47 Works

Causes of delayed outbreak responses and their impacts on epidemic spread

Yun Tao, Matthew Ferrari, Katriona Shea, William Probeert, Michael Runge, Kevin Lafferty & Michael Tildesley
Livestock diseases have devastating consequences economically, socially, and politically across the globe. In certain systems, pathogens remain viable after host death, which enables residual transmissions from infected carcasses. Rapid culling and carcass disposal are well-established strategies for stamping out an outbreak and limiting its impact, however, wait-times for these procedures, i.e., response delays, are typically farm-specific and time-varying due to logistical constraints. Failing to incorporate variable response delays in epidemiological models may understate outbreak projections...

Putative resistance and tolerance mechanisms have little impact on disease progression for an emerging salamander pathogen

Mark Wilber, Edward Carter, Matthew Gray & Cheryl Briggs
1. Resistance and tolerance are unique host defense strategies that can limit the impacts of a pathogen on a host. However, for most wildlife-pathogen systems there are still fundamental uncertainties regarding 1) how changes in resistance and tolerance can affect disease outcomes and 2) the mechanisms underlying resistance and tolerance in host populations. 2. Here, we first compared observed patterns of resistance and tolerance and their effects on disease outcomes among salamander species that are...

Land use impacts on parasitic infection: A cross-sectional epidemiological study on the role of irrigated agriculture in schistosome infection in a dammed landscape

Andrea Lund, David Rehkopf, Susanne Sokolow, M. Moustapha Sam, Nicolas Jouanard, Anne-Marie Schacht, Simon Senghor, Assane Fall, Gilles Riveau, Giulio De Leo & David Lopez-Carr
Background: Water resources development promotes agricultural expansion and food security. But are these benefits offset by increased infectious disease risk? Dam construction on the Senegal River in 1986 was followed by agricultural expansion and increased transmission of human schistosomes. Yet the mechanisms linking these processes at the individual and household levels remain unclear. We investigated the association between household land use and schistosome infection in children. Methods: We analyzed cross-sectional household survey data (n =...

Glassy dynamics and memory effects in an intrinsically disordered protein construct

Ian Morgan, Ram Avinery, Gil Rahamim, Roy Beck & Omar Saleh
Glassy, nonexponential relaxations in globular proteins are typically attributed to conformational behaviors that are missing from intrinsically disordered proteins. Yet, we show that single molecules of a disordered-protein construct display two signatures of glassy dynamics, logarithmic relaxations and a Kovacs memory effect, in response to changes in applied tension. We attribute this to the presence of multiple independent local structures in the chain, which we corroborate with a model that correctly predicts the force-dependence of...

Fastq files related to publication: At Palmyra Atoll, the fish‐community environmental DNA signal changes across habitats but not with tides

Kevin D. Lafferty, Ana E. Garcia‐Vedrenne, John P. McLaughlin, Jasmine N. Childress, Marisa F. Morse & Christopher L. Jerde
At Palmyra Atoll, the environmental DNA (eDNA) signal on tidal sand flats was associated with fish biomass density and captured 98%–100% of the expected species diversity there. Although eDNA spilled over across habitats, species associated with reef habitat contributed more eDNA to reef sites than to sand-flat sites, and species associated with sand-flat habitat contributed more eDNA to sand-flat sites than to reef sites. Tides did not disrupt the sand-flat habitat signal. At least 25...

Imaging orbital ferromagnetism in a moire Chern insulator

Charles Tschirhart, Marec Serlin, Hryhoriy Polshyn, Avi Shragai, Zhengchao Xia, Jiacheng Zhu, Yuxuan Zhang, Kenji Watanabe, Takashi Taniguchi, Martin Huber & Andrea Young
Electrons in moire flat band systems can spontaneously break time reversal symmetry, giving rise to a quantized anomalous Hall effect. Here we use a superconducting quantum interference device to image stray magnetic fields in twisted bilayer graphene aligned to hexagonal boron nitride. We find a magnetization of several Bohr magnetons per charge carrier, demonstrating that the magnetism is primarily orbital in nature. Our measurements reveal a large change in the magnetization as the chemical potential...

