Passivity Framework for Modeling, Composing and Mitigating Cyber Attacks

Thesis (Ph.D.)--University of Washington, 2016-08

A Scalable Design Framework for Variability Management in Large-Scale Software Product Lines

Variability management is one of the major challenges in software product line adoption, since it needs to be efficiently managed at various levels of the software product line development process (e.g., requirement analysis, design, implementation, etc.). One of the main challenges within variability management is the handling and effective visualization of large-scale (industry-size) models, which in many projects, can reach the order of thousands, along with the dependency relationships that exist among them. These have raised many concerns regarding the scalability of current variability management tools and techniques and their lack of industrial adoption. To address the scalability issues, this work employed a combination of quantitative and qualitative research methods to identify the reasons behind the limited scalability of existing variability management tools and techniques. In addition to producing a comprehensive catalogue of existing tools, the outcome form this stage helped understand the major limitations of existing tools. Based on the findings, a novel approach was created for managing variability that employed two main principles for supporting scalability. First, the separation-of-concerns principle was employed by creating multiple views of variability models to alleviate information overload. Second, hyperbolic trees were used to visualise models (compared to Euclidian space trees traditionally used). The result was an approach that can represent models encompassing hundreds of variability points and complex relationships. These concepts were demonstrated by implementing them in an existing variability management tool and using it to model a real-life product line with over a thousand variability points. Finally, in order to assess the work, an evaluation framework was designed based on various established usability assessment best practices and standards. The framework was then used with several case studies to benchmark the performance of this work against other existing tools.

Empowering single mothers in Iran : Applying a problem-solving model in learning groups to develop participants' capacities to improve their lives

Since 2000, a problem-solving model has been taught to the Society for Protecting the Rights of the Child, and teachers and  students of social work in two universities in Iran. Since 2006, with the initiation of UNICEF, social workers, psychologists  and even some psychiatrists in Iran have been learning this model. In 2008, a group of researchers created an empowerment-oriented  psycho-social group and private intervention project to assess whether a group of Iranian single mothers could use this model, which was traditionally used by professionals only, to effectively and independently meet challenges in their own lives. Our results show that all women used the model effectively and, consequently, made more deliberate decisions to improve their life situations. Some of the women succeeded in finding a job and many improved their family relationships. This study suggests that empowerment-oriented social work can help many clients to achieve their goals, and that this psycho-social intervention project can be a useful model for social work in Iran and many other societies.

Curricular training report: clinical studies coordination in a clinical research organization vs an investigational site perspective

This report describes my experience of nine months as a trainee of a CRO (Eurotrials, Scientific Consultants), as well as a trainee of a clinical research site (Clinical Academic Center – Braga, Association). This document describes the European framework about clinical research and the Portuguese situation compared to similar countries. The activities developed during this internship are also described. These activities are divided in two phases. The first one occurred in Eurotrials, Scientific Consultants, a CRO specialized in clinical research and scientific advice. The first weeks were dedicated to intensive self-training needed to perform CTA tasks. These tasks included qualification, initiation and monitoring activities related to clinical trials, as well as the development of a quality management system. The second phase took place on 2CA-Braga, a clinical research center located in Hospital of Braga. Clinical studies coordination was the main focus of this second phase of my internship, as well as negotiation of clinical studies agreements. I had also the opportunity to participate in “1as Jornadas de Investigação Clínica e Inovação” (1st Clinical Investigation and Innovation Conference) organized by 2CA-Braga. Globally, this internship was a great opportunity to get knowledge and experience in the implementation and management of clinical trials, in a CRO and clinical research site perspectives. These two perspectives provided an interesting overview about the scientific needs of different players involved in clinical research. To conclude, this internship strengthened the knowledge acquired from my academic background, which make me able to face and overcome new challenges in the clinical research area.

