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This paper aims to contribute to the evolving literature on the new landscape of scholarly journals. It builds on a series of experiences as a journal editor which span the print and digital eras, and focuses on two current activities with new journals. One was designed as a synoptic journal

This paper aims to contribute to the evolving literature on the new landscape of scholarly journals. It builds on a series of experiences as a journal editor which span the print and digital eras, and focuses on two current activities with new journals. One was designed as a synoptic journal in a broad multidisciplinary field, supported by a commercial publisher; the other a non-revenue journal which aims to showcase the work of undergraduates in the author’s institution. Despite the uniqueness of goals and delivery, some of the experiences—and challenges—have proved remarkably similar.

Created2015-09-25
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Restoration projects can have varying goals, depending on the specific focus, rationale, and aims for restoration. When restoration projects use project-specific goals to define activities and gauge success without considering broader ecological context, determination of project implications and success can be confounding. We used case studies from the Middle Rio

Restoration projects can have varying goals, depending on the specific focus, rationale, and aims for restoration. When restoration projects use project-specific goals to define activities and gauge success without considering broader ecological context, determination of project implications and success can be confounding. We used case studies from the Middle Rio Grande (MRG), southwest USA, to demonstrate how restoration outcomes can rank inconsistently when narrowly-based goals are used. Resource managers have chosen MRG for restoration due to impacts to the natural flood regime, reduced native tree recruitment, and establishment of non-native plants. We show restoration “success” ranks differently based upon three goals: increasing biodiversity, increasing specific ecosystem functions, or restoring native communities. We monitored 12 restored and control sites for seven years. Treatments ranked higher in reducing exotic woody populations, and increasing proportions of native plants and groundwater salvage, but generally worse at removing fuels, and increasing species and habitat structural diversity. Managers cannot rely on the term “restoration” to sufficiently describe a project’s aim. Specific desired outcomes must be defined and monitored. Long-term planning should include flexibility to incorporate provisions for adaptive management to refine treatments to avoid unintended ecological consequences.

Created2012-09-19
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Breast cancer is the leading cause of cancer-related deaths of women in the united states. Traditionally, Breast cancer is predominantly treated by a combination of surgery, chemotherapy, and radiation therapy. However, due to the significant negative side effects associated with these traditional treatments, there has been substantial efforts to develo

Breast cancer is the leading cause of cancer-related deaths of women in the united states. Traditionally, Breast cancer is predominantly treated by a combination of surgery, chemotherapy, and radiation therapy. However, due to the significant negative side effects associated with these traditional treatments, there has been substantial efforts to develop alternative therapies to treat cancer. One such alternative therapy is a peptide-based therapeutic cancer vaccine. Therapeutic cancer vaccines enhance an individual's immune response to a specific tumor. They are capable of doing this through artificial activation of tumor specific CTLs (Cytotoxic T Lymphocytes). However, in order to artificially activate tumor specific CTLs, a patient must be treated with immunogenic epitopes derived from their specific cancer type. We have identified that the tumor associated antigen, TPD52, is an ideal target for a therapeutic cancer vaccine. This designation was due to the overexpression of TPD52 in a variety of different cancer types. In order to start the development of a therapeutic cancer vaccine for TPD52-related cancers, we have devised a two-step strategy. First, we plan to create a list of potential TPD52 epitopes by using epitope binding and processing prediction tools. Second, we plan to attempt to experimentally identify MHC class I TPD52 epitopes in vitro. We identified 942 potential 9 and 10 amino acid epitopes for the HLAs A1, A2, A3, A11, A24, B07, B27, B35, B44. These epitopes were predicted by using a combination of 3 binding prediction tools and 2 processing prediction tools. From these 942 potential epitopes, we selected the top 50 epitopes ranked by a combination of binding and processing scores. Due to the promiscuity of some predicted epitopes for multiple HLAs, we ordered 38 synthetic epitopes from the list of the top 50 epitope. We also performed a frequency analysis of the TPD52 protein sequence and identified 3 high volume regions of high epitope production. After the epitope predictions were completed, we proceeded to attempt to experimentally detected presented TPD52 epitopes. First, we successful transduced parental K562 cells with TPD52. After transduction, we started the optimization process for the immunoprecipitation protocol. The optimization of the immunoprecipitation protocol proved to be more difficult than originally believed and was the main reason that we were unable to progress past the transduction of the parental cells. However, we believe that we have identified the issues and will be able to complete the experiment in the coming months.
ContributorsWilson, Eric Andrew (Author) / Anderson, Karen (Thesis director) / Borges, Chad (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
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Visual perceptual learning (VPL) is defined as visual performance improvement after visual experiences. VPL is often highly specific for a visual feature presented during training. Such specificity is observed in behavioral tuning function changes with the highest improvement centered on the trained feature and was originally thought to be evidence

Visual perceptual learning (VPL) is defined as visual performance improvement after visual experiences. VPL is often highly specific for a visual feature presented during training. Such specificity is observed in behavioral tuning function changes with the highest improvement centered on the trained feature and was originally thought to be evidence for changes in the early visual system associated with VPL. However, results of neurophysiological studies have been highly controversial concerning whether the plasticity underlying VPL occurs within the visual cortex. The controversy may be partially due to the lack of observation of neural tuning function changes in multiple visual areas in association with VPL. Here using human subjects we systematically compared behavioral tuning function changes after global motion detection training with decoded tuning function changes for 8 visual areas using pattern classification analysis on functional magnetic resonance imaging (fMRI) signals. We found that the behavioral tuning function changes were extremely highly correlated to decoded tuning function changes only in V3A, which is known to be highly responsive to global motion with human subjects. We conclude that VPL of a global motion detection task involves plasticity in a specific visual cortical area.

ContributorsShibata, Kazuhisa (Author) / Chang, Li-Hung (Author) / Kim, Dongho (Author) / Nanez, Jose (Author) / Kamitani, Yukiyasu (Author) / Watanabe, Takeo (Author) / Sasaki, Yuka (Author) / New College of Interdisciplinary Arts and Sciences (Contributor)
Created2012-08-28
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The purpose of my honors thesis project was to generate the tools needed for in vivo imaging by determining the optimal plasmid-fluorophore combination. To determine the optimal plasmid and fluorophore, asd plasmids were constructed with various promoters, origins of replications, and red fluorophores. The optimal asd plasmid for fluorescent in

The purpose of my honors thesis project was to generate the tools needed for in vivo imaging by determining the optimal plasmid-fluorophore combination. To determine the optimal plasmid and fluorophore, asd plasmids were constructed with various promoters, origins of replications, and red fluorophores. The optimal asd plasmid for fluorescent in vivo imaging was determined by the plasmid stability, growth rate, and growth phase dependence on fluorescent intensity. The end goal is to be able to use the asd plasmid in vaccine strains for the purpose of in vivo imaging of the recombinant attenuated Salmonella vaccine (RASV).
ContributorsEudy, L. Adam (Author) / Curtiss, Roy (Thesis director) / Roland, Kenneth (Committee member) / Forbes, Stephen (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2012-12