A Bayesian Approach for Decision Making on the Identification of Genes with Different Expression Levels: An Application to Escherichia coli Bacterium Data

A common interest in gene expression data analysis is to identify from a large pool of candidate genes the genes that present significant changes in expression levels between a treatment and a control biological condition. Usually, it is done using a statistic value and a cutoff value that are used to separate the genes differentially and nondifferentially expressed. In this paper, we propose a Bayesian approach to identify genes differentially expressed calculating sequentially credibility intervals from predictive densities which are constructed using the sampled mean treatment effect from all genes in study excluding the treatment effect of genes previously identified with statistical evidence for difference. We compare our Bayesian approach with the standard ones based on the use of the t-test and modified t-tests via a simulation study, using small sample sizes which are common in gene expression data analysis. Results obtained report evidence that the proposed approach performs better than standard ones, especially for cases with mean differences and increases in treatment variance in relation to control variance. We also apply the methodologies to a well-known publicly available data set on Escherichia coli bacterium.

A new method for decision making in multi-objective optimization problems

Many engineering sectors are challenged by multi-objective optimization problems. Even if the idea behind these problems is simple and well established, the implementation of any procedure to solve them is not a trivial task. The use of evolutionary algorithms to find candidate solutions is widespread. Usually they supply a discrete picture of the non-dominated solutions, a Pareto set. Although it is very interesting to know the non-dominated solutions, an additional criterion is needed to select one solution to be deployed. To better support the design process, this paper presents a new method of solving non-linear multi-objective optimization problems by adding a control function that will guide the optimization process over the Pareto set that does not need to be found explicitly. The proposed methodology differs from the classical methods that combine the objective functions in a single scale, and is based on a unique run of non-linear single-objective optimizers.

Post-decision Processes : Consolidation and value conflicts in decision making

The studies in the present thesis focus on post-decision processes using the theoretical framework of Differentiation and Consolidation Theory. This thesis consists of three studies. In all these studies, pre-decision evaluations are compared with post-decision evaluations in order to explore differences in evaluations of decision alternatives before and after a decision. The main aim of the studies was to describe and gain a clearer and better understanding of how people re-evaluate information, following a decision for which they have experienced the decision and outcome. The studies examine how the attractiveness evaluations of important attributes are restructured from the pre-decision to the post-decision phase; particularly restructuring processes of value conflicts. Value conflict attributes are those in which information speaks against the chosen alternative in a decision. The first study investigates an important real-life decision and illustrates different post-decision (consolidation) processes following the decision. The second study tests whether decisions with value conflicts follow the same consolidation (post-decision restructuring) processes when the conflict is controlled experimentally, as in earlier studies of less controlled real-life decisions. The third study investigates consolidation and value conflicts in decisions in which the consequences are controlled and of different magnitudes. The studies in the present thesis have shown how attractiveness restructuring of attributes in conflict occurs in the post-decision phase. Results from the three studies indicated that attractiveness restructuring of attributes in conflict was stronger for important real-life decisions (Study 1) and in situations in which real consequences followed a decision (Study 3) than in more controlled, hypothetical decision situations (Study 2). Finally, some proposals for future research are suggested, including studies of the effects of outcomes and consequences on consolidation of prior decisions and how a decision maker’s involvement affects his or her pre- and post-decision processes.

On uncertainty and robustness in evolutionary optimization-based multicriterio decision-making

Programa de Doctorado: Sistemas Inteligentes y Aplicaciones Numéricas en Ingeniería

Development of Clinical Decision Support Systems based on Mathematical Models of Physiological Systems

