25 Works

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...

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...

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...

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

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...

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,...

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.

RGB Camera Walnut Site 60 meters

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

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...

European high-skilled mobility data and Scientific publication & collaboration data

Alexander Petersen
Raw data files corresponding to longitudinal country-level observations for two types of variable: (i) publication, citation, and international collaboration data from SCImago Journal & Country Rank (www.scimagojr.com/) and (ii) high-skilled mobility data, corresponding to headcounts by source and destination country, from the “Professionals moving abroad (Establishment)” data hosted by the European Union's "The EU Single Market Regulated professionals database".

Thermal camera in walnut site 60 meters

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

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.

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...

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...

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.

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...

PLOS ONE publication and citation data

Alexander Petersen
Merged PLOS ONE publication metadata and Web of Science citation data, compiled in .dta files produced by STATA13. Included is a Do-file for reproducing the regression model estimates reported in Tables I and II reported in ("Megajournal Mismanagement", Petersen, 2018). 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 data...

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...

SWIR Camera in Walnut site 120 meters

Haoyu Niu, Tiebiao Zhao & YangQuan Chen
SWIR 120 meters

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...

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...

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....

Strategic Communication to Achieve Carbon Neutrality within the University of California

Jon Christensen, Roger Bales, Alex Heeren, Heather Hodges, Lisa Leombruni & Stacy Rebich-Hespanha

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...

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