Building trajectories through clinical data to model disease progression

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Clinical trials are typically conducted over a population within a defined time period in order to illuminate certain characteristics of a health issue or disease process. These cross-sectional studies provide a snapshot of these disease processes over a large number of people but do not allow us to model the temporal nature of disease, which is essential for modeling detailed prognostic predictions. Longitudinal studies, on the other hand, are used to explore how these processes develop over time in a number of people but can be expensive and time-consuming, and many studies only cover a relatively small window within the disease process. This thesis describes the application of intelligent data analysis techniques for extracting information from time series generated by different diseases. The aim of this thesis is to identify intermediate stages in a disease process and sub-categories of the disease exhibiting subtly different symptoms. It explores the use of a bootstrap technique that fits trajectories through the data generating “pseudo time-series”. It addresses issues including: how clinical variables interact as a disease progresses along the trajectories in the data; and how to automatically identify different disease states along these trajectories, as well as the transitions between them. The thesis documents how reliable time-series models can be created from large amounts of historical cross-sectional data and a novel relabling/latent variable approach has enabled the exploration of the temporal nature of disease progression. The proposed algorithms are tested extensively on simulated data and on three real clinical datasets. Finally, a study is carried out to explore whether we can “calibrate” pseudo time-series models with real longitudinal data in order to improve them. Plausible directions for future research are discussed at the end of the thesis

Effect of curing conditions and harvesting stage of maturity on Ethiopian onion bulb drying properties

The study was conducted to investigate the impact of curing conditions and harvesting stageson the drying quality of onion bulbs. The onion bulbs (Bombay Red cultivar) were harvested at three harvesting stages (early, optimum, and late maturity) and cured at three different temperatures (30, 40 and 50 oC) and relative humidity (30, 50 and 70%). The results revealed that curing temperature, RH, and maturity stage had significant effects on all measuredattributesexcept total soluble solids

DEVELOPMENT OF NANOPARTICLE RATE-MODULATING AND SYNCHROTRON PHASE CONTRAST-BASED ASSESSMENT TECHNIQUES FOR CARDIAC TISSUE ENGINEERING

Myocardial infarction (MI) is the most common cause of heart failure. Despite advancements in cardiovascular treatments and interventions, current therapies can only slow down the progression of heart failure, but not tackle the progressive loss of cardiomyocytes after MI. One aim of cardiac tissue engineering is to develop implantable constructs (e.g. cardiac patches) that provide physical and biochemical cues for myocardium regeneration. To this end, vascularization in these constructs is of great importance and one key issue involved is the spatiotemporal control of growth-factor (GF)-release profiles. The other key issue is to non-invasively quantitatively monitor the success of these constructs in-situ, which will be essential for longitudinal assessments as studies are advanced from ex-vivo to animal models and human patients. To address these issues, the present research aims to develop nanoparticles to modulate the temporal control of GF release in cardiac patches, and to develop synchrotron X-ray phase contrast tomography for visualization and quantitative assessment of 3D-printed cardiac patch implanted in a rat MI model, with four specific objectives presented below. The first research objective is to optimize nanoparticle-fabrication process in terms of particle size, polydispersity, loading capacity, zeta potential and morphology. To achieve this objective, a comprehensive experimental study was performed to examine various process parameters used in the fabrication of poly(lactide-co-glycolide) (PLGA) nanoparticles, along with the development of a novel computational approach for the nanoparticle-fabrication optimization. Results show that among various process parameters examined, the polymer and the external aqueous phase concentrations are the most significant ones to affect the nanoparticle physical and release characteristics. Also, the limitations of PLGA nanoparticles such as initial burst effect and the lack of time-delayed release patterns are identified. The second research objective is to develop bi-layer nanoparticles to achieve the controllable release of GFs, meanwhile overcoming the above identified limitations of PLGA nanoparticles. The bi-layer nanoparticle is composed of protein-encapsulating PLGA core and poly(L-lactide) (PLLA)-rate regulating shell, thus allowing for low burst effect, protein structural integrity and time-delayed release patterns. The bi-layer nanoparticles, along with PLGA ones, were successfully fabricated and then used to regulate simultaneous and/or sequential release of multiple angiogenic factors with the results demonstrating that they are effective to promote angiogenesis in fibrin matrix. The third objective is to develop novel mathematical models to represent the controlled-release of bioactive agents from nanoparticles. For this, two models, namely the mechanistic model and geno-mechanistic model, were developed based on the local and global volume averaging approaches, respectively, and then validated with experiments on both single- and bi-layer nanoparticles, by which the ovalbumin was used as a protein model for the release examination. The results illustrates the developed models are able to provide insight on the release mechanism and to predict nanoparticle transport and degradation properties of nanoparticles, thus providing a means to regulate and control the release of bioactive agents from the nanoparticles for tissue engineering applications. The fourth objective of this research is to develop a synchrotron-based phase contrast non-invasive imaging technique for visualization and quantitative assessment of cardiac patch implanted in a rat MI model. To this end, the patches were created from alginate strands using the three-dimensional (3D) printing technique and then surgically implanted on rat hearts for the assessment based on phase contrast tomography. The imaging of samples was performed at various sample-to-detector distances, CT-scan time, and areas of the region of interest (ROI) to examine their effects on imaging quality. Phase-retrieved images depict visible and quantifiable structural details of the patch at low radiation dose, which, however, are not seen from the images by means of dual absorption-phase and a 3T clinical magnetic resonance imaging. Taken together, this research represents a significant advance in cardiac tissue engineering by developing novel nano-guided approaches for vascularization in myocardium regeneration as well as non-invasive and quantitative monitoring techniques for longitudinal studies on the cardiac patch implanted in animal model and eventually in human patients

