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:: , Jeff H. Chang2,3,4 1 Department of Statistics, Oregon State University, Corvallis, Oregon, United

Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum

Creator:: Kimbrel, Jeffrey A., Thomas, William J., Jiang, Yuan, Creason, Allison L., Thireault, Caitlin A., Sachs, Joel L., and Chang, Jeff H.
Abstract:: Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. In one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. In the opposing...
Resource Type:: Article
Full Text:: Plant Biol 4: 336–342. 12. Dale C, Plague GR, Wang B, Ochman H, Moran NA (2002) Type III secretion

The Plant Actin Cytoskeleton Responds to Signals from Microbe-Associated Molecular Patterns

Creator:: Henty-Ridilla, Jessica L., Shimono, Masaki, Li, Jiejie, Chang, Jeff H., Day, Brad, and Staiger, Christopher J.
Abstract:: Plants are constantly exposed to a large and diverse array of microbes; however, most plants are immune to the majority of potential invaders and susceptible to only a small subset of pathogens. The cytoskeleton comprises a dynamic intracellular framework that responds rapidly to biotic stresses and supports numerous fundamental cellular...
Resource Type:: Article
Full Text:: , Jeff H. Chang3, Brad Day2*, Christopher J. Staiger1,4* 1 Department of Biological Sciences, Purdue

Survival and growth patterns of white spruce (Picea glauca [Moench] Voss) rangewide provenances and their implications for climate change adaptation

Creator:: Lu, Pengxin, Parker, William H., Cherry, Marilyn, Colombo, Steve, Parker, William C., Man, Rongzhou, and Roubal, Ngaire
Abstract:: Intraspecific assisted migration (ISAM) through seed transfer during artificial forest regeneration has been suggested as an adaptation strategy to enhance forest resilience and productivity under future climate. In this study, we assessed the risks and benefits of ISAM in white spruce based on long-term and multilocation, rangewide provenance test data....
Resource Type:: Article
Full Text:: implications for climate change adaptation Lu, P., Parker, W. H., Cherry, M., Colombo, S., Parker, W. C., Man

The VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx): goals, platforms, and field operations

Creator:: Wood, R., Mechoso, C. R., Bretherton, C. S., Weller, R. A., Huebert, B., Straneo, F., Albrecht, B. A., Coe, H., Allen, G., Vaughan, G., Daum, P., Fairall, C., Chand, D., Klenner, L. Gallardo, Garreaud, R., Grados, C., Covert, D. S., Bates, T. S., Krejci, R., Russell, L. M., de Szoeke, Simon P., Brewer, A., Yuter, S. E., Springston, S. R., Chaigneau, A., Toniazzo, T., Minnis, P., Palikonda, R., Abel, S. J., Brown, W. O. J., Williams, S., Fochesatto, J., Brioude, J., and Bower, K. N.
Abstract:: The VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx) was an international field program designed to make observations of poorly understood but critical components of the coupled climate system of the southeast Pacific. This region is characterized by strong coastal upwelling, the coolest SSTs in the tropical belt, and is home to...
Resource Type:: Article
Full Text:: . Straneo3, B. A. Albrecht5, H. Coe6, G. Allen6, G. Vaughan6, P. Daum7, C. Fairall8, D. Chand1,*, L. Gallardo

Isotopic constraints on the pre-industrial oceanic nitrogen budget

Creator:: Somes, C. J., Oschlies, A., and Schmittner, A.
Abstract:: The size of the bioavailable (i.e., “fixed”) nitrogen inventory in the ocean influences global marine productivity and the biological carbon pump. Despite its importance, the pre-industrial rates for the major source and sink terms of the oceanic fixed nitrogen budget, N₂ fixation and denitrification, respectively, are not well known. These...
Resource Type:: Article
Full Text:: nitrogen budget C. J. Somes1, A. Oschlies1, and A. Schmittner2 1GEOMAR Helmholtz-Zentrum f̈ur

