46 Works

No state change in pelagic fish production and biodiversity during the Eocene-Oligocene Transition

Elizabeth Sibert, Michelle Zill, Ella Frigyik & Richard Norris
The Eocene-Oligocene (E/O) boundary ~33.9 million years ago, has been described as a state change in the Earth system marked by the permanent glaciation of Antarctica and a proposed increase in oceanic productivity. Here we quantified the response of fish production and biodiversity to this event using microfossil fish teeth (ichthyoliths) in seven deep-sea sediment cores from around the world. Ichthyolith accumulation rate (a proxy for fish biomass production) shows no synchronous trends across the...

Quantifying the potential for biogeochemical feedbacks to create 'refugia' from ocean acidification on tropical coral reefs

Yuichiro Takeshita
Rising sea surface temperatures and ocean acidification (OA) may threaten the ability of calcified organisms to build carbonate reefs, but it is unclear if particular reefs have the capacity to tolerate global change. Current understanding of the effects of OA on coral reefs originates from single-species laboratory studies largely focused on scleractinian corals. Traditionally, these experiments attempt to mimic static future conditions under the assumption that coastal regimes are as constant as -- and will...

Data from: Stressed connections: cortisol levels following acute psychosocial stress disrupt affiliative mimicry in humans

Jonas P. Nitschke, Cecile S. Sunahara, Evan W. Carr, Piotr Winkielman, Jens C. Pruessner & Jennifer A. Bartz
Mimicry, and especially spontaneous facial mimicry, is a rudimentary element of social–emotional experience that is well-conserved across numerous species. Although such mimicry is thought to be a relatively automatic process, research indicates that contextual factors can influence mimicry, especially in humans. Here, we extend this work by investigating the effect of acute psychosocial stress on spontaneous facial mimicry. Participants performed a spontaneous facial mimicry task with facial electromyography (fEMG) at baseline and approximately one month...

Where New Words Are Born: Distributional Semantic Analysis of Neologisms and Their Semantic Neighborhoods

Maria Ryskina, Ella Rabinovich, Taylor Berg-Kirkpatrick, David R. Mortensen & Yulia Tsvetkov

Replication Files for Nutrition and the Gut Microbiota in 10–18-Month Old Children Living in Urban Slums of Mumbai, India

Samantha Huey, Aparna Thorat, Varsha Thakker, Julia L. Finkelstein, Lingjing Jiang, Marcus Fedarko, Daniel McDonald, Cameron Martino, Farhana Ali, David G. Russell, Harsha Chopra, Kripa Rajagopalan, Jere Douglas Haas, Rob Knight, S.A. Udipi & P. Ghugre

Uneven substrates constrain walking speed in ants through modulation of stride frequency more than stride length

Glenna Clifton, David Holway & Nick Gravish
Natural terrain is rarely flat. Substrate irregularities challenge walking animals to maintain stability, yet we lack quantitative assessments of walking performance and limb kinematics on naturally uneven ground. We measured how continually uneven 3D-printed substrates influence walking performance of Argentine ants by measuring walking speeds of workers from lab colonies and by testing colony-wide substrate preference in field experiments. Tracking limb motion in over 8,000 videos, we used statistical models that associate walking speed with...

Efficacy of metabarcoding for identification of fish eggs evaluated with mock communities

Elena Duke & Ron Burton
There is urgent need for effective and efficient monitoring of marine fish populations. Monitoring eggs and larval fish may be more informative that traditional fish surveys since ichthyoplankton surveys reveal the reproductive activities of fish populations, which directly impact their population trajectories. Ichthyoplankton surveys have turned to molecular methods (DNA barcoding & metabarcoding) for identification of eggs and larval fish due to challenges of morphological identification. In this study we examine the effectiveness of using...

