19 Works

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...

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...

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...

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...

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...

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...

Multi-scale drivers of soil resistance predict vulnerability of seasonally wet meadows to trampling by pack stock animals in the Sierra Nevada, USA

Joy S. Baccei, Mitchel P. McClaran, Tim J. Kuhn & Stephen C. Hart
Background Meadow ecosystems have important ecological functions and support socioeconomic services, yet are subject to multiple stressors that can lead to rapid degradation. In the Sierra Nevada of the western USA, recreational pack stock (horses and mules) use in seasonally wet mountain meadows may lead to soil trampling and meadow degradation, especially when soil water content is high and vegetation is developing. Methods In order to improve the ability to predict meadow vulnerability to soil...

Data from: Measuring attitude towards chemistry, biology, and math at a Hispanic-serving institution

Erik Menke & Jordan Chang
This work describes the evaluation of the Attitude toward the Subject of Chemistry Inventory (ASCI), as well as two modifications (one for attitude toward math and one for attitude toward biology), for college students at a Hispanic Serving Institution. Confirmatory factor analysis supported a two-factor structure, similar to an existing model of a revised version of the ASCI, for all three instruments. These instruments show little change in student attitude with respect to biology, chemistry,...

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...

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...

Data and code for: Microalgae-blend tilapia feed eliminates fishmeal and fish oil, improves growth, and is cost viable

Pallab Sarker, Anne Kapuscinski, Brandi McKuin, Devin Fitzgerald, Hannah Nash & Connor Greenwood
Aquafeed manufacturers have reduced, but not fully eliminated, fishmeal and fish oil and are seeking cost competitive replacements. We combined two commercially available microalgae, to produce a high-performing fish-free feed for Nile tilapia (Oreochromis niloticus) —the world’s second largest group of farmed fish. We substituted protein-rich defatted biomass of Nannochloropsis oculata (leftover after oil extraction for nutraceuticals) for fishmeal and whole cells of docosahexaenoic acid (DHA)-rich Schizochytrium sp. as substitute for fish oil. Here, we...

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...

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...

Soil microbial communities associated with giant sequoia: How does the world's largest tree affect some of the world's smallest organisms?

Stephen Hart, Chelsea J. Carey, Sydney I. Glassman, Thomas D. Bruns & Emma L. Aronson
Giant sequoia (Sequoiadendron giganteum) is an iconic conifer that lives in relic populations on the western slopes of the California Sierra Nevada. In these settings, it is unusual among the dominant trees in that it associates with arbuscular mycorrhizal fungi rather than ectomycorrhizal fungi. However, it is unclear whether differences in microbial associations extends more broadly to non-mycorrhizal components of the soil microbial community. To address this question, we characterized microbiomes associated with giant sequoia...

Snow depth, air temperature, humidity, soil moisture and temperature, and solar radiation data from the basin-scale wireless-sensor network in American River Hydrologic Observatory (ARHO)

Roger Bales, Guotao Cui, Robert Rice, Xiande Meng, Ziran Zhang, Peter Hartsough, Steven Glaser & Martha Conklin
Snow depth, air temperature, humidity, soil moisture and temperature, and solar radiation are measured by a basin-scale wireless-sensor network in the American River Hydrologic Observatory (ARHO). The wireless-sensor network is deployed across the upper, snow-covered areas of the American River basin from 1510 to 2723 m elevation on the western slope of the Sierra Nevada in California. The network comprises 13 sensor clusters (Schneiders, Echo Peak, MT Lincoln, Caples Lake, Alpha, Duncan Peak, Van Vleck,...

Iterative evolution of large-bodied hypercarnivory in canids benefits species but not clades

Mairin Balisi & Blaire Van Valkenburgh
Ecological specialization has costs and benefits at various scales: traits benefitting an individual may disadvantage its population, species or clade. In particular, large body size and hypercarnivory (diet over 70% meat) have evolved repeatedly in mammals; yet large hypercarnivores are thought to be trapped in a macroevolutionary “ratchet”, marching unilaterally toward decline. Here, we weigh the impact of this specialization on extinction risk using the rich fossil record of North American canids (dogs). In two...

Data from: Single-cell transcriptomic analysis of tumor-derived fibroblasts and normal tissue-resident fibroblasts reveals fibroblast heterogeneity in breast cancer

Nicholas Hum, Aimy Sebastian, Kelly Martin, Sean Gilmore, Stephen Byers, Elizabeth Wheeler, Matthew Coleman & Gabriela Loots
Cancer-associated fibroblasts (CAFs) are a prominent stromal cell type in solid tumors and molecules secreted by CAFs play an important role in tumor progression and metastasis. CAFs coexist as heterogeneous populations with potentially different biological functions. Although CAFs are a major component of the breast cancer stroma, molecular and phenotypic heterogeneity of CAFs in breast cancer is poorly understood. In this study, we investigated CAF heterogeneity in triple-negative breast cancer (TNBC) using a syngeneic mouse...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of California, Merced
  • University of California, Berkeley
  • Georgetown University
  • University of Arizona
  • University of California, Irvine
  • University of California, Davis
  • Rice University
  • Tencent (China)
  • University of Greifswald
  • Department of Plant Biology