In the last years of research, I focused my studies on different physiological problems. Together with my supervisors, I developed/improved different mathematical models in order to create valid tools useful for a better understanding of important clinical issues. The aim of all this work is to develop tools for learning and understanding cardiac and cerebrovascular physiology as well as pathology, generating research questions and developing clinical decision support systems useful for intensive care unit patients. I. ICP-model Designed for Medical Education We developed a comprehensive cerebral blood flow and intracranial pressure model to simulate and study the complex interactions in cerebrovascular dynamics caused by multiple simultaneous alterations, including normal and abnormal functional states of auto-regulation of the brain. Individual published equations (derived from prior animal and human studies) were implemented into a comprehensive simulation program. Included in the normal physiological modelling was: intracranial pressure, cerebral blood flow, blood pressure, and carbon dioxide (CO2) partial pressure. We also added external and pathological perturbations, such as head up position and intracranial haemorrhage. The model performed clinically realistically given inputs of published traumatized patients, and cases encountered by clinicians. The pulsatile nature of the output graphics was easy for clinicians to interpret. The manoeuvres simulated include changes of basic physiological inputs (e.g. blood pressure, central venous pressure, CO2 tension, head up position, and respiratory effects on vascular pressures) as well as pathological inputs (e.g. acute intracranial bleeding, and obstruction of cerebrospinal outflow). Based on the results, we believe the model would be useful to teach complex relationships of brain haemodynamics and study clinical research questions such as the optimal head-up position, the effects of intracranial haemorrhage on cerebral haemodynamics, as well as the best CO2 concentration to reach the optimal compromise between intracranial pressure and perfusion. We believe this model would be useful for both beginners and advanced learners. It could be used by practicing clinicians to model individual patients (entering the effects of needed clinical manipulations, and then running the model to test for optimal combinations of therapeutic manoeuvres). II. A Heterogeneous Cerebrovascular Mathematical Model Cerebrovascular pathologies are extremely complex, due to the multitude of factors acting simultaneously on cerebral haemodynamics. In this work, the mathematical model of cerebral haemodynamics and intracranial pressure dynamics, described in the point I, is extended to account for heterogeneity in cerebral blood flow. The model includes the Circle of Willis, six regional districts independently regulated by autoregulation and CO2 reactivity, distal cortical anastomoses, venous circulation, the cerebrospinal fluid circulation, and the intracranial pressure-volume relationship. Results agree with data in the literature and highlight the existence of a monotonic relationship between transient hyperemic response and the autoregulation gain. During unilateral internal carotid artery stenosis, local blood flow regulation is progressively lost in the ipsilateral territory with the presence of a steal phenomenon, while the anterior communicating artery plays the major role to redistribute the available blood flow. Conversely, distal collateral circulation plays a major role during unilateral occlusion of the middle cerebral artery. In conclusion, the model is able to reproduce several different pathological conditions characterized by heterogeneity in cerebrovascular haemodynamics and can not only explain generalized results in terms of physiological mechanisms involved, but also, by individualizing parameters, may represent a valuable tool to help with difficult clinical decisions. III. Effect of Cushing Response on Systemic Arterial Pressure. During cerebral hypoxic conditions, the sympathetic system causes an increase in arterial pressure (Cushing response), creating a link between the cerebral and the systemic circulation. This work investigates the complex relationships among cerebrovascular dynamics, intracranial pressure, Cushing response, and short-term systemic regulation, during plateau waves, by means of an original mathematical model. The model incorporates the pulsating heart, the pulmonary circulation and the systemic circulation, with an accurate description of the cerebral circulation and the intracranial pressure dynamics (same model as in the first paragraph). Various regulatory mechanisms are included: cerebral autoregulation, local blood flow control by oxygen (O2) and/or CO2 changes, sympathetic and vagal regulation of cardiovascular parameters by several reflex mechanisms (chemoreceptors, lung-stretch receptors, baroreceptors). The Cushing response has been described assuming a dramatic increase in sympathetic activity to vessels during a fall in brain O2 delivery. With this assumption, the model is able to simulate the cardiovascular effects experimentally observed when intracranial pressure is artificially elevated and maintained at constant level (arterial pressure increase and bradicardia). According to the model, these effects arise from the interaction between the Cushing response and the baroreflex response (secondary to arterial pressure increase). Then, patients with severe head injury have been simulated by reducing intracranial compliance and cerebrospinal fluid reabsorption. With these changes, oscillations with plateau waves developed. In these conditions, model results indicate that the Cushing response may have both positive effects, reducing the duration of the plateau phase via an increase in cerebral perfusion pressure, and negative effects, increasing the intracranial pressure plateau level, with a risk of greater compression of the cerebral vessels. This model may be of value to assist clinicians in finding the balance between clinical benefits of the Cushing response and its shortcomings. IV. Comprehensive Cardiopulmonary Simulation Model for the Analysis of Hypercapnic Respiratory Failure We developed a new comprehensive cardiopulmonary model that takes into account the mutual interactions between the cardiovascular and the respiratory systems along with their short-term regulatory mechanisms. The model includes the heart, systemic and pulmonary circulations, lung mechanics, gas exchange and transport equations, and cardio-ventilatory control. Results show good agreement with published patient data in case of normoxic and hyperoxic hypercapnia simulations. In particular, simulations predict a moderate increase in mean systemic arterial pressure and heart rate, with almost no change in cardiac output, paralleled by a relevant increase in minute ventilation, tidal volume and respiratory rate. The model can represent a valid tool for clinical practice and medical research, providing an alternative way to experience-based clinical decisions. In conclusion, models are not only capable of summarizing current knowledge, but also identifying missing knowledge. In the former case they can serve as training aids for teaching the operation of complex systems, especially if the model can be used to demonstrate the outcome of experiments. In the latter case they generate experiments to be performed to gather the missing data.

