Learning Models of Gene Expression from Synthetic DNA Sequences

Thesis (Ph.D.)--University of Washington, 2016-06

Mapping the determinants in owl monkey CD4 and CCR5 that allow entry of early-stage HIV-1 Env variants

Thesis (Master's)--University of Washington, 2016-06

Designing supramolecular structures from models of cyclic peptide scaffolds with heterocyclic constraints

Cyclic peptides containing oxazole and thiazole heterocycles have been examined for their capacity to be used as scaffolds in larger, more complex, protein-like structures. Both the macrocyclic scaffolds and the supramolecular structures derived therefrom have been visualised by molecular modelling techniques. These molecules are too symmetrical to examine structurally by NMR spectroscopy. The cyclic hexapeptide ([Aaa-Thz](3), [Aaa-Oxz](3)) and cyclic octapeptide ([Aaa-Thz](4), [Aaa-Oxz](4)) analogues are composed of dipeptide surrogates (Aaa: amino acid, Thz: thiazole, Oxz: oxazole) derived from intramolecular condensation of cysteine or serine/threonine side chains in dipeptides like Aaa-Cys, Aaa-Ser and Aaa-Thr. The five-membered heterocyclic rings, like thiazole, oxazole and reduced analogues like thiazoline, thiazolidine and oxazoline have profound influences on the structures and bioactivities of cyclic peptides derived therefrom. This work suggests that such constrained cyclic peptides can be used as scaffolds to create a range of novel protein-like supramolecular structures (e.g. cylinders, troughs, cones, multi-loop structures, helix bundles) that are comparable in size, shape and composition to bioactive surfaces of proteins. They may therefore represent interesting starting points for the design of novel artificial proteins and artificial enzymes. (C) 2002 Elsevier Science Inc. All rights reserved.

A convergent solution-phase synthesis of the macrocycle Ac-Phe-[Orn-Pro-D-Cha-Trp-Arg], a potent new antiinflammatory drug

Relatively few cyclic peptides have reached the pharmaceutical marketplace during the past decade, most produced through fermentation rather than made synthetically. Generally, this class of compounds is synthesized for research purposes on milligram scales by solid-phase methods, but if the potential of macrocyclic peptidomimetics is to be realized, low-cost larger scale solution-phase syntheses need to be devised and optimized to provide sufficient quantities for preclinical, clinical, and commercial uses. Here, we describe a cheap, medium-scale, solution-phase synthesis of the first reported highly potent, selective, and orally active antagonist of the human C5a receptor. This compound, Ac-Phe[Orn-Pro-D-Cha-Trp-Arg], known as 3D53, is a macrocyclic peptidomimetic of the human plasma protein C5a and displays excellent antiinflammatory activity in numerous animal models of human disease. In a convergent approach, two tripeptide fragments Ac-Phe-Orn-(Boc)-Pro-OH and H-D-Cha-Trp(For)-Arg-OEt were first prepared by high-yielding solution-phase couplings using a mixed anhydride method before coupling them to give a linear hexapeptide which, after deprotection, was obtained in 38% overall yield from the commercially available amino acids. Cyclization in solution using BOP reagent gave the antagonist in 33% yield (13% overall) after HPLC purification. Significant features of the synthesis were that the Arg side chain was left unprotected throughout, the component Boe-D-Cha-OH was obtained very efficiently via hydrogenation Of D-Phe with PtO2 in TFA/water, the tripeptides were coupled at the Pro-Cha junction to minimize racemization via the oxazolone pathway, and the entire synthesis was carried out without purification of any intermediates. The target cyclic product was purified (>97%) by reversed-phase HPLC. This convergent synthesis with minimal use of protecting groups allowed batches of 50100 g to be prepared efficiently in high yield using standard laboratory equipment. This type of procedure should be useful for making even larger quantities of this and other macrocyclic peptidomimetic drugs.

From a Vicious Circle of Anxiety to a Virtuous Circle of Learning: Experience of Teaching to a Heterogenous Clientele

A considerable body of literature suggests that significant psychological barrier and anxiety characterize the teaching and learning process in statistics. This study investigates the incidence of statistics anxiety, the extent to which it can be overcome and the factors that contribute to the process of overcoming it. Self-study and overall teaching quality, amongst others, significantly contributed to this outcome. This study identifies factors contributing to overall teaching quality. The teaching and learning process typified a highly effective communication mechanism based on an appropriate diagnosis of individual needs. This cumulative change resulted from circular causation. It is argued that given appropriate conditions the vicious circle of anxiety can be transformed into a virtuous circle of learning.

