Data from the 1995 National Health Interview Survey (NHIS) indicate that, due to chronic conditions, the onset of activity limitation typically occurs between age 40-70 years (i.e., the proportion of young adults with activity limitation is small and roughly constant with age and then it starts to change, roughly increasing). We use a Bayesian hierarchical model to detect the change point of a positive activity limitation status (ALS) across twelve domains based on race, gender, and education. We have two types of data: weighted and unweighted. We obtain weighted binomial counts using a regression analysis with the sample weights. Given the proportion of individuals in the population with positive ALS, we assume that the number of individuals with positive ALS at each age group has a binomial probability mass function. The proportions across age are different, and have the same beta distribution up to the change point (unknown), and the proportions after the change point have a different beta distribution. We consider two different analyses. The first considers each domain individually in its own model and the second considers the twelve domains simultaneously in a single model to“borrow strength" as in small area estimation. It is reasonable to assume that each domain has its own onset.In the first analysis, we use the Gibbs sampler to fit the model, and a computation of the marginal likelihoods, using an output analysis from the Gibbs sampler, provides the posterior distribution of the change point. We note that a reversible jump sampler fails in this analysis because it tends to get stuck either age 40 or age 70. In the second analysis, we use the Gibbs sampler to fit only the joint posterior distribution of the twelve change points. This is a difficult problem because the joint density requires the numerical computation of a triple integral at each iteration. The other parameters of the process are obtained using data augmentation by a Metropolis sampler and a Rao-Blackwellization. We found that overall the age of onset is about 50 to 60 years.

Modifying photopolymer structure on the molecular and nanoscale level permits tailoring materials for use in a wide variety of applications. Understanding the fundamentals behind polymer structure at these levels permits the control of material properties. This work gains insight into the modification of structure on two levels, the nanoscale by use of structure templates and the molecular scale through the modification of polymer network formation. Lyotropic liquid crystals (LLCs) are a type of self-assembling surfactant system, which in combination with photopolymerization can be used to template ordered nanostructure within polymer materials. This structure can be controlled and utilized to influence the properties of a polymer material. This research examines materials used as templating agents and the types of nanostructures that may be obtained. Additionally, their effects upon the LLC templating process and material properties is determined. Structured polymers are created using LLC templates in pursuit of materials for use in water purification processes and electrochemical devices. Through a more complete understanding of the fundamentals of the templating process, the work presented here extends the LLC templating technique to a greater variety of materials and applications in the water remediation and energy storage fields. The second portion of this research is the use of reversible addition fragmentation chain transfer (RAFT) to modify photopolymer networks. RAFT agents are utilized to control the propagation reaction to create networks with increased homogeneity between network crosslinks. By increasing the uniformity of the polymer network, increases in polymer elongation and toughness as well as decreases in polymer modulus are observed. The effects of RAFT agent addition on the network formation and the final properties of the photopolymer is examined. By understanding the mechanisms behind this modification technique, photopolymers can be extended into new applications where increased elongation and toughness is valued.

At this time the synthesis of reversible circuits for quantum computing is an active area of research. In the most restrictive quantum computing models there are no ancilla lines and the quantum cost, or latency, of performing a reversible form of the AND gate, or Toffoli gate, increases exponentially with the number of input variables. In contrast, the quantum cost of performing any combination of reversible EXOR gates, or CNOT gates, on n input variables requires at most O(n2/log2n) gates. It was under these conditions that EXOR-AND-EXOR, or EPOE, synthesis was developed. In this work, the GF(2) logic theory used in EPOE is expanded and the concept of an EXOR-AND product transform is introduced. Because of the generality of this logic theory, it is adapted to EXOR-AND-OR, or SPOE, synthesis. Three heuristic spectral logic synthesis algorithms are introduced, implemented in a program called XAX, and compared with previous work in classical logic circuits of up to 26 inputs. Three linear reversible circuit methods are also introduced and compared with previous work in linear reversible logic circuits of up to 100 inputs.