Analyzing environmental and social impacts of urban forestry practices in Tacoma, WA with PlanIT Geo

Joanne Pham, Veronica Weber & Rachel Conway
Urban forestry encompasses street trees, residential trees, park trees and greenbelt vegetation. Despite local groups’ efforts and trends in better forest management practices, there is an unequal distribution of urban forests and their associated ecosystem services across most of the United States. Evaluating canopy distribution is the first step to enable cities to better devote limited resources to marginalized communities, which often have additional equity concerns. Our project will help the urban forestry nonprofit, PlanIT...

Projected climate risk of aquatic food system benefits

Michelle Tigchelaar, William Cheung, Essam Mohammed, Michael Phillips, Hanna Payne, Elizabeth Selig, Colette Wabnitz, Muhammed Oyinlola, Thomas Frölicher, Jessica Gephart, Christopher Golden, Edward Allison, Abigail Bennett, Ling Cao, Jessica Fanzo, Benjamin Halpern, Fiorenza Micheli, Rosamond Naylor, Rashid Sumaila, Alessandro Tagliabue & Max Troell
Aquatic foods from marine and freshwater systems are critical to the nutrition, health, livelihoods, economies and culture of billions of people worldwide – but climate-related hazards may compromise their ability to provide these benefits. This analysis estimates national-level aquatic food system climate risk using a fuzzy logic modeling approach that connects climate hazards impacting marine and freshwater capture fisheries and aquaculture to their contributions to sustainable food system outcomes, and vulnerability to losing those contributions....

Relationships of climate, human activity, and fire history to spatiotemporal variation in annual fire probability across California: Source Code and Core Data

Isaac Park, Michael Mann, Lorraine Flint, Alan Flint & Max Moritz
In the face of recent wildfires across the Western United States, it is essential that we understand both the dynamics that drive the spatial distribution of wildfire, and the major obstacles to modeling the probability of wildfire over space and time. However, it is well documented that the precise relationships of local vegetation, climate, and ignitions, and how they influence fire dynamics, may vary over space and among local climate, vegetation, and land use regimes....

Data from: A food web including parasites for kelp forests of the Santa Barbara Channel, California

Dana Morton, Cristiana Antonino, Farallon Broughton, Dykman Lauren, Armand Kuris & Kevin Lafferty
We built a high-resolution topological food web for the kelp forests of the Santa Barbara Channel, California, USA that includes parasites and significantly improves resolution compared to previous webs. The 1,098 nodes and 21,956 links in the web describe an economically, socially, and ecologically vital system. Nodes are broken into life-stages. There are 549 free-living life-stages (comprising 492 species from 21 Phyla) and 549 parasitic life-stages (comprising 450 species from 10 Phyla). Links represent three...

Data From: Tactile Echoes: Multisensory Augmented Reality for the Hand

Anzu Kawazoe, Gregory Reardon, Erin Woo, Massimiliano Di Luca & Yon Visell
Touch interactions are central to many human activities, but there are few technologies for computationally augmenting free-hand interactions with real environments. Here, we describe Tactile Echoes, a finger-wearable system for augmenting touch interactions with physical objects. This system captures and processes touch-elicited vibrations in real-time in order to enliven tactile experiences. We process these signals via a parametric signal processing network in order to generate responsive tactile and auditory feedback. Just as acoustic echoes are...

The CALFISH database: open-sourcing a century of California’s non-confidential fisheries landings and participation data

Christopher Free, Camila Vargas Poulsen & Lyall Bellquist
California’s commercial and recreational fisheries support vibrant coastal economies and communities. Maintaining healthy fishing communities into the future requires a detailed understanding of their past. The California Department of Fish and Wildlife (CDFW) has been monitoring statewide fisheries landings and participation since 1916 and releases confidential versions of this data through authorized data requests and non-confidential summaries of this data in its quasi-annual landings reports. The non-confidential data published in the landings reports provide a...

Supporting information for: A pilot experiment on infrasonic lahar detection at Mount Adams, Cascades: Ambient infrasound and wind-noise characterization at a quiescent stratovolcano: time-lapse camera images

Richard Sanderson, Robin Matoza, Rachel Haymon & Jamison Steidl
Erosion, hydrothermal activity, and magmatism at volcanoes can cause large and unexpected mass wasting events. Large fluidized debris flows have occurred within the past 6,000 years at Mount Adams, WA, and present a hazard to communities downstream. In August 2017, we began a pilot experiment to investigate the potential of infrasound arrays for detecting and tracking debris flows at Mount Adams. We deployed a telemetered 4-element infrasound array (BEAR, 85-m aperture) ~11 km from a...

