New Statistical Algorithms for the Analysis of Mass Spectrometry Time-Of-Flight Mass Data with Applications in Clinical Diagnostics

Mass spectrometry (MS) based techniques have emerged as a standard forlarge-scale protein analysis. The ongoing progress in terms of more sensitive machines and improved data analysis algorithms led to a constant expansion of its fields of applications. Recently, MS was introduced into clinical proteomics with the prospect of early disease detection using proteomic pattern matching. Analyzing biological samples (e.g. blood) by mass spectrometry generates mass spectra that represent the components (molecules) contained in a sample as masses and their respective relative concentrations. In this work, we are interested in those components that are constant within a group of individuals but differ much between individuals of two distinct groups. These distinguishing components that dependent on a particular medical condition are generally called biomarkers. Since not all biomarkers found by the algorithms are of equal (discriminating) quality we are only interested in a small biomarker subset that - as a combination - can be used as a fingerprint for a disease. Once a fingerprint for a particular disease (or medical condition) is identified, it can be used in clinical diagnostics to classify unknown spectra. In this thesis we have developed new algorithms for automatic extraction of disease specific fingerprints from mass spectrometry data. Special emphasis has been put on designing highly sensitive methods with respect to signal detection. Thanks to our statistically based approach our methods are able to detect signals even below the noise level inherent in data acquired by common MS machines, such as hormones. To provide access to these new classes of algorithms to collaborating groups we have created a web-based analysis platform that provides all necessary interfaces for data transfer, data analysis and result inspection. To prove the platform's practical relevance it has been utilized in several clinical studies two of which are presented in this thesis. In these studies it could be shown that our platform is superior to commercial systems with respect to fingerprint identification. As an outcome of these studies several fingerprints for different cancer types (bladder, kidney, testicle, pancreas, colon and thyroid) have been detected and validated. The clinical partners in fact emphasize that these results would be impossible with a less sensitive analysis tool (such as the currently available systems). In addition to the issue of reliably finding and handling signals in noise we faced the problem to handle very large amounts of data, since an average dataset of an individual is about 2.5 Gigabytes in size and we have data of hundreds to thousands of persons. To cope with these large datasets, we developed a new framework for a heterogeneous (quasi) ad-hoc Grid - an infrastructure that allows to integrate thousands of computing resources (e.g. Desktop Computers, Computing Clusters or specialized hardware, such as IBM's Cell Processor in a Playstation 3)

Differentiating the medial patterns of operatic adaptations: Macbeth

The processes that underlie the creation of operatic adaptations are similar to those of film adaptations, yet the language and discourse that is used in the two fields is considerably different. In opera, the adaptation is viewed as being the notated music score which contains the libretto. In film, however, discourse related to film adaptation tends to focus on the qualities of the production of the screenplay, not on the screenplay itself, viewing the film as being based on the source text instead of it being based on the screenplay. While these differences may be due to contractual issues – screenplays involving only one film production, operas involving as many stage productions as requested – and similar cultural values as those ascribed to composers also being ascribed to directors instead of the screenplay writers, it nevertheless provides a reason to consider the implications that the operatic adaptations have for the understanding of other media, including but not limited to screen-based media. This dissertation therefore argues for a reassessment of product creation processes as viewed by Adaptation Studies and Intermedial Studies through the differentiation of medial patterns of operas in intermedial and intramedial contexts. A four-phase model divided into conception, adaptation/composition, production, and reception is proposed that could realign adaptation research away from a predominantly qualitative approach that combines reception based on the aesthetics of a production, to combine quantitative and qualitative methods that also examine the text-types created by adapters. In doing so, research and education in English Studies would benefit from clearer theoretical foundations that do not mostly link a source text with the aesthetic qualities of the production, but with the textual links to the structural conventions of the medial form involved. It is proposed here that the concept of fidelity to a source text, if it must be used in research or in education, should be discussed in various forms: fidelity to the text of the source text (textual fidelity), fidelity to the structural conventions of the text-type/medium (medial fidelity), and the subjective fidelity of the aesthetics of a production (aesthetic fidelity). The splitting of the fidelity concept proposed in this research could advantage English Studies – and many other academic fields – by providing a deeper understanding related to the interpretations of a source text: do the interpretations of the source text occur in the written form in the text-type formed in the adaptation/composition phase or in the visual and/or auditory mediation of the text-type into a directed adaptation during the production phase? Has an interpretation of the text occurred through mediation of text by the adapter (e.g. screenwriter) or the director? The quantitative analysis in this research involved 75 adaptations of Macbeth in two groups of adaptations, directed and printed, and eleven categories of media, including eight operas. The analysis provided data regarding the percentage of text in each medial category and the number and type of alterations made to the text that form the patterns of each medium. Following the intermedial findings, intramedial analysis of all 14 available operatic adaptations of Macbeth was also undertaken, including three individual case studies and two comparative case studies on some lesser known Macbeth operas. The theoretical basis of the dissertation revolves around concepts by Linda Hutcheon in Adaptation Studies and Lars Elleström in Intermedial Studies. Evidence and observations from the intermedial and intramedial analyses and the case studies provide support for the extension of some of Hutcheon’s concepts (e.g. adaptation as process, and knowing and unknowing audiences) and raise issues that highlight some problematic areas of others, such as modes of engagement