Semantic systems biology of prokaryotes : heterogeneous data integration to understand bacterial metabolism

The goal of this thesis is to improve the prediction of genotype to phenotypeassociations with a focus on metabolic phenotypes of prokaryotes. This goal isachieved through data integration, which in turn required the development ofsupporting solutions based on semantic web technologies. Chapter 1 providesan introduction to the challenges associated to data integration. Semantic webtechnologies provide solutions to some of these challenges and the basics ofthese technologies are explained in the Introduction. Furthermore, the ba-sics of constraint based metabolic modeling and construction of genome scalemodels (GEM) are also provided. The chapters in the thesis are separated inthree related topics: chapters 2, 3 and 4 focus on data integration based onheterogeneous networks and their application to the human pathogen M. tu-berculosis; chapters 5, 6, 7, 8 and 9 focus on the semantic web based solutionsto genome annotation and applications thereof; and chapter 10 focus on thefinal goal to associate genotypes to phenotypes using GEMs. Chapter 2 provides the prototype of a workflow to efficiently analyze in-formation generated by different inference and prediction methods. This me-thod relies on providing the user the means to simultaneously visualize andanalyze the coexisting networks generated by different algorithms, heteroge-neous data sets, and a suite of analysis tools. As a show case, we have ana-lyzed the gene co-expression networks of M. tuberculosis generated using over600 expression experiments. Hereby we gained new knowledge about theregulation of the DNA repair, dormancy, iron uptake and zinc uptake sys-tems. Furthermore, it enabled us to develop a pipeline to integrate ChIP-seqdat and a tool to uncover multiple regulatory layers. In chapter 3 the prototype presented in chapter 2 is further developedinto the Synchronous Network Data Integration (SyNDI) framework, whichis based on Cytoscape and Galaxy. The functionality and usability of theframework is highlighted with three biological examples. We analyzed thedistinct connectivity of plasma metabolites in networks associated with highor low latent cardiovascular disease risk. We obtained deeper insights froma few similar inflammatory response pathways in Staphylococcus aureus infec-tion common to human and mouse. We identified not yet reported regulatorymotifs associated with transcriptional adaptations of M. tuberculosis.In chapter 4 we present a review providing a systems level overview ofthe molecular and cellular components involved in divalent metal homeosta-sis and their role in regulating the three main virulence strategies of M. tu-berculosis: immune modulation, dormancy and phagosome escape. With theuse of the tools presented in chapter 2 and 3 we identified a single regulatorycascade for these three virulence strategies that respond to limited availabilityof divalent metals in the phagosome. The tools presented in chapter 2 and 3 achieve data integration throughthe use of multiple similarity, coexistence, coexpression and interaction geneand protein networks. However, the presented tools cannot store additional(genome) annotations. Therefore, we applied semantic web technologies tostore and integrate heterogeneous annotation data sets. An increasing num-ber of widely used biological resources are already available in the RDF datamodel. There are however, no tools available that provide structural overviewsof these resources. Such structural overviews are essential to efficiently querythese resources and to assess their structural integrity and design. There-fore, in chapter 5, I present RDF2Graph, a tool that automatically recoversthe structure of an RDF resource. The generated overview enables users tocreate complex queries on these resources and to structurally validate newlycreated resources. Direct functional comparison support genotype to phenotype predictions.A prerequisite for a direct functional comparison is consistent annotation ofthe genetic elements with evidence statements. However, the standard struc-tured formats used by the public sequence databases to present genome an-notations provide limited support for data mining, hampering comparativeanalyses at large scale. To enable interoperability of genome annotations fordata mining application, we have developed the Genome Biology OntologyLanguage (GBOL) and associated infrastructure (GBOL stack), which is pre-sented in chapter 6. GBOL is provenance aware and thus provides a consistentrepresentation of functional genome annotations linked to the provenance.The provenance of a genome annotation describes the contextual details andderivation history of the process that resulted in the annotation. GBOL is mod-ular in design, extensible and linked to existing ontologies. The GBOL stackof supporting tools enforces consistency within and between the GBOL defi-nitions in the ontology. Based on GBOL, we developed the genome annotation pipeline SAPP (Se-mantic Annotation Platform with Provenance) presented in chapter 7. SAPPautomatically predicts, tracks and stores structural and functional annotationsand associated dataset- and element-wise provenance in a Linked Data for-mat, thereby enabling information mining and retrieval with Semantic Webtechnologies. This greatly reduces the administrative burden of handling mul-tiple analysis tools and versions thereof and facilitates multi-level large scalecomparative analysis. In turn this can be used to make genotype to phenotypepredictions. The development of GBOL and SAPP was done simultaneously. Duringthe development we realized that we had to constantly validated the data ex-ported to RDF to ensure coherence with the ontology. This was an extremelytime consuming process and prone to error, therefore we developed the Em-pusa code generator. Empusa is presented in chapter 8. SAPP has been successfully used to annotate 432 sequenced Pseudomonas strains and integrate the resulting annotation in a large scale functional com-parison using protein domains. This comparison is presented in chapter 9.Additionally, data from six metabolic models, nearly a thousand transcrip-tome measurements and four large scale transposon mutagenesis experimentswere integrated with the genome annotations. In this way, we linked gene es-sentiality, persistence and expression variability. This gave us insight into thediversity, versatility and evolutionary history of the Pseudomonas genus, whichcontains some important pathogens as well some useful species for bioengi-neering and bioremediation purposes. Genome annotation can be used to create GEM, which can be used to betterlink genotypes to phenotypes. Bio-Growmatch, presented in chapter 10, istool that can automatically suggest modification to improve a GEM based onphenotype data. Thereby integrating growth data into the complete processof modelling the metabolism of an organism. Chapter 11 presents a general discussion on how the chapters contributedthe central goal. After which I discuss provenance requirements for data reuseand integration. I further discuss how this can be used to further improveknowledge generation. The acquired knowledge could, in turn, be used to de-sign new experiments. The principles of the dry-lab cycle and how semantictechnologies can contribute to establish these cycles are discussed in chapter11. Finally a discussion is presented on how to apply these principles to im-prove the creation and usability of GEM’s.</p

