70 Works

X-Ray Spectra (Mg, Ge)

Peter Beiersdorfer & Wyatt Joyce
Here are 4 x-ray emission spectra of the 3p1/2→2s1/2 transition in neonlike germanium and 2 x-ray emission spectra of Lyα1 and Lyα2 of hydrogenlike magnesium. These were taken at the electron beam ion trap at Lawrence Livermore National Laboratory. Two crystals were used and thus, there are two peaks detected for each line. The experiment was performed under the auspices of the U. S. Department of Energy by Lawrence Livermore National Laboratory under contract No....

Contrasting biogeography of fungal communities associated with roots versus soils and the role of root morphology in mycobiome assembly in coast redwood, Sequoia sempervirens

Claire Willing
As fungal communities generally assemble as roots grow through rhizosphere soil, it is important to understand how geography, climate, and environmental that influence the soil fungal community may also impact fungal community assembly in roots. Further, the heterogeneity of root morphology might also play an important role in fungal community assembly. The coast redwood (Sequoia sempervirens) is spans substantial geographic, climatic, and environmental gradients throughout its nearly contiguous range and, like many other tree species...

Unnatural selection of salmon life histories in a modified riverscape

Anna M. Sturrock, Stephanie M. Carlson, John D. Wikert, Tim Heyne, Sébastien Nusslé, Joseph E. Merz, Hugh J. W. Sturrock & Rachel C. Johnson
Altered river flows and fragmented habitats often simplify riverine communities and favor non‐native fishes, but their influence on life‐history expression and survival is less clear. Here, we quantify the expression and ultimate success of diverse salmon emigration behaviors in an anthropogenically altered California river system. We analyzed two decades of Chinook salmon monitoring data to explore the influence of regulated flows on juvenile emigration phenology, abundance, and recruitment. We then followed seven cohorts into adulthood...

Data from: Insect herbivory reshapes a native leaf microbiome

Parris Humphrey & Noah Whiteman
Publication abstract: Insect herbivory is pervasive in plant communities, but its impact on microbial plant colonizers is not well-studied in natural systems. By calibrating sequencing-based bacterial detection to absolute bacterial load, we find that the within-host abundance of most leaf microbiome (phyllosphere) taxa colonizing a native forb is amplified within leaves impacted by insect herbivory. Herbivore-associated bacterial amplification reflects community-wide compositional shifts towards lower ecological diversity, but the extent and direction of such compositional shifts...

Whole genome sequences of 23 species from the Drosophila montium species group (Diptera: Drosophilidae): a resource for testing evolutionary hypotheses

Michael Bronski, Ciera Martinez, Holli Weld & Michael Eisen
Large groups of species with well-defined phylogenies are excellent systems for testing evolutionary hypotheses. In this paper, we describe the creation of a comparative genomic resource consisting of 23 genomes from the species-rich Drosophila montium species group, 22 of which are presented here for the first time. The montium group is uniquely positioned for comparative studies. Within the montium clade, evolutionary distances are such that large numbers of sequences can be accurately aligned while also...

Extinct plants of North America north of Mexico

Wesley Knapp, Anne Frances, Reed Noss, Robert Naczi, Alan Weakley, George Gann, Bruce Baldwin, James Miller, Patrick McIntyre, Brent Mishler, Gerry Moore, Richard Olmstead, Anna Strong, Daniel Gluesenkamp & Kathryn Kennedy
The recent study by Humphreys et al., reporting extinction of almost 600 plant species globally, represents a groundbreaking effort at compiling direct data on seed plants. We applaud Humphreys et al. for quantifying plant extinctions because they formulate an important and testable hypothesis. However, their study missed many extinctions and rediscoveries of seed plants in the United States and Canada. Our team of experts has been compiling a list of extinct plants of North America...

Data from: Precession modulation of the South Pacific westerly wind belt over the past million years

John Chiang & Frank Lamy
This archive contain the model output used in the publication Lamy, F., J. C.H. Chiang, G. Martínez-Méndez, M. Thierens, H.W. Arz, J.H.C. Bosmans, D. Hebbeln, F. Lambert, L. Lembke-Jene, J-B. Stuut: "Precession modulation of the South Pacific westerly wind belt over the past million years". Revised for the Proceedings of the National Academy of Sciences, July 2019. They only contain the monthly mean climatological GFDL model output; output for EC Earth is archive elsewhere. The...

Data from: A small yet occasional meal: predatory drill holes in Paleocene ostracods from Argentina and methods to infer predation intensity

Jorge Villegas-Martín, Daiane Ceolin, Gerson Fauth & Adiël Klompmaker
Ostracods are common yet understudied prey in the fossil record. We document drill holes in Paleocene (Danian) ostracods from central Argentina using 9025 specimens representing 66 species. While the assemblage-level drilling percentage is only 2.3%, considerable variation exists within species (0.3–25%), suggesting prey preference by the drillers. This preference is not determined by abundance because no significant correlation is found between species abundance and drilling percentages. Seven methods were used, some of which are new,...

Personal thermal comfort models with wearable sensors

Shichao Liu & Stefano Schiavon
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...

Data from: Do genomics and sex predict migration in a partially migratory salmonid fish, Oncorhynchus mykiss?

