117 Works

Southern Sierra Critical Zone Observatory (SSCZO), Providence Creek meteorological data, soil moisture and temperature, snow depth and air temperature

Roger Bales, Matt Meadows, Erin Stacy, Martha Conklin, Xiande Meng & SSCZO Southern Sierra Critical Zone Observatory
Snow depth, soil moisture and soil temperature are measured at lower Providence South facing (LowMetS) and North facing (LowMetN), Upper Providence South facing (UpMetS), North facing (UpMetN) and Flat aspect (UpMetF), and Subcatchment basin P301 (P301) with a wireless sensor network, using a Campbell Scientific logger to control peripheral devices. Snow depth is measured in the open, at the drip edge and under canopies. Soil moisture and temperature are measured at 10, 30, 60 and...

Data from: Controlled comparison of species- and community-level models across novel climates and communities

Kaitlin Clare Maguire, Diego Nieto-Lugilde, Jessica Blois, Matthew Fitzpatrick, John Williams, Simon Ferrier & David Lorenz
Species distribution models (SDMs) assume species exist in isolation and do not influence one another's distributions, thus potentially limiting their ability to predict biodiversity patterns. Community-level models (CLMs) capitalize on species co-occurrences to fit shared environmental responses of species and communities, and therefore may result in more robust and transferable models. Here, we conduct a controlled comparison of five paired SDMs and CLMs across changing climates, using palaeoclimatic simulations and fossil-pollen records of eastern North...

Data from: How chimpanzees integrate sensory information to select figs

Nathaniel J. Dominy, Justin D. Yeakel, Uttam Bhat, Lawrence Ramsden, Richard W. Wrangham & Peter W. Lucas
Figs are keystone resources that sustain chimpanzees when preferred fruits are scarce. Many figs retain a green(ish) colour throughout development, a pattern that causes chimpanzees to evaluate edibility on the basis of achromatic accessory cues. Such behaviour is conspicuous because it entails a succession of discrete sensory assessments, including the deliberate palpation of individual figs, a task that requires advanced visuomotor control. These actions are strongly suggestive of domain-specific information processing and decision-making, and they...

Data from: Cooperative interactions between different classes of disordered proteins play a functional role in the nuclear pore complex of Baker's yeast

David E. Ando, Ajay Gopinathan & David Ando
Nucleocytoplasmic transport is highly selective, efficient, and is regulated by a poorly understood mechanism involving hundreds of disordered FG nucleoporin proteins (FG nups) lining the inside wall of the nuclear pore complex (NPC). Previous research has concluded that FG nups in Baker's yeast (S. cerevisiae) are present in a bimodal distribution, with the ``Forest Model'' classifying FG nups as either di-block polymer like ``trees'' or single-block polymer like ``shrubs''. Using a combination of coarse-grained modeling...

CoreShellShell, a quantum dot excitonic energy and charge density calculator

Anne Kelley
This program calculates electron and hole charge distributions for a spherical semiconductor quantum dot that may have up to three different materials in concentric shells (core-barrier-shell), each with different valence and/or conduction band potentials. It calculates the four lowest s-type (zero angular momentum) electron wavefunctions and the eight lowest s-type hole wavefunctions using the effective mass approximation particle in a sphere model. It then uses the excitons produced from these pairs of single-particle wavefunctions as...

A local and global sensitivity analysis of a mathematical model of coagulation and platelet deposition under flow

Kathryn Link, Michael Stobb, Jorge Di Paola, Keith Neeves, Aaron Fogelson, Suzanne Sindi & Karin Leiderman
The hemostatic response involves blood coagulation and platelet aggregation to stop blood loss from an injured blood vessel. The complexity of these processes make it difficult to intuit the overall hemostatic response without quantitative methods. Mathematical models aim to address this challenge but are often accompanied by numerous parameters choices and thus need to be analyzed for sensitivity to such choices. Here we use local and global sensitivity analyses to study a model of coagulation...

SWIR Camera in Walnut site 120 meters

Haoyu Niu, Tiebiao Zhao & YangQuan Chen
SWIR 120 meters

RGB Camera Walnut Site 60 meters

Haoyu Niu, Tiebiao Zhao & YangQuan Chen
RGB Camera Walnut Site 60 meters

Data from: Comparing methods for SNP calling from Genotyping-By-Sequencing (GBS) data for a large-genome conifer without a published genome sequence

Mengjun Shu & Emily Moran
Reduced-representation restriction-enzyme-based sequencing methods have been demonstrated to be robust and cost-effective genotyping methods to identify Single Nucleotide Polymorphisms (SNPs). While alignment of the short-read fragments to a genome sequence of the same species results in better SNP calling than de novo approaches, only a few tree species - and few conifers in particular - have an annotated sequence. Many conifer genomes are huge (>19 GB) and include a large proportion of repeat sequences, making...

