A Kinetic Vlasov Model for Plasma Simulation Using Discontinuous Galerkin Method on Many-Core Architectures

Thesis (Ph.D.)--University of Washington, 2016-03

Is Mindfulness Beneficial for Job Performance Following Positive and Negative Affective Events? The Attenuating Role of Mindfulness on Self-Serving Bias

Thesis (Ph.D.)--University of Washington, 2016-05

Dynamical properties of a strongly correlated model for quarter-filled layered organic molecular crystals

The dynamical properties of an extended Hubbard model, which is relevant to quarter-filled layered organic molecular crystals, are analyzed. We have computed the dynamical charge correlation function, spectral density, and optical conductivity using Lanczos diagonalization and large-N techniques. As the ratio of the nearest-neighbor Coulomb repulsion, V, to the hopping integral, t, increases there is a transition from a metallic phase to a charge-ordered phase. Dynamical properties close to the ordering transition are found to differ from the ones expected in a conventional metal. Large-N calculations display an enhancement of spectral weight at low frequencies as the system is driven closer to the charge-ordering transition in agreement with Lanczos calculations. As V is increased the charge correlation function displays a collective mode which, for wave vectors close to (pi,pi), increases in amplitude and softens as the charge-ordering transition is approached. We propose that inelastic x-ray scattering be used to detect this mode. Large-N calculations predict superconductivity with d(xy) symmetry close to the ordering transition. We find that this is consistent with Lanczos diagonalization calculations, on lattices of 20 sites, which find that the binding energy of two holes becomes negative close to the charge-ordering transition.

Attending to the distractor and old/new discriminations in negative priming

When participants ignore an irrelevant distractor they typically show impaired responding to that item if it becomes the relevant stimulus on a subsequent trial. In Experiment 1 (N = 64), a masked white colour name was presented briefly before a Stroop display. Negative priming in colour naming occurred when the colour of the lettering for the Stroop stimulus matched the colour name displayed in the first display, consistent with the proposal of temporal discrimination theory that negative priming arises because a recurrence of an unattended stimulus cannot readily be classified as old or new. Experiment 2 (N = 32) replicated negative priming in the interleaved-word display where participants had to name the red word from a pair of red and green words. In Experiment 3 (N = 32) and Experiment 4 (N = 28) the participants were required to attend to but not respond to the words in the prime display and name one of two interleaved words in the probe display. Negative priming was observed in this arrangement, consistent with the episodic retrieval theory of negative priming. The temporal discrimination model may need to be extended to situations in which the attended stimuli have different responses attached to them.

Negative regulation of prophenoloxidase (proPO) activation by a clip-domain serine proteinase homolog (SPH) from endoparasitoid venom

Most parasitic wasps inject maternal factors into the host hemocoel to suppress the host immune system and ensure successful development of their progeny. Melanization is one of the insect defence mechanisms against intruding pathogens or parasites. We previously isolated from the venom of Cotesia rubecula a 50 kDa protein that blocked melanization in the hemolymph of its host, Pieris rapae [Insect Biochem. Mol. Biol. 33 (2003) 1017]. This protein, designated Vn50, is a serine proteinase homolog (SPH) containing an amino-terminal clip domain. In this work, we demonstrated that recombinant Vn50 bound P. rapae hemolymph components that were recognized by antisera to Tenebrio molitor prophenoloxidase (proPO) and Manduca sexta proPO-activating proteinase (PAP). Vn50 is stable in the host hemolymph-it remained intact for at least 72 It after parasitization. Using M. sexta as a model system, we found that Vn50 efficiently down-regulated proPO activation mediated by M. sexta PAP-1, SPH-1, and SPH-2. Vn50 did not inhibit active phenoloxidase (PO) or PAP-1, but it significantly reduced the proteolysis of proPO. If recombinant Vn50 binds P. rapae proPO and PAP (as suggested by the antibody reactions), it is likely that the molecular interactions among M. sexta proPO, PAP-1, and SPHs were impaired by this venom protein. A similar strategy might be employed by C rubecula to negatively impact the proPO activation reaction in its natural host. (C) 2004 Elsevier Ltd. All rights reserved.

