67 Works

Stochastic Persistence in Nucleated Polymerization Model

Suzanne Sindi & Jason Dark
The code in this repository was created by Dr. Jason K. Dark in completing his PhD at the University of California, Merced. The stochastic model of prion persistence is detailed in Chapter 3 of his Dissertation which is available at the following link: https://escholarship.org/uc/item/8tq2w26b Questions should be emailed to: Prof Suzanne Sindi (ssindi@ucmerced.edu)

Data from: Decoding the dynamics of dental distributions: insights from shark demography and dispersal

Sora Kim, Justin Yeakel, Juergen Kriwet, Meghan Balk, Jaelyn Eberle, Sarah Zeichner & Dina Fieman
Shark teeth are the most abundant vertebrate fossil, and because tooth size generally correlates with body size, their accumulations document the size structure of populations. Understanding how ecological and environmental processes influence size structure, and how this extends to influence these dental distributions, may offer a window into the ecological and environmental dynamics of past and present shark populations. Here we examine the dental distributions of sand tigers, including extant Carcharias taurus and extinct Striatolamia...

Pronghorn (Antilocapra americana) enamel phosphate δ18O values reflect climate seasonality: implications for paleoclimate reconstruction

Danielle Fraser, Mark Clementz, Jeffrey Welker & Sora Kim
Stable oxygen isotope compositions from vertebrate tooth enamel are commonly used as biogeochemical proxies for paleoclimate reconstructions. However, the utility of enamel isotopic values across species varies due to differences in rates of enamel deposition and mineralization as well as sources of ingested water, body water residence times, and species’ physiology. We evaluate the use of stable oxygen isotope compositions from pronghorn (Antilocapra americana Gray, 1866) enamel for the amplitude reconstruction of terrestrial paleoclimate seasonality....

Comparative molecular analysis of cancer behavior cultured in vitro, in vivo, and ex vivo

Nicholas R. Hum, Aimy Sebastian, Sean F. Gilmore, Wei He, Kelly A. Martin, Aubree Hinckley, Karen R. Dubbin, Monica L. Moya, Elizabeth K. Wheeler, Matthew A. Coleman & Gabriela G. Loots
Current pre-clinical models of cancer fail to recapitulate the cancer cell behavior in primary tumors primarily because of the lack of a deeper understanding of the effects that the microenvironment has on cancer cell phenotype. Transcriptomic profiling of 4T1 murine mammary carcinoma cells from 2D and 3D cultures, subcutaneous or orthotopic allografts (from immunocompetent or immunodeficient mice), as well as ex vivo tumoroids, revealed differences in molecular signatures including altered expression of genes involved in...

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...

Data from: Evapotranspiration response to multiyear dry periods in the semiarid western United States

Joseph Rungee, Roger Bales, Michael Goulden, Gerald Flerchinger, Greg Barron-Gafford & Xiande Meng
Analysis of measured evapotranspiration shows that subsurface plant‐accessible water storage (PAWS) can sustain evapotranspiration through multiyear dry periods. Measurements at 25 flux tower sites in the semiarid western United States, distributed across five land cover types, show both resistance and vulnerability to multiyear dry periods. Average (±standard deviation) evapotranspiration ranged from 660 ± 230 mm yr−1 (October–September) in evergreen needleleaf forests to 310 ± 200 mm yr−1 in grasslands and shrublands. More than 52% of...

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...

Merced Vernal Pools and Grassland Reserve sUAS-LiDAR High Resolution 0.25-meter DEM

Michael Kalua, Joshua Viers & Andreas Anderson
The Merced Vernal Pools and Grassland Reserve is 6,500 acres of protected habitat adjacent to the University of California Merced containing rare and endangered species and a unique seasonal wetland habitat. These data were gathered to be used for hydrological modelling on the Reserve for potential restoration projects and to be made public for other researchers who may find very high resolution topographical information useful for their work. This dataset contains a Digital Elevation Model...

Evapotranspiration data from eddy-covariance flux-tower measurements and Landsat imagery in California’s Sierra Nevada from 1985 to 2019

Qin Ma, Roger Bales, Joseph Rungee, Martha Conklin, Xiande Meng & Michael Goulden
The gridded annual evapotranspiration (ET) from 1985 to 2019 were calculated based on the correlations between eddy-covariance flux-tower measurements of annual evapotranspiration and satellite imagery derived Normalized Difference Vegetation Index (NDVI). Annual ET observations from 12 flux-towers across the Sierra Nevada and Southern California were collected from 2001 to 2016, resulting 97 site-years of ET observations in five main vegetation types (Evergreen Needleleaf Forest, Grasslands, Mixed Forest, Open Shrublands, and Woody Savannas). The NDVI was...

