43 Works

Caltrans PEMS highway sensor average flows by occupancy

Clark Fitzgerald & Michael Zhang
This data summarizes average vehicle flow as a function of occupancy for traffic sensor data available from CalTrans Performance Management System (PEMS). It's useful because it shows the behavior of traffic in congested regimes, without requiring the preprocessing of several hundred GB of the raw data. Open the pdf files to see what this data looks like.

Heterotrophic N2-fixation contributes to nitrogen economy of a common wetland sedge, Schoenoplectus californicus

Eliska Rejmankova, Dagmara Sirova, Stephanie Castle, Jiri Barta & Heather Carpenter
These data sets document environmental characteristics of sampling locations of Schoenoplectus californicus, california bulrush, throughout its range in the Americas. In addition, the data on nif gene in rhizomes and roots of Schoenoplectus are provided.

Vibrational Neutron Scattering Spectra for Undoped and Doped P3HT

Thomas Harrelson, Jun Li & Adam Moule
Doped semiconducting polymers have garnered vast research interest in photovoltaic, transistor, thermoelectric, and sensor applications. P3HT is a canonical semiconducting polymer that self-assembles into a mixture of crystalline and amorphous domains. Doping P3HT can increase the observed conductivity by several orders of magnitude. The vibrations of the polymer are sensitive to the local morphology of the film, and the morphology of the film changes upon doping. Vibrational neutron spectroscopy is a method for identifying vibrational...

Regional and disease-related differences in properties of the equine temporomandibular joint disc

Derek Cissell
Temporomandibular joint (TMJ) disorders are increasingly recognized in animals. The articular disc plays a major role in TMJ disorders in people, but its role in the pathogenesis of TMJ disease in animals is not well understood. This study characterizes properties of the equine TMJ disc, including regional variation within discs as well as differences in properties associated with naturally-occurring TMJ osteoarthritis.

Incipits for the Catalogue of the Works of Hector Berlioz, Second edition, digital

Jonathan Minnick & D. Kern Holoman
This collection of PDFs contains all of the incipits for the Catalogue of the Works of Hector Berlioz, Second edition, digital, edited by D. Kern Holoman and Jonathan Minnick. Contents used with permission from Bärenreiter-Verlag / Kassel-Basel-London-New York-Praha / www.barenreiter.com

Defining hydrogel properties to instruct lineage- and cell-specific mesenchymal differentiation

Kent Leach
The maintenance and direction of stem cell lineage after implantation remains challenging for clinical translation. Aggregation and encapsulation into instructive biomaterials after preconditioning can bolster retention of differentiated phenotypes. Since these procedures do not depend on cell type or lineage, we hypothesized we could use a common, tunable platform to engineer formulations that retain and enhance multiple lineages from different cell populations. To test this, we varied alginate stiffness and adhesive ligand content, then encapsulated...

Data associated with manuscript \"Predicting wave-induced sediment resuspension at the perimeter of lakes using a steady-state spectral wave model\"

Derek Roberts, S. Geoffrey Schladow, Simon Hook, Shohei Watanabe & Patricio Moreno-Casas
This repository includes data associated with the manuscript, "Predicting wave-induced sediment resuspension at the perimeter of lakes using a steady-state spectral wave model," currently in press at Water Resources Research as of January 2019. Following American Geophysical Union standards, this repository serves to publically share all data associated with the manuscript. Plain lanuage summary of the manuscript: A tool that describes lake-wide wave conditions as a function of combinations of wind speeds and directions is...

Formica ant and Cinara aphid mutualisms on limber pines (Pinus flexilis)

Charles Chen, Lori Liu &
Ant-aphid mutualisms play important ecological roles in many ecosystems. While Formica ants are well studied model organisms, pine-specialist Cinara aphids remain understudied. Moreover, there is little research on ant-aphid mutualism in subalpine ecosystems. We investigated multiple species of Formica ants and their mutualistic interactions with Cinara aphids on the limber pine Pinus flexilis in a subalpine ecosystem. Cinara apini colonies were found tended to by silver, black, and red Formica ants, and they occupy older...

Alpine wet meadows: soil properties’ effect on plant diversity

Madeline Castro, Fidel Machado-Perez & Rebecca Raven
Alpine ecosystems are a harsh environment with little nutrients and the abiotic effect that the soil has on the plant community is relatively unknown. The focus of this study is to illuminate the role that soils play in the plant diversity of alpine wet meadows. In doing so we investigated the function of clay and root content, organic matter, pH and soil moisture in determining plant diversity in three meadows in the White Mountains, California....

