697 Works

A Benchmark Data Set for Hydrogen Combustion

Akshaya Das, Christopher J. Stein, Farnaz Heidar-Zadeh, Luke Bertels, Meili Liu, Xingyi Guan, Mojtaba Haghighatlari, Jie Li, Oufan Zhang, Hongxia Hao, Itai Leven, Martin Head-Gordon & Teresa Head-Gordon

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

Anthony Roger Byrne

ddRAD of Hawaiian Ariamnes spiders

Ellie Armstrong, Benoît Perez-Lamarque, Ke Bi, Leontine Becking, Jun Lim, Tyler Linderoth, Rosemary Gillespie & Henrik Krehenwinkel
The diversification of a host organism can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, coupled with a chronologically arranged series of volcanic mountains, to determine the evolutionary history of a host and its associated microbial communities, altogether forming the “holobiont”. Using the stick spider Ariamnes waikula (Araneae, Theridiidae) on the island of Hawaiʻi, and outgroup taxa on older islands, we tested whether...

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...

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...

Personal thermal comfort models with wearable sensors

Shichao Liu, Stefano Schiavon, Hari Prasanna Das, Ming Jin & Costas Spanos
A personal comfort model is an approach to thermal comfort modeling, for thermal environmental design and control, that predicts an individual’s thermal comfort response, instead of the average response of a large population. We developed personal thermal comfort models using lab grade wearable in normal daily activities. We collected physiological signals (e.g., skin temperature, heart rate) of 14 subjects (6 female and 8 male adults) and environmental parameters (e.g., air temperature, relative humidity) for 2-4...

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.

GEOS-Chem output for \"Lightning NOx Emissions: Reconciling measured and modeled emissions estimates with updated NOx chemistry\"

Joshua Laughner, Ronald Cohen & Benjamin Nault
These GEOS-Chem simulations examine the effect of recent advances to our understanding of upper tropospheric chemistry on our ability to constrain lightning NOx emissions. These simulations examine the effect of the addition of methyl peroxy nitrate chemistry, as well as better constraints on the formation of pernitric acid, dinitrogen pentoxide, and nitric acid at the temperatures and pressures of the upper troposphere. These simulations include a base case, simulations implementing each change individually, all four...

Demonstration retrievals from \"Quantification of the effect of modeled lightning NO2 on UV-visible air mass factors\"

Joshua Laughner & Ronald Cohen
Space-borne measurements of tropospheric nitrogen dioxide (NO2) are up to 10x more sensitive to upper tropospheric NO2 than near-surface NO2 over low reflectivity surfaces. This make the modeling of lightning NO2 in the a priori profiles imperative to accurately retrieve NO2 over regions with significant lightning activity. This is quantified in our work "Quantification of the effect of modeled lightning NO2 on UV-visible air mass factors." This dataset contains the NO2 retrievals used in Section...

Six subsets of all native vascular plant species of California used by Baldwin et al. (2017), and the R script to use to extract the subsets from the master spatial file

Bruce G. Baldwin, Andrew H. Thornhill, William A. Freyman, David. D. Ackerly, Matthew M. Kling, Naia Morueta-Holme & Brent D. Mishler
Spatial patterns of diversity and endemism across California were examined by Baldwin et al. (2017 Amer. J. Bot.) for six subsets of all native vascular plant species: (1) only vascular plants that are completely restricted (absolutely endemic) to California, (2) only vascular plants native to the California Floristic Province, (3) only angiosperms, (4) only gymnosperms, (5) only ‘pteridophytes’ (i.e., ferns and lycophytes), and (6) the set of California species belonging to the diverse genera examined...

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...

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...

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...

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

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...

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.

Causal Evidence for Lateral Prefrontal Cortex Dynamics Supporting Cognitive Control

Derek Nee & Mark D'Esposito
The lateral prefrontal cortex (LPFC) is essential for higher-level cognition, but how its interactions support cognitive control remains elusive. Previously (Nee and D'Esposito, 2016), dynamic causal modeling (DCM) indicated that mid LPFC integrates abstract, rostral and concrete, caudal influences to inform context-appropriate action. Here, we use continuous theta-burst transcranial magnetic stimulation (cTBS) to causally test this model. cTBS was applied to three LPFC sites and a control site in counterbalanced sessions. Behavioral modulations resulting from...

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.

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...

Data from: Phosphoprotein SAK1 is a regulator of acclimation to singlet oxygen in Chlamydomonas reinhardtii

Setsuko Wakao, Brian L. Chin, Krishna K. Niyogi, Heidi K. Ledford, David Casero, Matteo Pellegrini, Rachel M. Dent & Sabeeha S. Merchant
Singlet oxygen is a highly toxic and inevitable byproduct of oxygenic photosynthesis. The unicellular green alga Chlamydomonas reinhardtii is capable of acclimating specifically to singlet oxygen stress, but the retrograde signaling pathway from the chloroplast to the nucleus mediating this response is unknown. Here we describe a mutant, singlet oxygen acclimation knocked-out 1 (sak1), that lacks the acclimation response to singlet oxygen. Analysis of genome-wide changes in RNA abundance during acclimation to singlet oxygen revealed...

Data from: Nonlinear thermal gradients shape broad-scale patterns in geographic range size and can reverse Rapoport’s rule

Adam Tomasovych, David Jablonski, Sarah K. Berke, Andrew Z. Krug & James W. Valentine
Aim: Species living at latitudes that have greater annual temperature variations are expected to achieve broader geographic ranges than species living at latitudes that have smaller annual temperature variations, generating a positive relationship between range size and latitude (Rapoport's rule). However, this prediction fails to take into account the greater latitudinal extent of tropical temperatures relative to those at higher latitudes. Here we model the contributions of the broader latitudinal extent of equal-temperature habitats at...

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.

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

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...

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...

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