Differential surface activation of the A1 domain of von Willebrand factor

Creator:: Tronic, Elaine H., Yakovenko, Olga, Weidner, Tobias, Baio, Joe E., Penkala, Rebecca, Castner, David G., and Thomas, Wendy E.
Abstract:: The clotting protein von Willebrand factor (VWF) binds to platelet receptor glycoprotein Ibα (GPIbα) when VWF is activated by chemicals, high shear stress, or immobilization onto surfaces. Activation of VWF by surface immobilization is an important problem in the failure of cardiovascular implants, but is poorly understood. Here, the authors...
Resource Type:: Article
Full Text:: -bottom (MatTek) 96-well plates were incubated with 10 lg/ml A1 domain for 2 h at 37 �C, and blocked with

3,3'-Diindolylmethane Induces G₁ Arrest and Apoptosis in Human Acute T-Cell Lymphoblastic Leukemia Cells

Creator:: Shorey, Lyndsey E., Hagman, Amanda M., Williams, David E., Ho, Emily, Dashwood, Roderick H., and Benninghoff, Abby D.
Abstract:: Certain bioactive food components, including indole-3-carbinol (I3C) and 3,3'-diindolylmethane (DIM) from cruciferous vegetables, have been shown to target cellular pathways regulating carcinogenesis. Previously, our laboratory showed that dietary I3C is an effective transplacental chemopreventive agent in a dibenzo[def,p]chrysene (DBC)-dependent model of murine T-cell lymphoblastic lymphoma. The primary objective of the...
Resource Type:: Article
Full Text:: E. Williams1,2, Emily Ho2,4, Roderick H. Dashwood1,2, Abby D. Benninghoff3,5,6* 1 Department of

Circadian Regulation of Glutathione Levels and Biosynthesis in Drosophila melanogaster

Creator:: Beaver, Laura M., Klichko, Vladimir I., Chow, Eileen S., Kotwica-Rolinska, Joanna, Williamson, Marisa, Orr, William C., Radyuk, Svetlana N., and Giebultowicz, Jadwiga M.
Abstract:: Circadian clocks generate daily rhythms in neuronal, physiological, and metabolic functions. Previous studies in mammals reported daily fluctuations in levels of the major endogenous antioxidant, glutathione (GSH), but the molecular mechanisms that govern such fluctuations remained unknown. To address this question, we used the model species Drosophila, which has a...
Resource Type:: Article
Full Text:: melanogaster. Proc Natl Acad Sci U S A 99: 9562– 9567. 24. Claridge-Chang A, Wijnen H, Naef F, Boothroyd C

Initiation of Genome Instability and Preneoplastic Processes through Loss of Fhit Expression

Creator:: Saldivar, Joshua C., Miuma, Satoshi, Bene, Jessica, Hosseini, Seyed Ali, Shibata, Hidetaka, Sun, Jin, Wheeler, Linda J., Mathews, Christopher K., and Huebner, Kay
Abstract:: Genomic instability drives tumorigenesis, but how it is initiated in sporadic neoplasias is unknown. In early preneoplasias, alterations at chromosome fragile sites arise due to DNA replication stress. A frequent, perhaps earliest, genetic alteration in preneoplasias is deletion within the fragile FRA3B/FHIT locus, leading to loss of Fhit protein expression....
Resource Type:: Article
Full Text:: Preneoplastic Processes through Loss of Fhit Expression Joshua C. Saldivar1,2, Satoshi Miuma2, Jessica Bene2

ScholarsArchive@OSU

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum

The Plant Actin Cytoskeleton Responds to Signals from Microbe-Associated Molecular Patterns

Survival and growth patterns of white spruce (Picea glauca [Moench] Voss) rangewide provenances and their implications for climate change adaptation

The VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx): goals, platforms, and field operations

Isotopic constraints on the pre-industrial oceanic nitrogen budget

Differential surface activation of the A1 domain of von Willebrand factor

3,3'-Diindolylmethane Induces G₁ Arrest and Apoptosis in Human Acute T-Cell Lymphoblastic Leukemia Cells

Circadian Regulation of Glutathione Levels and Biosynthesis in Drosophila melanogaster

Initiation of Genome Instability and Preneoplastic Processes through Loss of Fhit Expression

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