An ancient forest on the move: Range shifts in bristlecone pines

Angela Delos Santos, Katherine Pratt, Grace Rosburg-Francot, Linnea Schaefer & George Sidarous
Recent changes in global climate are causing many species to shift their ranges towards higher elevations. The rate at which species can shift their ranges may determine whether or not they will be able to persist in light of such rapid environmental change. In this study, we examined the effect of elevation on recruitment, mortality, and intraspecific competition in Great Basin bristlecone pines (Pinus longaeva, BC), a long-lived subalpine species whose upper limit is often...

Habitat preference and species interactions of the desert woodrat (Neotoma lepida) in the Mojave Desert

Becca Cosmero, Emily Fieberling, Katherine Marlin, Ricardo Ruiz, & Lara Volski
Ecosystem engineers often have cascading impacts on the ecosystems in which they occur. Understanding the factors that contribute to their habitat selection can provide valuable information on how ecosystems function. Our study investigates the habitat distribution of desert woodrats (Neotoma lepida) in the Eastern Mojave Desert. We show that there is a difference in desert woodrat abundance among habitats, and found that specific aspects of these environments are associated with woodrats. These aspects include grass...

Data deposition for Complex electrophysiological remodeling in postinfarction ischemic heart failure

Bence Hegyi & Ye Chen-Izu
Heart failure (HF) following myocardial infarction (MI) is associated with high incidence of cardiac arrhythmias. Development of therapeutic strategy requires detailed understanding of electrophysiological remodeling. However, changes of ionic currents in ischemic HF remain incompletely understood, especially in translational large animal models. Here, we systematically measure the major ionic currents in ventricular myocytes from the infarct border and remote zones in a porcine model of post-MI HF. We recorded eight ionic currents during the cell’s...


Raquel Peixoto, Phillipe Rosado, Deborah Leite, Gustavo Duarte, Ricardo Chaloub, Guillaume Jospin, Jonathan Eisen, David Bourne, Ulisses Da Rocha, João Saraiva & Francisco Dini-Andreote
Although the early coral reef-bleaching warning system (NOAA/USA) is established, there is no feasible treatment that can minimize temperature bleaching and/or disease impacts on corals in the field. Here, we present the first attempts to extrapolate the widespread and well-established use of bacterial consortia to protect or improve health in other organisms (e.g., humans and plants) to corals. Manipulation of the coral-associated microbiome was facilitated through addition of a consortium of native (isolated from Pocillopora...

Temperature-Dependent Dynamics of Molecular Dopant in Conjugated Polymer

Jun Li, Tucker Murrey, Souleymane Diallo & Adam Moule
Understanding the nature of dopant dynamics in the solid state is critical for improving the longevity and stability of organic electronic devices and for optimizing the dopinginduced solubility control (DISC) patterning method. In this work, we use quasi-elastic neutron scattering (QENS) to study the dynamics of the soluble p-type molecular dopant tetrafluoromethyloxycarbonyltricyanoquinodimethane (F4MCTCNQ) in the semiconductive polymer poly(3-hexylthiophene-2,5-diyl) (P3HT). Specifically, fast dynamics (ps−ns) of the dopant, such as the methyl and the methoxycarbonyl group rotations,...

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...

Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris)

Paul Gepts
Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA...

Life on the edge: Abiotic stress and competitive exclusion affect plant communities across a subalpine edaphic gradient

, Willem Schep, Hanan Abels-Sullivan & Casey Kwok
Abiotic stress and heavy competition each limit the assemblages of plant communities, defining their composition as well as their boundaries. One plant community governed by stress and another by competition may abut one another, forming a biotic gradient called an ecotone. In California’s White Mountains, this gradient occurs across the meeting point between a calcareous (dolomite) and non-calcareous (quartzite) soil types. In this study, we tested the effects of this gradient on plant community compositions...

The fungus among us: Ecological succession within decomposer communities

Marta Alvarez, Ashlyn Bahrychuk, Kellie Cutsinger, Alexander Gallandt & Thomas Lenihan
The process of succession can be a major driving force in sculpting ecological communities over time. Decomposers play a crucial role in forest succession, recycling nutrients from fallen logs back into the ecosystem. In this study, we examined the community of plants, fungi, and invertebrates living in fallen log microhabitats across decomposition stages in a mixed conifer forest. We predicted there would be a shift in species composition among decomposer communities in Douglas fir logs...

