543 Works

Code review regression analysis of open source GitHub projects

Christopher Thompson & David Wagner
This dataset contains the repository data used for our study "A Large-Scale Study of Modern Code Review and Security in Open Source Projects". This dataset was collected from GitHub, and includes 3,126 projects in 143 languages, with 489,038 issues and 382,771 pull requests. We also include the regression analysis notebooks for reproducing our results from this data.

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

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...

Data from: Interaction of the westerlies with the Tibetan Plateau in determining the mei-yu termination

Wenwen Kong & John Chiang
Boundary topography and model output for "Interaction of the westerlies with the Tibetan Plateau in determining the mei-yu termination" This dataset contains the boundary topography files and key model outputs used in: Kong, W., and J. C. H. Chiang, Interaction of the westerlies with the Tibetan Plateau in determining the mei-yu termination. Accepted with minor revision, Journal of Climate, September 2019

Ancestral male recombination in Drosophila albomicans produced geographically restricted neo-Y chromosome haplotypes varying in age and onset of decay

Kevin Wei & Doris Bachtrog
Male Drosophila typically have achiasmatic meiosis, and fusions between autosomes and the Y chromosome have repeatedly created non-recombining neo-Y chromosomes that degenerate. Intriguingly, Drosophila nasuta males recombine, but their close relative D. albomicans reverted back to achiasmy after evolving neo-sex chromosomes. Here we use genome-wide polymorphism data to reconstruct the complex evolutionary history of neo-sex chromosomes in D. albomicans and examine the effect of recombination and its cessation on the initiation of neo-Y decay. Population...

Shape-controlled single-crystal growth of InP at low temperatures down to 220 ℃

Der-Hsien Lien, Mark Hettick, Hao Li, Ali Javey, Matthew Yeh, Tzu-Yi Yang, Niharika Gupta, Matin Amani, Daryl Chrzan & Yu-Lun Chueh
III-V compound semiconductors are widely used for electronic and optoelectronic applications. However, interfacing III-Vs with other materials has been fundamentally limited by the high growth temperatures and lattice-match requirements of traditional deposition processes. Recently, we developed the templated liquid phase (TLP) crystal growth method for enabling direct growth of shape-controlled single crystal III-Vs on amorphous substrates. Although in theory, the lowest temperature for TLP growth is that of the melting point of the group III...

Pretrained model for UCBShift

Jie Li
UCBShift is a program for predicting chemical shifts for backbone atoms and β-carbon of a protein in solution. It utilizes a machine learning module that makes predictions from features extracted from the 3D structures of the proteins. Provided here are the pre-trained machine learning models for making the predictions. The instructions for downloading UCBShift and use these .sav format pretrained models can be found at https://github.com/THGLab/CSpred

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.

Redefining Near-Unity Luminescence in Quantum Dots with Photothermal Threshold Quantum Yield

David Hanifi, Noah Bronstein, Brent Koscher, Zach Nett, Joseph Swabeck, Kaori Takano, Adam Schwartzberg, Lorenzo Maserati, Koen Vandewal, Yoeri Van De Burgt, Alberto Salleo & Paul Alivisatos
Herin is the code and example data sets for the publication titled: "Redefining Near-Unity Luminescence in Quantum Dots with Photothermal Threshold Quantum Yield." The abstract of this paper is as follows. A variety of optical applications rely on the absorption and reemission of light. The quantum yield of this process often plays an essential role. When the quantum yield deviates from unity by significantly less than 1%, applications such as luminescent concentrators and optical refrigerators...

Berkeley High Resolution (BEHR) OMI NO2 v3.0C - Native pixels, daily profiles

Qindan Zhu, Josh Laughner & Ron Cohen
The BEHR 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 monthly average) profiles...

Supporting data for \"Direct observation of changing NOx lifetime in North American cities\"

Joshua Laughner & Ronald Cohen
NOx lifetime can be directly observed from space, and has a nonlinear relationship with its own concentration. At high NOx concentrations, NOx lifetime decreases with decreasing concentration, but at intermediate concentrations, the reverse is true. Here we show that urban NOx lifetime in North America has changed between 2005 and 2014. The shape of these changes is qualitatively consistent with a steady-state model of NOx lifetime with decreasing NOx emissions. The pattern of change suggests...

Muntiacus muntjak and Muntiacus reevesi supporting files

Austin Mudd, Jessen Bredeson, Rachel Baum, Dirk Hockemeyer & Daniel Rokhsar
Available Files: Mmuntjak.cds.fasta.gz - Nucleotide sequences of the coding regions from M. muntjak gene annotations. Mmuntjak.gff.gz - Gene annotations for M. muntjak from Gene Model Mapper (v1.5.3). Mmuntjak.pep.fasta.gz - Peptide sequences of the coding regions from M. muntjak gene annotations. Mmuntjak.repeat_lib.fasta.gz - De novo repeats from RepeatModeler (v1.0.11) for M. muntjak as well as ancestral Cetartiodactyla repeats from RepBase (downloaded November 8, 2018). Mreevesi.cds.fasta.gz - Nucleotide sequences of the coding regions from M. reevesi gene...

Vegetation Change in the Natural Reserve of Orange County

Katherine Suding, Sara Jo Dickens & Samuel Bedgood
This data set describes vegetation change in 109 areas in the Nature Reserve of Orange County. The authors of this data were mainly interested in the success of artichoke thistle (Cynara cardunculus) control, but it could be approached in many different ways. Surveyors identified and recorded more than 375 plant species from the years 1998, 2008, and 2013.