Interactive Machine Learning for User-Innovation Toolkits – An Action Design Research approach

Machine learning offers great potential to developers and end users in the creative industries. However, to better support creative software developers' needs and empower them as machine learning users and innovators, the usability of and developer experience with machine learning tools must be considered and better understood. This thesis asks the following research questions: How can we apply a user-centred approach to the design of developer tools for rapid prototyping with Interactive Machine Learning? In what ways can we design better developer tools to accelerate and broaden innovation with machine learning? This thesis presents a three-year longitudinal action research study that I undertook within a multi-institutional consortium leading the EU H2020 -funded Innovation Action RAPID-MIX. The scope of the research presented here was the application of a user-centred approach to the design and evaluation of developer tools for rapid prototyping and product development with machine learning. This thesis presents my work in collaboration with other members of RAPID-MIX, including design and deployment of a user-centred methodology for the project, interventions for gathering requirements with RAPID-MIX consortium stakeholders and end users, and prototyping, development and evaluation of a software development toolkit for interactive machine learning. This thesis contributes with new understanding about the consequences and implications of a user-centred approach to the design and evaluation of developer tools for rapid prototyping of interactive machine learning systems. This includes 1) new understanding about the goals, needs, expectations, and challenges facing creative machine-learning non-expert developers and 2) an evaluation of the usability and design trade-offs of a toolkit for rapid prototyping with interactive machine learning. This thesis also contributes with 3) a methods framework of User-Centred Design Actions for harmonising User-Centred Design with Action Research and supporting the collaboration between action researchers and practitioners working in rapid innovation actions, and 4) recommendations for applying Action Research and User-Centred Design in similar contexts and scale

Introduction to Development Engineering

This open access textbook introduces the emerging field of Development Engineering and its constituent theories, methods, and applications. It is both a teaching text for students and a resource for researchers and practitioners engaged in the design and scaling of technologies for low-resource communities. The scope is broad, ranging from the development of mobile applications for low-literacy users to hardware and software solutions for providing electricity and water in remote settings. It is also highly interdisciplinary, drawing on methods and theory from the social sciences as well as engineering and the natural sciences. The opening section reviews the history of “technology-for-development” research, and presents a framework that formalizes this body of work and begins its transformation into an academic discipline. It identifies common challenges in development and explains the book’s iterative approach of “innovation, implementation, evaluation, adaptation.” Each of the next six thematic sections focuses on a different sector: energy and environment; market performance; education and labor; water, sanitation and health; digital governance; and connectivity. These thematic sections contain case studies from landmark research that directly integrates engineering innovation with technically rigorous methods from the social sciences. Each case study describes the design, evaluation, and/or scaling of a technology in the field and follows a single form, with common elements and discussion questions, to create continuity and pedagogical consistency. Together, they highlight successful solutions to development challenges, while also analyzing the rarely discussed failures. The book concludes by reiterating the core principles of development engineering illustrated in the case studies, highlighting common challenges that engineers and scientists will face in designing technology interventions that sustainably accelerate economic development. Development Engineering provides, for the first time, a coherent intellectual framework for attacking the challenges of poverty and global climate change through the design of better technologies. It offers the rigorous discipline needed to channel the energy of a new generation of scientists and engineers toward advancing social justice and improved living conditions in low-resource communities around the world

Introduction to development engineering: a framework with applications from the field