Epistolary Pamphlets

Rachael King & Edwin Roland
These spreadsheets show the results of an effort to identify the epistolary pamphlet genre within the ECCO-TCP database. Sheet 1 shows the model's predictions of whether a particular text was an epistolary pamphlet while Sheet 2 identifies the tokens used to build the model. Overall, the model was able to identify the genre with 76 percent accuracy.

Data from: Strong evidence for an intraspecific metabolic scaling coefficient near 0.89 in fish

Krista Kraskura, Christopher Jerde & Erika Eliason
We curated standard metabolic rate measurements of individual fish, temperature, and body mass. The database is grouped by studies, with independent trials, and fish species. The databse includes a total of n = 1456 observations that were used to quantify the body mass – metabolic rate relationship in fishes using the evidential approach to statistical inference.

Diet mediates thermal performance traits: implications for marine ectotherms

Emily Hardison, Emily A Hardison, Krista Kraskura, Jacey Van Wert, Tina Nguyen & Erika J Eliason
Thermal acclimation is a key process enabling ectotherms to cope with temperature change. To undergo a successful acclimation response, ectotherms require energy and nutritional building blocks obtained from their diet. However, diet is often overlooked as a factor that can alter acclimation responses. Using a temperate omnivorous fish, opaleye (Girella nigricans), as a model system, we tested the hypotheses that 1) diet can impact the magnitude of thermal acclimation responses and 2) traits vary in...

Protecting the global ocean for biodiversity, food and climate

Enric Sala, Juan Mayorga, Darcy Bradley, Reniel Cabral, Trisha Atwood, Arnaud Auber, William Cheung, Francesco Ferretti, Alan Friedlander, Steven Gaines, Cristina Garilao, Whitney Goodell, Benjamin Halpern, Audra Hinson, Kristin Kaschner, Kathleen Kesner-Reyes, Fabien Leprieur, Jennifer McGowan, Lance Morgan, David Mouillot, Juliano Palacios-Abrantes, Hugh Possingham, Kristin Rechberger, Boris Worm & Jane Lubchenco
The ocean contains unique biodiversity, provides valuable food resources, and is a major sink for anthropogenic carbon. Marine protected areas (MPAs) are an effective tool for restoring ocean biodiversity and ecosystem services but at present only 2.7% of the ocean is highly protected. This low level of ocean protection is due largely to conflicts with fisheries and other extractive uses. To address this issue, here we developed a conservation planning framework to prioritize highly protected...

Triennial migration and philopatry in the critically endangered soupfin shark (Galeorhinus galeus)

Andrew Nosal, Daniel Cartamil, Arnold Ammann, Lyall Bellquist, Noah Ben-Aderet, Kayla Blincow, Echelle Burns, Eric Chapman, Ryan Freedman, Peter Klimley, Ryan Logan, Christopher Lowe, Brice Semmens, Connor White & Philip Hastings
Globally, one-quarter of shark and ray species is threatened with extinction due to overfishing. Effective conservation and management can facilitate population recoveries; however, these efforts depend on robust data on movement patterns and stock structure, which are lacking for many threatened species, including the Critically Endangered soupfin shark (Galeorhinus galeus), a circumglobal coastal-pelagic species. Using passive acoustic telemetry, we continuously tracked 34 mature female soupfin sharks, surgically implanted with coded acoustic transmitters, for seven years...

Juan José Arreola y su estética del zigzag

Sara Poot Herrera
pp. 77-90 The work of Juan José Arreola, taken as a whole, represents a fluid and continuous coming and going between life and literature, reality and fiction. It is a back and forth trip, a zig zag between official and popular culture, literary genres, orality and writing, because Arreola is above all a thinker and a man of culture through multiple facets that accompanied him throughout his career: essayist, narrator, chronicler, biographer, philologist, teacher, actor,...