In 2010 Medicaid financed approximately 48% of all births in the United States and nearly 30% of all births in Virginia. Due to strict state-specific eligibility criteria, many low-income women qualify for Medicaid coverage exclusively as a result of pregnancy status. As the nation moves forward with the Patient Protection and Affordable Care Act (PPACA), state-elected Medicaid expansion has the potential to expand services to women of reproductive age that would precede pregnancy events and offer continuous access to care postpartum. Despite this potential influx of newly insured women, little is known about how this population may make decisions regarding reproductive healthcare services and if these selections influence process and outcome measures. This study examines two research aims that provide insight into these knowledge gaps. First, utility theory and discrete choice modeling is used to examine clinic and patient level factors associated with clinic type choice. Specifically, this study examines the role of high risk pregnancy status and travel distance to clinic as associated with clinic selection. Second, Donabedian’s Structure, Process, Outcome framework provides a conceptual lens to examine if clinic selection is associated with maternal and infant measures. The linear probability model and logistic regression models are employed to examine two process measures, including prenatal care inadequacy and postpartum visit nonattendance, and three outcome measures including maternal long acting reversible contraceptive method (LARC) use and infant birthweight and gestational age. Results examining clinic type selection reveal significant associations between independent and dependent variables. Women experiencing a high risk pregnancy are significantly more likely to select a hospital based clinic for care, compared to women experiencing a normal risk pregnancy. However, when specifically examining women experiencing their first pregnancy, this association is no longer significant. Additionally, as distance to clinic type increase, women are significantly less likely to select that clinic type for prenatal care. Clinic selection was found to be significantly associated with maternal measures, but not significantly associated with infant outcomes. Selecting a public health department or Federally Qualified Health Center for prenatal care services was associated with a significant decrease in inadequate prenatal care, postpartum visit nonattendance, and non-LARC use compared to a private physician office. Clinic type selection, however, was not found to be significantly associated with infant outcomes including preterm birth and low birthweight babies. Results from Research Aim 1 have a variety of implications for clinic and public policy and offer guidance for future research. Clinics that seek to provide care to pregnant Medicaid beneficiaries should examine local residential patterns of current and potential future pregnant Medicaid recipients and consider how these might affect decisions about future clinic locations. Results suggest that women are more likely to attend clinic types closer to their area of residence, and this close proximity may have additional implications beyond shorter travel time to clinic including the minimization of transportation and childcare issues. Results from Research Aim 2 analyses offer a variety of public policy implications and guidance for future research. This research provides evidence that public health facilities including public health departments and FQHCs have improved prenatal care adequacy and postpartum visit attendance compared to private physician offices, providing evidence that public funding should continue for these facility types. As the United States moves forward with PPACA, healthcare organization administration should turn to the public facilities in their communities to learn how to manage and improve the health of these patient populations and ultimately aim to improve access and quality care among the nation’s most vulnerable populations.

The present work is dealing with the first synthesis and characterisation of amphiphilic diblock copolymers bearing b-dicarbonyl (acetoacetoxy) chelating residues. Polymers were obtained by Group Transfer Polymerisation (GTP)/acetoacetylation and controlled radical polymerisation techniques (RAFT).<br><br>Different micellar morphologies of poly(n-butyl methacrylate)-block-poly[2-(acetoacetoxy)ethyl methacrylate] (pBuMA-b-pAEMA) were observed in cyclohexane as a selective solvent. Depending on the block length ratio, either spherical, elliptical, or cylindrical micelles were formed. The density of the polymer chains at the core/corona interface is considerably higher as compared to any other strongly segregating system reported in the literature. It is demonstrated that there are H-bond interactions existing between acetoacetoxy groups, which increase the incompatibility between block segments. In addition, such interactions lead to the formation of secondary structures (such as b-sheets or globular structures) and larger superstructures in the micrometer length scale.<br><br>Block copolymers were also used to solubilise metal ion salts of different geometries and oxidation states in organic media, in which are otherwise insoluble. Sterically stabilised colloidal hybrid materials are formed, i.e. monodisperse micelles having the metal ion salt incorporated in their core upon complexation with the ligating pAEMA block, whereas pBuMA forms the solvating corona responsible for stabilisation in solution. Systematic studies show that the aggregation behaviour is dependent on different factors, such as the tautomeric form of the beta-dicarbonyl ligand (keto/enol) as well as the nature and amount of added metal ion salt.

