78 Works

Data: Researcher Perspectives on the Use and Sharing of Software

Yasmin Alnoamany & John Borghi
We are interested in learning about perceptions, values, and behaviors around the computer software generated as part of the research process. To understand researchers' prespectives on software usage and sharing, we conducted an online survey sent to researchers at academic institutions throughout the United States. We used the Qualtrics platform to distribute our survey. This data set contains the responses of the survey participants after excluding any personally identifying data. All study materials and procedures...

Berkeley High Resolution (BEHR) OMI NO2 - Gridded pixels, daily profiles

Joshua Laughner, Ronald Cohen & Qindan Zhu
The BEHR OMI NO2 product reprocesses tropospheric NO2 columns from the Ozone Monitoring Instrument (OMI) satellite using high resolution a priori NO2 profiles, surface reflectivity, and surface elevation data. This product uses NO2 profiles for the day retrieved, simulated by the WRF-Chem model at 12 km spatial resolution. The use of high spatial resolution NO2 profiles has been shown to better resolve urban/rural differences in NO2 column densities, and the use of day-to-day (rather than...

A Bayesian method of evaluating discomfort due to glare: The effect of order bias from a large glare source

Toby Cheung, Michael Kent, Stefano Schiavon & Aleksandra Lipczyńska
to be confrim

Effect of non-Schmid Stresses on a-type Screw Dislocation Core Structure and Mobility in Titanium

Max Poschmann
Data summarizing DFT calculations concerning the effects of non-Schmid stresses on dislocation core structure and mobility in titanium.

Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia

Cassandra Ettinger, Laetitia Wilkins, Guillaume Jospin & Jonathan Eisen
Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and...

Data from: Quantifying the dark data in museum fossil collections as palaeontology undergoes a second digital revolution

Charles R. Marshall, Seth Finnegan, Erica C. Clites, Patricia A. Holroyd, Nicole Bonuso, Crystal Cortez, Edward Davis, Gregory P. Dietl, Patrick S. Druckenmiller, Ron C. Eng, Christine Garcia, Kathryn Estes-Smargiassi, Austin Hendy, Kathy A. Hollis, Holly Little, Elizabeth A. Nesbitt, Peter Roopnarine, Leslie Skibinski, Jann Vendetti & Lisa D. White
Large-scale analysis of the fossil record requires aggregation of palaeontological data from individual fossil localities. Prior to computers these synoptic datasets were compiled by hand, a laborious undertaking that took years of effort and forced palaeontologists to make difficult choices about what types of data to tabulate. The advent of desktop computers ushered in palaeontology’s first digital revolution – online literature-based databases, such as the Paleobiology Database (PBDB). However, the published literature represents only a...

Data from: Acid secretion by the boring organ of the burrowing giant clam, Tridacna crocea

Richard W. Hill, Eric J. Armstrong, Kazuo Inaba, Masaya Morita, Martin Tresguerres, Jonathon H. Stillman, Jinae N. Roa & Garfield T. Kwan
The giant clam Tridacna crocea, native to Indo-Pacific coral reefs, is noted for its unique ability to bore fully into coral rock and is a major agent of reef bioerosion. However, T. crocea’s mechanism of boring has remained a mystery despite decades of research. By exploiting a new, two-dimensional pH-sensing technology and manipulating clams to press their presumptive boring tissue (the pedal mantle) against pH-sensing foils, we show that this tissue lowers the pH of...

Data from: Migratory plasticity is not ubiquitous among large herbivores

Hall Sawyer, Jerod A. Merkle, Arthur D. Middleton, Samantha P.H. Dwinnell, Kevin L. Monteith & Samantha P. H. Dwinnell
1. The migratory movements of wild animals can promote abundance and support ecosystem functioning. For large herbivores, mounting evidence suggests that migratory behavior is an individually variable trait, where individuals can easily switch between migrant and resident tactics. The degree of migratory plasticity, including whether and where to migrate, has important implications for the ecology and conservation of large herbivores in a changing world. 2. Mule deer (Odocoileus hemionus) are an iconic species of western...

Data from: The role of red coloration and song in peacock spiders: insights into complex signaling systems

Madeline B. Girard, Michael M. Kasumovic & Damian O. Elias
Research on animal signaling enhances our understanding of links between sensory processing, decision-making, behavior, and evolution. Studies of sexually-selected signals may be particularly informative as mate choice provides access to decision patterns in the way that courtship leads to an easily observable behavioral output in choosers, i.e. mating. Male peacock spiders have some of the most elaborate and varied courtship displays known among animals. Particularly striking to human observers is the diversity of red, orange...

