Patients with cystic fibrosis (CF) are susceptible to respiratory tract infections at an early age; with the most frequent initial isolate being the Gram-positive pathogen Staphylococcus aureus. Subsequently, these patients become chronically...
The Border Gateway Protocol (BGP) that manages inter-domain routing on the Internet lacks security. Protective measures using public key cryptography introduce complexities and costs. To support authentication and other security functionality in...
Electronic data processing -- Distributed processing. ; Computer network architectures. ; Programming languages (Electronic computers) -- Semantics. ; Database management.
I tackle the problem of naming and sharing resources across administrative boundaries. Conventional systems manifest the hierarchy of typical administrative structure in the structure of their own mechanism. While natural for communication that...
We study the bijective combinatorics of reduced words. These are fundamental objects in the study of Coxeter groups. We restrict our focus to reduced words of permutations and signed permutations. Our results can all be situated within the context...
This thesis contains material relating to two separate subjects. The first section determines when the C*-algebra affiliated to a directed graph has continuous trace. We use groupoid methods and the focus is on producing conditions on a graph that...
Temperature has powerful effects on all scales of biological organization from biochemical reactions to ecosystem processes. Despite the well-appreciated influence and thorough understanding of the physiological and population consequences of...
The Mixed Lineage Leukemia (MLL1) gene was first cloned as a hot spot of chromosomal translocations in acute leukemia. More than 70 fusion proteins of MLL1 have been described in both lymphoid and myeloid leukemia and many are highly associated...
Pseudomonas aeruginosa is a virulent opportunistic pathogen that is frequently cultured from infectious sites, and is estimated to cause ~12% of nosocomial infections worldwide [1]. P. aeruginosa infections occur in a majority of adults with the...
In this thesis, we characterize and enumerate the permutations which are realized by the orbits of signed shifts, a family of discrete dynamical systems on words. The permutations, which are called patterns of the signed shifts, are given by the...
In Chapter 2 we look at the distribution of permutation statistics in the context of pattern-avoiding permutations. The first part of this chapter deals with a recursively defined bijection of Robertson [37] between 123- and 132-avoiding...
Robustness to genetic perturbations is a fundamental property of all living things. The genetic code is degenerate, RNA secondary structure is robust to sequence changes, and protein structure is robust to amino acid substitutions. Complex systems...
Digital integrated circuits -- Testing. Digital integrated circuits -- Testing -- Mathematical models. Digital integrated circuits -- Design and construction.
PDZ domains are protein:protein interaction domains that serve as molecular scaffolds, especially in the case of specialized cellular environments like polarized airway epithelial cells of the human lung. Historically the domains have been thought...
Vibrio cholerae is the etiologic agent of the severe diarrheal disease cholera. Colonization of the host environment by V. cholerae requires the type IV toxin co-regulated pilus (TCP). Adequate colonization by V. cholerae is essential for cholera...
Apoptosis is important for tissue homeostasis and is the mechanism of cell death induced by many anticancer agents. The apoptotic machinery is present in all cells, such that tight regulation must exist to prevent untimely cell and tissue death. To...
During an immune reaction to an invading pathogen, a population of lymphocytes with receptors that specifically recognize the pathogen are activated and become memory cells. Characteristically, memory lymphocytes persist for long periods of time...
In this dissertation, I present an examination of the role of two biotic interactions in the population dynamics of Vibrio cholerae. Traits with a genetic basis such as size, physiological processes, stress tolerance, and even behavior, are key...
This thesis centers around a generalization of the classical discrete Fourier transform. We first present a general diagrammatic approach to the construction of efficient algorithms for computing the Fourier transform of a function on a finite...
Despite immunogenicity, melanoma-specific vaccines have demonstrated minimal clinical efficacy in patients with established disease, but enhance survival when administered in the adjuvant setting. It has been shown that T cell infiltration of...
'Orthogonal modular forms are algebraic modular forms arising from lattices in quadratic spaces. In this thesis, we define orthogonal modular forms, establish their basic properties, and then apply them to a case of ternary quadratic spaces to...
For most cancers, the genetic mechanisms that predispose normal cells to neoplastic transformation and tumor cells to therapeutic eradication are poorly understood. High throughput genotyping technologies have allowed the rapid discovery of...
There are no Vassiliev invariants of degree one for classical knots. A. Henrich proved the existence of a sequence of three Vassiliev invariants of degree one for virtual knots. The invariants get stronger and stronger, and the final invariant is...
This thesis investigates a notion of Turing reducibility introduced by Winkler [8] that is total on all computably enumerable oracles. Groszek and Weber show in [7] that this is a new notion of reducibility and it is not transitive. They give su...
Interleukin-2 (IL-2) is an immunoregulatory cytokine whose biological effects are mediated through interaction with specific receptors (IL-2R) on the surface of target cells. Due to its presumed role in generating a normal immune response, IL-2 is...