Validation of a food-frequency questionnaire assessment of carotenoid and vitamin E intake using weighed food records and plasma biomarkers: The method of triads model

Background: Reliability or validity studies are important for the evaluation of measurement error in dietary assessment methods. An approach to validation known as the method of triads uses triangulation techniques to calculate the validity coefficient of a food-frequency questionnaire (FFQ). Objective: To assess the validity of an FFQ estimates of carotenoid and vitamin E intake against serum biomarker measurements and weighed food records (WFRs), by applying the method of triads. Design: The study population was a sub-sample of adult participants in a randomised controlled trial of beta-carotene and sunscreen in the prevention of skin cancer. Dietary intake was assessed by a self-administered FFQ and a WFR. Nonfasting blood samples were collected and plasma analysed for five carotenoids (alpha-carotene, beta-carotene, beta-cryptoxanthin, lutein, lycopene) and vitamin E. Correlation coefficients were calculated between each of the dietary methods and the validity coefficient was calculated using the method of triads. The 95% confidence intervals for the validity coefficients were estimated using bootstrap sampling. Results: The validity coefficients of the FFQ were highest for alpha-carotene (0.85) and lycopene (0.62), followed by beta- carotene (0.55) and total carotenoids (0.55), while the lowest validity coefficient was for lutein (0.19). The method of triads could not be used for b- cryptoxanthin and vitamin E, as one of the three underlying correlations was negative. Conclusions: Results were similar to other studies of validity using biomarkers and the method of triads. For many dietary factors, the upper limit of the validity coefficients was less than 0.5 and therefore only strong relationships between dietary exposure and disease will be detected.

Binomial leap methods for simulating stochastic chemical kinetics

This paper discusses efficient simulation methods for stochastic chemical kinetics. Based on the tau-leap and midpoint tau-leap methods of Gillespie [D. T. Gillespie, J. Chem. Phys. 115, 1716 (2001)], binomial random variables are used in these leap methods rather than Poisson random variables. The motivation for this approach is to improve the efficiency of the Poisson leap methods by using larger stepsizes. Unlike Poisson random variables whose range of sample values is from zero to infinity, binomial random variables have a finite range of sample values. This probabilistic property has been used to restrict possible reaction numbers and to avoid negative molecular numbers in stochastic simulations when larger stepsize is used. In this approach a binomial random variable is defined for a single reaction channel in order to keep the reaction number of this channel below the numbers of molecules that undergo this reaction channel. A sampling technique is also designed for the total reaction number of a reactant species that undergoes two or more reaction channels. Samples for the total reaction number are not greater than the molecular number of this species. In addition, probability properties of the binomial random variables provide stepsize conditions for restricting reaction numbers in a chosen time interval. These stepsize conditions are important properties of robust leap control strategies. Numerical results indicate that the proposed binomial leap methods can be applied to a wide range of chemical reaction systems with very good accuracy and significant improvement on efficiency over existing approaches. (C) 2004 American Institute of Physics.

Dynamic and regulated association of caveolin with lipid bodies: Modulation of lipid body motility and function by a dominant negative mutant

Caveolins are a crucial component of caveolae but have also been localized to the Golgi complex, and, under some experimental conditions, to lipid bodies (LBs). The physiological relevance and dynamics of LB association remain unclear. We now show that endogenous caveolin-1 and caveolin-2 redistribute to LBs in lipid loaded A431 and FRT cells. Association with LBs is regulated and reversible; removal of fatty acids causes caveolin to rapidly leave the lipid body. We also show by subcellular fractionation, light and electron microscopy that during the first hours of liver regeneration, caveolins show a dramatic redistribution from the cell surface to the newly formed LBs. At later stages of the regeneration process (when LBs are still abundant), the levels of caveolins in LBs decrease dramatically. As a model system to study association of caveolins with LBs we have used brefeldin A (BFA). BFA causes rapid redistribution of endogenous caveolins to LBs and this association was reversed upon BFA washout. Finally, we have used a dominant negative LB-associated caveolin mutant (cav(DGV)) to study LB formation and to examine its effect on LB function. We now show that the cav(DGV) mutant inhibits microtubule-dependent LB motility and blocks the reversal of lipid accumulation in LBs.