Data from: High-severity wildfire leads to multi-decadal impacts on soil biogeochemistry in mixed-conifer forests

Nicholas Dove & Stephen Hart
During the past century, systematic wildfire suppression has decreased fire frequency and increased fire severity in the western United States of America. While this has resulted in large ecological changes aboveground such as altered tree species composition and increased forest density, little is known about the long-term, belowground implications of altered, ecologically novel fire regimes, especially on soil biological processes. To better understand the long-term implications of ecologically novel, high-severity fire, we used a 44-y...

Energy and water co-benefits from covering canals with solar panels

Brandi McKuin, Andrew Zumkehr, Jenny Ta, Roger Bales, Joshua Viers, Tappan Pathak & J. Elliott Campbell
In the manuscript entitled, "Energy and water co-benefits from covering canals with solar panels", we quantified the evaporation savings and financial performance of over-canal solar in comparison to over-ground solar on land adjacent to canals, using regional-scale hydrologic and cost simulations. We conducted regional hydrologic and techno-economic simulations of solar PV panels covering California’s 6350 km canal network. We examined the net effect on the financial performance of three different solar PV structures at eight...

Reannotation of CCA-ends, initiator tRNAs, and other CAU-anticodon tRNAs of prokaryotic genomes in tRNAdb-CE 0.8

David H. Ardell & Ya-Ming Hou
Background: While the CCA sequence at the mature 3′ end of tRNAs is conserved and critical for translational function, a genetic template for this sequence is not always contained in tRNA genes. In eukaryotes and archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by CCA-adding enzymes. In bacteria, tRNA genes template CCA sporadically. Results: In order to understand the variation in how prokaryotic tRNA genes template CCA, we re-annotated tRNA genes in tRNAdb-CE database...

Climate, snow, and soil moisture data set for the Tuolumne and Merced River watersheds, California, USA

James Roche, Robert Rice, Xiande Meng, Daniel Cayan, Mike Dettinger, Douglas Alden, Sarina Patel, Megan Mason, Martha Conklin & Roger Bales
UCM sites. Snow depth, soil moisture and soil temperature are measured near the Merced Grove, Gin Flat, Smoky Jack Creek, and Olmsted Quarry with a distributed array of 6-7 sensor nodes at each location. Snow depth is measured in the open, at the drip edge and under canopies, as well as 3-4 other sites representative of an area of 1-2 hectares. Soil moisture and temperature are measured at 10, 30, 60 and 90 cm depths...

Southern Sierra Critical Zone Observatory (SSCZO), Wolverton Creek meteorological data, soil moisture and temperature

Roger Bales, Erin Stacy, Matt Meadows, Peter Kirchner, Martha Conklin & Xiande Meng
Wolverton basin in Sequoia National Park is instrumented with four instrument clusters (site 1 through site 4) and two meteorological stations (Panther met and Wolverton met). Soil moisture and temperature, snow depth, solar radiation and meteorological data (air temperature, relative humidity, wind speed, wind direction and precipitation) are measured across the network. Snow depth is measured in the open, at the drip edge and under tree canopies. Soil moisture and temperature are measured at 10,...

Juxtaposition of climate change contrarians and scientists in the media using Media Cloud data

Alexander Petersen
We document the media visibility and climate change research achievements of two groups of individuals representing some of the most prominent figures in their respective domains: 386 climate change contrarians (CCC) juxtaposed with 386 expert climate change scientists (CCS). These data were collected from the Media Cloud project (MC), an open data project hosted by the MIT Center for Civic Media and the Berkman Klein Center for Internet & Society at Harvard University. Enclosed are...

Sex, hormone status, and growth rate influence dietary isotope fractionation in laboratory rats

Sora Kim & Jessica Santollo
Stable isotope analysis of rat tissues to determine effects of gonadectomization. Four groups - female, ovarectomized, male, and castrated male - were fed a constant diet for 30 days. Fat, muscle, liver, and kidney were sampled at the experiment's end while serum and blood were sampled at days 0, 1, and 30. We found that sex and removal of gonadal hormones are factors either individually or interactive for carbon and nitrogen stable isotope composition in...

Supporting Files for Schiebelhut LM, Puritz JB & Dawson MN (2018) \"Decimation by sea star wasting disease and rapid genetic change in a keystone species, Pisaster ochraceus\" PNAS

Lauren Schiebelhut
The data files associated with Schiebelhut LM, Puritz JB & Dawson MN (2018) "Decimation by sea star wasting disease and rapid genetic change in a keystone species, Pisaster ochraceus" are deposited here, including: the commented bioinformatics code, raw SNP calls, filtered SNPs, and final haplotype calls.

