Visualisation of curved tubular structures in medical databases: An application to virtual colonoscopy

Medical conditions affecting the colon are problematic to diagnose due to the difficulty in examining this particular internal organ. To date, the most widely used approach is to perform a colonoscopy; a procedure in which a small camera is inserted into the colon to examine its surface. This procedure is unpleasant and potentially dangerous for the patient, and is expensive and time consuming for the hospital. As a result, patients at risk of developing the conditions are not always screened as often as would be desirable. Over the last few years a new approach known as virtual colonoscopy has been gaining popularity. The method uses information from a CT scan to reconstruct a 3D model of the colon which can then be examined without the patient needing to undergo a colonoscopy. This approach is now commonly used when screening for polyps (an indication of colon cancer) but can not be so easily used on conditions such as Inflammatory Bowel Disease (IBD) where information beyond the shape of the surface is required. This thesis forms part of a larger project which aims to diagnose conditions such as IBD by using image processing algorithms on CT data and presenting the results to the user in an easy to interpret way. Specifically we are concerned with this visualisation stage of the system and so have developed a new visualisation approach which we call Volumetric CPR. This can be used to supplement the more traditional virtual flythrough visualisation and is applicable to IBD detection as well as screening for polyps. Our technique builds on the concept of Curved Planar Reformation (CPR), which has proved to be a practical and widely used tool for the visualisation of curved tubular structures within the human body. It has been useful in medical procedures involving the examination of blood vessels and the spine. However, it is more difficult to use it for structures such as the colon because abnormalities are smaller relative to the size of the structure and may not have such distinct density and shape characteristics. Our new approach improves on this situation by using volume rendering for hollow regions of the structure and standard CPR, for the surrounding tissue. This effectively combines grey scale contextual information with detailed colour information from the area of interest. The approach is successfully used with each of the standard CPR types and the resulting images are promising as an alternative for virtual colonoscopy. We also demonstrate how systems can effectively utilize this new visualisation in order to convey maximum information to the user. We show how overlays can be used to present surface coverage data and how sophisticated lighting models can improve the users understanding of the 3D structure. We also present details of how to integrate our visualisation into existing systems and work flows

Complex genetic approaches to neurodegenerative diseases.

Neurodegenerative diseases are fatal disorders in which disease pathogenesis results in the progressive degeneration of the central and/or the peripheral nervous systems. These diseases currently affect -2% of the population but are expected to increase in prevalence as average life expectancy increases. The majority of these diseases have a complex genetic basis. The work presented in this thesis aimed to investigate the genetic basis of two neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and the human prion diseases kuru and sporadic Creutzfeldt-Jakob disease (sCJD), using novel complex genetic approaches. ALS is a fatal neurodegenerative disease in which motor neurons are seen to degenerate. It is a complex disease with 10% of individuals having a family history and the remaining 90% of non-familial cases having some genetic component. The gene DYNC1H1 is involved in retrograde axonal transport and is a good candidate for ALS. In this thesis the genetic architecture of DYNC1H1 was elucidated and a mutation screen of exons 8, 13 and 14 was undertaken in familial forms of ALS and other motor neuron diseases. No mutations were found. A linkage disequilibrium (LD) based association study was conducted using two tagging single nucleotide polymorphisms (tSNPs) which were identified as sufficient to represent genetic variation across DYNC1HI. These tSNPs were tested for an association with sporadic ALS (SALS) in 261 cases and 225 matched controls but no association was identified. Kuru is a devastating epidemic prion disease which affected a highly geographically restricted area of the Papua New Guinea highlands, predominantly affected adult women and children. Its incidence has steadily declined since the cessation of its route of transmission, endocannibalism, in the late 1950's. Kuru imposed strong balancing selection on codon 129 of the prion gene (PRNP). Analysis of kuru-exposed and unexposed populations showed significant deviations from Hardy-Weinberg equilibrium (HWE) consistent with the known protective effect of codon 129 heterozygosity. Signatures of selection were investigated in the surviving populations, such as deviations from HWE and an increasing cline in codon 129 valine allele frequency, which covaried with disease exposure. A novel PRNP G127V polymorphism was detected which, while common in the area of highest kuru incidence, was absent from kuru patients and unexposed population groups. Genealogical analysis revealed that the heterozygous PRNP G127V genotype confers strong prion disease resistance, which has been selected by the kuru epidemic. Finally, PRNP copy number was investigated as a possible genetic mechanism for susceptibility to kuru and sCJD. No conclusive copy number changes were identified

Towards BIM/GIS interoperability: A theoretical framework and practical generation of spaces to support infrastructure Asset Management

The past ten years have seen the widespread adoption of Building Information Modelling (BIM) among both the Architectural, Engineering and Construction (AEC) and the Asset Management/ Facilities Management (AM/FM) communities. This has been driven by the use of digital information to support collaborative working and a vision for more efficient reuse of data. Within this context, spatial information is either held in a Geographic Information Systems (GIS) or as Computer-Aided Design (CAD) models in a Common Data Environment (CDE). However, these being heterogeneous systems, there are inevitable interoperability issues that result in poor integration. For this thesis, the interoperability challenges were investigated within a case study to ask: Can a better understanding of the conceptual and technical challenges to the integration of BIM and GIS provide improved support for the management of asset information in the context of a major infrastructure project? Within their respective fields, the terms BIM and GIS have acquired a range of accepted meanings, that do not align well with each other. A seven-level socio-technical framework is developed to harmonise concepts in spatial information systems. This framework is used to explore the interoperability gaps that must be resolved to enable design and construction information to be joined up with operational asset information. The Crossrail GIS and BIM systems were used to investigate some of the interoperability challenges that arise during the design, construction and operation of an infrastructure asset. One particular challenge concerns a missing link between AM-based information and CAD-based geometry which hinders engineering assets from being located within the geometric model and preventing geospatial analysis. A process is developed to link these CAD-based elements with AM-based assets using defined 3D spaces to locate assets. However, other interoperability challenges must first be overcome; firstly, the extraction, transformation and loading of geometry from CAD to GIS; secondly, the creation of an explicit representation of each 3D space from the implicit enclosing geometry. This thesis develops an implementation of the watershed transform algorithm to use real-world Crossrail geometry to generate voxelated interior spaces that can then be converted into a B-Rep mesh for use in 3D GIS. The issues faced at the technical level in this case study provide insight into the differences that must also be addressed at the conceptual level. With this in mind, this thesis develops a Spatial Information System Framework to classify the nature of differences between BIM, GIS and other spatial information systems

