Statistical Hurdle Models for Single Cell Gene Expression: Differential Expression and Graphical Modeling

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

The functions of societies and the evolution of group living: Spider societies as a test case

Many models have been advanced to suggest how different expressions of sociality have evolved and are maintained. However these models ignore the function of groups for the particular species in question. Here we present a new perspective on sociality where the function of the group takes a central role. We argue that sociality may have primarily a reproductive, protective, or foraging function, depending on whether it enhances the reproductive, protective or foraging aspect of the animal's life (sociality may serve a mixture of these functions). Different functions can potentially cause the development of the same social behaviour. By identifying which function influences a particular social behaviour we can determine how that social behaviour will change with changing conditions, and which models are most pertinent. To test our approach we examined spider sociality, which has often been seen as the poor cousin to insect sociality. By using our approach we found that the group characteristics of eusocial insects is largely governed by the reproductive function of their groups, while the group characteristics of social spiders is largely governed by the foraging function of the group. This means that models relevant to insects may not be relevant to spiders. It also explains why eusocial insects have developed a strict caste system while spider societies are more egalitarian. We also used our approach to explain the differences between different types of spider groups. For example, differences in the characteristics of colonial and kleptoparasitic groups can be explained by differences in foraging methods, while differences between colonial and cooperative spiders can be explained by the role of the reproductive function in the formation of cooperative spider groups. Although the interactions within cooperative spider colonies are largely those of a foraging society, demographic traits and colony dynamics are strongly influenced by the reproductive function. We argue that functional explanations help to understand the social structure of spider groups and therefore the evolutionary potential for speciation in social spiders.

The effectiveness of an inpatient group cognitive behavioral therapy program for alcohol dependence

The present study evaluated the effectiveness of attendance at a clinically based, short-term, in-patient group CBT program largely based on Monti, Abrams, Kadden, and Cooney(1) to treat problem drinking. Participants were 37 males and 34 females diagnosed with alcohol dependence. Patients attended 42 CBT sessions over three weeks, with each session being one hour in duration. Measures included the Khavari Alcohol Test (KAT), the Short Alcohol Dependence Data Questionnaire (SADD), the Beck Anxiety Index (BAI), the Symptom Checklist-90-Revised (SCL-90), a General Self-Efficacy scale (GSE), and the Drinking Expectancy Profile (DEP). Group attendance rates were monitored daily. Two structured phone calls were conducted at one month and three months post-discharge. Results showed that attendance rates at CBT group sessions were not associated with improvements found at the end of therapy or in drinking behaviors at three-month follow-up. Full support could not be found for the effectiveness of group CBT and cognitive models of problem drinking.

Cognitive change process during group cognitive behaviour therapy for depression

Background: This study extended that of Kwon and Oei [Kwon, S.M., Oei, T.P.S., 2003. Cognitive change processes in a group cognitive behavior therapy of depression. J. Behav. Ther. Exp. Psychiatry, 3, 73-85], which outlined a number of testable models based on Beck's cognitive theory of depression. Specifically, the current study tested the following four competing models: the causal, consequential, fully and partially interactive cognitive models in patients with major depressive disorder. Methods: A total of 168 clinically depressed outpatients were recruited into a 12-week group cognitive behaviour therapy program. Data was collected at three time points: baseline, mid- and at termination of therapy using the ATQ DAS and BD1. The data were analysed with Amos 4.01 (Arbuckle, J.L., 1999. Amos 4.1. Smallwaters, Chicago.) structural equation modelling. Results: Results indicated that dysfunctional attitudes, negative automatic thoughts and symptoms of depression reduced significantly during treatment. Both the causal and consequential models equally provided an adequate fit to the data. The fully interactive model provided the best fit. However, after removing non-significant pathways, it was found that reduced depressive symptom contributed to reduced depressogenic automatic thoughts and dysfunctional attitudes, not the reverse. Conclusion: These findings did not fully support Beck's cognitive theory of depression that cognitions are primary in the reduction of depressed mood. (c) 2006 Elsevier B.V. All rights reserved.