Questioning to Resolve Transduction Problems

Eric Meinhardt, Anna Mai, Eric Bakovic & Adam McCollum

Data from: Nutrient availability controls the impact of mammalian herbivores on soil carbon and nitrogen pools in grasslands

Judith Sitters, E.R. Jasper Wubs, Elisabeth S. Bakker, Thomas W. Crowther, Peter B. Adler, Sumanta Bagchi, Jonathan D. Bakker, Lori Biederman, Elizabeth T. Borer, Elsa E. Cleland, Nico Eisenhauer, Jennifer Firn, Laureano Gherardi, Nicole Hagenah, Yann Hautier, Sarah E. Hobbie, Johannes M.H. Knops, Andrew S. MacDougall, Rebecca L. McCulley, Joslin L. Moore, Brent Mortensen, Pablo L. Peri, Suzanne M. Prober, Charlotte Riggs, Anita C. Risch … &
Grasslands have been subject to considerable alteration due to human activities globally, including widespread changes in populations and composition of large mammalian herbivores and elevated supply of nutrients. Grassland soils remain important reservoirs of carbon (C) and nitrogen (N). Herbivores may affect both C and N pools and these changes likely interact with increases in soil nutrient availability. Given the scale of grassland soil fluxes, such changes can have striking consequences for atmospheric C concentrations...

VELB watershed data 2005

Michael Dobbins, Theresa Talley & Marcel Holyoak
The Valley Elderberry Longhorn Beetle (“VELB,” Desmocerus californicus dimorphus) is a rare and cryptic species that is found on or near its host plant, blue elderberry (Sambucus mexicana), and is native to California’s Central Valley. Over the past 100 years, the riparian forests of Central California have shrunk by over 90%, resulting in highly fragmented, and often isolated, remaining VELB habitat patches. This has created the need for robust monitoring and demographic data to assess...

Data from: Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): developing a model system for the evolution of marine bioluminescence

Jessica A. Goodheart, Geetanjali Minsky, Mira N. Brynjegard-Bialik, Michael S. Drummond, J. David Munoz, Timothy R. Fallon, Darrin T. Schultz, Jing-Ke Weng, Elizabeth Torres & Todd H. Oakley
Bioluminescence, or the production of light by living organisms via chemical reaction, is widespread across Metazoa. Laboratory culture of bioluminescent organisms from diverse taxonomic groups is important for determining the biosynthetic pathways of bioluminescent substrates, which may lead to new tools for biotechnology and biomedicine. Some bioluminescent groups may be cultured, including some cnidarians, ctenophores, and brittle stars, but those use luminescent substrates (luciferins) obtained from their diets, and therefore are not informative for determination...

Dataset for: Cascading effects of freshwater salinization on plankton communities in the Sierra Nevada

Emma Moffett, Henry Baker, Christine Bonadonna, Jonathan Shurin & Celia Symons
Runoff containing road salt (sodium chloride, NaCl) causes the salinization of inland freshwaters, with potentially severe impacts on aquatic species. We performed a mesocosm experiment to test the effects of salinization on plankton community structure in an oligotrophic mountain lake with a limited history of elevated salt concentrations. We exposed plankton communities to a gradient of 30 salt concentrations ranging from 1-2900 Cl– mg L-1 for six weeks. Adding salt increased zooplankton biomass at concentrations...

Collaborative research: Quantifying the biological, chemical, and physical linkages between chemosynthetic communities and the surrounding deep sea

Oliver Ashford
The deep ocean supplies food, energy, novel drugs and materials, and plays essential roles in the global cycling of carbon, the nutrient replenishment for shallow waters, and the maintenance of biodiversity. Despite the crucial contribution of the deep sea to the larger functioning of global marine ecosystems, there is only a cursory understanding of this vast region and the connectivity among its communities and the rest of the oceans. Cold seeps, active areas of the...

Dataset marmoset Snowdrift

Alejandro Sanchez Amaro, Judith Burkart & Federico Rossano
Social primates constantly face situations in which their preferences collide and they need to engineer strategies to overcome conflicts of interest. Studies with chimpanzees have found that they use competitive strategies to overcome social dilemmas, maximizing their own benefits while minimizing the loss of rewards. However, little is known about how other primates that rely more on cooperation would overcome similar dilemmas. We therefore presented male-female pairs of common marmosets (cooperative breeders) with two experiments...