The etiology of social phobia: Empirical evidence and an initial model

Research into the etiology of social phobia has lagged far behind that of descriptive and maintaining factors. The current paper reviews data from a variety of sources that have some bearing on questions of the origins of social fears. Areas examined include genetic factors, temperament, childrearing, negative life events, and adverse social experiences. Epidemiological data are examined in detail and factors associated with social phobia such as cognitive distortions and social skills are also covered. The paper concludes with an initial model that draws together some of the current findings and aims to provide a platform for future research directions. (C) 2004 Elsevier Ltd. All rights reserved.

Swash overtopping and sediment overwash on a truncated beach

New experimental laboratory data are presented on swash overtopping and sediment overwash on a truncated beach, approximating the conditions at the crest of a beach berm or inter-tidal ridge-runnel. The experiments provide a measure of the uprush sediment transport rate in the swash zone that is unaffected by the difficulties inherent in deploying instrumentation or sediment trapping techniques at laboratory scale. Overtopping flow volumes are compared with an analytical solution for swash flows as well as a simple numerical model, both of which are restricted to individual swash events. The analytical solution underestimates the overtopping volume by an order of magnitude while the model provides good overall agreement with the data and the reason for this difference is discussed. Modelled flow velocities are input to simple sediment transport formulae appropriate to the swash zone in order to predict the overwash sediment transport rates. Calculations performed with traditional expressions for the wave friction factor tend to underestimate the measured transport. Additional sediment transport calculations using standard total load equations are used to derive an optimum constant wave friction factor of f(w)=0.024. This is in good agreement with a broad range of published field and laboratory data. However, the influence of long waves and irregular wave run-up on the overtopping and overwash remains to be assessed. The good agreement between modelled and measured sediment transport rates suggests that the model provides accurate predictions of the uprush sediment transport rates in the swash zone, which has application in predicting the growth and height of beach berms. (c) 2005 Elsevier B.V. All rights reserved.

Relations between coping and positive and negative outcomes in carers of persons with multiple sclerosis (MS)

This study examined relations between stress and coping predictors and negative and positive outcomes in MS caregiving. A total of 222 carers and their care-recipients completed questionnaires at Time 1 and three months later, Time 2 ( n = 155). Predictors included care-recipient characteristics ( age, time since diagnosis, course and life satisfaction), and Times 1 and 2 carer problems, stress appraisal and coping. Dependent variables were Time 2 negative ( anxiety, depression) and positive outcomes ( life satisfaction, positive affect, benefits). Regressions indicated that, overall, the hypothesised direct effects of stress appraisal and coping strategies on positive and negative outcomes were supported. The hypothesised stress-buffering effects of positive reframing coping were also supported. All but one of the coping strategies were related to both positive and negative outcomes; specifically, practical assistance coping emerged as a unique predictor of distress. Of the model predictors, care-recipient life satisfaction emerged as the strongest and most consistent predictor of both positive and negative outcomes except benefit finding. Findings support the role of care-recipient characteristics and the carer's appraisal and coping processes in shaping both positive and negative outcomes. The guiding framework and findings have the potential to inform interventions designed to promote well-being in carers.

Study of the integrated cognitive model of depression among Latin-Americans

Objective: The objective of the present study is to test the validity of the integrated cognitive model (ICM) of depression proposed by Kwon and Oei with a Latin-American sample. The ICM of depression postulates that the interaction between negative life events with dysfunctional attitudes increases the frequency of negative automatic thoughts, which in turns affects the depressive symptomatology of a person. This model was developed for Western Europeans such as Americans and Australians and the validity of this model has not been tested on Latin-Americans. Method: Participants were 101 Latin-American migrants living permanently in Brisbane, including people from Chile, El Salvador, Nicaragua, Argentina and Guatemala. Participants completed the Beck Depression Inventory, the Dysfunctional Attitudes Scale, the Automatic Thoughts Questionnaire and the Life Events Inventory. Alternative or competing models of depression were examined, including the alternative aetiologies model, the linear mediational model and the symptom model. Results: Six models were tested and the results of the structural equation modelling analysis indicated that the symptom model only fits the Latin-American data. Conclusions: Results show that in the Latin-American sample depression symptoms can have an impact on negative cognitions. This finding adds to growing evidence in the literature that the relationship between cognitions and depression is bidirectional, rather than unidirectional from cognitions to symptoms.