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.

Kick'n'on: The design and evaluation of a group programme for young males with psychotic disorders

Young men with psychotic disorders have persistently poorer outcomes in social functioning when interventions aimed at arresting social isolation are not implemented. Recent literature has indicated that it is important to develop rehabilitation programmes that are based on areas of needs that are identified by the participants. To assist in the design of a group programme, a qualitative (focus group) investigation of the perceptions of young males concerning male roles and identity in today’s society was conducted. The participants were six young males with psychotic disorders who had been referred to an Australian regional rehabilitation service to address poor social functioning and social isolation. Three main themes emerged from the focus groups. These were role models, concept of what is a man, and societal expectations. The findings were used to develop a group programme called Kick’n’On.

Ontological clarity and comprehension in health data models

Conceptual modeling forms an important part of systems analysis. If this is done incorrectly or incompletely, there can be serious implications for the resultant system, specifically in terms of rework and useability. One approach to improving the conceptual modelling process is to evaluate how well the model represents reality. Emergence of the Bunge-Wand-Weber (BWW) ontological model introduced a platform to classify and compare the grammar of conceptual modelling languages. This work applies the BWW theory to a real world example in the health arena. The general practice computing group data model was developed using the Barker Entity Relationship Modelling technique. We describe an experiment, grounded in ontological theory, which evaluates how well the GPCG data model is understood by domain experts. The results show that with the exception of the use of entities to represent events, the raw model is better understood by domain experts

Dissecting query performance in logical data models: Parsimony vs. greater ontological clarity

Even when data repositories exhibit near perfect data quality, users may formulate queries that do not correspond to the information requested. Users’ poor information retrieval performance may arise from either problems understanding of the data models that represent the real world systems, or their query skills. This research focuses on users’ understanding of the data structures, i.e., their ability to map the information request and the data model. The Bunge-Wand-Weber ontology was used to formulate three sets of hypotheses. Two laboratory experiments (one using a small data model and one using a larger data model) tested the effect of ontological clarity on users’ performance when undertaking component, record, and aggregate level tasks. The results indicate for the hypotheses associated with different representations but equivalent semantics that parsimonious data model participants performed better for component level tasks but that ontologically clearer data model participants performed better for record and aggregate level tasks.

Changes in social identity when joining a new group: The role of individual-level and group-level adaptation processes

While classic intergroup theories have specified the processes explaining situational shifts in social identification, the processes whereby social identities change more profoundly and become integrated within the self have to be proposed. To this aim, the present studies investigate the processes by which group members integrate a new social identity as they are joining a new group. Combining a social identity approach and stress and coping models, this research tests if social factors (i.e., needs satisfied by fellow group members, social support), have an impact on the adaptation strategies group members use to deal with the novelty of the situation and to fit into their new group (seeking information & adopting group norms vs. disengaging). These strategies, in turn, should predict changes in level of identification with the new social group over time, as well as enhanced psychological adjustment. These associations are tested among university students over the course of their first academic year (Study 1), and among online gamers joining a newly established online community (Study 2). Path analyses provide support for the hypothesised associations. The results are discussed in light of recent theoretical developments pertaining to intraindividual changes in social identities and their integration in the self.

A comparison of linear forecasting models and neural networks:an application to Euro inflation and Euro Divisia

Linear models reach their limitations in applications with nonlinearities in the data. In this paper new empirical evidence is provided on the relative Euro inflation forecasting performance of linear and non-linear models. The well established and widely used univariate ARIMA and multivariate VAR models are used as linear forecasting models whereas neural networks (NN) are used as non-linear forecasting models. It is endeavoured to keep the level of subjectivity in the NN building process to a minimum in an attempt to exploit the full potentials of the NN. It is also investigated whether the historically poor performance of the theoretically superior measure of the monetary services flow, Divisia, relative to the traditional Simple Sum measure could be attributed to a certain extent to the evaluation of these indices within a linear framework. Results obtained suggest that non-linear models provide better within-sample and out-of-sample forecasts and linear models are simply a subset of them. The Divisia index also outperforms the Simple Sum index when evaluated in a non-linear framework. © 2005 Taylor & Francis Group Ltd.