This open access textbook introduces the emerging field of Development Engineering and its constituent theories, methods, and applications. It is both a teaching text for students and a resource for researchers and practitioners engaged in the design and scaling of technologies for low-resource communities. The scope is broad, ranging from the development of mobile applications for low-literacy users to hardware and software solutions for providing electricity and water in remote settings. It is also highly interdisciplinary, drawing on methods and theory from the social sciences as well as engineering and the natural sciences. The opening section reviews the history of “technology-for-development” research, and presents a framework that formalizes this body of work and begins its transformation into an academic discipline. It identifies common challenges in development and explains the book’s iterative approach of “innovation, implementation, evaluation, adaptation.” Each of the next six thematic sections focuses on a different sector: energy and environment; market performance; education and labor; water, sanitation and health; digital governance; and connectivity. These thematic sections contain case studies from landmark research that directly integrates engineering innovation with technically rigorous methods from the social sciences. Each case study describes the design, evaluation, and/or scaling of a technology in the field and follows a single form, with common elements and discussion questions, to create continuity and pedagogical consistency. Together, they highlight successful solutions to development challenges, while also analyzing the rarely discussed failures. The book concludes by reiterating the core principles of development engineering illustrated in the case studies, highlighting common challenges that engineers and scientists will face in designing technology interventions that sustainably accelerate economic development. Development Engineering provides, for the first time, a coherent intellectual framework for attacking the challenges of poverty and global climate change through the design of better technologies. It offers the rigorous discipline needed to channel the energy of a new generation of scientists and engineers toward advancing social justice and improved living conditions in low-resource communities around the world

Introduction to Development Engineering

This open access textbook introduces the emerging field of Development Engineering and its constituent theories, methods, and applications. It is both a teaching text for students and a resource for researchers and practitioners engaged in the design and scaling of technologies for low-resource communities. The scope is broad, ranging from the development of mobile applications for low-literacy users to hardware and software solutions for providing electricity and water in remote settings. It is also highly interdisciplinary, drawing on methods and theory from the social sciences as well as engineering and the natural sciences. The opening section reviews the history of “technology-for-development” research, and presents a framework that formalizes this body of work and begins its transformation into an academic discipline. It identifies common challenges in development and explains the book’s iterative approach of “innovation, implementation, evaluation, adaptation.” Each of the next six thematic sections focuses on a different sector: energy and environment; market performance; education and labor; water, sanitation and health; digital governance; and connectivity. These thematic sections contain case studies from landmark research that directly integrates engineering innovation with technically rigorous methods from the social sciences. Each case study describes the design, evaluation, and/or scaling of a technology in the field and follows a single form, with common elements and discussion questions, to create continuity and pedagogical consistency. Together, they highlight successful solutions to development challenges, while also analyzing the rarely discussed failures. The book concludes by reiterating the core principles of development engineering illustrated in the case studies, highlighting common challenges that engineers and scientists will face in designing technology interventions that sustainably accelerate economic development. Development Engineering provides, for the first time, a coherent intellectual framework for attacking the challenges of poverty and global climate change through the design of better technologies. It offers the rigorous discipline needed to channel the energy of a new generation of scientists and engineers toward advancing social justice and improved living conditions in low-resource communities around the world