Root uptake under mismatched distributions of water and nutrients in the root zone

Jing Yan, Nathaniel Bogie & Teamrat Ghezzehei
Most plants derive their water and nutrient needs from soils, where the resources are often scarce, patchy, and ephemeral. It is not uncommon for plant roots to encounter mismatched patches of water-rich and nutrient-rich regions in natural environments. Such an uneven distribution of resources necessitates plants to rely on strategies to explore and acquire nutrients from relatively dry patches. We conducted a laboratory study that elucidates the biophysical mechanisms that enable this adaptation. The roots...

Data from: Probing the ecology and climate of the Eocene Southern Ocean with sand tiger sharks Striatolamia macrota

Sora Kim, Sarah Zeichner, Albert Colman, Howie Scher, Jürgen Kriwet & Thomas Mörs
During the Eocene, the Earth climate system transitioned from greenhouse to icehouse conditions. Central to many explanations is the Southern Ocean—where tectonic configurations influenced oceanic gateways, ocean circulation reduced heat transport, and/or greenhouse gas declines prompted glaciation. To date, few studies have explored the implications of this climate transition on high latitude, marine vertebrates. Seymour Island near the Antarctic Peninsula preserves a rich, diverse fossil assemblage in the Tertiary Eocene La Meseta (TELM) Formation (Fm)....

Electronic properties of oligothiophenes

Chee-Kong Lee, Chengqiang Lu, Yue Yu, Qiming Sun, Chang-Yu Hsieh, Shengyu Zhang, Qi Liu & Liang Shi
Despite the remarkable progress of machine learning (ML) techniques in chemistry, modeling the optoelectronic properties of long conjugated oligomers and polymers with ML remains challenging due to the difficulty in obtaining sufficient training data. Here we use transfer learning to address the data scarcity issue by pre-training graph neural networks using data from short oligomers. With only a few hundred training data, we are able to achieve an average error of about 0.1 eV for...

2009 modeled electricity prices from HiGRID for the California grid

Brian Tarroja, Joshua H. Viers, Aditya Sood & Gustavo Facincani Dourado
This dataset was developed to be used in the CenSierraPywr model, created for the project "Optimizing Hydropower Operations While Sustaining Ecosystem Functions in a Changing Climate", for the California Energy Commission. The model that includes hydroeconomic optimization for hydropower production in the Stanislaus and Upper San Joaquin River basins in the Central Sierra Nevada, California. The two basins have high elevation reservoirs that are typically operated to maximize revenue from hydropower production. Therefore, to better...

CCMI nursery coral disease 2019

Anya Brown, Dagny-Elyse Anastasiou, Monica Schul, Sophia MacVittie, Lindsay Spiers, Julie Meyer, Carrie Manfrino & Thomas Frazer
Marine infectious diseases are a leading cause of population declines globally due, in large part, to challenges in diagnosis and limited treatment options. Mitigating disease spread is particularly important for species targeted for conservation. In some systems, the strategic arrangement of organisms in space can constrain disease outbreaks, however, this approach has not been used in marine restoration. Reef-building corals have been particularly devastated by disease and continue to experience catastrophic population declines. Here, we...

Data for: Thermal vulnerability in a mountain stream network: Temporal, spatial, and biological data

Kyle Leathers, David Herbst, Mohammad Safeeq & Albert Ruhi
As climate change continues to increase air temperature in high-altitude ecosystems, it has become critical to understand the controls and scales of aquatic habitat vulnerability to warming. Here we used a nested array of high-frequency sensors, and advances in time-series models, to examine spatiotemporal variation in thermal vulnerability in a model Sierra Nevada watershed. Stream thermal sensitivity to atmospheric warming fluctuated strongly over the year and peaked in spring and summer—when hot days threaten invertebrate...

Additional file 2 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 2: Supplemental Table S1. Impact of adding different concentrations of non-ionic detergents to the SIP gradient medium on percent DNA recovery (n=3).

Additional file 4 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 4: Supplemental Table S3. Assembly statistics, taxonomic lineage, and atom percent excess (APE) of the metagenome amplified genomes (MAGs) created in this study.

