69 Works

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.

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....

Metabolite, qPCR, and metadata for relationships between Sphaerulina musiva infection and the Populus microbiome and metabolome

Nicholas Dove
Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigate the microbiome and metabolome of P....

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...

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...

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...

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...

Computed tomography reveals hip dysplasia in the extinct Pleistocene saber-tooth cat Smilodon

Mairin Balisi, Abhinav Sharma, Carrie Howard, Christopher Shaw, Robert Klapper & Emily Lindsey
Reconstructing the behavior of extinct species is challenging, particularly for those with no living analogues. However, damage preserved as paleopathologies on bone can record how an animal moved in life, potentially reflecting behavioral patterns. Here, we assess hypothesized etiologies of pathology in a pelvis and associated right femur of a Smilodon fatalis saber-toothed cat, one of the best-studied species from the Pleistocene-age Rancho La Brea asphalt seeps, California, USA, using visualization by computed tomography (CT)....

Supplemental material for Climate forcing by battered-and-breaded fillets and crab-flavored sticks from Alaska pollock

Brandi McKuin, Jordan Watson, Alan Haynie & J. Elliott Campbell
Detailed supplemental datasets: inputs and output information and emission factors for ingredients, non-ingredient materials, and embodied energy of pollock products.

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...

Dataset for: Physics-informed neural networks with monotonicity constraints for Richardson-Richards equation: Estimation of constitutive relationships and soil water flux density from volumetric water content measurements by Toshiyuki Bandai and Teamrat A. Ghezzehei

Toshiyuki Bandai & Teamrat Ghezzehei
Simulation of soil moisture dynamics is important for various fields, such as agriculture, hydrological modeling, and natural disasters. Such simulations are conducted by solving a partial differential equation (PDE) called the Richardson-Richards equation (RRE). Because the RRE is a highly non-linear PDE, we need to solve it numerically. Various numerical methods have been used to solve the RRE, such as the finite difference, finite element, and finite element volume method. In order for those numerical...

Active nematic order and dynamic lane formation of microtubules driven by membrane-bound diffusing motors

Linda Hirst
Dynamic lane formation and long-range active nematic alignment is reported using a geometry in which kinesin motors are directly coupled to a lipid bilayer, allowing for in-plane motor diffusion during microtubule gliding. We use fluorescence microscopy to image protein distributions in and below the dense two-dimensional microtubule layer, revealing evidence of diffusion-enabled kinesin restructuring within the fluid membrane substrate as microtubules collectively glide above. We find that the lipid membrane acts to promote filament-filament alignment...

Shape multistability in flexible tubular crystals through interactions of mobile dislocations: Simulation data

Daniel Beller & Andrei Zakharov
We study avenues to shape multistability and shape-morphing in flexible crystalline membranes of cylindrical topology, enabled by glide mobility of dislocations. Using computational modeling, we obtain states of mechanical equilibrium presenting a wide variety of tubular crystal deformation geometries, due to an interplay of effective defect interactions with out-of-tangent-plane deformations that reorient the tube axis. Importantly, this interplay often stabilizes defect configurations quite distinct from those predicted for a two-dimensional crystal confined to the surface...

Mapping subjectivities on wildlife trafficking: Implications for management and governance

Felber Arroyave & Jeffrey Jenkins
Illegal wildlife trade or wildlife trafficking is a problem that affects societies and ecosystems alike. However, it remains unclear which management strategies are suitable for addressing this issue, particularly when one considers the diversity of actors, interests, and nuances of the problem. We argue that better management strategies require multiple – and at times, even opposite – actors to coalesce around the fundamentals of the problem. An initial step towards formulating management strategies is to...

Bias-corrected VIC historical runoff data (1950-2013) for the Central Sierra Nevada

Gustavo Facincani Dourado, David E. Rheinheimer, Aditya Sood, Anna M. Rallings, Ann Willis, Mahesh L. Maskey, Alan Cai & Joshua H. Viers
This data was 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. For hydrology inputs, the model requires runoff at the sub-basin level. For this study, we used VIC the historical (1950 to 2013) daily gridded (1/16o) runoff data generated by the Variable Infiltration Capacity (VIC) hydrologic model, forced with observed meteorological data from NOAA/OAR/ESRL PSD, Boulder, Colorado, USA....

Large dataset of disambiguated publication profiles for studying researcher mobility

Alexander Petersen
Researcher mobility facilitates the exchange of scientific, institutional, and cultural knowledge. Yet whether globalization and advances in virtual communication technologies have altered the impact of researcher mobility is a relevant and open question. To this end, we developed and leveraged a large and internationally broad disambiguated dataset of researchers in physics over the period 1985-2009; we used the article-level metadata contained in the American Physical Society "Article and Citations dataset" as the starting point. After...

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