245 Works

Towards the introgression of PvPdh1 for increased resistance to pod shattering in common bean

Travis Parker, Lorenna Lopes De Sousa, Talissa De Oliveira Floriani, Antonia Palkovic & Paul Gepts
Some varieties of common bean (Phaseolus vulgaris L.) suffer from pod shattering, which can severely reduce yields, especially in arid conditions. The PvPdh1 locus on chromosome Pv03 has recently been described as a major locus controlling pod shattering in common bean and could be used to mitigate pod shattering in the future. Despite this, the role of a possible second locus on chromosome Pv08 remains unclear and patterns of dominance and epistasis between alleles of...

Vibrational Neutron Spectroscopy Data for Small Molecule Organic Semiconductors

Thomas Harrelson, Varuni Dantanarayana, Roland Faller & Adam Moule
Organic semiconductors are a class of molecules that self-assemble into materials that have semiconducting properties. Recently, they have generated a large amount of research interest due to their solution processability, mechanical flexibility, and conducting properties. Small molecule organic semiconductors are highly crystalline, which means molecular vibrations/phonons are the dominant factors affecting charge transport properties. A key to improving small-molecule semiconductors involves designing materials that minimize the effects of vibrations/phonons on charge transport. Vibrational neutron spectroscopy...

Water uptake, cloud condensation nuclei and surface tension: results from the MadFACTS campaign

Sara Forestieri, Sean Staudt, Thomas Kuborn, Christopher Ruehl, Timothy Bertram & Christopher Cappa
This data set is associated with the manuscript “Establishing the Impact of Model Surfactants on Cloud Condensation Nuclei Activity of Sea Spray Aerosols” by Forestieri et al. that has been submitted to Atmospheric Chemistry and Physics. The abstract to this manuscript is provided below. By reducing surface tension (σ), surfactants present in aerosols can increase their cloud condensation nuclei (CCN) activation efficiency. However, the importance of this effect is poorly constrained. Here we present estimates...

Emergence of complex institutions in a large population of self-governing communities

Seth Frey
Most aspects of our lives are governed by large, highly developed institutions that integrate several governance tasks under one authority structure. But theorists differ as to the mechanisms that drive the development of such concentrated governance systems from rudimentary beginnings. Is the emergence of regime consolidation a symptom of the runaway capture by opportunists? Or does integration occur because a consolidated institution is better adapted to a complex environment? Here we examine the emergence of...

Initial application of the noise-sorted scanning clustering algorithm to the analysis of composition-dependent organic aerosol thermal desorption measurements

Christopher Cappa, Ziyue Li, Emma D'Ambro, Siegfried Schobesberger, John Shilling, Felipe Lopez-Hilfiker, Jiumeng Liu, Cassandra Gaston & Joel Thornton
The FIGAERO-CIMS (Filter Inlet for Gases and AEROsols + chemical ionization mass spectrometer) measures thermal desorption profiles for individual ions evolved from evaporation of organic aerosol components. Often, hundreds of individual thermograms are obtained, reflecting the compositional complexity of organic aerosol. We have developed a novel clustering algorithm, Noise-Sorted Scanning Clustering (NSSC), that provides a robust, reproducible analysis of the FIGAERO temperature-dependent mass spectral data. The NSSC allows for determination of thermal profiles for compositionally...

Data from: What is in a general plan? using natural language processing to read 461 California city general plans

Carl Stahmer & Catherine Brinkley
This repository contains all data outputs related to reasearch that analyzed General Plans from cities across the state of California to understand what topics are adressed and the spacial distribution of topic rerpresentation. We assembles a database of 421 California city-level General Plans and used Natural Language Processing to read their contents. The plans contained over 60 discrete topics and wer generally optimistic in sentiment. A quarter of the topics were reagionally specific. Housing is...

Survey data for: Planning and policymaking for TOD, transit, and AT in California cities

Elisa Barbour
This in-progress two-year research project for the California Department of Transportation, through the National Center for Sustainable Transportation, is assessing planning and policymaking for transit-oriented development , transit, and active transport in California cities located in the state's four largest regions, the San Francisco Bay, Los Angeles, San Diego, and Sacramento areas. The dataset we provide here is an anonymous version of our survey results of city planning directors in these regions, conducted between April...

Differing, multi-scale landscape effects on genetic diversity and differentiation in eastern chipmunks

Elizabeth Kierepka, Sara Anderson, Robert Swihart &
Understanding how habitat loss and fragmentation impact genetic variation is a major goal in landscape genetics, but to date, most studies have focused solely on the correlation between intervening matrix and genetic differentiation at a single spatial scale. Several caveats exist in these study designs, among them is the inability to include measures of genetic diversity in addition to differentiation. Both genetic metrics help predict population persistence, but are expected to function at differing spatial...

