Nicolas Gauthier, Jonathan A. Sobota, Makoto Hashimoto, Heike Pfau, Dong-Hui Lu, Eric D. Bauer, Filip Ronning, Patrick S. Kirchmann & Zhi-Xun Shen
This HDF5 file contains the data that supports the findings of "Quantum well states in fractured crystals of the heavy fermion material CeCoIn5" authored by N. Gauthier, J. A. Sobota, M. Hashimoto, H. Pfau, D.-H. Lu, E. D. Bauer, F. Ronning, P. S. Kirchmann, and Z.-X. Shen. Preprint available at https://arxiv.org/abs/2006.16301.

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