Index Catalog // ScholarsArchive@OSU

Characterization of Neurospora crassa “Fatty Acid Regulator” transcription factors, FAR-1 and FAR-2, by ChIP- and RNA-sequencing

Creator:: Bredeweg, Erin L. and Freitag, Michael
Abstract:: Transcription factor (TF) genes were modified endogenously to include epitope tags for identification of TF protein binding sites by Chromatin Immunoprecipitation (ChIP), followed by high throughput sequencing. We used RNA-sequencing in carbon sources of sucrose, butyrate, and oleate in far-1, far-2, and a double far-1; far-2 mutant to find transcripts...
Resource Type:: Dataset

Host and Habitat Index for Phytophthora Species in Oregon: Supplemental Spreadsheet

Creator:: Hansen, Everett, Reeser, Paul, Sutton, Wendy, and Sims, Laura
Resource Type:: Dataset
Full Text:: cryptogea 33-2-S.2 Forest soil Lane 2010 Sims (in prep) europaea close to europaea VI 1-2P Forest stream

ICESat-2 Bathymetry Training and Testing Database

Creator:: Ohlwiler, Ellery E., Ghartey, Charles E., McCullough, Ruth M., Parrish, Christopher E., Magruder, Lori A., Dietrich, James T., Holwill, Matthew, and Markel, Jonathan
Abstract:: NASA’s ICESat-2 satellite, which launched in 2018, carries the Advanced Topographic Laser Altimeter System (ATLAS), a green-wavelength, photon-counting lidar. While ICESat-2’s primary mission focuses on measurement of elevation of ice sheets, glaciers, sea ice, and vegetation, ATLAS has also proven remarkably effective at measurement of bathymetry, or water depths. However,...
Resource Type:: Dataset

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition

Creator:: Koslicki, David, Chatterjee, Saikat, Shahrivar, Damon, Walker, Alan W., Francis, Suzanna C., Fraser, Louise J., Vehkaperä, Mikko, Lan, Yueheng, and Corander, Jukka
Abstract:: Motivation: Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of...
Resource Type:: Article
Full Text:: test set and sub- sets can be written as pðxÞ ¼ PQq¼1 Pq pðxjx 2 RqÞ; pðxjx 2 RqÞ ¼ PM m¼1 pðCmjx 2

Usage, Costs, and Benefits of Continuous Integration in Open-Source Projects

Creator:: Hilton, Michael, Tunnell, Timothy, Huang, Kai, Marinov, Darko, and Dig, Danny
Abstract:: Continuous integration (CI) systems automate the compilation, building, and testing of software. Despite CI rising as a big success story in automated software engineering, it has received almost no attention from the research community. For example, how widely is CI used in practice, and what are some costs and benefits...
Resource Type:: Technical Report
Full Text:: focus more research on CI. 1. INTRODUCTION Continuous Integration (CI) is emerging as one of the

Direct numerical simulation results for turbulent hydrogen/air flame: mixture-averaged diffusion model

Creator:: Fillo, Aaron J., Schlup, Jason, Beardsell, Guillaume, Blanquart, Guillaume, and Niemeyer, Kyle E.
Abstract:: This data contains results from direct numerical simulations of three-dimensional, premixed, hydrogen/air flames, using the mixture-averaged diffusion model. We performed the simulations using the finite-difference code NGA; simulation details are described completely in the associated article.
Resource Type:: Dataset

Blended sea level anomaly fields with enhanced coastal coverage along the U.S. West Coast. Version 3

Creator:: Risien, Craig M. and Strub, P. Ted
Abstract:: We form a new data set of fields of sea level anomalies by combining gridded daily fields derived from altimeter data with coastal tide gauge data. Within approximately 50-80 km of the coast, the altimeter data are discarded and replaced by a linear interpolation between the tide gauge and remaining...
Resource Type:: Dataset

A low-cost acoustic permeameter

Creator:: Drake, Stephen A., Selker, John S., and Higgins, Chad W.
Abstract:: This dataset was used to determine the attenuation of an audio signal by reticulated foam samples that span the natural range of intrinsic permeability for seasonal snow. Data are audio measurements acquired on a two-channel oscilloscope.
Resource Type:: Dataset

Re-coding of the Dataset for Status of the European Green Crab, Carcinus maenas, in Oregon and Washington coastal Estuaries in 2019 and 2020

Creator:: Sims, Kimberly, Behrens Yamada, Sylvia, Schooler, Shon, Heller, Renee, Donaldson, Luke, Takacs, Graham T., Randall, Andrea, and Buffington, Chelsey
Abstract:: European green crab, Carcinus maenas, trapped and collected in coastal Oregon and Washington coastal estuaries during the 2019. Data for individual crabs include: estuary, site, date of collection, sex, carapace width, weight, molt stage (color of abdomen), missing limbs, estimated year class, method of collection, and name of collector. This...
Resource Type:: Dataset

Supplemental data to "Casting a broader net: Using microfluidic metagenomics to capture aquatic biodiversity data from diverse taxonomic targets"

Creator:: Hauck, Laura L., Weitemier, Kevin A., Penaluna, Brooke E., Garcia, Tiffany, and Cronn, Richard
Abstract:: This dataset contains the taxonomic classifications of environmental DNA (eDNA) sequences obtained from Fall Creek, Oregon, via microfluidic multiplex PCR (Fluidigm Access Array) and high-throughput sequencing. It is accompanied by electrofishing counts taken at the same time as the eDNA samples. Metadata and R scripts are provided to analyze the...
Resource Type:: Dataset

ScholarsArchive@OSU

Characterization of Neurospora crassa “Fatty Acid Regulator” transcription factors, FAR-1 and FAR-2, by ChIP- and RNA-sequencing

Host and Habitat Index for Phytophthora Species in Oregon: Supplemental Spreadsheet

ICESat-2 Bathymetry Training and Testing Database

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition

Usage, Costs, and Benefits of Continuous Integration in Open-Source Projects

Direct numerical simulation results for turbulent hydrogen/air flame: mixture-averaged diffusion model

Blended sea level anomaly fields with enhanced coastal coverage along the U.S. West Coast. Version 3

A low-cost acoustic permeameter

Re-coding of the Dataset for Status of the European Green Crab, Carcinus maenas, in Oregon and Washington coastal Estuaries in 2019 and 2020

Supplemental data to "Casting a broader net: Using microfluidic metagenomics to capture aquatic biodiversity data from diverse taxonomic targets"

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