65 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...

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...

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)....

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...

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...

RGB Camera Walnut Site 60 meters

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

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...

SWIR Camera in Walnut site 120 meters

Haoyu Niu, Tiebiao Zhao & YangQuan Chen
SWIR 120 meters

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...

Heritability of plastic trait changes in drought-exposed ponderosa pine seedlings

Dean Wu, Mengjun Shu & Emily Moran
Climate change is imposing new selective pressures on forest tree populations. Evolutionary responses may be important for trees, despite long generation times, since many populations harbor significant genetic variation in environmentally relevant traits. However, the heritability of climate responses (e.g. how much growth differs under drought) has been investigated in only one tree species previously. Here, we quantify heritable variation in environmental response traits of Pinus ponderosa using a greenhouse trial. Five seedlings from each...

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...

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...

Ambient and nitrogen environment friction data for various materials and surface treatments for space applications

Azhar Vellore, Sergio Romero Garcia, Duval Johnson & Ashlie Martini
A multivariate tribological evaluation of candidate materials, surface treatments and dry film lubricants is necessary for design of moving mechanical components that function reliably in extreme conditions, including for long duration space missions. In this study, linear reciprocating or unidirectional sliding friction data was collected using ball-on-flat tests. The balls were hardened 440C stainless steel (either uncoated or sputtered with MoS2) and flat surfaces were 440C stainless steel, Nitronic 60 stainless steel or Ti6Al4V titanium...

Thermal camera in walnut site 60 meters

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

CALeDNA Anacapa/CRUX Dat Container (Linux/HPC)

Maxwell Ogden
As part of the CALeDNA project this includes Anacapa Container which includes all the necessary software dependencies to run the Anacapa and CRUX pipelines on Linux/HPCs.

Data from: Identifying genetic variation associated with environmental variation and drought-tolerance phenotypes in ponderosa pine

Mengjun Shu & Emily Moran
Background Genotype-to-environment (G2E) association analysis coupled with genotype-to-phenotype (G2P) association analysis promises exciting advances towards discovering genes responsible for local adaptation. We combine G2E and G2P analysis with gene annotation in Pinus ponderosa (ponderosa pine), an ecologically and economically important conifer that lacks a sequenced genome, to identify genetic variants and gene functions that may be associated with local adaptation to drought. Results We identified SNP markers in 223 genotypes from across the Sierra Nevada...

CALeDNA Anacapa/CRUX Dat Container (Windows/Mac Vagrant Version)

Max Ogden
This dataset contains the Vagrant version of Anacapa Container for Windows/Mac with virtualization. For the recommended Linux/HPC version, see https://doi.org/10.6071/M31H29.

Assessing the impact of product inhibition in a chromogenic assay

Michael Stobb, Karin Leiderman, Suzanne Sindi & Dougald Monroe
Chromogenic substrates (CS) are synthetic substrates used to monitor the activity of a target enzyme. It has been reported that some CSs display competitive product inhibition with their target enzyme. Thus, in assays where enzyme activity is continuously monitored over long periods of time, the product inhibition may significantly interfere with the reactions being monitored. Despite this knowledge, it is rare for CSs to be directly incorporated into mathematical models that simulate these assays. This...

Remineralizing Enamel : A Literature Review

Carolina Karuppiah
Background: Tooth enamel is a non-living tissue, once matured it can no longer remineralization itself. Unfortunately, there are only a few studies that analyze the risks and benefits in applications towards remineralization. The objective was to examine the effectiveness and risks of synthetic applications towards remineralizing tooth enamel. Methods: Experimental trials focusing on the effect of synthetic applications on tooth enamel such as, surface hardness, surface thickness and overall effectiveness were included in this review....

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...

Near-term modeled forest fire area and fuel aridity projections

John Abatzoglou
Escalating burned area in western US forests has heightened the need to refine near-term forest fire projections. One critical knowledge gap is how fire-fuel feedbacks may constrain such projections. We use both static climate-fire models and dynamic models that incorporate feedbacks to project future western US forest-fire area. Compared to 1991-2020, static models for 2021-2050 project a doubling in forest-fire area, increased year-to-year variability, and increased occurrence of years with forest-fire area exceeding the 2020...

Files associated with: Species’ attributes predict the relative magnitude of ecological and genetic recovery following mass mortality

Lauren Schiebelhut, Gaylord Brian, Richard Grosberg, Laura Jurgens & Michael Dawson
Theoretically, species’ characteristics should allow estimation of dispersal potential and, in turn, explain levels of population genetic differentiation. However, a mismatch between traits and genetic patterns is often reported in marine species and interpreted as evidence that life-history traits do not influence dispersal. Here, we couple ecological and genomic methods to test the hypothesis that species with attributes favoring greater dispersal potential — e.g. longer pelagic duration, higher fecundity, and larger population size — have...

Data associated with: Minor genetic consequences of a major mass mortality: Short-term effects in Pisaster ochraceus

Lauren Schiebelhut, Melina Giakoumis, Rita Castilho, Paige Duffin, Jonathan Puritz, John Wares, Gary Wessel & Michael Dawson
Mass mortality events (MMEs) are increasing globally in frequency and magnitude, largely due to human-induced change. The effects of these MMEs, both in the long- and short-term, are of imminent concern because of their ecosystem impacts. Genomic data can be used to reveal some of the population-level changes associated with MMEs. Here, we use reduced-representation sequencing to identify potential short-term genetic impacts of an MME associated with a sea star wasting (SSW) outbreak. We tested...

Are geometric morphometric analyses replicable? Evaluating landmark measurement error and its impact on extant and fossil Microtus classification

Nathaniel Fox, Joseph Veneracion & Jessica Blois
Geometric morphometric analyses are frequently employed to quantify biological shape and shape variation. Despite the popularity of this technique, quantification of measurement error in geometric morphometric datasets and its impact on statistical results is seldom assessed in the literature. Here, we evaluate error on 2D landmark coordinate configurations of the lower first molar of five North American Microtus (vole) species. We acquired data from the same specimens several times to quantify error from four data...

Multiplex networks reveal geographic constraints on illicit wildlife trafficking

Felber Arroyave, Alexander Petersen, Jeffrey Jenkins & Rafael Hurtado
Illicit wildlife trafficking poses a threat to the conservation of species and ecosystems, and represents a fundamental source of biodiversity loss, alongside climate change and large-scale land degradation. Despite the seriousness of this issue, little is known about various socio-cultural demand sources underlying trafficking networks, for example the forthright consumption of endangered species on different cultural contexts. Our study illustrates how wildlife trafficking represents a wicked problem at the intersection of criminal enforcement, cultural heritage...

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