Through space and time: Vertebrate coexistence through circadian changes in community composition

Mark Arenas, Danielle Davis, Mikala Haptonstall, Brendan Kyle & Eric Stubbs
Many mechanisms of biodiversity exist in nature. Temporal niche partitioning is an overlooked mechanism that could explain how species coexist in the same space. We hypothesized that different vertebrate communities would be using a shared habitat space (rock bars) at different times of day. To test this hypothesis, we surveyed the total number of vertebrates present on six different rock bars during morning, midday, and night. We documented strong differences between vertebrate communities by time...

Coastal dune invasion and restoration at Point Reyes: the ecology of European sea rocket, Cakile maritime

Shay McGraw, Jay Luce Nelson, Yuxin Shen & Aidé Villegas
California coastal dune ecosystems are prime targets for conservation and restoration efforts due to their high native plant diversity and rates of endemism. Invasive dune species such as European sea rocket (Cakile maritima) may disrupt key ecosystem processes by altering dune physical processes and outcompeting native species, decreasing the success of the endangered species beach layia (Layia carnosa) and Tidestrom's lupine (Lupinus tidestromii) at Point Reyes National Seashore in Marin County, California. We investigated potential...

PhyloSift Markers Database

Guillaume Jospin
Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection. In this work we present an approach to leverage phylogenetic analysis of metagenomic...

Measurement and modeling of the multi-wavelength optical properties of uncoated flame-generated soot: Data from the BC2, BC3, BC3+ and BC4 studies

Sara Forestieri & Christopher Cappa
Optical properties of flame-generated black carbon (BC) containing soot particles were quantified at multiple wavelengths during the BC2, BC3, BC3+ and BC4 campaigns. The particles were produced using two different flames, either an ethylene premixed flame (sampled at multiple heights above the flame front) or a methane diffusion flame. Measurements were made both for size-selected nascent soot particles and for particles that were coated (with either dioctyl sebacate, sulfuric acid or secondary organic aerosol) and...

Genetic Patterns of Common-Bean Seed Acquisition and Early-stage Adoption among Farmer Groups in Western Uganda

Paul Gepts, Erin Wilkus, Jorge Carlos Berny Mier Y Teran, Clare Mukankusi, Saarah Kuzaay & Paige Hamilton-Conaty
Widespread adoption of new varieties can be valuable, especially in developing countries, which tend to lack access to improved agricultural production technologies. However, as farmers adopt new varieties, in situ population structure and genetic diversity of their seed holdings can change drastically. Consequences of adoption are still poorly understood due to a lack of crop genetic diversity assessments and detailed surveys of farmers’ seed management practices. Common bean (Phaseolus vulgaris) is an excellent model for...

Falk et al Plot Data

Adele Igel, Nicholas Falk & Matthew Igel
Plot data for Falk et al 2019. Falk, N. M., A. L. Igel and M. R. Igel, 2019: The Relative Impact of Ice Fall Speeds and Microphysics Parameterization Complexity on Supercell Evolution. Monthly Weather Review https://doi.org/10.1175/MWR-D-18-0417.1

Dynamics of riparian disturbance: Overstory effects on river ecosystems

Ryan Blaich, Laurel Bowling, Meghan Green, Sandra Hamilton & Carina Motta
Ecological disrupting events can drastically alter biotic communities. Riparian assemblages are subject to significant amounts of such disturbance, resulting in succession. In a river system prone to annual and catastrophic disruptive events, we examined the ecological effects of the successional return of alder overstory on aquatic communities. To test for overstory effects, we measured aquatic invertebrate populations, fish populations, and river structure (speed and depth) between alder and control sites. Both mayflies (Ephemeroptera) and stoneflies...

Registration Year

  • 2018

Resource Types

  • Text
  • Dataset


  • University of California, Davis
  • Helmholtz Centre for Environmental Research
  • University of California, Berkeley
  • Nederlands Instituut voor Ecologie
  • Oak Ridge National Laboratory
  • University of Wisconsin-Madison
  • California Air Resources Board
  • Jet Propulsion Lab
  • Universidad de Los Andes
  • Uganda Clays (Uganda)