Kinetic sequencing (k-Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters

Yuning Shen, Abe Pressman, Evan Janzen & Irene Chen
Characterizing genotype-phenotype relationships of biomolecules (e.g., ribozymes) requires accurate ways to measure activity for a large set of molecules. Kinetic measurement using high-throughput sequencing (e.g., k-Seq) is an emerging assay applicable in various domains that potentially scales up measurement throughput to over 106 unique nucleic acid sequences. However, maximizing the return of such assays requires understanding the technical challenges introduced by sequence heterogeneity and DNA sequencing. We characterized the k-Seq method in terms of model...

Spenders versus savers: climate-induced carbon allocation tradeoffs in a recently introduced woody plant

Randall Long, Tom Dudley, Carla D'Antonio, Kevin Grady, Susan Bush & Kevin Hultine
Non-structural carbohydrate(NSC) storage may be under strong selection in woody plant species that occur across strong environmental gradients. We therefore investigated carbon allocation strategies in a widely distributed, introduced woody plant. We predicted genotypes from cold climates with exposure to episodic freeze events, would have elevated NSC concentrations with the tradeoff of reduced growth and reproduction relative to warm-adapted genotypes. We established an experimental common garden using genotypes of Tamarix spp., sourced across a large...

A distributed circuit for associating environmental context to motor choice in retrosplenial cortex

Luis Franco & Michael Goard
During navigation, animals often use recognition of familiar environmental contexts to guide motor action selection. The retrosplenial cortex (RSC) receives inputs from both visual cortex and subcortical regions required for spatial memory, and projects to motor planning regions. However, it is not known whether RSC is important for associating familiar environmental contexts with specific motor actions. Here, we test this possibility by developing a task in which trajectories are chosen based on the context. We...

Using acoustic telemetry to quantify potential contaminant exposure of Vermilion Rockfish (Sebastes miniatus), Hornyhead Turbot (Pleuronichthys verticalis), and White Croaker (Genyonemus lineatus) at wastewater outfalls in southern California

Echelle Burns, Barrett Wolfe, Jeff Armstrong, Danny Tang, Ken Sakamoto & Christopher Lowe
Contaminant Exposure Models (CEMs) were developed to predict population-level tissue contaminant concentrations in fishes by pairing sediment-bound contaminant concentrations (DDTs, PCBs) and fine-scale acoustic telemetry data from a habitat- associated species (Vermilion Rockfish, Sebastes miniatus), nomadic flatfish species (Hornyhead Turbot, Pleuronichthys verticalis), and nomadic benthic/midwater schooling species (White Croaker, Genyonemus lineatus) tagged near wastewater outfalls in southern California. Model results were compared to contaminant concentrations in tissue samples. The CEMs developed require further refinement before...

Value of Curation Survey, January 2021

Lisa R Johnston, Renata Gonçalves Curty, Sophia Lafferty-Hess, Hannah Hadley, Jonathan Petters, Hoa Luong, Susan Braxton, Jake Carlson & Wendy A Kozlowski

Exposure, hazard and vulnerability all contribute to Schistosoma haematobium re-infection in northern Senegal

Andrea Lund, Susanne Sokolow, Isabel Jones, Chelsea Wood, Sofia Ali, Andrew Chamberlin, Alioune Sy, M. Moustapha Sam, Nicolas Jouanard, Anne-Marie Schacht, Simon Senghor, Assane Fall, Raphael Ndione, Gilles Riveau, Giulio De Leo & David Lopez-Carr
The risk of infectious diseases, including snail-borne schistosomiasis, is determined by three interrelated components: exposure, hazard and vulnerability. For schistosomiasis, exposure occurs through behaviors involving water contact, but not without the environmental hazard of snails and parasites in the water. Socio-economic vulnerability makes it difficult to reduce exposure in the presence of hazard, because it increases reliance on hazardous activities and environments. We aimed to quantify the contributions of exposure, hazard and vulnerability to schistosome...

Registration Year

  • 2021

Resource Types

  • Dataset
  • Text
  • Preprint


  • University of California, Santa Barbara
  • Stanford University
  • University of British Columbia
  • University of Washington
  • United States Geological Survey
  • California State University, Long Beach
  • Desert Botanical Garden
  • University of Queensland
  • Oregon State University
  • Espoir pour la Sante