Data from: Avoiding topsy-turvy: how Anna's Hummingbirds (Calypte anna) fly through upward gusts

Marc A. Badger, Hao Wang & Robert Dudley
Flying organisms frequently confront the challenge of maintaining stability when moving within highly dynamic airflows near the Earth's surface. Either aerodynamic or inertial forces generated by appendages and other structures, such as the tail, may be used to offset aerial perturbations, but these responses have not been well characterized. To better understand how hummingbirds modify wing and tail motions in response to individual gusts, we filmed Anna's Hummingbirds as they negotiated an upward jet of...

Data from: Does biological intimacy shape ecological network structure? A test using a brood pollination mutualism on continental and oceanic islands

David H. Hembry, Rafael L. G. Raimundo, Erica A. Newman, Lesje Atkinson, Chang Guo, & Rosemary G. Gillespie
Biological intimacy—the degree of physical proximity or integration of partner taxa during their life cycles—is thought to promote the evolution of reciprocal specialization and modularity in the networks formed by co‐occurring mutualistic species, but this hypothesis has rarely been tested. Here, we test this “biological intimacy hypothesis” by comparing the network architecture of brood pollination mutualisms, in which specialized insects are simultaneously parasites (as larvae) and pollinators (as adults) of their host plants to that...

Data from: Random heteropolymers preserve protein function in foreign environments

Brian Panganiban, Baofu Qiao, Tao Jiang, Christopher DelRe, Mona M. Obadia, Trung Dac Nguyen, Anton A. A. Smith, Aaron Hall, Izaac Sit, Marquise G. Crosby, Patrick B. Dennis, Eric Drockenmuller, Monica Olvera De La Cruz & Ting Xu
The successful incorporation of active proteins into synthetic polymers could lead to a new class of materials with functions found only in living systems. However, proteins rarely function under the conditions suitable for polymer processing. On the basis of an analysis of trends in protein sequences and characteristic chemical patterns on protein surfaces, we designed four-monomer random heteropolymers to mimic intrinsically disordered proteins for protein solubilization and stabilization in non-native environments. The heteropolymers, with optimized...

Data from: Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty

Michael J. Landis, William A. Freyman & Bruce G. Baldwin
The Hawaiian silversword alliance (Asteraceae) is an iconic adaptive radiation. However, like many island plant lineages, no fossils have been assigned to the clade. As a result, the clade's age and diversification rate are not known precisely, making it difficult to test biogeographic hypotheses about the radiation. Without fossils, paleogeographically structured biogeographic processes may inform species divergence times; for example, an island must first exist for a clade to radiate upon it. We date the...

Training and Support for Student Library Employees in a Tiered Reference Service Model: Supporting Materials

Brian Quigley, Jeffery Loo, Lisa Ngo, Susan Powell, Samantha Teplitzky, Anna Sackmann & Kortney Rupp
To cultivate students’ reference skills, the Engineering and Physical Sciences Division of the UC Berkeley Library developed an active training program based upon a dynamic online reference manual continuously improved with student feedback. We evaluate the effectiveness of our training program and share procedures and tools for enhancing student training. Students were given a pre-test of reference skills and self-efficacy prior to attending an annual training session. One month afterwards, we distributed a post-test and...

Thermal and energetic ion dynamics in Ganymede's magnetosphere

This dataset accompanies the manuscript "Thermal and energetic dynamics in Ganymede's magnetosphere", JGR Space Physics, 2018.

2D attenuation model of Long Valley (CA)

Janire Prudencio, Michael Manga & Taka'aki Taira
We image seismic intrinsic (Qi-1) and scattering (Qs-1) attenuation in Long Valley caldera, California, by analyzing more than 1700 vertical-component waveforms from local earthquakes. Observed energy envelopes are fit to the diffusion model (data files) and seismic attenuation images (anomalies files) are produced using two-dimensional space-weighting functions.

Supporting data for \"Evaluation of version 3.0B of the BEHR OMI NO2 product\"

Joshua Laughner, Qindan Zhu & Ronald Cohen
This dataset contains supporting data for the paper "Evaluation of version 3.0B of the BEHR OMI NO2 product" by Laughner, Zhu, and Cohen. Evaluation of new satellite trace gas products is an important step in proving their usefulness, and, in the case of NO2, is typically done by comparing the satellite-observed vertical column densities to independent measurements taken by aircraft or ground-based spectrometers. Input data required by the satellite retrieval may also be directly compared...

Restoration of incomplete oceanographic datasets

Siavash Ameli & Shawn Shadden
Remote sensing of oceanographic data often yields incomplete coverage of the measurement domain. This can limit interpretability of the data and identification of coherent features informative of ocean dynamics. Several methods exist to fill gaps of missing oceanographic data, and are often based on projecting the measurements onto basis functions or a statistical model. Herein, we use an information transport approach inspired from an image processing algorithm. This approach aims to restore gaps in data...