The relationship between the mismatch negativity (MMN) and psycholinguistic models of spoken word processing

Background: The results from previous studies have indicated that a pre-attentive component of the event-related potential (ERP), the mismatch negativity (MMN), may be an objective measure of the automatic auditory processing of phonemes and words. Aims: This article reviews the relationship between the MMN data and psycholinguistic models of spoken word processing, in order to determine whether the MMN may be used to objectively pinpoint spoken word processing deficits in individuals with aphasia. Main Contribution: This article outlines the ways in which the MMN data support psycholinguistic models currently used in the clinical management of aphasic individuals. Furthermore, the cell assembly model of the neurophysiological mechanisms underlying spoken word processing is discussed in relation to the MMN and psycholinguistic models. Conclusions: The MMN data support current theoretical psycholinguistic and neurophysiological models of spoken word processing. Future MMN studies that include normal and aphasic populations will further elucidate the role that the MMN may play in the clinical management of aphasic individuals.

Energy level statistics for models of coupled single-mode Bose-Einstein condensates

We study the distribution of energy level spacings in two models describing coupled single-mode Bose-Einstein condensates. Both models have a fixed number of degrees of freedom, which is small compared to the number of interaction parameters, and is independent of the dimensionality of the Hilbert space. We find that the distribution follows a universal Poisson form independent of the choice of coupling parameters, which is indicative of the integrability of both models. These results complement those for integrable lattice models where the number of degrees of freedom increases with increasing dimensionality of the Hilbert space. Finally, we also show that for one model the inclusion of an additional interaction which breaks the integrability leads to a non-Poisson distribution.

Images of desire: Cognitive models of craving

Cognitive modelling of phenomena in clinical practice allows the operationalisation of otherwise diffuse descriptive terms such as craving or flashbacks. This supports the empirical investigation of the clinical phenomena and the development of targeted treatment interventions. This paper focuses on the cognitive processes underpinning craving, which is recognised as a motivating experience in substance dependence. We use a high-level cognitive architecture, Interacting Cognitive Subsystems (ICS), to compare two theories of craving: Tiffany's theory, centred on the control of automated action schemata, and our own Elaborated Intrusion theory of craving. Data from a questionnaire study of the subjective aspects of everyday desires experienced by a large non-clinical population are presented. Both the data and the high-level modelling support the central claim of the Elaborated Intrusion theory that imagery is a key element of craving, providing the subjective experience and mediating much of the associated disruption of concurrent cognition.

Borrowing from models of motor control to translate cognitive processes: Evidence for hypokinetic-hyperkinetic linguistic homologues?

In relation to motor control, the basal ganglia have been implicated in both the scaling and focusing of movement. Hypokinetic and hyperkinetic movement disorders manifest as a consequence of overshooting and undershooting GPi (globus pallidus internus) activity thresholds, respectively. Recently, models of motor control have been borrowed to translate cognitive processes relating to the overshooting and undershooting of GPi activity, including attention and executive function. Linguistic correlates, however, are yet to be extrapolated in sufficient detail. The aims of the present investigation were to: (1) characterise cognitive-linguistic processes within hypokinetic and hyperkinetic neural systems, as defined by motor disturbances; (2) investigate the impact of surgically-induced GPi lesions upon language abilities. Two Parkinsonian cases with opposing motor symptoms (akinetic versus dystonic/dyskinetic) served as experimental subjects in this research. Assessments were conducted both prior to as well as 3 and 12 months following bilateral posteroventral pallidotomy (PVP). Reliable changes in performance (i.e. both improvements and decrements) were typically restricted to tasks demanding complex linguistic operations across subjects. Hyperkinetic motor symptoms were associated with an initial overall improvement in complex language function as a consequence of bilateral PVP, which diminished over time, suggesting a decrescendo effect relative to surgical beneficence. In contrast, hypokinetic symptoms were associated with a more stable longitudinal linguistic profile, albeit defined by higher proportions of reliable decline versus improvement in postoperative assessment scores. The above findings endorsed the integration of the GPi within cognitive mechanisms involved in the arbitration of complex language functions. In relation to models of motor control, 'focusing' was postulated to represent the neural processes underpinning lexical-semantic manipulation, and 'scaling' the potential allocation of cognitive resources during the mediation of high-level linguistic tasks. (c) 2005 Elsevier Ltd. All rights reserved.

On minimal models of process systems

Minimal representations are known to have no redundant elements, and are therefore of great importance. Based on the notions of performance and size indices and measures for process systems, the paper proposes conditions for a process model being minimal in a set of functionally equivalent models with respect to a size norm. Generalized versions of known procedures to obtain minimal process models for a given modelling goal, model reduction based on sensitivity analysis and incremental model building are proposed and discussed. The notions and procedures are illustrated and compared on a simple example, that of a simple nonlinear fermentation process with different modelling goals and on a case study of a heat exchanger modelling. (C) 2004 Elsevier Ltd. All rights reserved.