Fitness assessment of document model

Document classification is a supervised machine learning process, where predefined category labels are assigned to documents based on the hypothesis derived from training set of labelled documents. Documents cannot be directly interpreted by a computer system unless they have been modelled as a collection of computable features. Rogati and Yang [M. Rogati and Y. Yang, Resource selection for domain-specific cross-lingual IR, in SIGIR 2004: Proceedings of the 27th annual international conference on Research and Development in Information Retrieval, ACM Press, Sheffied: United Kingdom, pp. 154-161.] pointed out that the effectiveness of document classification system may vary in different domains. This implies that the quality of document model contributes to the effectiveness of document classification. Conventionally, model evaluation is accomplished by comparing the effectiveness scores of classifiers on model candidates. However, this kind of evaluation methods may encounter either under-fitting or over-fitting problems, because the effectiveness scores are restricted by the learning capacities of classifiers. We propose a model fitness evaluation method to determine whether a model is sufficient to distinguish positive and negative instances while still competent to provide satisfactory effectiveness with a small feature subset. Our experiments demonstrated how the fitness of models are assessed. The results of our work contribute to the researches of feature selection, dimensionality reduction and document classification.

Modelling predicts positive and negative interactions between three Australian tropical tree species in monoculture and binary mixture

Computer modelling promises to. be an important tool for analysing and predicting interactions between trees within mixed species forest plantations. This study explored the use of an individual-based mechanistic model as a predictive tool for designing mixed species plantations of Australian tropical trees. The 'spatially explicit individually based-forest simulator' (SeXI-FS) modelling system was used to describe the spatial interaction of individual tree crowns within a binary mixed-species experiment. The three-dimensional model was developed and verified with field data from three forest tree species grown in tropical Australia. The model predicted the interactions within monocultures and binary mixtures of Flindersia brayleyana, Eucalyptus pellita and Elaeocarpus grandis, accounting for an average of 42% of the growth variation exhibited by species in different treatments. The model requires only structural dimensions and shade tolerance as species parameters. By modelling interactions in existing tree mixtures, the model predicted both increases and reductions in the growth of mixtures (up to +/- 50% of stem volume at 7 years) compared to monocultures. This modelling approach may be useful for designing mixed tree plantations. (c) 2006 Published by Elsevier B.V.

Relations between social support, appraisal and coping and both positive and negative outcomes for children of a parent with multiple sclerosis and comparisons with children of healthy parents

Objective: To examine adjustment in children of a parent with multiple sclerosis within a stress and coping framework and compare them with those who have 'healthy' parents. Subjects: A total of 193 participants between 10 and 25 years completed questionnaires; 48 youngsters who had a parent with multiple sclerosis and 145 youngsters who reported that they did not have a parent with an illness or disability. Method: A questionnaire survey methodology was used. Variable sets included caregiving context (e.g. additional parental illness, family responsibilities, parental functional impairment, choice in helping), social support (network size, satisfaction), stress appraisal, coping (problem solving, seeking support, acceptance, wishful thinking, denial), and positive (life satisfaction, positive affect, benefits) and negative (distress, health) adjustment outcomes. Results: Caregiving context variables significantly correlated with poorer adjustment in children of a parent with multiple sclerosis included additional parental illness, higher family responsibilities, parental functional impairment and unpredictability of the parent's multiple sclerosis, and less choice in helping. As predicted, better adjustment in children of a parent with multiple sclerosis was related to higher levels of social support, lower stress appraisals, greater reliance on approach coping strategies (problem solving, seeking support and acceptance) and less reliance on avoidant coping (wishful thinking and denial). Compared with children of 'healthy' parents, children of a parent with multiple sclerosis reported greater family responsibilities, less reliance on problem solving and seeking social support coping, higher somatization and lower life satisfaction and positive affect. Conclusions: Findings delineate the key impacts of young caregiving and support a stress and coping model of adjustment in children of a parent with multiple sclerosis.