Life with sheepdogs:alternative metaphorical models of the doctoral research process revisited

The doctoral research process is the entry path for the academic profession. Traditionally it is explained by reference to another professional entry path, the industrial apprenticeship. Revisiting a paper and discussion originally held at the Marketing Education Group conference in 1991, we explore the implications and limitations of this metaphorical model, suggest alternatives and consider the interaction between student characteristics and supervisory approach. Through this process we offer marketing academics a vast range of unflattering metaphors to employ in describing themselves, their students, their supervisors and their colleagues.

Ethnic diversity as a multilevel construct:the combined effects of dissimilarity, group diversity, and societal status on learning performance in work groups

The authors present a model of the multilevel effects of diversity on individual learning performance in work groups. For ethnically diverse work groups, the model predicts that group diversity elicits either positive or negative effects on individual learning performance, depending on whether a focal individual’s ethnic dissimilarity from other group members is high or low. By further considering the societal status of an individual’s ethnic origin within society (Anglo versus non-Anglo for our U.K. context), the authors hypothesize that the model’s predictions hold more strongly for non-Anglo group members than for Anglo group members. We test this model with data from 412 individuals working on a 24-week business simulation in 87 four- to seven-person groups with varying degrees of ethnic diversity. Two of the three hypotheses derived from the model received full support and one hypothesis received partial support. Implications for theory development, methods, and practice in applied group diversity research are discussed.

Short-term electricity demand and gas price forecasts using wavelet transforms and adaptive models

This paper presents some forecasting techniques for energy demand and price prediction, one day ahead. These techniques combine wavelet transform (WT) with fixed and adaptive machine learning/time series models (multi-layer perceptron (MLP), radial basis functions, linear regression, or GARCH). To create an adaptive model, we use an extended Kalman filter or particle filter to update the parameters continuously on the test set. The adaptive GARCH model is a new contribution, broadening the applicability of GARCH methods. We empirically compared two approaches of combining the WT with prediction models: multicomponent forecasts and direct forecasts. These techniques are applied to large sets of real data (both stationary and non-stationary) from the UK energy markets, so as to provide comparative results that are statistically stronger than those previously reported. The results showed that the forecasting accuracy is significantly improved by using the WT and adaptive models. The best models on the electricity demand/gas price forecast are the adaptive MLP/GARCH with the multicomponent forecast; their MSEs are 0.02314 and 0.15384 respectively.

Development of performance models for co-operative information systems in an organisational context

The thesis reports of a study into the effect upon organisations of co-operative information systems (CIS) incorporating flexible communications, group support and group working technologies. A review of the literature leads to the development of a model of effect based upon co-operative business tasks. CIS have the potential to change how co-operative business tasks are carried out and their principal effect (or performance) may therefore be evaluated by determining to what extent they are being employed to perform these tasks. A significant feature of CIS use identified is the extent to which they may be designed to fulfil particular tasks, or by contrast, may be applied creatively by users in an emergent fashion to perform tasks. A research instrument is developed using a survey questionnaire to elicit users judgements of the extent to which a CIS is employed to fulfil a range of co-operative tasks. This research instrument is applied to a longitudinal study of Novell GroupWise introduction at Northamptonshire County Council during which qualitative as well as quantitative data were gathered. A method of analysis of questionnaire results using principles from fuzzy mathematics and artificial intelligence is developed and demonstrated. Conclusions from the longitudinal study include the importance of early experiences in setting patterns for use for CIS, the persistence of patterns of use over time and the dominance of designed usage of the technology over emergent use.