<p>Evolutionary dynamics can be notoriously complex and difficult to analyze. In this dissertation I describe a population genetic regime where the dynamics are simple enough to allow a relatively complete and elegant treatment. Consider a haploid, asexual population, where each possible genotype has been assigned a fitness. When mutations enter a population sufficiently rarely, we can model the evolution of this population as a Markov chain where the population jumps from one genotype to another at the birth of each new mutant destined for fixation. Furthermore, if the mutation rates are assigned in such a manner that the Markov chain is reversible when all genotypes are assigned the same fitness, then it is still reversible when genotypes are assigned differing fitnesses. </p><p>The key insight is that this Markov chain can be analyzed using the spectral theory of finite-state, reversible Markov chains. I describe the spectral decomposition of the transition matrix and use it to build a general framework with which I address a variety of both classical and novel topics. These topics include a method for creating low-dimensional visualizations of fitness landscapes; a measure of how easy it is for the evolutionary process to `find' a specific genotype or phenotype; the index of dispersion of the molecular clock and its generalizations; a definition for the neighborhood of a genotype based on evolutionary dynamics; and the expected fitness and number of substitutions that have occurred given that a population has been evolving on the fitness landscape for a given period of time. I apply these various analyses to both a simple one-codon fitness landscape and to a large neutral network derived from computational RNA secondary structure predictions.</p> / Dissertation

Green chemistry principles have been applied to the enhancement of two industrial chemistry problems. An industrially used reaction to form alcohols from aldehydes and ketones, the Meerwein-Ponndorf-Verley reduction, was improved by introducing a new catalyst Al(OtBu)₃. Due to the lower state of aggregation of this catalyst versus the conventional Al(OiPr)₃ catalyst, reduction rates were found to be faster in both pure iPrOH and mixed solvent systems for three model compounds: benzaldehyde, acetophenone, and a complex, chiral ketone, (S)-CMK. This allowed for the successful implementation of two important milestones; lowering the amount of catalyst needed necessary to complete the reactions (an economic benefit and lower waste) and the conversion from traditional batch reactions to continuous flow (a processing benefit) whereby reactions can be scaled-out rather than scaled-up. Another industrially important field of research that was focused on was CO₂ capture. High energy demands from current CO₂ capture methods such as aqueous amine solvents, specifically from coal-fired power plant flue gas, led to the development of non-aqueous reversible ionic liquids based on silylated amines. Structural modifications of the substitution around the silicon atom, the length of the alkyl chain bonding the silicon and amine, branching along the alkyl backbone, and investigating secondary and primary amines within this class of silylated amines were completed. These amines were reacted with CO₂ and the CO₂ capacity, the ionic liquid viscosity, reversal temperature and reaction enthalpy were all considered as a function of structure. In all cases the capacity was found to be not only greater than that of monethanolamine, an industrial standard, but higher than theoretical predictions through the formation of carbamic acid. Viscosity, reversal temperature, and reaction enthalpy were all found to be tunable through structure. These modifications gave significant insight into the necessary direction for optimization of these solvents as energy-efficient replacements of current CO₂ capture technology.

<p>Dynamic Combinatorial Chemistry (DCC) is a recently introduced supramolecular approach to generate dynamically interchanging libraries of compounds. These libraries are made of different building blocks that reversibly interact with one another and spontaneously assemble to encompass all possible combinations. If a target molecule, for instance a receptor is added to the system and one or more molecules show affinity to the target species, these compounds will, according to Le Châtelier´s principle, be amplified on the expense of the other non-bonding constituents. To date, only a handful of different systems and formats have been used. Hence, to further advance the technique, especially when biological systems are targeted, new reaction types and new screening methods are necessary. This thesis describes the development of reversible sulfur reactions, thiol/disulfide interchange and transthiolesterification (the latter being a new reaction type for DCC), as means of generating reversible covalent bond reactions. Two different types of target proteins are used, enzymes belonging to the hydrolase family and the plant lectin Concanavalin A. Furthermore, two new screening/analysis methods not previously used in DCC are also presented; the quartz crystal microbalance (QCM)-technique and catalytic self-screening.</p>

