Cancer is among the leading causes of death worldwide. In 2012, there were 14 million new cases and 8.2 million cancer-related deaths worldwide. The number of new cancer cases is expected rise to 22 million within the next two decades. Most chronic cancers cannot be cured. However, if the precise cancer cell type is diagnosed at an earlier, less aggressive stage then the chance of curing the disease increases with accurate drug delivery. This work is a humble contribution to the advancement of cancer research. This work delves into biological cell phenotyping under a dielectrophoresis setup using computer vision. Dielectrophoresis is a well-known phenomenon in which dielectric particles are subjected to a non-homogeneous electric field. This work is an analytical part of a larger proposed system replete with hardware, software and microfluidics integration to achieve cancer cell characterization, separation and enrichment using contactless dielectrophoresis. To analyze the cell morphology, various detection and tracking algorithms have been implemented and tested on a diverse dataset comprising cell-separation video sequences. Other related applications like cell-counting and cell-proximity detection have also been implemented. Performances were evaluated against ground truth using metrics like precision, recall and RMS cell-count error. A detection approach using difference of Gaussian and super-pixel algorithm gave the highest average F-measure of 0.745. A nearest neighbor tracker and Kalman tracking method gave the best overall tracking performance with an average F-measure of 0.95. This combination of detection and tracking methods proved to be best suited for this dataset. A graphical user interface to automate the experimentation process of the proposed system was also designed. / Master of Science

Bien que le rejet humoral en transplantation rénale soit de mieux en mieux caractérisé, des difficultés diagnostiques persistent et son pronostic reste sombre. Objectifs : dans un tel contexte, nous avons privilégié 2 objectifs : (1) préciser les mécanismes physiopathologiques en cause lorsque des signes d’inflammation microvasculaire tels qu’une glomérulite sont observés isolément sur biopsie systématique ; (2) évaluer le rôle de l’autoimmunité au cours de la transplantation dans le but d’identifier d’éventuels marqueurs prédictifs d’une évolution particulière au cours de la greffe. Méthodes : dans un premier temps, nous avons effectué une analyse clinico-pathologique d’une cohorte de 20 patients avec glomérulite isolée sur biopsie systématique à 3 mois de la greffe, couplée à un phénotypage par analyse transcriptomique. Après cette première étape, les distorsions du répertoire B induites par la greffe ont été évaluées de manière séquentielle par technique d’immuno-empreinte chez 43 patients transplantés rénaux dans l’optique de la caractérisation éventuelle de nouveaux biomarqueurs à valeur diagnostique et pronostique. Résultats et conclusion : il n’y avait pas de différence significative à 3 ans de la transplantation entre le groupe de patients avec glomérulite isolée et le groupe témoin.Cependant, la cohorte de patients étudiée est hétérogène puisqu’une évolution péjorative a été observée chez une minorité de patients, pour lesquels des anticorps anti-HLA (non spécifiques du donneur) étaient plus souvent présents et le grade lésionnel plus élevé. L’étude du répertoire B illustre l’importante hétérogénéité interindividuelle des profils de réactivitévis à vis du tissu rénal. Après transplantation, l’apparition de bandes de réactivité additionnelles était notée chez 19/43 patients, et ce dans toutes les catégories anatomocliniques représentées. L’identification des cibles antigéniques est un complément indispensable de cette approche. / X

