70 Works

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

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...

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: Tropical arboreal ants form dominance hierarchies over nesting resources

Senay Yitbarek & Stacy M. Philpott
Interspecific dominance hierarchies have been widely reported across animal systems. High-ranking species are expected to monopolize more resources than low-ranking species via resource monopolization. In some ant species, dominance hierarchies have been used to explain species coexistence and community structure. However, it remains unclear whether or in what contexts dominance hierarchies occur in tropical ant communities. This study seeks to examine whether arboreal twig-nesting ants competing for nesting resources in a Mexican coffee agricultural ecosystem...

Data from: The 15-year post-treatment response of a mixed-conifer understory plant community to thinning and burning treatments

Matthew Hurteau, Marrissa Goodwin, Malcolm North, Harold Zald & Brandon Collins
Disturbance is central to maintaining diversity in forest ecosystems. In the dry forests of the western United States, over a century of fire exclusion has altered the fire regimes of these forests, resulting in high fuel loads and a loss of plant diversity. Mechanical thinning and prescribed fire are widely used to restore structural complexity and species diversity in many western U.S. forests. While studies have shown that the reintroduction of fire into these forests...

Predicted percentage dissatisfied with ankle draft

Shichao Liu & Stefano Schiavon
We collected subjective responses on thermal comfort from 110 college students when their lower legs and ankles were exposed to air at different environment conditions (e.g., air speed and temperature). A draft risk model was developed based on the laboratory results. One can find more description in our original papers. S. Liu, S. Schiavon, A. Kabanshi, W.W. Nazaroff, Predicted percentage dissatisfied with ankle draft, Indoor Air. 27 (2017) 852–862. S. Schiavon, D. Rim, W. Pasut,...

Data from: Spider webs, stable isotopes and molecular gut content analysis: multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders

Susan Kennedy, Jun Ying Lim, Joanne Clavel, Henrik Krehenwinkel & Rosemary G. Gillespie
1. Adaptive radiations are typically characterized by niche partitioning among their constituent species. Trophic niche partitioning is particularly important in predatory animals, which rely on limited food resources for survival. 2. We test for trophic niche partitioning in an adaptive radiation of Hawaiian Tetragnatha spiders, which have diversified in situ on the Hawaiian Islands. We focus on a community of nine species belonging to two different clades, one web building and the other actively hunting,...

Data from: Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode datasets

Emily E. Curd, Zack Gold, Gaurav S. Kandlikar, Jesse Gomer, Max Ogden, Taylor O'Connell, Lenore Pipes, Teia M. Schweizer, Laura Rabichow, Meixi Lin, Baochen Shi, Paul H. Barber, Nathan Kraft, Robert Wayne & Rachel S. Meyer
1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable, and non-invasive. Longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high-throughput sequencing platforms, fast multilocus metabarcode processing, and accurate taxonomic assignment. As bioinformatics tools continue to improve, addressing each of these demands within a single bioinformatics toolkit is becoming a reality. 2. Here we present an open...

Data from: Differential gene expression in relation to mating system in Peromyscine rodents

Jesyka Melendez-Rosa, Ke Bi & Eileen A. Lacey
Behaviors that increase an individual's exposure to pathogens are expected to have important effects on immunoactivity. Because sexual reproduction typically requires close contact among conspecifics, mating systems provide an ideal opportunity to study the immunogenetic correlates of behaviors with high versus low risks of pathogen exposure. Despite logical links between polygynandrous mating behavior, increased pathogen exposure, and greater immunoactivity, these relationships have seldom been examined in nonhuman vertebrates. To explore interactions among these variables in...

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...

Videos of Gold Nanorods Etching in Graphene Liquid Cell Transmission Electron Microscopy- 28 mM FeCl3

Matthew Hauwiller, Justin Ondry & A. Paul Alivisatos
Premade gold nanorods 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 28mM. 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.

Videos of Gold Nanorods Etching in Graphene Liquid Cell Transmission Electron Microscopy- 34 mM FeCl3

Matthew Hauwiller, Justin Ondry & A. Paul Alivisatos
Premade gold nanorods 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 34 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.