Suzanne J. Kelson, Michael R. Miller, Tasha Q. Thompson, Sean M. O'Rourke & Stephanie M. Carlson
Partial migration is a common phenomenon wherein populations include migratory and resident individuals. Whether an individual migrates or not has important ecological and management implications, particularly within protected populations. Within partially migratory populations of O. mykiss, migration is highly correlated with a specific genomic region, but it is unclear how well this region predicts migration at the individual level. Here, we relate sex and life history genotype, determined using >400 SNPs on the migratory-linked genomic...

Videos of Gold Nanorods Etching in Graphene Liquid Cell Transmission Electron Microscopy- 38 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 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.

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

Qindan Zhu, Joshua 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...

Xenon hydrate as an analogue of methane hydrate in geologic systems out of thermodynamic equilibrium

Xiaojing Fu, William Waite, Luis Cueto-Felgueroso & Ruben Juanes
This data set contains simulation results of hydrate growth on a gas-liquid interface for both methane and xenon hydrate systems. The simulations are performed on a 1D domain of 115 micron in length and for a duration of 40 minutes. The data set contains two MATLAB data files (methane_data.mat and xenon_data.mat) and one file to help users to visualize the data (plot_data.m). In the file plot_data.m, we also use experimental data from Taylor et al....

Polysome fractionation analysis reveals features important for human nonsense-mediated mRNA decay

James Lloyd, Courtney French & Steven Brenner
Nonsense-mediated mRNA decay (NMD) is a translation-dependent mRNA surveillance pathway that eliminates transcripts with premature termination codons. Several studies have tried defined the features governing which transcripts are targeted to NMD. However, these approaches often rely on inhibiting core NMD factors, which often have roles in non-NMD processes within the cell. Based on reports that NMD-targeted transcripts are often bound by a single ribosome, we analyzed RNA-Seq data from a polysome fractionation experiment (TrIP-Seq) to...

Building deformation caused by tunnelling: centrifuge modelling

Stefan Ritter, Giorgia Giardina, Andrea Franza & Matthew DeJong
This paper investigates the deformation of buildings due to tunnelling-induced soil displacements. Centrifuge model tests of 3D printed building models subject to a plane-strain tunnel excavation in dense, dry sand are discussed. The small-scale structures replicate important building characteristics including brittle material properties similar to masonry, a realistic building layout, façade openings, strip footings and a rough soil-structure interface. Digital images were captured during the experiments, enabling image-based measurements of the building response. Results demonstrate...

Data from: Global patterns in fine root decomposition: climate, chemistry, mycorrhizal association, and woodiness

Craig R. See, Michael Luke McCormack, Sarah E. Hobbie, Habacuc Flores-Moreno, Whendee L. Silver & Peter G. Kennedy
Fine root decomposition constitutes a critical yet poorly understood flux of carbon and nutrients in terrestrial ecosystems. Here, we present the first large‐scale synthesis of species trait effects on the early stages of fine root decomposition at both global and local scales. Based on decomposition rates for 279 plant species across 105 studies and 176 sites, we found that mycorrhizal association and woodiness are the best categorical traits for predicting rates of fine root decomposition....

Data from: High-throughput synapse-resolving two-photon fluorescence microendoscopy for deep-brain volumetric imaging in vivo

Guanghan Meng, Yajie Liang, Sarah Sarsfield, Wan-Chen Jiang, Rongwen Lu, Joshua Tate Dudman, Yeka Aponte & Na Ji
Optical imaging has become a powerful tool for studying brains in vivo. The opacity of adult brains makes microendoscopy, with an optical probe such as a gradient index (GRIN) lens embedded into brain tissue to provide optical relay, the method of choice for imaging neurons and neural activity in deeply buried brain structures. Incorporating a Bessel focus scanning module into two-photon fluorescence microendoscopy, we extended the excitation focus axially and improved its lateral resolution. Scanning...

Data from: Rapid evolution of invasive traits facilitates the invasion of common ragweed, Ambrosia artemisiifolia

Yan Sun & George K. Roderick
1. Invasive alien plants, together with organisms introduced for biological control, are ideal study systems with which to address questions of whether, and how fast, organisms adapt to changing environments. We compared populations of common ragweed, Ambrosia artemisiifolia, from native (USA) and introduced (China) ranges at similar latitudes, together with herbivores introduced for biological control, to understand the rate of evolutionary adaptive response of an invasive plant to novel environments. 2. Evolution of phenotypic traits...

Data from: Successional loss of two key food tree species best explains decline in group size of Panamanian howler monkeys (Alouatta palliata)

Katharine Milton, David W. Armitage & Wayne P. Sousa.
Negative impacts of discrete, short-term disturbances to wildlife populations are well-documented. The consequences of more gradual environmental change are less apparent and harder to study because they play out over longer periods and are often indirect in their action. Yet, they can drive the decline of wildlife populations even in seemingly pristine and currently well-protected habitats. One such environmental change is a successional shift in a community’s species composition as it regenerates from disturbance caused...

NetCDF data from: Numerical investigation of baroclinic channel-shoal interaction in partially stratified estuaries

Jian Zhou, Mark Stacey, Rusty C. Holleman, Emma Nuss & David B. Senn
These NetCDF files are the simulation result files for the eleven scenarios listed in Table 1 of the manuscript. They are generated using a two-dimensional cross-sectional mode of the General Estuarine Transport Model (GETM). They include a reference scenario and a number of sensitivity scenarios with variation of the longitudinal salinity radient, the cross-sectionally averaged tidal velocity magnitude, the averaged shoal depth, the slope of the shoal, and the quasi-lateral eddy diffusivities. To be specific,...

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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...

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

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...

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