215 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

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...

Data from: Predators can influence the host-parasite dynamics of their prey via non-consumptive effects

Nicolette Zukowski, Devin Kirk, Kiran Wadhawan, Dylan Shea, Denon Start & Martin Krkosek
Ecological communities are partly structured by indirect interactions, where one species can indirectly affect another by altering its interactions with a third species. In the absence of direct predation, non-consumptive effects of predators on prey have important implications for subsequent community interactions. To better understand these interactions, we used a Daphnia-parasite-predator cue system to evaluate if predation risk affects Daphnia responses to a parasite. We investigated the effects of predator cues on two aspects of...

Snowpack, precipitation, and temperature measurements at the Central Sierra Snow Laboratory for water years 1971 to 2019

Randall Osterhuber & Andrew Schwartz
The snowpack of the Sierra Nevada Mountains is an indispensable freshwater resource for large portions of western North America. The Central Sierra Snow Laboratory (CSSL) has had an intigral role in the measurement of snowfall and snowpack properties within the Sierra Nevada Mountains, and has worked to develop a physical understanding of the processes that govern snow since 1946. This dataset contains measurements of temperature, precipiation quantity, snowfall, and snowpack characteristics including 24-hour snowfall, snowpack...

Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti)

Timothy O'Connor, Marissa Sandoval, Jiarui Wang, Jacob Hans, Risa Takenaka, & Noah Whiteman
Color polymorphic species can offer exceptional insight into the ecology and genetics of adaptation. Although the genetic architecture of animal coloration is diverse, many color polymorphisms are associated with large structural variants and maintained by biotic interactions. Grasshoppers are notably polymorphic in both color and karyotype, making them excellent models for understanding the ecological drivers and genetic underpinnings of color variation. Banded and uniform morphs of the desert clicker grasshopper (Ligurotettix coquilletti) are found across...

Data from: Aridity drives coordinated trait shifts but not decreased trait variance across the geographic range of eight Australian trees

Leander Anderegg, Xingwen Loy, Ian Markham, Christina Elmer, Mark Hovenden, Janneke HilleRisLambers & Margaret Mayfield
Large intraspecific functional trait variation strongly impacts many aspects of communities and ecosystems, and is the medium upon which evolution works. Yet intraspecific trait variation is inconsistent and hard to predict across traits, species, and locations. We measured within-species variation in leaf mass per area (LMA), leaf dry matter content (LDMC), branch wood density (WD), and allocation to stem area vs. leaf area in branches (branch Huber value, HV) across the aridity range of seven...

Data from: Indirect genetic control of migration in a salmonid fish

Suzanne Kelson, Stephanie Carlson & Michael Miller
The paper titled "Indirect genetic control of migration in a salmonid fish" examines the genetic architecture of migration in a partially migratory salmonid fish, Oncorhynchus mykiss. We assess the shared genetic basis between early life growth and migration, and find a shared allelic basis on the Omy05 region of the genome. We then test if early life growth differs among resident/migratory genotype juvenile fish in streams in the South Fork Eel River watershed, in Northern...

Gold Nanorods with PEG-Alkanethiol Ligands Etching in Graphene Liquid Cell Electron Microscopy-38 mM FeCl3

Matthew Hauwiller & A. Paul Alivisatos
Premade gold nanorods with PEG-Alkanethiol ligands were etched in a graphene liquid cell and imaged using Transmission Electron Microscopy (TEM). An aqueous solution of gold nanorods, Tris Buffer-HCl, and FeCl3 was encapsulated between graphene sheets. The final concentration of FeCl3 was 38 mM. Through a combination of the electron beam-generated radiolysis products and the FeCl3, the nanorods underwent non-equilibrium etching. See associated papers for more details.

The effect of influenza vaccination for the elderly on hospitalization and mortality: an observational study with a regression-discontinuity design

, Carlos Dobkin & Devon Gorry
Replication files for "The Effect of Influenza Vaccination for the Elderly on Hospitalization and Mortality: An Observational Study with a Regression-Discontinuity Design", published in the Annals of Internal Medicine.

Data from: Modifications during early plant development promote the evolution of nature’s most complex woods

Joyce G. Chery, Marcelo R. Pace, Pedro Acevedo-Rodriguez, Chelsea D. Specht & Carl J. Rothfels
Secondary growth is the developmental process by which woody plants grow radially. The most complex presentations of secondary growth are found in lianas (woody vines) as a result of their unique demand to maintain stems that can twist without breaking. The complex woody forms in lianas arise as non-circular stem outlines, aberrant tissue configurations, and/or shifts in the relative abundance of secondary tissues. Previous studies demonstrate that abnormal activity of the vascular cambium leads to...

In transition: avian biogeographic responses to a century of climate change across desert biomes

Kelly Iknayan & Steven Beissinger
Transition zones between biomes, also known as ecotones, are areas of pronounced ecological change. They are primarily maintained by abiotic factors and disturbance regimes that could hinder or promote species range shifts in response to climate change. We evaluated how climate change has affected metacommunity dynamics in two adjacent biomes and across their ecotone by resurveying 106 sites that were originally surveyed for avian diversity in the early 20th century by Joseph Grinnell and colleagues....

Long-term evidence shows crop-rotation diversification increases agricultural resilience to adverse growing conditions in North America

Timothy Bowles, Maria Mooshammer, Yvonne Socolar, Franciso Calderón, Michel Cavigelli, Steve Culman, William Dean, Axel Garcia Y Garcia, Amélie Gaudin, W Scott Harkom, Michael Lehman, Shannon Osborne, G Philip Robertson, Jonathan Salerno, Marty Schmer, Jeffrey Strock, A Stuart Grandy & Craig Drury
A grand challenge facing humanity is how to produce food for a growing population in the face of a changing climate and environmental degradation. Though empirical evidence remains sparse, management strategies that increase environmental sustainability, like increasing agroecosystem diversity through crop rotations, may also increase resilience to weather extremes without sacrificing yields. We used multilevel regression analyses of long-term crop yield datasets across a continental precipitation gradient to assess how temporal crop diversification affects maize...

Data from: Low temperatures impact species distributions of jumping spiders across a desert elevational cline

Erin E. Brandt, Kevin T. Roberts, Caroline M. Williams & Damian O. Elias
Temperature is known to influence many aspects of organisms and is frequently linked to geographical species distributions. Despite the importance of a broad understanding of an animal’s thermal biology, few studies in- corporate more than one metric of thermal biology. Here we examined an elevational assemblage of Habronattus jumping spiders to measure different aspects of their thermal biology including thermal limits (CTmin , CTmax), thermal preference, V̇CO2 as proxy for metabolic rate, locomotor behavior and...

Data from: The utility of information flow in formulating discharge forecast models: a case study from an arid snow-dominated catchment

Dino Bellugi, Chris Tennant, Larsen Laurel, Edom Moges, Liang Zhang & Hongxu Ma
These data accompany the manuscript “The utility of information flow in formulating discharge forecast models: a case study from an arid snow-dominated catchment”, in review at WRR. They were compiled from Boise State’s University’s Dry Creek Experimental Watershed (DCEW) web site, and consist of measurements of climatic data and discharge at various stations in the watershed from 1 January 2001 through 19 July 2017. The data quality-controlled, gap-filled, and aggregated at scales varying from 1...

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Affiliations

  • University of California, Berkeley
    215
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    4
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