Direct mapping of curve-crossing dynamics in IBr by attosecond transient absorption spectroscopy

Yuki Kobayashi, Kristina Chang, Tao Zeng, Daniel Neumark & Stephen Leone
Herein is the experimental data set for the publication titled "Direct mapping of curve-crossing dynamics in IBr by attosecond transient absorption spectroscopy." The abstract of the paper is as follows: The electronic character of photoexcited molecules can abruptly change at avoided crossings and conical intersections. Here, we report direct mapping of the coupled interplay between electrons and nuclei in a prototype molecule, iodine monobromide (IBr), using attosecond transient absorption spectroscopy. A few-femtosecond visible pulse resonantly...

As the Wind Blows: The Effects of Long-Term Exposure to Air Pollution on Mortality

Replication files for "As the Wind Blows: The Effects of Long-Term Exposure to Air Pollution on Mortality", published in the Journal of the European Economic Association.

Supplementary information for: Deterministic assembly of arrays of lithographically defined WS_2 and MoS_2 monolayer features directly from multilayer sources into van der Waals heterostructures

Hayden Taylor, Vu Nguyen, Hannah Gramling, Clarissa Towle, Wan Li, Der-Hsien Lien, Hyungjin Kim, Daryl Chrzan, Ali Javey, Ke Xu & Joel Ager
One of the major challenges in the van der Waals (vdW) integration of 2D materials is achieving high-yield and high-throughput assembly of pre-defined sequences of monolayers into heterostructure arrays. Mechanical exfoliation has recently been studied as a promising technique to transfer monolayers from a multilayer source synthesized by other techniques, allowing the deposition of a wide variety of 2D materials without exposing the target substrate to harsh synthesis conditions. Although a variety of processes have...

Data from: Genome-wide epigenetic isolation by environment in a widespread Anolis lizard

Ian Wang, Guinevere Wogan, Michael Yuan & D. Luke Mahler
Epigenetic changes can provide a pathway for organisms to respond to local environmental conditions by influencing gene expression. However, we still know little about the spatial distribution of epigenetic variation in natural systems, how it relates to the distribution of genetic variation and the environmental structure of the landscape, and the processes that generate and maintain it. Studies examining spatial patterns of genetic and epigenetic variation can provide valuable insights into how ecological and population...

Data from: Megaphylogeny resolves global patterns of mushroom evolution

Torda Varga, Krisztina Krizsán, Csenge Földi, Bálint Dima, Marisol Sánchez-García, Santiago Sánchez-Ramírez, Gergely J. Szöllősi, János G. Szarkándi, Viktor Papp, László Albert, William Andreopoulos, Claudio Angelini, Vladimír Antonín, Kerrie W. Barry, Neale L. Bougher, Peter Buchanan, Bart Buyck, Viktória Bense, Pam Catcheside, Mansi Chovatia, Jerry Cooper, Wolfgang Dämon, Dennis Desjardin, Péter Finy, József Geml … & László G. Nagy
Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfill diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree...

The many population genetic and demographic routes to islands of genomic divergence

Claudio Quilodrán, Kristen Ruegg, Ashley Sendell-Price, Eric Anderson, Tim Coulson & Sonya Clegg
The way that organisms diverge into reproductively isolated species is a major question in biology. The recent accumulation of genomic data provides promising opportunities to understand the genomic landscape of divergence, which describes the distribution of differences across genomes. Genomic areas of unusually high differentiation have been called genomic islands of divergence. Their formation has been attributed to a variety of mechanisms, but a prominent hypothesis is that they result from divergent selection over a...

Contrasting impacts of a novel specialist vector on multi-host viral pathogen epidemiology in wild and managed bees

Robyn Manley, Ben Temperton, Mike Boots & Wilfert Lena
Typically pathogens infect multiple host species. Such multi-host pathogens can show considerable variation in their degree of infection and transmission specificity, which has important implications for potential disease emergence. Transmission of multi-host pathogens can be driven by key host species and changes in such transmission networks can lead to disease emergence. We study two viruses that show contrasting patterns of prevalence and specificity in managed honeybees and wild bumblebees, black queen cell virus (BQCV) and...

Registration Year

  • 2019
    70

Resource Types

  • Dataset
    70

Affiliations

  • University of California, Berkeley
    70
  • University of Minnesota
    2
  • United States Department of Agriculture
    2
  • Lawrence Berkeley National Laboratory
    2
  • University of Toronto
    2
  • Technical University of Madrid
    2
  • University of Exeter
    2
  • Worcester Polytechnic Institute
    2
  • University of California, Davis
    2
  • Norwegian University of Science and Technology
    2