Data from: Training data from SPCAM for machine learning in moist physics

Guang Zhang, Yilun Han, Xiaomeng Huang & Yong Wang
Current moist physics parameterization schemes in general circulation models (GCMs) are the main source of biases in simulated precipitation and atmospheric circulation. Recent advances in machine learning make it possible to explore data-driven approaches to developing parameterization for moist physics processes such as convection and clouds. This study aims to develop a new moist physics parameterization scheme based on deep learning. We use a residual convolutional neural network (ResNet) for this purpose. It is trained...

Oxygen exposure of common benthic megafauna off San Diego, CA

Ed Parnell
Oxygen decline poses increasing risks to global shelf communities. This study was conducted to measure species oxygen exposures in situ, and to assess risks of low oxygen based on the hypothesis that species risk varies spatially and is dependent on the interaction of shelf oxygen dynamics with habitat pattern, species mobility and tolerance to low oxygen. Here, we report concomitant observations of oxygen, depth, and habitat for the most common benthic and epibenthic megafauna on...

Data from: Validation of serum neurofilaments as prognostic & potential pharmacodynamic biomarkers for ALS

Michael Benatar, Lanyu Zhang, Lily Wang, Volkan Granit, Jeffrey Statland, Richard Barohn, Andrea Swenson, John Ravitz, Carlayne Jackson, Ted Burns, Jaya Trivedi, Erik Pioro, James Caress, Jonathan Katz, Jacob McCauley, Rosa Rademakers, Andrea Malaspina, Lyle Ostrow & Joanne Wuu
Objective. Identify preferred neurofilament assays, and clinically validate serum NfL and pNfH as prognostic and potential pharmacodynamic biomarkers relevant to ALS therapy development. Methods. Prospective, multi-center, longitudinal observational study of patients with ALS (n=229), primary lateral sclerosis (PLS, n=20) and progressive muscular atrophy (PMA, n=11). Biological specimens were collected, processed and stored according to strict standard operating procedures (SOPs) 1. Neurofilament assays were performed in a blinded manner by independent contract research organizations (CROs). Results....

Kelp forests at the end of the earth: 45 years later

Alan Friedlander, Enric Ballesteros, Tom Bell, Jennifer Caselle, Claudio Campagna, Mathias Hune, Alex Munoz, Pelayo Salinas-De-Leon, Enric Sala & Paul Dayton
The kelp forests of southern South America are some of the least disturbed on the planet. The remoteness of this region has, until recently, spared it from many of the direct anthropogenic stressors that have negatively affected these ecosystems elsewhere. Re-surveys of 11 locations at the easternmost extent of Tierra del Fuego originally conducted in 1973 showed no significant differences in the densities of adult and juvenile Macrocystis pyrifera kelp or kelp holdfast diameter between...

Mitonuclear mismatch alters performance and reproductive success in naturally-introgressed populations of a montane leaf beetle

Nathan Rank, Nathan E Rank, Patrick Mardulyn, Sarah J Heidl, Kevin T Roberts, Nicolas A Zavala, John T Smiley & Elizabeth P Dahlhoff
Coordination between nuclear and mitochondrial genomes is critical to metabolic processes underlying animals' ability to adapt to local environments, yet consequences of mitonuclear interactions have rarely been investigated in populations where individuals with divergent mitochondrial and nuclear genomes naturally interbreed. Genetic variation in the leaf beetle Chrysomela aeneicollis was assessed along a latitudinal thermal gradient in California's Sierra Nevada. Variation at mitochondrial cytochrome oxidase II (COII) and the nuclear gene phosphoglucose isomerase (PGI) shows concordance...

Phylogenomic analysis and morphological data suggest left-right swimming behavior evolved prior to the origin of the pelagic Phylliroidae (Gastropoda: Nudibranchia)

Jessica Goodheart & Heike Wägele
Evolutionary transitions from benthic to pelagic habitats are major adaptive shifts. Investigations into such shifts are critical for understanding the complex interaction between co-opting existing traits for new functions and novel traits that originate during or post-transition. Gastropod mollusks are of particular interest in regard to benthic-pelagic evolutionary transitions, as shifts from benthic to pelagic habitats are uncommon. Phylliroe is one such pelagic lineage in Phylliroidae, a family of holoplanktonic nudibranchs with a highly aberrant...