Extraterritorialities in Occupied Worlds

The concept of extraterritoriality designates certain relationships between space, law, and representation. This collection of essays explores contemporary manifestations of extraterritoriality and the diverse ways in which the concept has been put to use in various disciplines. Some of the essays were written especially for this volume; others are brought here together for the first time. The inquiry into extraterritoriality found in these essays is not confined to the established boundaries of political, conceptual, and representational territories or fields of knowledge; rather, it is an invitation to navigate the margins of the legal–juridical and the political, but also the edges of forms of representation and poetics. Within its accepted legal and political contexts, the concept of extraterritoriality has traditionally been applied to people and to spaces. In the first case, extraterritorial arrangements could either exclude or exempt an individual or a group of people from the territorial jurisdiction in which they were physically located; in the second, such arrangements could exempt or exclude a space from the territorial jurisdiction by which it was surrounded. The special status accorded to people and spaces had political, economic, and juridical implications, ranging from immunity and various privileges to extreme disadvantages. In both cases, a person or a space physically included within a certain territory was removed from the usual system of laws and subjected to another. In other words, the extraterritorial person or space was held at what could be described as a legal distance. (In this respect, the concept of extraterritoriality presupposes the existence of several competing or overlapping legal systems.) It is this notion of being held at a legal distance around which the concept of extraterritoriality may be understood as revolving. This volume is a part of Amir and Sela’s Exterritory Project, an ongoing art project that wishes to encourage both the theoretical and practical exploration of ideas concerning extraterritoriality in an interdisciplinary context. The project aims not only to draw on existing definitions of extraterritoriality but seeks also to charge it with new meanings, searching for ways in which the notion of extraterritoriality could produce a critique of discriminating power structures and re-articulate new practical, conceptual, and poetical possibilities

Extraterritorialities in Occupied Worlds

The concept of extraterritoriality designates certain relationships between space, law, and representation. This collection of essays explores contemporary manifestations of extraterritoriality and the diverse ways in which the concept has been put to use in various disciplines. Some of the essays were written especially for this volume; others are brought here together for the first time. The inquiry into extraterritoriality found in these essays is not confined to the established boundaries of political, conceptual, and representational territories or fields of knowledge; rather, it is an invitation to navigate the margins of the legal–juridical and the political, but also the edges of forms of representation and poetics. Within its accepted legal and political contexts, the concept of extraterritoriality has traditionally been applied to people and to spaces. In the first case, extraterritorial arrangements could either exclude or exempt an individual or a group of people from the territorial jurisdiction in which they were physically located; in the second, such arrangements could exempt or exclude a space from the territorial jurisdiction by which it was surrounded. The special status accorded to people and spaces had political, economic, and juridical implications, ranging from immunity and various privileges to extreme disadvantages. In both cases, a person or a space physically included within a certain territory was removed from the usual system of laws and subjected to another. In other words, the extraterritorial person or space was held at what could be described as a legal distance. (In this respect, the concept of extraterritoriality presupposes the existence of several competing or overlapping legal systems.) It is this notion of being held at a legal distance around which the concept of extraterritoriality may be understood as revolving. This volume is a part of Amir and Sela’s Exterritory Project, an ongoing art project that wishes to encourage both the theoretical and practical exploration of ideas concerning extraterritoriality in an interdisciplinary context. The project aims not only to draw on existing definitions of extraterritoriality but seeks also to charge it with new meanings, searching for ways in which the notion of extraterritoriality could produce a critique of discriminating power structures and re-articulate new practical, conceptual, and poetical possibilities