Sustainability indicators for environmental management and decision making

The general objective of this research is to explore theories and methodologies of sustainability indicators, environmental management and decision making disciplines with the operational purpose of producing scientific, robust and relevant information for supporting system understanding and decision making in real case studies. Several tools have been applied in order to increase the understanding of socio-ecological systems as well as providing relevant information on the choice between alternatives. These tools have always been applied having in mind the complexity of the issues and the uncertainty tied to the partial knowledge of the systems under study. Two case studies with specific application to performances measurement (environmental performances in the case of the K8 approach and sustainable development performances in the case of the EU Sustainable Development Strategy) and a case study about the selection of sustainable development indicators amongst Municipalities in Scotland, are discussed in the first part of the work. In the second part of the work, the common denominator among subjects consists in the application of spatial indices and indicators to address operational problems in land use management within the territory of the Ravenna province (Italy). The main conclusion of the thesis is that a ‘perfect’ methodological approach which always produces the best results in assessing sustainability performances does not exist. Rather, there is a pool of correct approaches answering different evaluation questions, to be used when methodologies fit the purpose of the analysis. For this reason, methodological limits and conceptual assumptions as well as consistency and transparency of the assessment, become the key factors for assessing the quality of the analysis.

Variability analysis of discrete event series and wavefront patterns in surface electrocardiogram: contributions to psychophysiological and clinical research

The surface electrocardiogram (ECG) is an established diagnostic tool for the detection of abnormalities in the electrical activity of the heart. The interest of the ECG, however, extends beyond the diagnostic purpose. In recent years, studies in cognitive psychophysiology have related heart rate variability (HRV) to memory performance and mental workload. The aim of this thesis was to analyze the variability of surface ECG derived rhythms, at two different time scales: the discrete-event time scale, typical of beat-related features (Objective I), and the “continuous” time scale of separated sources in the ECG (Objective II), in selected scenarios relevant to psychophysiological and clinical research, respectively. Objective I) Joint time-frequency and non-linear analysis of HRV was carried out, with the goal of assessing psychophysiological workload (PPW) in response to working memory engaging tasks. Results from fourteen healthy young subjects suggest the potential use of the proposed indices in discriminating PPW levels in response to varying memory-search task difficulty. Objective II) A novel source-cancellation method based on morphology clustering was proposed for the estimation of the atrial wavefront in atrial fibrillation (AF) from body surface potential maps. Strong direct correlation between spectral concentration (SC) of atrial wavefront and temporal variability of the spectral distribution was shown in persistent AF patients, suggesting that with higher SC, shorter observation time is required to collect spectral distribution, from which the fibrillatory rate is estimated. This could be time and cost effective in clinical decision-making. The results held for reduced leads sets, suggesting that a simplified setup could also be considered, further reducing the costs. In designing the methods of this thesis, an online signal processing approach was kept, with the goal of contributing to real-world applicability. An algorithm for automatic assessment of ambulatory ECG quality, and an automatic ECG delineation algorithm were designed and validated.