Bicultural individuals as workforce in Australian MNCs

This study focuses on bicultural individuals as workforce in multinational companies in Australia. The aim of the study is to research the role of these individuals in these companies, with three sub-questions; to research (bi)cultural identity biculturals have, exploiting biculturals’ competencies in multinational companies, and challenges in managing biculturals in these companies. The main theoretical concepts related to this research are biculture and a cross-cultural work environment. Furthermore, discussing biculturals as part of workforce in MNCs, by presenting opportunities and challenges, has been taken into account. The empirical part for the research was collected by semi-structured interviews between January and March 2016. The findings of this study suggest that the role of biculturals in MNCs is not established. Biculturals can be viewed as appreciated workforce but MNCs lack recognition and awareness of biculturals’ competencies. The competencies of biculturals’ are related to bicultural identity integration and sometimes competencies can be latent. Competencies bicultural individuals possess are often related to cultural knowledge, cultural frame switching, understanding and perception towards others. Australia as a nation faces cultural diversity daily but the potential behind it remains fairly untouched even on the individual level. The potential is everywhere but a more universal approach how to handle the potential still remains vague for most. There seem to be different approaches to diversity and to biculturalism, which lead to either advantage or challenge. It is found that in case the potential is recognized the result is more likely positive. Challenges may still occur yet if challenges are managed appropriately the company may be able to learn from them. Alternatively, ignorance is more likely to cause challenges that lead to a loss of resources. Biculturalism is not achieved overnight, as it was emphasized throughout this study, which highlights the role of competencies. For the future research it is necessary to find approaches how to enhance awareness and highlight possibilities, to capture currently lost potential.

New challenges for the EU internal security strategy

In recent years, the EU and its member states have experienced a number of changes, as well as challenges, in the areas of politics, economics, security and law. As these areas are interconnected, changes and challenges to any of them have implications for the others, as well as implications for the populations and institutions of the EU or those coming into contact with its international power and influence. This edited collection focuses primarily on security and law, particularly the EU’s internal security strategy. The EU’s Internal Security Strategy, adopted by the Spanish presidency early in 2010, followed the Lisbon Treaty in 2009, building on previous developments within the EU in the Area of Freedom Security and Justice (AFSJ) policy. The focus of the EU Internal Security Strategy is to prevent and combat “serious and organised crime, terrorism and cybercrime, in strengthening the management of our external borders and in building resilience to natural and man-made disasters”. The Internal Security strategy intersects and overlaps with the European Union’s Counter-terrorism strategy, the Strategy for the External Dimension of JHA, and the EU’s Security Strategy. The role of and interaction between these strategies, their supplementing documents, and their implications for crime, victims, the law, political relations, democracy and human rights, form the backdrop against which the chapters in this collection are written. Building on original research by its contributors, this collection comprises work by authors from a wide variety of academic and professional areas and perspectives, as well as different countries, on a variety of areas and issues related to or raised by the EU’s Internal Security Strategy, from intelligence-led policing to human trafficking and port security. This book examines, from a wide variety of disciplinary perspectives including law, geography, politics and practice, both this further refinement of existing internal provisions on cross-border crime, and the increasing external relations of the EU in the AFSJ.

DATA DRIVEN APPROACHES TO IDENTIFY DETERMINANTS OF HEART DISEASES AND CANCER RESISTANCE

Cancer and cardio-vascular diseases are the leading causes of death world-wide. Caused by systemic genetic and molecular disruptions in cells, these disorders are the manifestation of profound disturbance of normal cellular homeostasis. People suffering or at high risk for these disorders need early diagnosis and personalized therapeutic intervention. Successful implementation of such clinical measures can significantly improve global health. However, development of effective therapies is hindered by the challenges in identifying genetic and molecular determinants of the onset of diseases; and in cases where therapies already exist, the main challenge is to identify molecular determinants that drive resistance to the therapies. Due to the progress in sequencing technologies, the access to a large genome-wide biological data is now extended far beyond few experimental labs to the global research community. The unprecedented availability of the data has revolutionized the capabilities of computational researchers, enabling them to collaboratively address the long standing problems from many different perspectives. Likewise, this thesis tackles the two main public health related challenges using data driven approaches. Numerous association studies have been proposed to identify genomic variants that determine disease. However, their clinical utility remains limited due to their inability to distinguish causal variants from associated variants. In the presented thesis, we first propose a simple scheme that improves association studies in supervised fashion and has shown its applicability in identifying genomic regulatory variants associated with hypertension. Next, we propose a coupled Bayesian regression approach -- eQTeL, which leverages epigenetic data to estimate regulatory and gene interaction potential, and identifies combinations of regulatory genomic variants that explain the gene expression variance. On human heart data, eQTeL not only explains a significantly greater proportion of expression variance in samples, but also predicts gene expression more accurately than other methods. We demonstrate that eQTeL accurately detects causal regulatory SNPs by simulation, particularly those with small effect sizes. Using various functional data, we show that SNPs detected by eQTeL are enriched for allele-specific protein binding and histone modifications, which potentially disrupt binding of core cardiac transcription factors and are spatially proximal to their target. eQTeL SNPs capture a substantial proportion of genetic determinants of expression variance and we estimate that 58% of these SNPs are putatively causal. The challenge of identifying molecular determinants of cancer resistance so far could only be dealt with labor intensive and costly experimental studies, and in case of experimental drugs such studies are infeasible. Here we take a fundamentally different data driven approach to understand the evolving landscape of emerging resistance. We introduce a novel class of genetic interactions termed synthetic rescues (SR) in cancer, which denotes a functional interaction between two genes where a change in the activity of one vulnerable gene (which may be a target of a cancer drug) is lethal, but subsequently altered activity of its partner rescuer gene restores cell viability. Next we describe a comprehensive computational framework --termed INCISOR-- for identifying SR underlying cancer resistance. Applying INCISOR to mine The Cancer Genome Atlas (TCGA), a large collection of cancer patient data, we identified the first pan-cancer SR networks, composed of interactions common to many cancer types. We experimentally test and validate a subset of these interactions involving the master regulator gene mTOR. We find that rescuer genes become increasingly activated as breast cancer progresses, testifying to pervasive ongoing rescue processes. We show that SRs can be utilized to successfully predict patients' survival and response to the majority of current cancer drugs, and importantly, for predicting the emergence of drug resistance from the initial tumor biopsy. Our analysis suggests a potential new strategy for enhancing the effectiveness of existing cancer therapies by targeting their rescuer genes to counteract resistance. The thesis provides statistical frameworks that can harness ever increasing high throughput genomic data to address challenges in determining the molecular underpinnings of hypertension, cardiovascular disease and cancer resistance. We discover novel molecular mechanistic insights that will advance the progress in early disease prevention and personalized therapeutics. Our analyses sheds light on the fundamental biological understanding of gene regulation and interaction, and opens up exciting avenues of translational applications in risk prediction and therapeutics.