Data from: Mutual fitness benefits arise during coevolution in a nematode-defensive microbe model

Charlotte Rafaluk-Mohr, Ben Ashby, Dylan A. Dahan & Kayla C. King
Species interactions can shift along the parasitism-mutualism continuum. However, the consequences of these transitions for coevolutionary interactions remain unclear. We experimentally coevolved a novel species interaction between Caenorhabditis elegans hosts and a mildly parasitic bacterium, Enterococcus faecalis, with host-protective properties against virulent Staphylococcus aureus. Coinfections drove the evolutionary transition of the C.elegans-E. faecalis relationship towards a reciprocally beneficial interaction. As E. faecalis evolved to protect nematodes against S. aureus infection, hosts adapted by accommodating greater...

Data from: Glucocorticoid-environment relationships align with responses to environmental change in two co-occurring congeners

Talisin T. Hammond, Rupert Palme & Eileen A. Lacey
As more species undergo range shifts in response to climate change, it is increasingly important to understand the factors that determine an organism’s realized niche. Physiological limits imposed by abiotic factors constrain the distributions of many species. Because glucocorticoids are essential to the maintenance of physiological homeostasis, identifying glucocorticoid-environment relationships may generate critical insights into both limits on species distributions and potential responses to environmental change. We explored relationships between variability in baseline glucocorticoids and...

Data from: Bayesian vector transmission model detects conflicting interactions from transgenic disease‐resistant grapevines

Adam R. Zeilinger, Daniel Turek, Daniele Cornara, Anne Sicard, Steven E. Lindow & Rodrigo P. P. Almeida
Effective management of vector-borne plant pathogens often relies on disease-resistant cultivars. While heterogeneity in host resistance and in pathogen population density at the host population level play important and well-recognized roles in epidemiology, the effects of resistance traits on pathogen distribution at the individual host level, and the epidemiological consequences in turn, are poorly understood. Transgenic disease-resistant plants that produce bacterial Diffusible Signaling Factor (DSF) could provide resistance to the vector-borne bacterium Xylella fastidiosa by...

Data from: Genomic analysis of MHC-based mate choice in the monogamous California mouse

Jesyka Meléndez-Rosa, Ke Bi, Elieen A. Lacey & Eileen A Lacey
Variation at Major Histocompatibility Complex (MHC) genes is thought to be an important mechanism underlying mate choice in vertebrates, with individuals typically predicted to prefer MHC-dissimilar reproductive partners. However, analyses based on individual MHC loci have generated contradictory results regarding the role of these genes in mate choice decisions. To provide a more comprehensive assessment of relationships between MHC variation and mating behavior, we used an exome capture strategy to characterize variability at 13 MHC...

Data from: Microbiome interactions shape host fitness

Alison L. Gould, Vivian Zhang, Lisa Lamberti, Eric W. Jones, Benjamin Obadia, Nikolaos Korasidis, Alex Gavryushkin, Jean M. Carlson, Niko Beerenwinkel & William B. Ludington
Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host, in turn, shapes the gut microbiome. However, it is unclear to what extent individual species versus community interactions within the microbiome are linked to host fitness. Here, we combinatorially dissect the natural microbiome of Drosophila melanogaster and reveal that interactions between bacteria shape host fitness through life history tradeoffs. Empirically, we made germ-free flies colonized with each...

Data from: The Metapopulation Microcosm Plate: a modified 96-well plate for use in microbial metapopulation experiments

Helen Kurkjian & Helen M. Kurkjian
1. Researchers in many sub-fields of ecology and evolutionary biology test hypotheses relating to metapopulation dynamics and landscape spatial structure. Key aspects of these hypotheses are often (a) large numbers of subpopulations and dispersal corridors and (b) their positions relative to each other. Testing such spatial hypotheses using traditional lab equipment and methods can be impractical, unwieldy, expensive, or impossible. 2. The Metapopulation Microcosm Plate (MMP) overcomes these difficulties. This device resembles a 96-well microtiter...

Data from: Native grass ground covers provide multiple ecosystem services in Californian vineyards

Kent M. Daane, Brian N. Hogg, Houston Wilson & Glenn Y. Yokota
1. The mechanisms responsible for the success or failure of agricultural diversification are often unknown. Most studies of arthropod pest management focus on enhancing the effectiveness of natural enemies, but non-crop plants can also improve or hamper pest suppression by changing the host quality of crop plants by reducing or adding available soil nutrients or water. Native perennial ground covers may provide resources and long-term habitat to resident natural enemies and be more compatible than...

Registration Year

  • 2018
    78

Resource Types

  • Dataset
    78

Affiliations

  • University of California, Berkeley
    78
  • University of Minnesota
    4
  • University of Washington
    3
  • Columbia University
    3
  • University of California System
    3
  • Museum of Vertebrate Zoology
    3
  • Dayton Foundation
    3
  • Cornell University
    3
  • Stanford University
    2
  • University of California, San Diego
    2