German wage theories; a history of their development,

Pub. also as author's thesis (PH. D.) Columbia University.

Learning Models of Gene Expression from Synthetic DNA Sequences

Thesis (Ph.D.)--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.

Hurt feelings in couple relationships: Towards integrative models of the negative effects of hurtful events

Previous research suggests that hurt feelings can have powerful effects on individual and relational outcomes. This study examined a typology of hurtful events in couple relationships, together with integrative models predicting ongoing effects on victims and relationships. Participants were 224 students from introductory and third-year psychology classes, who completed open-ended and structured measures concerning an event in which a partner had hurt their feelings. By tailoring Leary et al.'s (1998) typology to the context of romantic relationships, five categories of hurtful events were proposed: active disassociation, passive disassociation, criticism, infidelity, and deception. Analyses assessing similarities and differences among the categories confirmed the utility of the typology. Structural equation modeling showed that longer-term effects on the victim were predicted by relationship anxiety and by the victim's immediate reactions to the event (negative emotions and self-perceptions; feelings of rejection and powerlessness). In contrast, ongoing effects on the relationship were predicted by avoidance, the victim's attributions and perceptions of offender remorse, and the victim's own behavior. The results highlight the utility of an integrated approach to hurt, incorporating emotional, cognitive, and behavioral responses, and dimensions of attachment security.

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.

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.

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.

An evaluation of different models of water recovery in flotation

Water recovery is one of the key parameters in flotation modelling for the purposes of plant design and process control, as it determines the circulating flow and residence time in the individual process units in the plant and has a significant effect on entrainment and froth recovery. This paper reviews some of the water recovery models available in the literature, including both empirical and fundamental models. The selected models are tested using the data obtained from the experimental work conducted in an Outokumpu 3 m(3) tank cell at the Xstrata Mt Isa copper concentrator. It is found that all the models fit the experimental data reasonably well for a given flotation system. However, the empirical models are either unable to distinguish the effect of different cell operating conditions or required to determine the empirical model parameters to be derived in an existing flotation system. The model developed by [Neethling, SJ., Lee, H.T., Cilliers, J.J., 2003, Simple relationships for predicting the recovery of liquid from flowing foams and froths. Minerals Engineering 16, 1123-1130] is based on fundamental understanding of the froth structure and transfer of the water in the froth. It describes the water recovery as a function of the cell operating conditions and the froth properties which can all be determined on-line. Hence, the fundamental model can be used for process control purposes in practice. By incorporating additional models to relate the air recovery and surface bubble size directly to the cell operating conditions, the fundamental model can also be used for prediction purposes. (C) 2005 Elsevier Ltd. All rights reserved.

Models of adding relations to an organization structure of a complete K-ary tree

This paper proposes three models of adding relations to an organization structure which is a complete K-ary tree of height H: (i) a model of adding an edge between two nodes with the same depth N, (ii) a model of adding edges between every pair of nodes with the same depth N and (iii) a model of adding edges between every pair of siblings with the same depth N. For each of the three models, an optimal depth N* is obtained by maximizing the total shortening path length which is the sum of shortening lengths of shortest paths between every pair of all nodes. (c) 2005 Elsevier B.V. All rights reserved.

Physiologically based synthetic models of hepatic disposition

Current Physiologically based pharmacokinetic (PBPK) models are inductive. We present an additional, different approach that is based on the synthetic rather than the inductive approach to modeling and simulation. It relies on object-oriented programming A model of the referent system in its experimental context is synthesized by assembling objects that represent components such as molecules, cells, aspects of tissue architecture, catheters, etc. The single pass perfused rat liver has been well described in evaluating hepatic drug pharmacokinetics (PK) and is the system on which we focus. In silico experiments begin with administration of objects representing actual compounds. Data are collected in a manner analogous to that in the referent PK experiments. The synthetic modeling method allows for recognition and representation of discrete event and discrete time processes, as well as heterogeneity in organization, function, and spatial effects. An application is developed for sucrose and antipyrine, administered separately and together PBPK modeling has made extensive progress in characterizing abstracted PK properties but this has also been its limitation. Now, other important questions and possible extensions emerge. How are these PK properties and the observed behaviors generated? The inherent heuristic limitations of traditional models have hindered getting meaningful, detailed answers to such questions. Synthetic models of the type described here are specifically intended to help answer such questions. Analogous to wet-lab experimental models, they retain their applicability even when broken apart into sub-components. Having and applying this new class of models along with traditional PK modeling methods is expected to increase the productivity of pharmaceutical research at all levels that make use of modeling and simulation.