Cancer is arguably one of the most dangerous diseases and the major causes of death in the modern day. It becomes increasingly harder to treat and cure the disease as it makes progress. Detecting cancer at an early stage can help in preventing it from affecting an organism. However, it is very hard to detect at an early stage. The best possible way to tackle this disease is to first study it at a cellular level. This study aims at identifying various phenotypic traits of these cells in the Dielectrophoresis (DEP) based microfluidic device experimental setup and subsequently classifying the cells from the rest. A general framework for automatic labeling, identifying and classifying the malignant from the dead cells is developed in this work. The framework shows a top-down approach starting from static background subtraction, tracking, automatic labeling, feature extraction and finally classification. The data used in this work are videos of live and dead human prostate cancer (PC-3) cells flowing through the microfluidic device. Previous studies have shown that there are significant differences in morphological attributes between cancerous and non-cancerous cells. We focus mainly on shape, texture and geometry as the prominent attribute in our work and subsequently use them for classification. In this work we obtain good tracking results through optical flow as compared to previous work. For classification, linear classifiers such as logistic regression and linear Support Vector Machine (SVM) showed decent results. The machine learning algorithms use Histogram of Oriented Gradient (HOG) features plus the elliptical features as a combined feature vector. The elliptic features branch out this study to another direction that is useful in calculation of physical properties such as the cell elasticity through video processing and we propose a model for the same for the given setup. Currently, the elasticity of a single cell is calculated using expensive and time consuming procedures such as the atomic force microscopy (AFM). Using our framework, we can potentially obtain elasticity for a batch of cells in much less time. Also, our cell classification algorithm procedure is suitable for real time applications and can be a proposed futuristic concept for selective killing of cells. / Master of Science / Cancer is one of the most dangerous disease and a major cause of death in the modern day. It becomes increasingly harder to treat and cure the disease as it makes progress. Detecting cancer at an early stage can help in preventing it from affecting an organism. However, it is very hard to detect at an early stage. The best possible way to tackle this disease is to first study it at the cellular scale. Our study aims at identifying various characteristics of these cells from videos recorded in a dielectrophoresis (DEP) based cell sorting setup. A general framework for identifying and classifying the malignant from the dead cells is developed in this work. We use computer vision algorithms for detection, tracking and analyzing characteristics of the cells. We use these characteristics to classify the cells into live and dead with an accuracy of 95% using standard classification algorithms used in machine learning such as support vector machine and logistic regression. The study of such properties of the cells also enables us to propose a model to estimate Young’s modulus of elasticity of the cells. Currently, time consuming techniques such as the atomic force microscopy (AFM) are being used to determine the elasticity of a single cell at a time. Using our work, we can potentially obtain elasticity for a batch of cells in much less time. Our cell classification algorithm procedure is suitable for real time applications and can be a proposed futuristic concept for selective killing of cells.

Yes / Background/purpose Coronary heart disease is the leading cause of morbidity in patients with type 2 diabetes mellitus (T2DM), frequently resulting in a requirement for coronary revascularization using the internal mammary artery (IMA) or saphenous vein (SV). Patency rates of SV grafts are inferior to IMA and further impaired by T2DM whilst IMA patencies appear similar in both populations. Smooth muscle cells (SMC) play a pivotal role in graft integration; we therefore examined the phenotype and proliferative function of IMA- and SV-SMC isolated from non-diabetic (ND) patients or those diagnosed with T2DM. Methods/materials SMC were cultured from fragments of SV or IMA. Morphology was analyzed under light microscopy (spread cell area measurements) and confocal microscopy (F-actin staining). Proliferation was analyzed by cell counting. Levels of RhoA mRNA, protein and activity were measured by real-time RT-PCR, western blotting and G-LISA respectively. Results IMA-SMC from T2DM and ND patients were indistinguishable in both morphology and function. By comparison, SV-SMC from T2DM patients exhibited significantly larger spread cell areas (1.5-fold increase, P < 0.05), truncated F-actin fibers and reduced proliferation (33% reduction, P < 0.05). Furthermore, lower expression and activity of RhoA were observed in SV-SMC of T2DM patients (37% reduction in expression, P < 0.05 and 43% reduction in activity, P < 0.01). Conclusions IMA-SMC appear impervious to phenotypic modulation by T2DM. In contrast, SV-SMC from T2DM patients exhibit phenotypic and functional changes accompanied by reduced RhoA activity. These aberrancies may be epigenetic in nature, compromising SMC plasticity and SV graft adaptation in T2DM patients.

Yes / (1) Abdominal aortic aneurysm (AAA) is a silent, progressive disease with significant mortality from rupture. Whilst screening programmes are now able to detect this pathology early in its development, no therapeutic intervention has yet been identified to halt or retard aortic expansion. The inability to obtain aortic tissue from humans at early stages has created a necessity for laboratory models, yet it is essential to create a timeline of events from EARLY to END stage AAA progression. (2) We used a previously validated ex vivo porcine bioreactor model pre-treated with protease enzyme to create "aneurysm" tissue. Mechanical properties, histological changes in the intact vessel wall, and phenotype/function of vascular smooth muscle cells (SMC) cultured from the same vessels were investigated. (3) The principal finding was significant hyperproliferation of SMC from EARLY stage vessels, but without obvious histological or SMC aberrancies. END stage tissue exhibited histological loss of α-smooth muscle actin and elastin; mechanical impairment; and, in SMC, multiple indications of senescence. (4) Aortic SMC may offer a therapeutic target for intervention, although detailed studies incorporating intervening time points between EARLY and END stage are required. Such investigations may reveal mechanisms of SMC dysfunction in AAA development and hence a therapeutic window during which SMC differentiation could be preserved or reinstated. / This research was funded in part by The Leeds Teaching Hospitals Charitable Foundation (R11/8002). E.R.C. was supported by a PhD studentship from the Engineering and Physical Sciences Research Council (EPSRC; EP/F500513/1). R.J.H. was the recipient of an Intercalated Batchelor of Science Degree in Science award from the Royal College of Surgeons of England. M.A.B.(FS/18/12/33270 and FS/12/54/29671), K.I.B. (FS/12/26/29395), and K.J.G. (FS/11/91/29090) were supported by BHF Clinical Research Training Fellowships.