VCC User Survey Results

Angela Sanguinetti
PROJECT: Strategies to promote plug-in electric vehicle (PEV) adoption include consumer education about potential energy cost savings. However, the complexity of comparing gasoline and electricity prices makes it difficult to quantify. Vehicle energy cost calculators (VCCs) help consumers navigate this complexity, and research shows they can increase consumer knowledge and positive attitudes about PEVs. At least 12 of these calculators exist, but none appear to be based on behavioral research. They vary in terms of...

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...

Utilizing Highway Rest Areas for Electric Vehicle Charging: Economics and Impacts of Renewable Energy Penetration in California

Behdad Kiani, Joan Ogden, F. Alex Sheldon & Lauren Cordano
California policy is incentivizing rapid adoption of zero emission electric vehicles for light duty and freight applications. In this project, we explored how locating charging facilities at California’s highway rest stops, might impact electricity demand, grid operation, and integration of renewables like solar and wind into California’s energy mix. Assuming a growing population of electric vehicles to meet state goals, we estimated state-wide growth of electricity demand, and identified the most attractive rest stop locations...

Data from: The effect of early burn injury on sensitivity to future painful stimuli in dairy heifers

Sarah Adcock & Cassandra Tucker
Animals that experience painful procedures as neonates are more sensitive to pain later in life. We evaluated whether disbudding with a heated iron at 3 (n=12), 35 (n=9), or 56 (n=20) d of age affected heifers’ pain responses to vaccine injections at 11 mo of age. Heifers responded to the injection procedure with struggling and changes in eye temperature and heart rate variability compared to a sham procedure the day before, and still had a...

Data from: Wildfire reveals transient changes to individual traits and population responses of a native bumble bee (Bombus vosnesenskii)

John Mola, Michael Miller, Sean O'Rourke & Neal Williams
1. Fire-induced changes in the abundance and distribution of organisms, especially plants, can alter resource landscapes for mobile consumers driving bottom-up effects on their population sizes, morphologies, and reproductive potential. We expect these impacts to be most striking for obligate visitors of plants, like bees and other pollinators, but these impacts can be difficult to interpret due to the limited information provided by forager counts in the absence of survival or fitness proxies. 2. Increased...

Data from: Behavioral changes in calves 11 days after cautery disbudding: effect of local anesthesia

Cassandra Tucker, Sarah Adcock & Danielle Cruz
Hot-iron disbudding results in painful burn wounds that take weeks to heal. Spontaneous behaviors indicative of pain are apparent in the immediate hours after disbudding, but whether they occur later in the healing process is unknown. To evaluate whether ongoing pain was present around the time the necrotic tissue loosens from the scalp, we tested the effect of administration of local anesthetic 11 d after the procedure. Disbudded female Holstein and Jersey calves (n=24) were...

zigzag: A Hierarchical Bayesian Mixture Model for Inferring the Expression State of Genes in Transcriptomes

Ammon Thompson, Michael May, Brian Moore & Artyom Kopp
Transcriptomes are key to understanding the relationship between genotype and phenotype. The ability to infer the expression state (active or inactive) of genes in the transcriptome offers unique benefits for addressing this issue. For example, qualitative changes in gene expression may underly the origin of novel phenotypes, and expression states are readily comparable between tissues and species. However, inferring the expression state of genes is a surprisingly difficult problem, owing to the complex biological and...

0 ns and 75 ns configurations of glycosylated ACE2-FC and its interaction with SARS-CoV-2 binding domains

Roland Faller, Austen Bernardi, Yihan Huang, Bradley Harris, Yongao Xiong, Somen Nandi & Karen McDonald
These are initial and final (75ns) configurations in PDB format of glycosylated ACE2-FC fusion proteins which are promising targets for a COVID-19 therapeutic. Some of them are in interaction witha fragment of the receptor-binding domain (RBD) of the Spike Protein S of the SARS-CoV-2 virus. We used two glycosylation variants for ACE2-FC, variant 1 is fully glycosylated with Man8 glycans, variant 2 is fully glycosylated with GnGnXF3. The Spike RBD is glycosylated with ANaF^6.

Delimitation of tribes in the subfamily Leptanillinae (Hymenoptera: Formicidae), with a description of the male of Protanilla lini Terayama, 2009

Zachary Griebenow
The subfamily Leptanillinae Emery, 1910 (Hymenoptera, Formicidae) is a clade of cryptic subterranean ants, which is restricted to the tropics and warm temperate regions of the Old World. Due to acquisition bias against the minute and hypogaeic workers, most known leptanilline specimens are male, with four genera described solely from males. The sexes have been associated in only two out of 68 described species, meaning that redundant naming of taxa is likely. Herein the phylogeny...