Models of psychological service provision under Australia's better outcomes in mental health care program

The Access to Allied Psychological Services component of Australia's Better Outcomes in Mental Health Care program enables eligible general practitioners to refer consumers to allied health professionals for affordable, evidence-based mental health care, via 108 projects conducted by Divisions of General Practice. The current study profiled the models of service delivery across these projects, and examined whether particular models were associated with differential levels of access to services. We found: 76% of projects were retaining their allied health professionals under contract, 28% via direct employment, and 7% some other way; Allied health professionals were providing services from GPs' rooms in 63% of projects, from their own rooms in 63%, from a third location in 42%; and The referral mechanism of choice was direct referral in 51% of projects, a voucher system in 27%, a brokerage system in 24%, and a register system in 25%. Many of these models were being used in combination. No model was predictive of differential levels of access, suggesting that the approach of adapting models to the local context is proving successful.

Anisotropic viscous models of large-deformation Mohr-Coulomb failure

We have developed a way to represent Mohr-Coulomb failure within a mantle-convection fluid dynamics code. We use a viscous model of deformation with an orthotropic viscoplasticity (a different viscosity is used for pure shear to that used for simple shear) to define a prefered plane for slip to occur given the local stress field. The simple-shear viscosity and the deformation can then be iterated to ensure that the yield criterion is always satisfied. We again assume the Boussinesq approximation, neglecting any effect of dilatancy on the stress field. An additional criterion is required to ensure that deformation occurs along the plane aligned with maximum shear strain-rate rather than the perpendicular plane, which is formally equivalent in any symmetric formulation. We also allow for strain-weakening of the material. The material can remember both the accumulated failure history and the direction of failure. We have included this capacity in a Lagrangian-integration-point finite element code and show a number of examples of extension and compression of a crustal block with a Mohr-Coulomb failure criterion. The formulation itself is general and applies to 2- and 3-dimensional problems.

Stirring in 3-d spherical models of convection in the Earth's mantle

On a global scale basalts from mid-ocean ridges are strikingly more homogeneous than basalts from intraplate volcanism. The observed geochemical heterogeneity argues strongly for the existence of distinct reservoirs in the Earth's mantle. It is an unresolved problem of Geodynamics as to how these findings can be reconciled with large-scale convection. We review observational constraints, and investigate stirring properties of numerical models of mantle convection. Conditions in the early Earth may have supported layered convection with rapid stirring in the upper layers. Material that has been altered near the surface is transported downwards by small-scale convection. Thereby a layer of homogeneous depleted material develops above pristine mantle. As the mantle cools over Earth history, the effects leading to layering become reduced and models show the large-scale convection favoured for the Earth today. Laterally averaged, the upper mantle below the lithosphere is least affected by material that has experienced near-surface differentiation. The geochemical signature obtained during the previous episode of small-scale convection may be preserved there for the longest time. Additionally, stirring is less effective in the high viscosity layer of the central lower mantle [1, 2], supporting the survival of medium-scale heterogeneities there. These models are the first, using 3-d spherical geometry and mostly Earth-like parameters, to address the suggested change of convective style. Although the models are still far from reproducing our planet, we find that proposal might be helpful towards reconciling geochemical and geophysical constraints.

Towards developing reliable models of leaf area on grapevines (Vitis vinifera L.)

A field study in three vineyards in southern Queensland (Australia) was carried out to develop predictive models for individual leaf area and shoot leaf area of two cultivars (Cabernet Sauvignon and Shiraz) of grapevines (Vitis Vinifera L.). Digital image analysis was used to measure leaf vein length and leaf area. Stepwise regressions of untransformed and transformed models consisting of up to six predictor variables for leaf area and three predictor variables for shoot leaf area were carried out to obtain the most efficient models. High correlation coefficients were found for log10 transformed individual leaf and shoot leaf area models. The significance of predictor variables in the models varied across vineyards and cultivars, demonstrating the discontinuous and heterogeneous nature of vineyards. The application of this work in a grapevine modeling environment and in a dynamic vineyard management context are discussed. Sample sizes for quantification of individual leaf areas and areas of leaves on shoots are proposed based on target margins of errors of sampled data.