Data Mining in Clinical Practice for the Quantification of Motor Impairment in Parkinson's Disease

Advances in biomedical signal acquisition systems for motion analysis have led to lowcost and ubiquitous wearable sensors which can be used to record movement data in different settings. This implies the potential availability of large amounts of quantitative data. It is then crucial to identify and to extract the information of clinical relevance from the large amount of available data. This quantitative and objective information can be an important aid for clinical decision making. Data mining is the process of discovering such information in databases through data processing, selection of informative data, and identification of relevant patterns. The databases considered in this thesis store motion data from wearable sensors (specifically accelerometers) and clinical information (clinical data, scores, tests). The main goal of this thesis is to develop data mining tools which can provide quantitative information to the clinician in the field of movement disorders. This thesis will focus on motor impairment in Parkinson's disease (PD). Different databases related to Parkinson subjects in different stages of the disease were considered for this thesis. Each database is characterized by the data recorded during a specific motor task performed by different groups of subjects. The data mining techniques that were used in this thesis are feature selection (a technique which was used to find relevant information and to discard useless or redundant data), classification, clustering, and regression. The aims were to identify high risk subjects for PD, characterize the differences between early PD subjects and healthy ones, characterize PD subtypes and automatically assess the severity of symptoms in the home setting.

Integration of cognitive and affective processes in perception and decision-making

The relationship between emotion and cognition is a topic that raises great interest in research. Recently, a view of these two processes as interactive and mutually influencing each other has become predominant. This dissertation investigates the reciprocal influences of emotion and cognition, both at behavioral and neural level, in two specific fields, such as attention and decision-making. Experimental evidence on how emotional responses may affect perceptual and attentional processes has been reported. In addition, the impact of three factors, such as personality traits, motivational needs and social context, in modulating the influence that emotion exerts on perception and attention has been investigated. Moreover, the influence of cognition on emotional responses in decision-making has been demonstrated. The current experimental evidence showed that cognitive brain regions such as the dorsolateral prefrontal cortex are causally implicated in regulation of emotional responses and that this has an effect at both pre and post decisional stages. There are two main conclusions of this dissertation: firstly, emotion exerts a strong influence on perceptual and attentional processes but, at the same time, this influence may also be modulated by other factors internal and external to the individuals. Secondly, cognitive processes may modulate emotional prepotent responses, by serving a regulative function critical to driving and shaping human behavior in line with current goals.

Diversity and local democracy. The case of Republic of Macedonia - implications of ethnic diversity on municipal decision making and organizational performance

This research seeks to review the level of knowledge achieved in interpreting the relationship between the ethnic diversity at the workplace in the public sector and the organizational performance; as well as seeks to contribute in understanding the implications of this relationship. The study commenced with investigating the academic research in the relevant area addressing the following research questions: (a) How are diversity management and organizational performance conceptualized? (b) What are the existing findings of research concerning diversity at the workplace in the public organizations and organizational performance? (c) What factors intervene the relationship between the diversity and organizational performance? Based on the findings from the review of the academic research, this study seeks to contribute in understanding the ethnic diversity – performance relationship and its mplications at the local level in the Macedonian context. The reform process in Macedonia as a multicultural society, where for many years, inter-ethnic relations have been one of the most sensitive political issues, affecting both the stability of the country and the progress, focused mainly on the implementation of the decentralization and inclusion of ethnic minorities in the decision making process. With the implementation of the Ohrid Framework Agreement workforce at the units of local self-government in Republic of Macedonia is becoming more balanced with respect to ethnic minorities, with more workforce participation than ever by Albanians, Turks, Roma and other minorities. As public organizations at local level become more diverse along ethnic lines, it makes sense to pay more attention to how different ethnic groups interact with one another at work. Thus it gives additional importance on the research question addressed in the study and gives significance of the research in a broader scope.

Teoria dei giochi e Multi-criteria decision-making per reti mobili Ad-hoc: un protocollo di routing

Nell'elaborato si analizzano aspetti della teoria dei giochi e della multi-criteria decision-making. La riflessione serve a proporre le basi per un nuovo modello di protocollo di routing in ambito Mobile Ad-hoc Networks. Questo prototipo mira a generare una rete che riesca a gestirsi in maniera ottimale grazie ad un'acuta tecnica di clusterizzazione. Allo stesso tempo si propone come obiettivo il risparmio energetico e la partecipazione collaborativa di tutti i componenti.