Exploring the contradictions between Brazil’s role in the global climate change regime and its position in regional environmental governance.

Similar to other developing countries Brazil’s position on climate change emphasises national sovereignty and the principle of “common but differentiated responsibilities”. However, in recent years Brasilia has also announced voluntary reductions in carbon emissions, making Brazil one of the leading emerging countries in its approach to climate change, while enhancing its international reputation and legitimacy. Compared to its neighbours Brazil has older and more developed domestic environmental institutions and movements. Yet, Brazil’s global leadership on climate change does not translate into a similar role in regional environmental governance. In the 2000s Argentina and Uruguay became embroiled in a bitter environmental conflict involving a shared natural resource, the Uruguay River. Brazil not only refused to mediate, but also kept it out of regional forums insisting on the conflict’s bilateral nature. Furthermore, Mercosur’s environmental agenda has progressively become eroded while Brazilian-led Unasur lacks an institutional framework dedicated to environmental concerns. This indicates that environmental concerns are far more important for Brazil’s global image than for its role as a regional leader. It also highlights the limited scope of the climate change negotiations which focus narrowly on reducing carbon emissions, without taking wider concerns over energy generation or environmental and social justice into account. Brazil has promoted hydropower generation, portrayed as “clean” energy. Yet, these projects have sparked strong domestic and regional civil society opposition due to their social and environmental costs which make it difficult for Brazil to claim a regional leadership role on environmental concerns.

Strategic tillage in no-till farming systems in Australia's northern grains-growing regions: I. Drivers and implementation

Development of no-tillage (NT) farming has revolutionized agricultural systems by allowing growers to manage greater areas of land with reduced energy, labour and machinery inputs to control erosion, improve soil health and reduce greenhouse gas emission. However, NT farming systems have resulted in a build-up of herbicide-resistant weeds, an increased incidence of soil- and stubble-borne diseases and enrichment of nutrients and carbon near the soil surface. Consequently, there is an increased interest in the use of an occasional tillage (termed strategic tillage, ST) to address such emerging constraints in otherwise-NT farming systems. Decisions around ST uses will depend upon the specific issues present on the individual field or farm, and profitability and effectiveness of available options for management. This paper explores some of the issues with the implementation of ST in NT farming systems. The impact of contrasting soil properties, the timing of the tillage and the prevailing climate exert a strong influence on the success of ST. Decisions around timing of tillage are very complex and depend on the interactions between soil water content and the purpose for which the ST is intended. The soil needs to be at the right water content before executing any tillage, while the objective of the ST will influence the frequency and type of tillage implement used. The use of ST in long-term NT systems will depend on factors associated with system costs and profitability, soil health and environmental impacts. For many farmers maintaining farm profitability is a priority, so economic considerations are likely to be a primary factor dictating adoption. However, impacts on soil health and environment, especially the risk of erosion and the loss of soil carbon, will also influence a grower's choice to adopt ST, as will the impact on soil moisture reserves in rainfed cropping systems. © 2015 Elsevier B.V.