Index Catalog // ScholarsArchive@OSU

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

Creator:: Mi, Gu, Di, Yanming, Emerson, Sarah, Cumbie, Jason S., and Chang, Jeff H.
Abstract:: When assessing differential gene expression from RNA sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. This phenomenon, called "length bias", will influence subsequent analyses such as Gene Ontology enrichment analysis. In the presence of length bias, Gene Ontology...
Resource Type:: Article
Full Text:: Enrichment Analysis Using Logistic Regression Gu Mi1*, Yanming Di1,2, Sarah Emerson1, Jason S. Cumbie2,3

Lymphocytic Choriomeningitis Virus Infection in FVB Mouse Produces Hemorrhagic Disease

Creator:: Schnell, Frederick J., Sundholm, Sarah, Crumley, Stacy, Iversen, Patrick L., and Mourich, Dan V.
Abstract:: The viral family Arenaviridae includes a number of viruses that can cause hemorrhagic fever in humans. Arenavirus infection often involves multiple organs and can lead to capillary instability, impaired hemostasis, and death. Preclinical testing for development of antiviral or therapeutics is in part hampered due to a lack of an...
Resource Type:: Article
Full Text:: in FVB Mouse Produces Hemorrhagic Disease Frederick J. Schnell1, Sarah Sundholm1, Stacy Crumley1

High-Throughput Sequencing of Arabidopsis microRNAs : Evidence for Frequent Birth and Death of MIRNA Genes

Creator:: Fahlgren, Noah, Howell, Miya D., Kasschau, Kristin D., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., Law, Theresa F., Grant, Sarah R., Dangl, Jeffrey L., and Carrington, James C.
Abstract:: In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep...
Resource Type:: Article
Full Text:: . Kasschau1, Elisabeth J. Chapman1,2, Christopher M. Sullivan1, Jason S. Cumbie1, Scott A. Givan1, Theresa F

The plant phenology monitoring design for The National Ecological Observatory Network

Creator:: Elmendorf, Sarah C., Jones, Katherine D., Cook, Benjamin I., Diez, Jeffrey M., Enquist, Carolyn A. F., Hufft, Rebecca A., Jones, Matthew O., Mazer, Susan J., Miller-Rushing, Abraham J., Moore, David J. P., Schwartz, Mark D., and Weltzin, Jake F.
Abstract:: Phenology is an integrative science that comprises the study of recurring biological activities or events. In an era of rapidly changing climate, the relationship between the timing of those events and environmental cues such as temperature, snowmelt, water availability, or day length are of particular interest. This article provides an...
Resource Type:: Article
Full Text:: phenology monitoring design for The National Ecological Observatory Network Sarah C. Elmendorf,1,2

A Multi-Year Longitudinal Study of Water Quality Parameters in Four Salmon-Bearing and Recreational Streams on Mount Hood, Oregon

Creator:: Wasowski, Ronald, Alexander, David, Kolmes, Steven, Banet, Nathan, Card, Amy, Haines, Morgan, Kolmes, Elijah, Northcutt, Kelly, Roemer, Derek, and Webber, Sarah
Abstract:: Four streams-Clear Fork, Lost Creek, Camp Creek and Still Creek-in northwestern Oregon's Sandy River Basin were monitored for temperature, dissolved oxygen levels, and fecal bacterial concentrations in a multi-year analysis examining stream health for recreational users and anchor habitat for Pacific Salmon. Temperatures were recorded using micro -T temperature loggers...
Resource Type:: Article
Full Text:: , Kelly Northcutt1,6, Derek Roemer1,7, Sarah Webber1,8 1 Environmental Science Department, University of

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Creator:: Kasschau, Kristin D., Fahlgren, Noah, Chapman, Elisabeth J., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., and Carrington, James C.
Abstract:: Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants...
Resource Type:: Article
Full Text:: siRNAs Kristin D. Kasschau 1,2 , Noah Fahlgren 1,2,3 , Elisabeth J. Chapman 1,2,3 , Christopher M

Regional variation in stand structure and development in forests of Oregon, Washington, and inland Northern California

Creator:: Reilly, Matthew J. and Spies, Thomas A.
Abstract:: Despite its importance to biodiversity and ecosystem function, patterns and drivers of regional scale variation in forest structure and development are poorly understood. We characterize structural variation, create a hierarchical classification of forest structure, and develop an empirically based framework for conceptualizing structural development from 11,091 plots across 25 million...
Resource Type:: Article
Full Text:: development in forests of Oregon, Washington, and inland Northern California Reilly, M. J., & Spies, T. A

Post-fire tree establishment and early cohort development in conifer forests of the western Cascades of Oregon, USA

Creator:: Tepley, Alan J., Swanson, Frederick J., and Spies, Thomas A.
Abstract:: Early‐seral ecosystems make important contributions to regional biodiversity by supporting high abundance and diversity of many plant and animal species that are otherwise rare or absent from closed‐canopy forests. Therefore, the period of post‐fire tree establishment is a key stage in forest stand and ecosystem development that can be viewed...
Resource Type:: Article
Full Text:: Cascade Range. Elevation ranges from 316 to 1,753 m and most major ridges are higher than 1,200 m. The

Feeding Healthy Beagles Medium-Chain Triglycerides, Fish Oil, and Carnitine Offsets Age-Related Changes in Serum Fatty Acids and Carnitine Metabolites

Creator:: Hall, Jean A. and Jewell, Dennis E.
Abstract:: The purpose of this study was to determine if feeding dogs medium-chain triglycerides (MCT), fish oil, and L-carnitine enriched foods offsets age-associated changes in serum fatty acids (FA) and carnitine metabolites. Forty-one healthy Beagles, mean age 9.9 years (range 3.1 to 14.8), were fed control or one of two treatment...
Resource Type:: Article
Full Text:: PLOS ONE | www.plosone.org 5 November 2012 | Volume 7 | Issue 11 | e49510 T a b le 3 . Se ru m

Predation on an Upper Trophic Marine Predator, the Steller Sea Lion: Evaluating High Juvenile Mortality in a Density Dependent Conceptual Framework

Creator:: Horning, Markus and Mellish, Jo-Ann E.
Abstract:: The endangered western stock of the Steller sea lion (Eumetopias jubatus) - the largest of the eared seals - has declined by 80% from population levels encountered four decades ago. Current overall trends from the Gulf of Alaska to the Aleutian Islands appear neutral with strong regional heterogeneities. A published...
Resource Type:: Article
Full Text:: differential impact of predation on multiple vital rates. Citation: Horning M, Mellish J-AE (2012) Predation

ScholarsArchive@OSU

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

Lymphocytic Choriomeningitis Virus Infection in FVB Mouse Produces Hemorrhagic Disease

High-Throughput Sequencing of Arabidopsis microRNAs : Evidence for Frequent Birth and Death of MIRNA Genes

The plant phenology monitoring design for The National Ecological Observatory Network

A Multi-Year Longitudinal Study of Water Quality Parameters in Four Salmon-Bearing and Recreational Streams on Mount Hood, Oregon

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Regional variation in stand structure and development in forests of Oregon, Washington, and inland Northern California

Post-fire tree establishment and early cohort development in conifer forests of the western Cascades of Oregon, USA

Feeding Healthy Beagles Medium-Chain Triglycerides, Fish Oil, and Carnitine Offsets Age-Related Changes in Serum Fatty Acids and Carnitine Metabolites

Predation on an Upper Trophic Marine Predator, the Steller Sea Lion: Evaluating High Juvenile Mortality in a Density Dependent Conceptual Framework

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