Man and the Variable Vulnerability of Island Life: A Study of Recent Vegetation Change in the Bahamas, 1972

Anthony Roger Byrne

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: Zooming in on mechanistic predator-prey ecology: integrating camera traps with experimental methods to reveal the drivers of ecological interactions

Justine Smith, Justin Suraci, Jennifer Hunter, Kaitlyn Gaynor, Carson Keller, Meredith Palmer, Justine Atkins, Irene Castañeda, Michael Cherry, Patrick Garvey, Sarah Huebner, Dana Morin, Lisa Teckentrup, Martijn Weterings & Lydia Beaudrot
1. Camera trap technology has galvanized the study of predator-prey ecology in wild animal communities by expanding the scale and diversity of predator-prey interactions that can be analyzed. While observational data from systematic camera arrays have informed inferences on the spatiotemporal outcomes of predator-prey interactions, the capacity for observational studies to identify mechanistic drivers of species interactions is limited. 2. Experimental study designs that utilize camera traps uniquely allow for testing hypothesized mechanisms that drive...

Data from: Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest

Tom Callens, Peter Galbusera, Erik Matthysen, Eric Y Durand, Mwangi Githiru, Jeroen R Huyghe & Luc Lens
Habitat fragmentation can restrict geneflow, reduce neighbourhood effective population size, and increase genetic drift and inbreeding in small, isolated habitat remnants. The extent to which habitat fragmentation leads to population fragmentation, however, differs among landscapes and taxa. Commonly, researchers use information on the current status of a species to predict population effects of habitat fragmentation. Such methods, however, do not convey information on species-specific responses to fragmentation. Here we compare levels of past population differentiation,...

Data from: Host and habitat specialization of avian malaria in Africa

Claire Loiseau, Ryan J. Harrigan, Alexandre Robert, Rauri C. K. Bowie, Henri A. Thomassen, Thomas B. Smith & Ravinder N. M. Sehgal
Studies of both vertebrates and invertebrates have suggested that specialists, as compared to generalists, are likely to suffer more serious declines in response to environmental change. Less is known about the effects of environmental conditions on specialist vs. generalist parasites. Here, we study the evolutionary strategies of malaria parasites (Plasmodium spp.) among different bird host communities. We determined the parasite diversity and prevalence of avian malaria in three bird communities in the lowland forests in...

Data from: Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs

Rayna C Bell, Jason B MacKenzie, Michael J Hickerson, Krystle L Chavarría, Michael Cunningham, Stephen Williams, Craig Moritz & K. L. Chavarria
Though Pleistocene refugia are frequently cited as drivers of species diversification, comparisons of molecular divergence among sister species typically indicate a continuum of divergence times from the late Miocene, rather than a clear pulse of speciation events at the Last Glacial Maximum (LGM). Community-scale inference methods that explicitly test for multiple vicariance events, and account for differences in ancestral effective population size and gene flow, are well suited for detecting heterogeneity of species’ responses to...

Data from: The sampling and estimation of marine paleodiversity patterns: implications of a Pliocene model

James W. Valentine, David Jablonski, Andrew Z. Krug & Sarah K. Berke
Data that accurately capture the spatial structure of biodiversity are required for many paleobiological questions, from assessments of changing provinciality and the role of geographic ranges in extinction and originations, to estimates of global taxonomic or morphological diversity through time. Studies of temporal changes in diversity and global biogeographic patterns have attempted to overcome fossil sampling biases through sampling standardization protocols, but such approaches must ultimately be limited by available literature and museum collections. One...

Data from: Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids

Margaret R. Woodhouse, Haibao Tang & Michael Freeling
Certain types of gene families, such as those encoding most families of transcription factors, maintain their chromosomal syntenic positions throughout Angiosperm evolutionary time. Other, non-syntenic gene families are prone to deletion, tandem duplication, and transposition. Here we describe the chromosomal positional history of all genes in Arabidopsis thaliana (A. thaliana) throughout the rosid superorder. We introduce a public database where researchers can look up the positional history of their favorite A. thaliana gene or gene...

Data from: Diversification and phylogeographic structure in widespread Azteca plant-ants from the northern Neotropics

Elizabeth G. Pringle, Timothy C. Bonebrake, Santiago R. Ramírez, Deborah M. Gordon & Rodolfo Dirzo
The Neotropical myrmecophytic tree Cordia alliodora hosts symbiotic Azteca ants in most of its widespread range. The taxonomy of the genus Azteca is notoriously difficult, which has frequently obscured species identity in ecological studies. We used sequence data from one mitochondrial and four nuclear loci to infer phylogenetic relationships, patterns of geographic distribution, and timing of diversification for 181 colonies of Azteca from Mexico to Colombia. We identified at least eight lineages of C. alliodora-dwelling...

Data from: Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules

Kabir G. Peay, Max G. Schubert, Nhu H. Nguyen & Thomas D. Bruns
Dispersal plays a prominent role in most conceptual models of community assembly. However, direct measurement of dispersal across a whole community is difficult at ecologically relevant spatial scales. For cryptic organisms, such as fungi and bacteria, the scale and importance of dispersal limitation has become a major point of debate. We use an experimental island biogeographic approach to measure the effects of dispersal limitation on the ecological dynamics of an important group of plant symbionts,...

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