660 Works

Forcing files and Model output for \"Contrasting impacts of the South Pacific Split Jet and the Southern Annular Mode modulation on Southern Ocean circulation and biogeochemistry\"

John Chiang, Kathy Tokos, Shih-Yu Lee & Katsumi Matsumoto
This contains the CESM forcing files and ocean model output used in Chiang J.C.H, K. Tokos, S.-Y. Lee, and K. Matsumoto, Contrasting impacts of the South Pacific Split Jet and the Southern Annular Mode modulation on Southern Ocean circulation and biogeochemistry. In revision for Paleoceanography, Oct 2017.

Dataset for Large-Scale Analysis of Modern Code Review Practices and Software Security in Open Source Software

Christopher Thompson
Dataset for my thesis titled "Large-Scale Analysis of Modern Code Review Practices and Software Security in Open Source Software. Contains: Labeled issues data used to train and test the quantifier models. Post-quantification datasets the analyses were performed on. Scripts (R, Python) for all analyses performed.

Thermal and energetic ion dynamics in Ganymede's magnetosphere

This dataset accompanies the manuscript "Thermal and energetic dynamics in Ganymede's magnetosphere", JGR Space Physics, 2018.

2D attenuation model of Long Valley (CA)

Janire Prudencio, Michael Manga & Taka'aki Taira
We image seismic intrinsic (Qi-1) and scattering (Qs-1) attenuation in Long Valley caldera, California, by analyzing more than 1700 vertical-component waveforms from local earthquakes. Observed energy envelopes are fit to the diffusion model (data files) and seismic attenuation images (anomalies files) are produced using two-dimensional space-weighting functions.

Supporting data for \"Evaluation of version 3.0B of the BEHR OMI NO2 product\"

Joshua Laughner, Qindan Zhu & Ronald Cohen
This dataset contains supporting data for the paper "Evaluation of version 3.0B of the BEHR OMI NO2 product" by Laughner, Zhu, and Cohen. Evaluation of new satellite trace gas products is an important step in proving their usefulness, and, in the case of NO2, is typically done by comparing the satellite-observed vertical column densities to independent measurements taken by aircraft or ground-based spectrometers. Input data required by the satellite retrieval may also be directly compared...

Restoration of incomplete oceanographic datasets

Siavash Ameli & Shawn Shadden
Remote sensing of oceanographic data often yields incomplete coverage of the measurement domain. This can limit interpretability of the data and identification of coherent features informative of ocean dynamics. Several methods exist to fill gaps of missing oceanographic data, and are often based on projecting the measurements onto basis functions or a statistical model. Herein, we use an information transport approach inspired from an image processing algorithm. This approach aims to restore gaps in data...

Toxic Y-chromosome in D. miranda

Kevin Wei
Large portions of eukaryotic genomes consist of transposable elements (TEs), and the establishment of transcription-repressing heterochromatin during early development safeguards genome integrity. Repeat-rich Y chromosomes can act as reservoirs for TEs (toxic Y effect), and TEs may exploit vulnerabilities associated with incomplete genomic defenses during early development. Here, we contrast the dynamics of early TE activation in two Drosophila species with vastly different Y chromosomes of different age. Zygotic TE expression is elevated in male...

Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene

Augusto Berrocal, Nicholas Lammers, Hernan Garcia & Michael Eisen
We used live imaging to visualize the transcriptional dynamics of the Drosophila melanogaster even-skipped gene at single-cell and high temporal resolution as its seven stripe expression pattern forms, and developed tools to characterize and visualize how transcriptional bursting varies over time and space. We find that despite being created by the independent activity of five enhancers, even-skipped stripes are sculpted by the same kinetic phenomena: a coupled increase of burst frequency and amplitude. By tracking...

Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology

Sean Wu, Penny Hancock, Arnaud Le Menach, Tanya Russell, Thomas Burkot, , Derek Cummings, Kelly Compton, Daniel Citron, John Marshall, Biyonka Liang, Catherine Moyes, Qian Zhang, David Smith, Samson Kiware, Anne Wilson, Thomas Scott, John Henry, Steven Lindsay, Amit Verma & Hector Sanchez C.
Mosquitoes are important vectors for pathogens that infect humans and other vertebrate animals. Some aspects of adult mosquito behavior and mosquito ecology play an important role in determining the capacity of vector populations to transmit pathogens. Here, we re-examine factors affecting the transmission of pathogens by mosquitoes using a new approach. Unlike most previous models, this framework considers the behavioral states and state transitions of adult mosquitoes through a sequence of activity bouts. We developed...