The aortic valve functions in a complex mechanical environment which leads to force dependent cellular and tissue responses. Characterization of these responses provides a fundamental understanding of valve pathogenesis. The aim of this work was to develop an ex vivo organ culture system capable of simulating physiological aortic pressures and flow rates, and study the biological characteristics of native porcine aortic valves cultured in the system. Collagen, sGAG and elastin content of the valve leaflets were measured and cusp morphology, cell phenotype, cell proliferation and apoptosis were examined. Presence of endothelial cells (ECs) on the leaflet surface was also evaluated. The differences in collagen, sGAG and elastin contents were not significant (p greater than0.05) between the cultured and fresh valve leaflets. The cultured valves maintained the structural integrity of the leaflets while preserving the native morphology and cell phenotype. Cell phenotype in leaflets incubated statically under atmospheric conditions decreased compared to fresh and cultured valve leaflets, indicating the importance of mechanical forces in maintaining the natural biology of the valve leaflets. ECs were retained on the surfaces of cultured leaflets with no remodeling of the leaflets. The number of apoptotic cells in the cultured leaflets was significantly (p less than 0.05) less than in the statically incubated leaflets and comparable to fresh leaflets. The sterile ex vivo organ culture system thus maintained the viability and native biological characteristics of the aortic valves that were cultured under dynamic conditions for a period of 48 hours.

Abdominal aortic aneurysm (AAA) is a disease of the aorta characterized by pathological remodeling and progressive weakening of the vessel resulting in the increased risk of rupture and sudden death. In a mouse model of the disease induced by chronic Angiotensin II (AngII) infusion, progression of AAAs is associated with reduced differentiation of smooth muscle cells (SMCs) at the site of lesion development. In the mouse model, the effectiveness of cyclooxygenase-2 (COX-2) inhibition for attenuating AAA progression is associated with maintenance of a differentiated SMC phenotype. However, the safety of COX-2 inhibitors is currently in question due to the increased risk of adverse cardiovascular events. Thus, it is crucial to identify mediators downstream of COX-2 that may provide new targets for treatment of this disease. Recent studies in humans and mouse models have suggested that the microsomal prostaglandin E synthase (mPGES-1) enzyme, which acts downstream of COX-2, may also be involved in the pathogenesis of the disease. We hypothesized that increased prostaglandin E2 (PGE2) synthesis resulting from the induction of both COX-2 and mPGES-1 may result in reduced differentiation of SMCs, and that disruption of this pathway would preserve the differentiated phenotype. To test this hypothesis, human aortic smooth muscle cells (hASMCs) were utilized to examine the effects of a variety of agents involved in AAA development and the COX-2 pathway. My findings suggest that one of the effects of exposing hASMCs to AngII involves a specific induction of mPGES-1 expression. Furthermore, although different COX-2-derived products may have opposing effects, mPGES-1-derived PGE2 may be the primary prostanoid synthesized by SMCs which functions to attenuate differentiation. Therefore, mPGES-1 inhibition may provide inhibition of PGE2 that is more specific than COX-2 inhibitor treatment and may serve as a therapeutic target for attenuating AAA progression by maintaining a differentiated SMC phenotype.