This dissertation is divided into three major sections (one on dendrimers, one on tripodal metal ligands and one on a research oriented chemistry curricula) with a primary focus on different types of multicomponent assemblies. In the first chapter, a system is described that used a multicomponent assembly of AT-PAMAM dendrimers and an indicator, carboxyfluorescein, to detect and identify various polyanions at a low micromolar concentration. The system was able to successfully differentiate twelve anions, many of biological interest, including three tricarboxylates. The tricarboxylates were differentiated based primarily on the regiochemistry of the anionic groups. In the second chapter, further studies with AT-PAMAM dendrimers were carried out to provide some understanding of the thermodynamic origins of binding. Utilizing isothermal titration calorimetry, the binding of the dendrimers to large polyanionic dendrons with increasing numbers of charges was studied. Through these studies, the thermodynamic values of the binding events were obtained allowing us to explore the properties of the dendrimers. The cooperativity of the system was measured, and primarily negative cooperativity determined by the entropic contributions was uncovered. As the dendrimers increased in size, the thermodynamic origins of binding were determined to a greater extent by the entropy of binding. In the third chapter, a novel dynamic ligand system for metal binding is described. In the presence of a metal salt, a heterocyclic aldehyde and a secondary amine with two heterocyclic arms reversibly condense to form a hemiaminal with a tripodal metal binding site. This chapter describes studies on the metal binding ability, the variety of metals that will lead to this formation, the effects of anions and the range of aldehydes that can be used are described. Furthermore, the system’s reversibility was explored. Finally, the use of a bistriazole secondary amine was explored. The modular nature of triazole formation could lead to the introduction of additional functionalities. The fourth chapter discusses how the novel ligand system could be used to study the enantiomeric excess (ee) of chiral thiols. Based upon the system’s ability to form a stable hemiaminal thioether, a CD signal could be generated that is proportional to the amount of a particular enantiomer in solution. Using this system, a calibration curve relating CD signal and ee can be generated giving the ee of an unknown solution. In the final chapter, a look at the Freshman Research Initiative will be carried out with a focus on the ability to teach basic skills in an introductory laboratory through research. Four different skills or techniques will be explored through three different FRI streams,x and how they teach the four skills. Finally, analysis of the success of the program, particularly students’ success in the next laboratory course in the sequence, is discussed, and a model for adopting this type of teaching at other universities is given. / text