Data from: Enriched East Asian oxygen isotope of precipitation indicates reduced summer seasonality in regional climate and westerlies

John Chiang, Michael Herman, Kei Yoshimura & Inez Fung
This archive contain the isoGSM2 model output used in the publication Chiang, J. C. H., M. J. Herman, K. Yoshimura, and I. Y. Fung: Enriched East Asian oxygen isotope of precipitation indicates reduced summer seasonality in regional climate and westerlies. In press for Proceedings of the National Academy of Sciences, April 2020

Data from: Spatial phylogenetics of the North American flora

Brent Mishler, Robert Guralnick, Pamela Soltis, Stephen Smith, Douglas Soltis, Narayani Barve, Julie Allen & Shawn Laffan
North America is a large continent with extensive climatic, geological, soil, and biological diversity. That biota is under threat from habitat destruction and climate change, making a quantitative assessment of biodiversity of critical importance. Rapid digitization of plant specimen records and accumulation of DNA sequence data enable a much-needed broad synthesis of species occurrences with phylogenetic data. Here we attempted the first such synthesis of a flora from such a large and diverse part of...

BErkeley High Resolution (BEHR) OMI NO2 Prototype High Temporal Resolution Product

Joshua Laughner
The BErkeley High Resolution (BEHR) OMI NO2 Prototype High Temporal Resolution Product makes use of high spatial and temporal resolution a priori NO2 profiles for a limited domain in the southeast United States, covering 1 June-30 Aug 2013. These retrievals have been used to evaluate the impact of daily temporal resolution of the high-spatial-resolution a priori NO2 profiles needed for the retrieval

SanFranciscoBay_Adapt2SeaLevelRise_CaseStudies

Daniella Hirschfeld, Kristina Hill & Ellen Plane
As awareness of climate change increases more projects are beginning to include sea level rise in their planning and design. To better understand cutting edge examples of sea level rise adaptation we examined the current conditions and projected future changes from nine physical sea level rise adaptation projects in the San Francisco Bay.

Minimum Depth to Groundwater for the Coastal San Francisco Bay Area

Ellen Plane, Kristina Hill & Kris May
This dataset shows estimated values for minimum depth to groundwater in the coastal Bay Area. The estimation is based on an interpolation that uses ground elevation data and minimum depth to water values measured at monitoring wells in the nine Bay Area counties over the past 20 years. NOTE: The most recently uploaded data file (August 24, 2018) has the highest accuracy in the interpolation. Please use this file rather than the older versions. A...

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...

Temporal dynamics of migration-linked genetic variation are driven by streamflows and riverscape permeability

Suzanne Kelson, Michael Miller, Tasha Thompson, Sean O'Rourke & Stephanie Carlson
The permeability of landscapes is often explored spatially, but may also vary across time. For example, highways are more passable with low traffic, and mountain landscapes are more passable once snow-free. Landscape permeability especially influences migratory animals. Partial barriers are features that are passable in some conditions. Partial barriers are common in rivers due to the two-dimensional nature of river networks: aquatic organisms cannot circumvent in-river barriers. Barriers in river networks include waterfalls, logjams, or...

Behavioral, morphological, and ecological trait evolution in two clades of New World sparrows (Aimophila and Peucaea, Passerellidae)

Carla Cicero, Nicholas Mason, Lauryn Benedict & James Rising
The New World sparrows (Passerellidae) are a large and diverse group of songbirds that have been the subject of many studies on ecology, behavior, and evolutionary relationships. Here, we studied two clades of sparrows (Aimophila, Peucaea) to examine the evolution of behavioral, morphological, and ecological traits in a phylogenetic framework. Specifically, we inferred phylogenetic relationships in these clades, conducted ancestral state reconstructions, and asked whether patterns of trait evolution extend more broadly to New World...

Junco hyemalis Bone Microstructure

Leeann Louis, Rauri Bowie & Robert Dudley
Migration is the primary strategy that temperate birds use to avoid overwintering under harsh conditions. As a consequence, migratory birds have evolved specific morphological features in their wings and skeleton. However, in addition to varying in overall shape and size, bone can also change at the microstructural level by, for example, increasing its thickness. Such changes are critical to preventing fracture and damage under repeated loading (fatigue), yet it is not known whether migratory behaviour...

Data from: Topographic heterogeneity lengthens the duration of pollinator resources

Rachael Olliff-Yang & David Ackerly
The availability of sufficient and diverse resources across time is important for maintenance of biodiversity and ecosystem functioning. In this study we examine the potential for variation in environmental conditions across topographic gradients to extend floral resource timing. Flowering time on a landscape may vary across topography due to differences in abiotic factors, species turnover, or genotypic differences. However, the extent to which this variation in phenology affects overall flowering duration on a landscape, and...

Data from: Acrobatic squirrels learn to leap and land on tree branches without falling

Robert Full, Nathaniel Hunt, Lucia Jacobs & Judy Jinn
Arboreal animals often leap through complex canopies to travel and avoid predators. Their success at making split-second potentially life-threatening decisions of biomechanical capability depends on skillful use of acrobatic maneuvers and learning from past efforts. Here, we found that free-ranging fox squirrels (Sciurus niger) leaping across novel, simulated branches decided where to launch by balancing a trade-off between gap distance and branch-bending compliance. Squirrels quickly learned to modify impulse generation upon repeated leaps from novel,...

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