Identifying novel regulators of ciliogenesis

Primary cilia are microtubule-based “antennae-like” organelles extending from the apical surface of most mammalian cells. They integrate mechanical or chemical signals essential for cell homeostasis and differentiation through several cooperating compartments. Mutations in genes that encode ciliary proteins or proteins essential for correct ciliary function are the cause of a major group of inherited and variable developmental disorders known as ciliopathies. Functional interactions between ciliary compartments, the molecular basis of variable clinical phenotypes, and the mechanisms of cilia formation are all still poorly understood. The presence or absence of cilia can be easily imaged and quantitated. This lends itself to high-throughput, high-content imaging in reverse genetic screens of cellular phenotypes. siRNA reverse genetic screens were performed to assess increased cilia incidence and identified a key negative regulator of ciliogenesis. Analysis showed this regulator acts through a mechanism involving actin remodelling and acto-myosin contraction. Pharmacological inhibition of this target may therefore comprise a novel therapeutic approach for treatment of a broad group of ciliopathy disease classes. Further screening of a data-set for supernumerary primary cilia, added to the evidence that cytokinesis is not a prerequisite for ciliogenesis. Disruption of the centralspindilin complex caused mitotic failure and maturation of supernumerary centrosomes, leading to the formation of the supernumerary cilia, a known cellular phenotype of severe ciliopathies. Finally, a combinatorial screening approach to generate double genetic perturbations of ciliary genes identified reciprocal synthetic genetic interactions between anterograde intraflagellar transport (the IFT B complex) and the transition zone. Reverse genetics screening techniques have identified novel regulators and pathways of ciliogenesis, and a potential therapeutic target for ciliopathies. Furthermore, combinatorial screening has highlighted a novel and complex interaction in ciliary biology, that may provide potential new insights into ciliary organisation and disease pathomechanisms

Exploring the developmental functions of fat cadherins in Drosophila and mammals

The large cadherin Fat has important functions in morphogenetic processes during development of Drosophila and mammals. Yet, its molecular partners and signaling pathways are poorly understood. Here I studied a physical link between Drosophila Fat and the Hippo pathway regulator Expanded. I found that Expanded interacts with distinct domains of Fat through its FERM domain. This finding offers a possible explanation of how Fat regulates the apical localization of Expanded and its activity in the Hippo pathway. In order to better understand Expanded signaling, I further studied its phosphorylation and determined novel Expanded interactors, including the Yorkie co-factor Mask. The size and transmembrane nature of the mammalian Fat cadherin Fat4 had previously hindered the use of biochemical approaches to gain insight into its molecular functions. Here I developed several cell culture tools that allowed me to overcome some of these limitations and to study Fat4 localization and function. I performed proximity-dependent biotin identification (BioID) and identified an array of potential novel Fat4 interactors that will serve as a useful resource for future studies. Beside a variety of developmental defects, Fat4 mutant mice exhibit prenatal renal cysts with regions of abnormal primary cilia. Therefore, to understand if Fat4 regulates primary cilia, as has been suggested for several PCP proteins, I tested the effect of Fat4 depletion on cilia formation and maintenance in cell culture. Dramatic effects on cilia maintenance and centrosome positioning and coherence were found by knockdown with several independent siRNAs. However, CRISPR/Cas9-mediated Fat4 knockout did not confirm a requirement of Fat4 in these processes and indicated that cilia and centrosome defects were likely RNAi off-target effects. This highlights the potential pitfalls of RNAi and should be regarded as a cautionary tale

Combined immunotherapy approaches in preclinical models of mismatch-repair-deficiency-associated tumorigenesis

In this thesis, different immunotherapy strategies we employed to combat mismatch-repair-deficient (dMMR) cancer. We used two preclinical mouse models, either having constitutional (Mlh1) or conditional (Msh2) knock out. To prevent resistance development and improve outcome, we focused on combination strategies including whole tumor vaccines, immune checkpoint-inhibitors (α-PD-L1), classical chemotherapy or the Cyclin-dependent kinase inhibitor abemaciclib. By applying different combination strategies, a significant survival benefit was reached in all investigated treatments.Ziel dieser Arbeit war es, verschiedene Immuntherapien zu testen, um Mismatch-Reparatur-Defiziente (dMMR) Tumoren zu behandeln. Wir nutzten zwei präklinische Mausmodelle, die entweder einen konstitutionellen (Mlh1) oder einen konditionellen (Msh2) Knock-out tragen. Zur Verbesserung der Therapie, wurden verschiedene Kombinationsansätze getestet inklusive Tumorvakzinen, Immun-Checkpoint-Inhibitoren (anti-PD-L1), klassischer Chemotherapie oder dem Cyklin-abhängigen Kinase-Inhibitor Abemaciclib. Die Gabe verschiedener Kombinationstherapien konnte das Überleben signifikant verlängern