Die Wespengiftallergie stellt eine typische allergische Sofortreaktion dar. Für diese IgE-vermittelten, pathologischen Immunreaktionen ist die spezifische Immuntherapie (IT) die einzige zur Zeit zur Verfügung stehende kausale Therapie. Die Wirkmechanismen sind trotz intensiver Bemühungen weiterhin nicht vollständig aufgeklärt. Als wichtigste These wird zur Zeit eine Verlagerung des pathologischen, TH2-dominierten Zytokinmilieus in Richtung "normales" TH1-Milieu diskutiert. Es wurde auch eine reduzierte Mediatorfreisetzung von Effektorzellen, eine verminderte Leukozytenproliferation, eine verminderte Endorganantwort und charakteristische Ig-Titer-Veränderungen mit initialem Anstieg und längerfristigem Abfall des sIgE und Anstieg des sIgG4 beschrieben. In der vorliegenden Arbeit wurde der Einfluß der IT auf periphere B-Zellen hinsichtlich ihrer Ig-Produktion und ihres Phänotyps untersucht. 15 Patienten mit systemischen Reaktionen nach Wespenstich, Nachweis von spezifischem IgE und positivem Hauttest, bei denen eine Schnell-Immuntherapie eingeleitet wurde, wurden vor Beginn der Therapie (Tag 1), am Tag ihrer Entlassung (Tag 6), also einen Tag, nachdem die Erhaltungsdosis von 100 µg erreicht wurde, und vor der 2. ambulanten Allergeninjektion am 26. Tag untersucht. Die Expression von CD5, CD23, CD32, CD40, CD54, CD86, CD95, HLA-I-ABC und HLA-II-DR wurde auf peripheren mononukleären Blutzellen durchflußzytometrisch bestimmt. Anti-CD19 FITC wurde als spezifischer B-Zellmarker benutzt. Die Serum-Titer des Gesamt-IgE, Wespengift-spezifischen IgE und Wespengift-spezifischen IgG4 wurden mittels ELISA bestimmt. Zur statistischen Auswertung wurde der Wilcoxontest für nicht-parametrische, verbundene Daten benutzt. Die Expression von CD54, CD5, CD32 und HLA-II-DR wurde durch die IT signifikant und die von CD23 tendentiell modifiziert. So war die Expression dieser Moleküle auf der Oberfläche peripherer B-Zellen am Tag 6 im Vergleich zum Ausgangswert vom Tag 1 reduziert. Am 26. Tag wurden wieder Werte auf der Höhe der Ausgangswerte vom Tag 1 gemessen. Dagegen veränderte sich die Expression von CD40, CD86, CD95 und HLA-I-ABC während der untersuchten Zeitpunkte nicht. Die Ig-Titer veränderten sich in der für die IT charakteristischen Weise. So stieg nach 3 Wochen der Gesamt-IgE-, sIgE- und sIgG4-Titer hochsignifikant an. Die Expression der untersuchten Oberflächenmoleküle ist als Indikator für Veränderungen der Aktivationslage und des funktionellen Status der Zellen während der IT zu interpretieren. So spricht die Reduktion der Expression von CD32, CD54 und HLA-II für eine verminderte Aktivierungslage der peripheren B-Zellen. Ferner deutet die Reduktion von CD5 und CD32 auf eine Anergie der B-Zellen hin. Durch die reduzierte Expression von CD23 und CD54 könnte die T-B-Zell-Interaktion verschlechtert werden, die für die Effektorfunktionen beider Zellen bedeutsam ist.Einen wesentlichen Beitrag zur Wirksamkeit der IT könnte auch die verminderte Expression des HLA-II leisten, da HLA-II für die Ag-Präsentation essentiell ist. In dieser Arbeit wurde gezeigt, daß die spezifische Immuntherapie einen Einfluß nicht nur auf die Ig-Produktion der B-Zellen hat, sondern auch auf deren Phänotyp. Dies könnte Hinweise auf bisher nicht bekannte Mechanismen bieten, die an der Wirksamkeit der IT beteiligt sind. / Wasp-venom allergy is a typical IgE-mediated allergic reaction. Specific immunotherapy (IT) is the only currently available causal therapy for IgE-mediated allergies. The mechanisms responsible for the efficacy of IT are still not fully understood. So far, the main focus of research has been on changes of T-helper cell (TH) cytokine production with a shift from TH2 to TH1 cytokines. Reduced mediator secretion from effector cells of allergic reactions, decreased leukocyte proliferation, lowered responsiveness of end organs and changes in immunoglobulin levels have been reported as well. The purpose of this study was to investigate the influence of IT on phenotype and Ig-production of B-lymphocytes. 15 venom allergic patients with a history of systemic reactions after a wasp sting and venom-specific skin test reactivity as well as serum IgE were investigated before VIT (day 1), one day after reaching maintenance dose of 100 µg (day 6) during inpatient rush VIT, and again on day 26 during continued outpatient maintenance therapy. Changes in the serum levels of total IgE, allergen-specific IgE (sIgE) and sIgG4 were measured by ELISA. Expression of CD5, CD23, CD32, CD40, CD54, CD86, CD95, HLA-I-ABC and HLA-II-DR on double labeled B cells was studied by flow cytometry of peripheral blood mononuclear cells. On day 6, cell surface expression of CD54, CD5, CD32 and HLA-II-DR was decreased significantly in intensity and numbers of positive cells, compared to day 1, while on day 26, expression of these molecules approached again baseline levels. Furthermore, a trend to decreased CD23 was noted on day 6. No changes were observed for CD40, CD86, CD95 and HLA-I-ABC. Levels of total IgE, sIgE and sIgG4 showed a significant increase after 26 days of VIT. These data show that initiation of rush VIT has profound effects on B-cell phenotype and Ig-production. Reduced expression of surface molecules can be interpreted as a reduction of activation status of B-cells as well as reduced ability to present antigen and to costimulate other leukocytes. B cells may thus be additional direct or indirect targets of high dose antigen therapy and contribute to the efficacy of IT.