Additional file 5 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 5: Supplemental Table S4. Number of CAZyme family domains in the highly enriched MAGs (>10 atom% excess 13C). AOA = archaeal ammonia oxidizer, Fibro = Fibrobacterota, Myxo = Myxococcota (Myxococcaceae).

Data from: Complex phylogeography and historical hybridization between sister taxa of freshwater sculpin (Cottus).

Jason Baumsteiger, Andrew P. Kinziger, Stewart B. Reid & Andres Aguilar
Species ranges which span different geographic landscapes frequently contain cryptic species or population-level structure. Identifying these possible diversification factors can often be accomplished under a comparative phylogeographic framework. However comparisons suffer if previous studies are limited to a particular group or habitat type. In California, a complex landscape has led to several phylogeographic breaks, primarily in terrestrial species. However two sister taxa of freshwater fish, riffle sculpin (Cottus gulosus) and Pit sculpin (C. pitensis), display...

Data from: Downscaled and debiased climate simulations for North America from 21,000 years ago to 2100AD

David J. Lorenz, Diego Nieto-Lugilde, Jessica L. Blois, Matthew C. Fitzpatrick & John W. Williams
Increasingly, ecological modellers are integrating paleodata with future projections to understand climate-driven biodiversity dynamics from the past through the current century. Climate simulations from earth system models are necessary to this effort, but must be debiased and downscaled before they can be used by ecological models. Downscaling methods and observational baselines vary among researchers, which produces confounding biases among downscaled climate simulations. We present unified datasets of debiased and downscaled climate simulations for North America...

TWOSTATE, a resonance Raman excitation profile and absorption spectrum simulator

Anne Kelley
This Fortran code calculates resonance Raman and absorption spectra using the time-dependent wavepacket method with two excited electronic states for a molecule with up to 30 vibronically active vibrations. The ground and excited state vibrational frequencies may be different and coordinate dependence of the electronic transition moment may be included in any number of modes, but the ground and excited state normal modes are assumed to be parallel (no Duschinsky rotation). Up to three of...

Data from: Climate and landscape drive the pace and pattern of conifer encroachment into subalpine meadows

Kaitlin C. Lubetkin, Anthony Leroy Westerling & Lara M. Kueppers
Mountain meadows have high biodiversity and help regulate stream water release following the snowmelt pulse. However, many meadows are experiencing woody plant encroachment, threatening these ecosystem services. While there have been field surveys of individual meadows and remote sensing-based landscape-scale studies of encroachment, what is missing is a broad scale, ground-based study to understand common regional drivers, especially at high elevations, where land management has often played a less direct role. With this study we...

Data from: An initial comparative genomic autopsy of wasting disease in sea stars

Dannise V. Ruiz‐Ramos, Lauren M. Schiebelhut, Katharina J. Hoff, John P. Wares & Michael N. Dawson
Beginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as ‘asteroid idiopathic wasting syndrome’ (AIWS) due to its elusive etiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progression from morbidity to death was rapid, leaving few tell-tale symptoms. Here we take a forensic genomic approach to discover candidate genes that may help explain...

Growth rate assays reveal fitness consequences of β-lactamases

Fabian Santiago, Evin Doscher, Jay Kim, Manel Camps, Juan Meza, Suzanne Sindi & Miriam Barlow
Clinical resistance determination is critical for monitoring the spread of antibiotic resistance. However, clinical methods of detecting resistance lack the sensitivity necessary to make strong conclusions about fitness. Growth rates are a far more sensitive method of measuring resistance, but they differ from clinical methods in that a single concentration of antibiotic is used for the assay. Here we show that in spite of this key difference, the results of growth rates correlate well with...

Thermal camera in walnut site 60 meters

Haoyu Niu, Tiebiao Zhao & YangQuan Chen
Thermal camera in walnut site 60 meters

Registration Year

  • 2022
    43
  • 2021
    14
  • 2020
    20
  • 2019
    12
  • 2018
    13
  • 2017
    6
  • 2016
    6
  • 2015
    1
  • 2014
    2

Resource Types

  • Dataset
    117

Affiliations

  • University of California, Merced
    117
  • University of California, Berkeley
    18
  • Lawrence Livermore National Laboratory
    16
  • Lawrence Berkeley National Laboratory
    15
  • University of Massachusetts Amherst
    14
  • Joint Genome Institute
    14
  • University of California, Davis
    6
  • University of California, Irvine
    5
  • University of Colorado Boulder
    4
  • University of Nevada Reno
    3