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  • Dairy Cattle Nutrition and its Effect on Production, Milk, and Human Health

    Creator:
    Swanson, Katherine L.
    Abstract:
    As the world population continues to grow we must look for smarter and more sustainable ways to feed everyone. Milk is the first food humans consume and is a good source of protein, fat, and carbohydrates. The following studies sought to determine the effect of feeding blackberry pomace as a...
    Resource Type:
    Dissertation
    Full Text:
    AN ABSTRACT OF THE DISSERTATION OF Katherine

  • Gene expression analysis in feline injection-site sarcoma : differential expression of the ΔNp63 and TAp63 isoforms

    Creator:
    Dien, Thalia
    Abstract:
    Background Feline injection-site sarcoma (FISS) is a rare and aggressive tumor associated with vaccines, drug injections, and skin trauma in cats. The understanding of FISS remains limited, posing challenges in its diagnosis, treatment, and prevention. In this study, we analyzed the differential expression of miRNAs and their target genes in...
    Resource Type:
    Undergraduate Thesis
    Full Text:
    : _____________________________________________________ Stephen Ramsey, Department of Biomedical Sciences/EECS

  • Gene Networks of the Skeletal Muscle Cell

    Creator:
    Singh, Arun J.
    Abstract:
    Skeletal muscle is the largest organ in the body by mass, comprising roughly 40% of total bodyweight in adults. It plays diverse and unique roles that include movement, locomotion, and support for posture and internal organs, among others. The structural foundation for all skeletal muscle in adults is formed early...
    Resource Type:
    Dissertation
    Full Text:
    Development and Disease Chapter 1 Arun J. Singh, Stephen A. Ramsey, Theresa M. Filtz, Chrissa

  • Transformers for representing microbiome data: an empirical evaluation

    Creator:
    Varma, Rohan
    Abstract:
    As the link between human microbiomes and health has become more established, the interest in applying statistical approaches to microbiome data to understand the mechanisms behind these links has grown. However, microbiome data is often of unmanageable size, and consequently, producing quality lower dimensional representations of samples is a significant...
    Resource Type:
    Honors College Thesis
    Full Text:
    , representing Microbiology Stephen Ramsey, Committee Member, representing Electrical Engineering and Computer

  • Integration of Amino Acid Sequence and Alphafold2 Structural Predictions for Chlamydia trachomatis Polymorphic Membrane Proteins

    Creator:
    DeBrine, Abigail
    Abstract:
    Chlamydia trachomatis is an obligate intracellular bacterium that causes diseases of the eye and urogenital tract in humans. It is the cause of the sexual transmitted infection (STI) chlamydia, the most prevalent STI worldwide, and the ocular disease trachoma, the leading cause of infectious blindness. To date there is no...
    Resource Type:
    Honors College Thesis
    Full Text:
    Microbiol 2012, 50 (8), 2601–2608. 26. Suchland, R. J.; Carrell, S. J.; Ramsey, S. A.; Hybiske, K

  • Classification and Analysis of Nucleotide - Nucleotide Interactions in RNA

    Creator:
    Rouches, Mason
    Abstract:
    Base-pairing interaction are the fundamental blocks of an RNA structure. With increased ability to determine the structure of RNA molecules, an accurate and informative way of classifying these interactions would help to study RNA structure at many levels. Apart from the well-known complementary base pairs and wobble pairs, other interactions...
    Resource Type:
    Honors College Thesis
    Full Text:
    _____________________________________________________________________ Stephen Ramsey, Committee Member, representing the Department of Biomedical Sciences and the

  • Position-Dependent Codon Usage Bias in the Human Transcriptome

    Creator:
    Subramanian, Kaavya
    Abstract:
    All life depends on the reliable translation of RNA to protein according to complex interactions between translation machinery and RNA sequence features. While ribosomal occupancy and codon frequencies vary across coding regions, well-established metrics for computing coding potential of RNA do not capture such positional dependence. Here, we investigate position-dependent...
    Resource Type:
    Honors College Thesis
    Full Text:
    _____________________________________________________________________ Stephen Ramsey, Committee Member, representing Electrical Engineering and Computer Science

  • The Dynamics of Random Pulse-Coupled Oscillator Networks

    Creator:
    Kadhim, Kyra L.
    Abstract:
    The pulse-coupled oscillator model is widely used to simulate the dynamics of neural systems. For networks with particular internal (Mirollo-Strogatz) dynamics, I will define three broad patterns of collective behaviors found in literature in terms of inter-spike interval (ISI) statistics. These patterns are i) temporally-regular, characterized by all oscillators in...
    Resource Type:
    Honors College Thesis
    Full Text:
    , representing Janelia Research Campus Stephen Ramsey, Committee Member, representing Oregon State University

  • Visualization and analysis of sensor data for detecting microclimate cold air pools

    Creator:
    Singh, Satpreet Harcharan
    Abstract:
    Cold air pools are spatiotemporal phenomena that occur when cold air from higher elevations roll down the slope to accumulate in lower elevations. Behaviors like this lead to microclimate anomalies such as the city of Corvallis (Oregon) experiencing persistent cold weather even on a sunny day. We analyze multivariate temperature...
    Resource Type:
    Masters Thesis
    Full Text:
    committee: Dr. Raviv Raich, Dr. Stephen Ramsey and Dr. Rebecca Hutchinson (and Dr. Matthew Campbell, GCR

  • Deep Learning for Human and Biological Languages

    Creator:
    Hong, Junki
    Abstract:
    We explore the application of deep learning to the disparate fields of natural language processing and computational biology. Both the sentences uttered by humans as well as the RNA and protein sequences found within the cells of their bodies can be considered formal languages in computer science, as sets of...
    Resource Type:
    Dissertation
    Full Text:
    Alan Fern, Stephen Ramsey, Prasad Tadepalli, and my Graduate Council Representative Professor Jimmy