Recent bark beetle outbreaks influence wildfire severity in mixed-conifer forests of the Sierra Nevada, California, USA

Rebecca Wayman & Hugh Safford
In temperate forests, elevated frequency of drought related disturbances will likely increase the incidence of interactions between disturbances such as bark beetle epidemics and wildfires. Our understanding of the influence of recent drought and insect-induced tree mortality on wildfire severity has largely lacked information from forests adapted to frequent fire. A recent unprecedented tree mortality event in California’s Sierra Nevada provides an opportunity to examine this disturbance interaction in historically frequent-fire forests. Using field data...

Data from: Ectothermy and the macroecology of home range scaling in snakes

Brian Todd & Aaron Nowakowski
Aim: A central question in ecology has been that of why animal home ranges scale more steeply with body size than do metabolic rates. Yet, the generality of this notion has scarcely been tested in non-model species like ectotherms, which have lower metabolic requirements than endotherms and which may therefore have different home range area requirements. Our aim was to examine how home range area scales with body size in snakes and to shed light...

Data for: Environmentally-driven escalation of host egg-rejection decimates success of an avian brood parasite

John Eadie & Bruce Lyon
The black-headed duck (Heteronetta atricapilla) of South America is the only known avian obligate brood parasite with precocial offspring. In Argentina, it relies on two species of coots as primary hosts, which typically reject 35-65% of duck eggs. We show that environmentally-driven increases in host egg-rejection behavior lead to substantial reductions in the reproductive success of the brood parasite. Episodes of flooding and vegetation loss caused dramatic shifts in host egg rejection behavior, resulting in...

Rancho Seco vernal pool community data

Julia Michaels
Disturbance often increases local-scale (α) diversity by suppressing dominant competitors. However, widespread disturbances may also reduce biotic heterogeneity (β diversity) by making the identities and abundances of species more similar among patches. Landscape-scale (γ) diversity may also decline if disturbance-sensitive species are lost. California’s vernal pool plant communities are species-rich due in part to two scales of β diversity: (1) within pools, as species composition changes with depth (referred to here as vertical β diversity),...

Catastrophes, connectivity and Allee effects in the design of marine reserve networks

Easton White, Marissa Baskett & Alan Hastings
Catastrophic events, like oil spills and hurricanes, occur in many marine systems. One potential role of marine reserves is buffering populations against disturbances, including the potential for disturbance-driven population collapses under Allee effects. This buffering capacity depends on reserves in a network providing rescue effects, setting up a trade-off where reserves need to be connected to facilitate rescue, but also distributed in space to prevent simultaneous extinction. We use a set of population models to...

Data from: A phylogeny for the Drosophila montium species group: a model clade for comparative analyses

William Conner, Emily Delaney, Michael Bronski, Paul Ginsberg, Timothy Wheeler, Kelly Richardson, Brooke Peckenpaugh, Kevin Kim, Masayoshi Watada, Ary Hoffmann, Michael Eisen, Artyom Kopp, Brandon Cooper & Michael Turelli
The Drosophila montium species group is a clade of 94 named species closely related to the model D. melanogaster species group. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times...

Data and Supplemental Material from: A multifunction trade-off has contrasting effects on the evolution of form and function

Katherine Corn, Christopher Martinez, Edward Burress & Peter Wainwright
Trade-offs caused by the use of an anatomical apparatus for more than one function are thought to be an important constraint on evolution. However, whether multifunctionality suppresses diversification of biomechanical systems is challenged by recent literature showing that traits more closely tied to trade-offs evolve more rapidly. We contrast the evolutionary dynamics of feeding mechanics and morphology between fishes that exclusively capture prey with suction and multifunctional species that augment this mechanism with biting behaviors...

A case study for the implementation of an integrated variable speed limit (VSL) control strategy in a freeway section of I-80 based on SUMO simulations

Hang Gao & Michael Zhang
This project aims at reducing fuel consumption and greenhouse gas emission by applying variable speed control (VSL) strategies to the traffic corridors with multi-segment and multi-bottleneck. The dataset is composed of inputs and outputs of the SUMO simulation model via TraCI API. SUMO is a microscopic traffic simulation platform which allows to simulate a given traffic demand through a given network. Namely, the inputs consist of the vehicle trip data obtained from the PeMS database...

Registration Year

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Affiliations

  • University of California, Davis
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