Strategic decision making in international firms: effect of top management team internationalization on international strategic decision process

In this research project, I have integrated two research streams on international strategic decisions making in international firms: upper echelons or top management teams (TMT) internationalization research and international strategic decision making process research. Both research streams in international business literature have evolved independently, but there is a potential in combining these two streams of research. The first empirical paper “TMT internationalization and international strategic decision making process: a decision level analysis of rationality, speed, and performance” explores the influence of TMT internationalization on strategic decision rationality and speed and, subsequently, their effect on international strategic decision effectiveness (performance). The results show that the internationalization of TMT is positively related to decision effectiveness and this relationship is mediated by decision rationality while the hypotheses regarding the association between TMT internationalization and decision speed, and the mediating effect of speed were not supported. The second paper “TMT internationalization and international strategic decision rationality: the mediating role of international information” of my thesis is a simple but logical extension of first paper. The first paper showed that TMT Internationalization has a significant positive effect on international strategic decision rationality. The second paper explicitly showed that TMT internationalization affect on international strategic decision rationality comes from two sources: international experience (personal international knowledge and information) and international information collected from managerial international contacts. For this research project, I have collected data from international software firms in Pakistan. My research contributes to the literature on upper echelons theory and strategic decision making in context of international business and international firms by explicitly examining the link between TMT internationalization and characteristics of strategic decisions making process (i.e. rationality and speed) in international firms and their possible mediating effect on performance.

Cost-Effectiveness of Alternative Retrofit Options to Support Decision Making

How to evaluate the cost-effectiveness of repair/retrofit intervention vs. demolition/replacement and what level of shaking intensity can the chosen repairing/retrofit technique sustain are open questions affecting either the pre-earthquake prevention, the post-earthquake emergency and the reconstruction phases. The (mis)conception that the cost of retrofit interventions would increase linearly with the achieved seismic performance (%NBS) often discourages stakeholders to consider repair/retrofit options in a post-earthquake damage situation. Similarly, in a pre-earthquake phase, the minimum (by-law) level of %NBS might be targeted, leading in some cases to no-action. Furthermore, the performance measure enforcing owners to take action, the %NBS, is generally evaluated deterministically. Not directly reflecting epistemic and aleatory uncertainties, the assessment can result in misleading confidence on the expected performance. The present study aims at contributing to the delicate decision-making process of repair/retrofit vs. demolition/replacement, by developing a framework to assist stakeholders with the evaluation of the effects in terms of long-term losses and benefits of an increment in their initial investment (targeted retrofit level) and highlighting the uncertainties hidden behind a deterministic approach. For a pre-1970 case study building, different retrofit solutions are considered, targeting different levels of %NBS, and the actual probability of reaching Collapse when considering a suite of ground-motions is evaluated, providing a correlation between %NBS and Risk. Both a simplified and a probabilistic loss modelling are then undertaken to study the relationship between %NBS and expected direct and indirect losses.

Decision making nella robotica collettiva

Nel testo viene esposta la presa di decisione nella robotica collettiva, cioè il comportamento collettivo esibito dagli animali sociali in sciame migrato in un gruppo di robot. Questa tesi si prefigge di analizzare come un insieme di individui, all'interno di un gruppo, possano giungere tutti ad avere una stessa opinione comune, o come essi siano in grado di dividersi autonomamente il lavoro senza alcun bisogno di controllo centrale. Inizialmente, viene introdotta la robotica collettiva, esponendone origini, caratteristiche e ambiti di ricerca. Viene in seguito presentato il collective decision making, all'interno del comportamento collettivo generale, esponendone le origini biologiche fino ai primi esperimenti su dei semplici robot. Vengono poi analizzati i due aspetti del decision making, vale a dire il raggiungimento del consenso e la suddivisione del lavoro. Per entrambi gli argomenti, sono presentati studi sia di carattere biologico che robotico, allo scopo di trarne similitudini e differenze e realizzare una valida analisi critica. Infine, vengono esposti i possibili sviluppi del comportamento e della robotica collettiva, mostrando possibili scenari di utilizzo futuro e gli attuali limiti allo sviluppo.