Modifying Faug\`ere's F5 Algorithm to ensure termination

The structure of the F5 algorithm to compute Gr\"obner bases makes it very efficient. However, while it is believed to terminate for so-called regular sequences, it is not clear whether it terminates for all inputs. This paper has two major parts. In the first part, we describe in detail the difficulties related to a proof of termination. In the second part, we explore three variants that ensure termination. Two of these have appeared previously only in dissertations, and ensure termination by checking for a Gr\"obner basis using traditional criteria. The third variant, F5+, identifies a degree bound using a distinction between "necessary" and "redundant" critical pairs that follows from the analysis in the first part. Experimental evidence suggests this third approach is the most efficient of the three.Comment: 19 pages, 1 tabl

Economic Base in Emerging Economies: Estimating Regional Multipliers in Ecuador

When a subnational input-output matrix is unavailable, a non-governmental organization (NGO) may turn to a shortcut method in order to project its indirect economic impact in a region. The location quotient is the most common choice in developed nations, but has serious theoretical flaws in a developing-nation context. We explore the minimum requirements method as a cost-effective yet robust method to project the impact of an NGO in the Imbabura province of Ecuador. We find that every $1 of exogenous local spending stimulates between$1.32 and $1.62 of indirect economic impact in the region

THERMAL DEGRADATION OF FIREFIGHTER TURNOUT GEAR DUE TO THE EFFECTS OF MOISTURE

This research examines the effect of moisture on firefighting turnout gear. As moisture from perspiration penetrates a firefighters clothing and eventually migrates into his turnout gear, the thermal properties of the fabric are altered, resulting in thermal degradation. A numerical simulation was developed using a one dimensional heat conduction equation solved using Crank Nicholson finite difference methodology. Moisture was prescribed to penetrate the inner layers of the turnout gear and tracked using a regain measurement. Experimental tests were then performed under conditions with and without moisture with a radiant panel suspended over a guarded sweatplate to validate the results from the numerical simulation. The numerical simulation developed will be used in combination with future testing to design more effective firefighter turnout gear

Muscle Inflammatory Signaling Regulates Eccentric Contraction-Induced Protein Synthesis during Cancer Cachexia

Cancer-related cachexia is a complex metabolic syndrome that involves the unintentional loss of skeletal muscle mass that cannot be reversed by standard nutritional intervention. Skeletal muscle mass depletion directly impacts patient survival and life quality, and therefore treatments that preserve muscle mass and function may have significant implications for cancer patient treatment and survival. Systemic and muscle inflammation has been implicated in the regulation of skeletal muscle homeostasis, and the cytokine interleukin-6 (IL-6) and muscle gp130 receptor signaling have established roles in cancer-induced muscle wasting. Resistance exercise is a nonpharmacological treatment that can improve physical function and metabolic health in many disease conditions, and has proven beneficial outcomes during cancer patient treatment and survival. Unfortunately, no studies to date have examined the effects of exercise in the cachectic cancer patient, and significant gaps remain in our understanding of the interaction between exercise and the systemic cachectic environment during cancer. Therefore, the purpose of this dissertation was to determine how cancer-induced inflammation affects wasting muscles ability to respond to eccentric contractions (ECC). We hypothesized that chronic muscle inflammatory signaling would attenuate the anabolic response to acute ECC. In experiment 1, we determined if muscle inflammatory signaling regulated the cachectic muscle’s acute anabolic response to ECC. We found that muscle inflammatory signaling regulated basal and ECC-induced protein synthesis. In experiment 2, we determined if systemic IL-6 and muscle gp130 signaling regulated basal and ECC- induced protein synthesis and mTORC1 signaling. We found that systemic IL-6 signaling regulated basal and ECC-induced protein synthesis. In addition, muscle gp130 could regulate ECC-induced protein synthesis. In experiment 3, we determined if altering muscle inflammatory signaling by training improved basal and ECC-induced protein synthesis and mTORC1 signaling. We found that training could improve basal and ECC-induced protein synthesis. These findings provide initial evidence that cachectic muscle is responsive to acute responses and training adaptations induced by exercise. Additionally, we provide evidence for a potential interaction between muscle inflammation, protein synthesis, and oxidative metabolism, which can be influenced by exercise during cancer cachexia

Understanding the Interactions of Developing Thymocytes and Antigen Presenting Cells in the Thymic Medulla

Various thymic APC subsets have been invoked in deletional tolerance and Treg cell induction, but previous studies either assessed total T cell numbers or used TCR transgenic lines, obscuring roles that individual thymic APC subsets might serve for particular antigen-specific T cell populations. Utilizing T cell receptor sequencing, we found that medullary thymic epithelial cells (mTECs) and bone marrow-derived (BM) APCs delete or select unique conventional and Treg cell TCR repertoires, demonstrating distinct roles for these APCs. We show that BM APCs and mTECs each contribute to Aire-dependent T cell tolerance development, albeit through either cooperative or autologous antigen presentation respectively, and that cooperative antigen transfer is likely performed by thymic CD8+ DCs. Using our established TCR sequencing approach, In addition, we sought to understand CD8+ DC-mediated cooperative antigen presentation further. We quantified the extent of CD8+ DC-dependent Treg cell and negative selection and the proportion of this selection that is achieved through Aire-dependent cooperative antigen transfer. We also found that CD36 expression by CD8+ DCs facilitates Aire-dependent cooperative antigen transfer both in vivo and via TCR sequencing. Finally, we found that in the absence of thymic CD8+ DCs or CD36 expression; direct allo-tolerance fails to develop leading to catastrophic acute GVHD

A high-throughput screening method for determining the substrate scope of nitrilases