FACING EXPERIENCE: A PAINTER’S CANVAS IN VIRTUAL REALITY

Full version unavailable due to 3rd party copyright restrictions.This research investigates how shifts in perception might be brought about through the development of visual imagery created by the use of virtual environment technology. Through a discussion of historical uses of immersion in art, this thesis will explore how immersion functions and why immersion has been a goal for artists throughout history. It begins with a discussion of ancient cave drawings and the relevance of Plato’s Allegory of the Cave. Next it examines the biological origins of “making special.” The research will discuss how this concept, combined with the ideas of “action” and “reaction,” has reinforced the view that art is fundamentally experiential rather than static. The research emphasizes how present-day virtual environment art, in providing a space that engages visitors in computer graphics, expands on previous immersive artistic practices. The thesis examines the technical context in which the research occurs by briefly describing the use of computer science technologies, the fundamentals of visual arts practices, and the importance of aesthetics in new media and provides a description of my artistic practice. The aim is to investigate how combining these approaches can enhance virtual environments as artworks. The computer science of virtual environments includes both hardware and software programming. The resultant virtual environment experiences are technologically dependent on the types of visual displays being used, including screens and monitors, and their subsequent viewing affordances. Virtual environments fill the field of view and can be experienced with a head mounted display (HMD) or a large screen display. The sense of immersion gained through the experience depends on how tracking devices and related peripheral devices are used to facilitate interaction. The thesis discusses visual arts practices with a focus on how illusions shift our cognition and perception in the visual modalities. This discussion includes how perceptual thinking is the foundation of art experiences, how analogies are the foundation of cognitive experiences and how the two intertwine in art experiences for virtual environments. An examination of the aesthetic strategies used by artists and new media critics are presented to discuss new media art. This thesis investigates the visual elements used in virtual environments and prescribes strategies for creating art for virtual environments. Methods constituting a unique virtual environment practice that focuses on visual analogies are discussed. The artistic practice that is discussed as the basis for this research also concentrates on experiential moments and shifts in perception and cognition and references Douglas Hofstadter, Rudolf Arnheim and John Dewey. iv Virtual environments provide for experiences in which the imagery generated updates in real time. Following an analysis of existing artwork and critical writing relative to the field, the process of inquiry has required the creation of artworks that involve tracking systems, projection displays, sound work, and an understanding of the importance of the visitor. In practice, the research has shown that the visitor should be seen as an interlocutor, interacting from a first-person perspective with virtual environment events, where avatars or other instrumental intermediaries, such as guns, vehicles, or menu systems, do not to occlude the view. The aesthetic outcomes of this research are the result of combining visual analogies, real time interactive animation, and operatic performance in immersive space. The environments designed in this research were informed initially by paintings created with imagery generated in a hypnopompic state or during the moments of transitioning from sleeping to waking. The drawings often emphasize emotional moments as caricatures and/or elements of the face as seen from a number of perspectives simultaneously, in the way of some cartoons, primitive artwork or Cubist imagery. In the imagery, the faces indicate situations, emotions and confrontations which can offer moments of humour and reflective exploration. At times, the faces usurp the space and stand in representation as both face and figure. The power of the placement of the caricatures in the paintings become apparent as the imagery stages the expressive moment. The placement of faces sets the scene, establishes relationships and promotes the honesty and emotions that develop over time as the paintings are scrutinized. The development process of creating virtual environment imagery starts with hand drawn sketches of characters, develops further as paintings on “digital canvas”, are built as animated, three-dimensional models and finally incorporated into a virtual environment. The imagery is generated while drawing, typically with paper and pencil, in a stream of consciousness during the hypnopompic state. This method became an aesthetic strategy for producing a snappy straightforward sketch. The sketches are explored further as they are worked up as paintings. During the painting process, the figures become fleshed out and their placement on the page, in essence brings them to life. These characters inhabit a world that I explore even further by building them into three dimensional models and placing them in computer generated virtual environments. The methodology of developing and placing the faces/figures became an operational strategy for building virtual environments. In order to open up the range of art virtual environments, and develop operational strategies for visitors’ experience, the characters and their facial features are used as navigational strategies, signposts and methods of wayfinding in order to sustain a stream of consciousness type of navigation. Faces and characters were designed to represent those intimate moments of self-reflection and confrontation that occur daily within ourselves and with others. They sought to reflect moments of wonderment, hurt, curiosity and humour that could subsequently be relinquished for more practical or purposeful endeavours. They were intended to create conditions in which visitors might reflect upon their emotional state, v enabling their understanding and trust of their personal space, in which decisions are made and the nature of world is determined. In order to extend the split-second, frozen moment of recognition that a painting affords, the caricatures and their scenes are given new dimensions as they become characters in a performative virtual reality. Emotables, distinct from avatars, are characters confronting visitors in the virtual environment to engage them in an interactive, stream of consciousness, non-linear dialogue. Visitors are also situated with a role in a virtual world, where they were required to adapt to the language of the environment in order to progress through the dynamics of a drama. The research showed that imagery created in a context of whimsy and fantasy could bring ontological meaning and aesthetic experience into the interactive environment, such that emotables or facially expressive computer graphic characters could be seen as another brushstroke in painting a world of virtual reality

Radio, the Resilient Medium Papers from the Third Conference of the ECREA Radio Research Section

Radio is a resilient medium. It has evolved considerably over its hundred-year history and we have every reason to believe that evolution will continue. This book is a peer- reviewed collection of papers from the third conference of the Radio Research Section of the European Research and Education Association (ECREA), held at the London Campus of the University of Sunderland in September 2013. It represents some of the best research presented at the conference, but every chapter has been revised and edited prior to publication. The book, like the conference, is an initiative of the Centre for Research in Media and Cultural Studies (CRMCS), which is based in Sunderland. Published by the Centre for Research in Media and Cultural Studies, University of Sunderland, Sunderland, United Kingdom SR1 3SD