A mathematical model of flow-mediated coagulation identifies factor V as a modifier of thrombin generation in hemophilia A

Michael Stobb, Kathryn Link, Matthew Sorrells, Maria Bortot, Katherine Ruegg, Marilyn Manco-Johnson, Jorge DiPaola, Suzanne Sindi, Aaron Fogelson, Karin Leiderman & Keith Neeves
Hemophilia A is a bleeding disorder categorized as severe, mild, and moderate deficiencies in factor VIII (FVIII). Within these categories the variance in bleeding severity is significant and the origins unknown. The number of parameters that could modify bleeding are so numerous that experimental approaches are not feasible for considering all possible combinations. Consequently, we turn to a mathematical model of coagulation under flow to act as a screening tool to identify parameters that are...

PLOS ONE publication and citation data

Alexander Petersen
Merged PLOS ONE and Web of Science data compiled in .dta files produced by STATA13. Included is a Do-file for reproducing the regression model estimates reported in the pre-print (Tables I and II) and published version (Table 1). Each observation (.dta line) corresponds to a given PLOS ONE article, with various article-level and editor-level characteristics used as explanatory and control variables. This summary provides a brief description of each variable and its source. If you...

Linguistic laws in speech: the case of Catalan and Spanish

Ivan González Torre, Antoni Hernández-Fernández, Juan-María Garrido & Lucas Lacasa
In this work we explore in an oral corpus of Catalan and Spanish (Glissando Corpus) four classical linguistic laws (Zipf's law, Herdan's law, Brevity law, and Menzerath-Altmann's law) in oral communication, both in physical units and in symbolic units measured in speech transcriptions, and we also reviewed two more laws recently reformulated: lognormality law and size-rank law. Our results reinforce with empirical evidence in two more languages the 'physical hypothesis' according to which linguistic laws...

Saturated Hydraulic Conductivity Pedotransfer Models

Samuel N. Araya & Teamrat A. Ghezzehei
This repository contains machine learning-based pedotransfer models that predict saturated hydraulic conductivity (Ks). An app with a graphical user interface to run these models and other relevant materials including R codes used to build and test the models are available at the author's GitHub repository: https://github.com/saraya209/soil_ksat. Detailed description of this work is available in our paper published in the Journal of Water Resources Research: Araya and Ghezzehei (2019).

Continental-scale patterns of extracellular enzyme activity in the subsoil: an overlooked reservoir of microbial activity

Nicholas Dove
Chemical stabilization of microbial-derived products such as extracellular enzymes (EE) onto mineral surfaces has gained attention as a possibly important mechanism leading to the persistence of soil organic carbon (SOC). While the controls on EE activities and their stabilization in the surface soil are reasonably well-understood, how these activities change with soil depth and possibly diverge from those at the soil surface due to distinct physical, chemical, and biotic conditions remains unclear. We assessed EE...

Single cell RNA sequencing (scRNAseq) of transplanted mT3 tumors

Ivana Peran
Background & Aims: Pancreatic ductal adenocarcinomas (PDAC) are characterized by fibrosis and an abundance of cancer-associated fibroblasts (CAFs). We investigated strategies to disrupt interactions among CAFs, the immune system, and cancer cells, focusing on adhesion molecule cadherin 11 (CDH11), which has been associated with other fibrotic disorders and is expressed by activated fibroblasts. Methods: We compared levels of CDH11mRNA in human pancreatitis and pancreatic cancer tissues and cells, compared with normal pancreas, and measured levels...

Data from: Rethinking sustainability in seafood: synergies and trade-offs between fisheries and climate change

Brandi McKuin, Jordan Watson, Stephen Stohs & J. Elliott Campbell
In the manuscript entitled, "Rethinking sustainability in seafood: synergies and trade-offs between fisheries and climate change", we quantified the climate forcing per unit fish protein associated with several different U.S. tuna fishing fleets, among the most important capture fisheries by both volume and value. The fishing fleets include the U.S. purse seine that operates in the Western Central Pacific Fisheries Commission convention area, the U.S. North Pacific albacore surface gear (which includes both troll and...

Thermal camera data

Haoyu Niu & Tiebiao Zhao
TIR flight 4 2:17pm pome 30m 1011 flight 5 2:44pm peach 30m 1887 flight 6 3:24pm peach 60m 2990 flight 7 4:15pm onion 15m 4093

Registration Year

  • 2022
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Resource Types

  • Dataset


  • University of California, Merced
  • University of California, Santa Cruz
  • University of California, Davis
  • University of California, Berkeley
  • University of California, Irvine
  • Colorado School of Mines
  • Georgetown University
  • University of Colorado Boulder
  • University of Arizona
  • University of Vienna