Evaluation of 1-site and 5-site models of methane on its adsorption on graphite and in graphitic slit pores

In this paper, we evaluate the performance of the 1- and 5-site models of methane on the description of adsorption on graphite surfaces and in graphitic slit pores. These models have been known to perform well in the description of the fluid-phase behavior and vapor-liquid equilibria. Their performance in adsorption is evaluated in this work for nonporous graphitized thermal carbon black, and simulation results are compared with the experimental data of Avgul and Kiselev (Chemistry and Physics of Carbon; Dekker: New York, 1970; Vol. 6, p 1). On this nonporous surface, it is found that these models perform as well on isotherms at various temperatures as they do on the experimental isosteric heat for adsorption on a graphite surface. They are then tested for their performance in predicting the adsorption isotherms in graphitic slit pores, in which we would like to explore the effect of confinement on the molecule packing. Pore widths of 10 and 20 angstrom are chosen in this investigation, and we also study the effects of temperature by choosing 90.7, 113, and 273 K. The first two are for subcritical conditions, with 90.7 K being the triple point of methane and 113 K being its boiling point. The last temperature is chosen to represent the supercritical condition so that we can investigate the performance of these models at extremely high pressures. We have found that for the case of slit pores investigated in this paper, although the two models yield comparable pore densities (provided the accessible pore width is used in the calculation of pore density), the number of particles predicted by the I-site model is always greater than that predicted by the 5-site model, regardless of whether temperature is subcritical or supercritical. This is due to the packing effect in the confined space such that a methane molecule modeled as a spherical particle in the I-site model would pack better than the fused five-sphere model in the case of the 5-site model. Because the 5-site model better describes the liquid- and solid-phase behavior, we would argue that the packing density in small pores is better described with a more detailed 5-site model, and care should be exercised when using the 1-site model to study adsorption in small pores.

Variability in time delay between two models of pulse oximeters for deriving the photoplethysmographic signals

Pulse oximetry is commonly used as an arterial blood oxygen saturation (SaO(2)) measure. However, its other serial output, the photoplethysmography (PPG) signal, is not as well studied. Raw PPG signals can be used to estimate cardiovascular measures like pulse transit time (PTT) and possibly heart rate (HR). These timing-related measurements are heavily dependent on the minimal variability in phase delay of the PPG signals. Masimo SET (R) Rad-9 (TM) and Novametrix Oxypleth oximeters were investigated for their PPG phase characteristics on nine healthy adults. To facilitate comparison, PPG signals were acquired from fingers on the same hand in a random fashion. Results showed that mean PTT variations acquired from the Masimo oximeter (37.89 ms) were much greater than the Novametrix (5.66 ms). Documented evidence suggests that I ms variation in PTT is equivalent to I mmHg change in blood pressure. Moreover, the PTT trend derived from the Masimo oximeter can be mistaken as obstructive sleep apnoeas based on the known criteria. HR comparison was evaluated against estimates attained from an electrocardiogram (ECG). Novametrix differed from ECG by 0.71 +/- 0.58% (p < 0.05) while Masimo differed by 4.51 +/- 3.66% (p > 0.05). Modem oximeters can be attractive for their improved SaO(2) measurement. However, using raw PPG signals obtained directly from these oximeters for timing-related measurements warrants further investigations.

Fundamental considerations of beta-adrenoceptor subtypes in human heart failure

beta-Adrenoceptor antagonists have revolutionized the management of heart failure in humans. However, fundamental questions remain concerning their use. Currently, there is considerable debate about the role of beta(2)-adrenoceptors in heart failure and whether incremental clinical benefit can be obtained by blockade of beta(2)-adrenoceptors in addition to beta(1)-adrenoceptors. Polymorphic forms of beta(1)- and beta(2)-adrenoceptors exist, which might contribute to the variable clinical outcomes that are observed with P-adrenoceptor antagonists. There is evidence for a low-affinity state of beta(1)-adrenoceptors and ventricular beta(3)-adrenoceptors, and these are discussed in the context of heart failure. Finally, there is seemingly paradoxical evidence that restoration and normalization of the beta-adrenoceptor system is beneficial in animal models of heart failure. We reconcile this view with the current clinical use and proven benefit of beta-adrenoceptor antagonists.

Cardiac chymase: pathophysiological role and therapeutic potential of chymase inhibitors

On release from cardiac mast cells, alpha-chymase converts angiotensin I (Ang I) to Ang II. In addition to Ang II formation, alpha-chymase is capable of activating TGF-beta 1 and IL-1 beta, forming endothelins consisting of 31 amino acids, degrading endothelin-1, altering lipid metabolism, and degrading the extracellular matrix. Under physiological conditions the role of chymase in the mast cells of the heart is uncertain. In pathological situations, chymase may be secreted and have important effects on the heart. Thus, in animal models of cardiomyopathy, pressure overload, and myocardial infarction, there are increases in both chymase mRNA levels and chymase activity in the heart. In human diseased heart homogenates, alterations in chymase activity have also been reported. These findings have raised the possibility that inhibition of chymase may have a role in the therapy of cardiac disease. The selective chymase inhibitors developed to date include TY-51076, SUN-C8257, BCEAB, NK320, and TEI-E548. These have yet to be tested in humans, but promising results have been obtained in animal models of myocardial infarction, cardiomyopathy, and tachycardia-induced heart failure. It seems likely that orally active inhibitors of chymase could have a place in the treatment of cardiac diseases where injury-induced mast cell degranulation contributes to the pathology.