Nitrile compounds are intermediates in the synthesis of pharmaceuticals such as atorvastatin. We have developed a chromogenic reagent to screen for nitrilase activity as an alternative to Nessler's reagent. It produces a semi-quantifiable blue colour and hydrolysis of 38 nitrile substrates by 23 nitrilases as cell-free extracts has been shown

Academic Self-Efficacy Among Urban Health Care Students

Consistent with social-cognitive career theory, previous research has found empirical support for the role of social cognitive factors, such as stress and academic self-efficacy, in determining academic performance (Zajacova, Lynch, & Espenshade, 2005). The current study examined vocational identity status (Vocational Identity Status Assessment, VISA; Porfeli, Lee, Vondracek, & Weigold, 2011) and college stress (College Stress Inventory; Solberg, O’Brien, Villareal, Kennel, & Davis, 1993) as predictors of college self-efficacy, defined as a student’s confidence in his/her ability to complete a college-related task (Solberg, Hale, Villareal, & Kavanagh, 1993). We explored the notion of whether more adaptive dimensions of vocational identity would be related to higher levels of college self-efficacy, as measured by the College Self-Efficacy Inventory (Solberg et al., 1993), among pre-medical college students enrolled in an urban primary care track program

Academic Self-Efficacy Among Urban Health Care Students

Consistent with social-cognitive career theory, previous research has found empirical support for the role of social cognitive factors, such as stress and academic self-efficacy, in determining academic performance (Zajacova, Lynch, & Espenshade, 2005). The current study examined vocational identity status (Vocational Identity Status Assessment, VISA; Porfeli, Lee, Vondracek, & Weigold, 2011) and college stress (College Stress Inventory; Solberg, O’Brien, Villareal, Kennel, & Davis, 1993) as predictors of college self-efficacy, defined as a student’s confidence in his/her ability to complete a college-related task (Solberg, Hale, Villareal, & Kavanagh, 1993). We explored the notion of whether more adaptive dimensions of vocational identity would be related to higher levels of college self-efficacy, as measured by the College Self-Efficacy Inventory (Solberg et al., 1993), among pre-medical college students enrolled in an urban primary care track program

Dyslipidemia and Its Role in the Pathogenesis of Atherosclerotic Cardiovascular Disease: Implications for Evaluation and Targets for Treatment of Dyslipidemia Based on Recent Guidelines

The clinical presentations of atherosclerotic disease are the result of a constellation of diverse metabolic and immunologic mechanisms ultimately set into motion by the formation of fatty acid streaks and the accompanying inflammatory cell activation, endothelial damage, smooth muscle proliferation, vascular fibrosis, and end-organ infarction and necrosis. At the heart of atherosclerosis are the byproducts of lipid metabolism, lipoproteins containing triglycerides, phospholipids, and cholesterol, and the changes they undergo that eventually lead to macrophage activation, foam cell formation, and other downstream atherosclerotic changes. Understanding the functionality of cholesterol, triglycerides, and lipoproteins in the cascade of atherosclerotic pathways has tremendous implications on current guidelines for the evaluation and targets in the management of dyslipidemia, and serves as the foundation for future investigations into targets of atherosclerotic therapies

Assessing the monophyly of red algae and green plants via conserved core informational genes

For well over a century the existence of a monophyletic relationship between red algae and green plants has been debated. Many scholars have sought to address this issue, however, a consistent solution to the problem has not been found. Addressing a monophyletic relationship of red algae and green plants is important for understanding early eukaryotic evolution. Elucidating this relationship will allow for a more in depth evaluation of the origin and spread of photosynthesis in eukaryotes, and will further develop an understanding of the evolution of primary producers, which are of paramount importance in supporting the earth's ecosystems. The goal of this project is to apply a method that provides an accurate and consistent way to classify more ancient phylogenetic relationships. Although a great deal of work has been done in the past on this question, the need for a more consistent method that is minimally affected by phylogenetic artifacts has never been greater. This is because of the rapid increase in the amount of available sequence data, as well as the number of new taxa that are being sequenced. By providing a more accurate methodology for investigating broad scale relationships we hope to ameliorate some of the issues seen previously in evaluations of deep phylogenetic relationships. The first goal of this project was to develop a set of core conserved genes related to information processing in cells that span the broad range of eukaryotic life to circumvent known issues from previous studies where selection of markers was problematic. These genes perform highly conserved functions in the cell and, therefore, are less likely to be negatively influenced by problems that create phylogenetic discontinuities. For example, all living organisms must transcribe and translate their genes into proteins. As such, the transcriptional and transitional machinery required to accomplish this task is highly conserved across all forms of life. Although they are responsible for functioning of the central dogma of molecular biology, this research shows that universal conservation of many of these genes across the broad range of eukaryotic life is uncertain. Thorough analyses of 47 conserved genes indicated that the most reliable markers for ancient phylogenetic inferences are core subunits of DNA-dependent RNA polymerases. Genes encoding the two largest subunits of each of three eukaryotic RNA polymerases were recovered from a list of organisms that span eukaryotic diversity via BLAST searches of two major bioinformatics databases National Center for Biotechnology Information (NCBI) and the Department of Energy's Joint Genomics Institute (JGI). The sequences were aligned using multiple sequence alignment software packages, edited by hand, and then used as input into phylogenetic analysis programs. The resulting alignments recovered a polyphyletic relationship among red algae and green plants. Statistical analyses were applied to each tree, allowing for a clear determination that polyphyly was strongly supported by these data. The further hope is that this project will provide a method that is useful, not only for addressing red/green monophyletic issues, but also for future problematic phylogenies.M.S