Dense seismic three-component nodal array at the Ramona Reservation

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High-Resolution imaging and monitoring of the subsurface structure and seismicity at a site along the San Jacinto fault zone using a dense seismic nodal array. The site is located about 6 km northwest of the town of Anza, California. The type of nodal sensor employed is the Fairfield Zland 3-component 5 Hz geophones (records ground velocity continuously at 500 sps). The array consists of 97 sensors, with 65 located along a linear across-fault profile and...

Data from: Sierra Nevada mountain lake microbial communities are structured by temperature, resources, and geographic location

Marika Schulhof, Andrew Allen, Eric Allen, Natalie Mladenov, John McCrow, Natalie Jones, Jessica Blanton, Hamanda Badona Cavalheri, Drishti Kaul, Celia Symons & Jonathan Shurin
Warming, eutrophication (nutrient fertilization) and brownification (increased loading of allochthonous organic matter) are three global trends impacting lake ecosystems. However, the independent and synergistic effects of resource addition and warming on autotrophic and heterotrophic microorganisms are largely unknown. In this study, we investigate the independent and interactive effects of temperature, dissolved organic carbon (DOC, both allochthonous and autochthonous), and nitrogen (N) supply, in addition to the effect of spatial variables, on the composition, richness, and...

Data from: Allocation of gene products to daughter cells is determined by the age of the mother in single Escherichia coli cells

Ulla Rang, Chao Shi, Lin Chao, Audrey Proenca, Andrew Qiu & Jasper Chao
Gene expression and growth rate are highly stochastic in E. coli. Some of the growth rate variations result from the deterministic and asymmetric partitioning of damage by the mother to its daughters. One daughter, denoted the old daughter, receives more damage, grows more slowly, and ages. To determine if expressed gene products are also allocated asymmetrically, we compared the levels of expressed green fluorescence protein in growing daughters descending from the same mother. Our results...

Data from: Anticholinergic medications: A potentially modifiable risk factor for development of MCI

Alexandra Weigand, Mark W. Bondi, Kelsey R. Thomas, Noll L Campbell, Douglas Galasko, David P. Salmon, Daniel Sewell, James B. Brewer, Howard H Feldman & Lisa Delano-Wood
Objective: To determine the cognitive consequences of anticholinergic medications (aCH) in cognitively normal older adults as well as interactive effects of genetic and cerebrospinal fluid (CSF) Alzheimer’s disease (AD) risk factors. Methods: 688 cognitively normal participants from the Alzheimer’s Disease Neuroimaging Initiative were evaluated (mean age = 73.5, 49.6% female). Cox regression examined risk of progression to mild cognitive impairment (MCI) over a 10-year period, and linear mixed effects models examined 3-year rates of decline...

Data from: Phytoplankton growth and stoichiometric responses to warming, nutrient addition and grazing depend on lake productivity and cell size

Dedmer Van De Waal, Marika A. Schulhof, Jonathan B. Shurin & Steven A. J. Declerck
Global change involves shifts in multiple environmental factors that act in concert to shape ecological systems in ways that depend on local biotic and abiotic conditions. Little is known about the effects of combined global change stressors on phytoplankton communities, and particularly how these are mediated by distinct community properties such as productivity, grazing pressure and size distribution. Here, we tested for the effects of warming and eutrophication on phytoplankton net growth rate and C:N:P...

Registration Year

  • 2020

Resource Types

  • Dataset
  • Text
  • Output Management Plan


  • University of California, San Diego
  • University of Kentucky
  • Harvard University
  • Sun Yat-sen University
  • Boston Children's Hospital
  • Peking University Cancer Hospital
  • Sichuan University
  • Fudan University
  • Capital Medical University
  • Xi'an Jiaotong University