This thesis investigates the design, synthesis and biological assay of cysteine protease inhibitors within the papain superfamily of cysteine proteases. This is achieved by examining the effect of inhibitor design, especially warheads, on IC₅₀ values and structureactivity relationships between cysteine protease inhibitors of the papain superfamily. The representative proteases used are m-calpain, μ-calpain, cathepsin B and papain. Chapter One is an introductory chapter; Chapters Two-Four describe the design and synthesis of cysteine protease inhibitors; Chapter Five discusses assay protocol; and Chapter Six contains the assay results and structure-activity relationships of the synthesised inhibitors. Chapter One introduces cysteine proteases of the papain family and examines the structure, physiology and role in disease of papain, cathepsin B, m-calpain and μ-calpain. The close structural homology that exists between these members of the papain superfamily is identified, as well characteristics unique to each protease. Covalent reversible, covalent irreversible and non-covalent warheads are defined. The generic inhibitor scaffold of address region, recognition and warhead, upon which the inhibitors synthesised in this thesis are based, is also introduced. Chapter Two introduces reversible cysteine protease inhibitors found in the literature and that little is known about the effect of inhibitor warhead on selectivity within the papain superfamily. Oxidation of the dipeptidyl alcohols 2.6, 2.26, 2.29, 2.30, 2.35 and 2.36 utilising the sulfur trioxide-pyridine complex gave the aldehydes 2.3, 2.27, 2.19, 2.2, 2.21 and 2.22. Semicarbazones 2.37-2.40 were synthesised by a condensation reaction between the alcohol 2.3 and four available semicarbazides. The amidoximes 2.48 and 2.49 separately underwent thermal intramolecular cyclodehydration to give the 3-methyl-1,2,4- oxadiazoles 2.41 and 2.50. The aldehydes 2.3 and 2.27 were reacted with potassium cyanide to give the cyanohydrins 2.51 and 2.52. The cyanohydrins 2.51 and 2.52 were separately reacted to give 1) the α-ketotetrazoles 2.43 and 2.55; 2) the α-ketooxazolines 2.42 and 2.58; 3) the esterified cyanohydrins 2.60 and 2.61. A two step SN2 displacement reaction of the alcohol 2.6 to give the azide 2.62, an example of a non-covalent cysteine protease inhibitor. Chapter Three introduces inhibitors with irreversible warheads. The well-known examples of epoxysuccinic acids 3.1 and 3.5 are discussed in detail, highlighting the lack of irreversible cysteine protease specific inhibitors. The aldehydes 2.3 and 2.27 were reacted under Wittig conditions to give the α,β-unsaturated carbonyls 3.14-3.18. Horner- Emmons-Wadsworth methodology was utilised for the synthesis of the vinyl sulfones 3.20- 3.23. The dipeptidyl acids 2.24 and 2.28 were separately reacted with diazomethane to give the diazoketones 3.25 and 3.26. The diazoketones 3.25 and 3.26 were separately reacted with hydrogen bromide in acetic acid (33%) to give the α-bromomethyl ketones 3.27 and 3.28, which were subsequently reduced to give the α-bromomethyl alcohols 3.29-3.32. Under basic conditions the α-bromomethyl alcohols 3.29-3.32 ring-closed to form the peptidyl epoxides 3.33-3.36. Chapter Four introduces the disadvantages of peptide-based inhibitors. A discussion is given on the benefits of constraining inhibitors into the extended bioactive conformation known as a β-strand. Ring closing metathesis is utilised in the synthesis of the macrocyclic aldehyde 4.4, macrocyclic semicarbazone 4.15, the macrocyclic cyanohydrin 4.16, the macrocyclic α-ketotetrazole 4.18 and the macrocyclic azide 4.19. Chapter Five introduces enzyme inhibition studies. The BODIPY-casein fluorogenic assay used for establishing inhibitor potency against m-calpain and μ-calpain is validated. Assay protocols are also established and validated for cathepsin B, papain, pepsin and α- chymotrypsin. A discussion of the effect of solvent on enzyme activity is also included as part of this study. Chapter Six presents the assay results for all the inhibitors synthesised throughout this thesis and an extensive structure-activity relationship study between inhibitors is included. The alcohols 2.26 and 2.30 are unprecedented examples of non-covalent, potent, cathepsin B inhibitors (IC₅₀ = 0.075 μM selectivity 80-fold and 1.1 μM, selectivity 18-fold). The macrocyclic semicarbazone 4.15 is an unprecedented example of a potent macrocyclic cysteine protease inhibitor (m-calpain: IC₅₀ = 0.16 μM, selectivity 8-fold). The cyanohydrin 2.51 contains an unprecedented cysteine protease warhead and is a potent and selective inhibitor of papain (IC₅₀ = 0.030 μM, selectivity 3-fold). The O-protected cyanohydrin 2.61 is a potent and selective inhibitor of pepsin (IC₅₀ = 1.6 μM, selectivity 1.5-fold). The top ten warheads for potent, selective cathepsin B inhibition are: carboxylic acid, methyl ester, diazoketone, esterified cyanohydrin, α-bromomethyl ketone, α,β- unsaturated aldehyde, vinyl sulfones, α-bromomethyl-C₃-S,R-alcohol, alcohol and α,β- unsaturated ethyl ester. The selectivity of these warheads was between 5- and 130-fold for cathepsin B. The best inhibitors for cathepsin B were the α-bromomethyl ketone 3.26 (IC₅₀ = 0.075 μM, selectivity 16-fold), the α,β-unsaturated aldehyde 3.18 (IC₅₀ = 0.13 μM, selectivity 13-fold) and the esterified cyanohydrin 3.59 (IC₅₀ = 0.35 μM, selectivity 22- fold). Chapter Seven outlines the experimental details and synthesis of the compounds prepared in this thesis.