Vascular tissue engineering (VTE) with the use of polymeric scaffolds offers the potential to generate small-diameter (<6 mm) arteries. In this thesis, a degradable polar hydrophobic ionic (D-PHI) polyurethane porous scaffold was synthesized with the objective of demonstrating its potential application for VTE. D-PHI scaffold synthesis was optimized, maximizing isocyanate and methacrylate monomer conversion. Through the incorporation of a lysine-based crosslinker, scaffold mechanical properties and swelling were manipulated. Furthermore, D-PHI scaffolds demonstrated the ability to support the growth and adhesion of A10 vascular smooth muscle cells (VSMCs) during two weeks of culture. This study also investigated the effect of a double porogen approach on D-PHI scaffold properties, demonstrating an increase in the total scaffold porosity and pore interconnectivity. Specifically, it was found that the use of 10 wt% polyethylene glycol and 65 wt% sodium bicarbonate porogens resulted in a porous (79±3%) D-PHI scaffold with the mechanical properties (elastic modulus=0.16±0.03 MPa, elongation-at-yield=31±5%, and tensile strength=0.04±0.01 MPa) required to withstand the physiologically-relevant cyclic mechanical strain (CMS) that is experienced by VSMCs in vivo. Furthermore, the effects of uniaxial CMS (10% strain, 1 Hz, 4 weeks) on human coronary artery smooth muscle cells (hCASMCs), which were cultured in a porous D-PHI scaffold, were studied using a customized bioreactor. Four weeks of CMS was shown to yield greater DNA mass, more cell area coverage, a better distribution of cells within the scaffold, the maintenance of contractile protein expression and the improvement of tensile mechanical properties. The in vitro and in vivo degradation as well as the in vivo biocompatibility of D-PHI scaffolds were also investigated. Following their subcutaneous implantation in rats (100 days), porous D-PHI scaffolds demonstrated more cell/tissue infiltration within their pores and degraded in a controlled manner and at a faster rate when compared to in vitro studies (120 days), retaining the mechanical integrity required during neo-tissue formation. This thesis provides significant insight into the role of the D-PHI scaffold in combination with physiologically-relevant CMS in modulating VSMC proliferation and phenotype. The findings of this work can be used to tailor vascular tissue regeneration by regulating VSMC function in a directed manner.

Vascular tissue engineering (VTE) with the use of polymeric scaffolds offers the potential to generate small-diameter (<6 mm) arteries. In this thesis, a degradable polar hydrophobic ionic (D-PHI) polyurethane porous scaffold was synthesized with the objective of demonstrating its potential application for VTE. D-PHI scaffold synthesis was optimized, maximizing isocyanate and methacrylate monomer conversion. Through the incorporation of a lysine-based crosslinker, scaffold mechanical properties and swelling were manipulated. Furthermore, D-PHI scaffolds demonstrated the ability to support the growth and adhesion of A10 vascular smooth muscle cells (VSMCs) during two weeks of culture. This study also investigated the effect of a double porogen approach on D-PHI scaffold properties, demonstrating an increase in the total scaffold porosity and pore interconnectivity. Specifically, it was found that the use of 10 wt% polyethylene glycol and 65 wt% sodium bicarbonate porogens resulted in a porous (79±3%) D-PHI scaffold with the mechanical properties (elastic modulus=0.16±0.03 MPa, elongation-at-yield=31±5%, and tensile strength=0.04±0.01 MPa) required to withstand the physiologically-relevant cyclic mechanical strain (CMS) that is experienced by VSMCs in vivo. Furthermore, the effects of uniaxial CMS (10% strain, 1 Hz, 4 weeks) on human coronary artery smooth muscle cells (hCASMCs), which were cultured in a porous D-PHI scaffold, were studied using a customized bioreactor. Four weeks of CMS was shown to yield greater DNA mass, more cell area coverage, a better distribution of cells within the scaffold, the maintenance of contractile protein expression and the improvement of tensile mechanical properties. The in vitro and in vivo degradation as well as the in vivo biocompatibility of D-PHI scaffolds were also investigated. Following their subcutaneous implantation in rats (100 days), porous D-PHI scaffolds demonstrated more cell/tissue infiltration within their pores and degraded in a controlled manner and at a faster rate when compared to in vitro studies (120 days), retaining the mechanical integrity required during neo-tissue formation. This thesis provides significant insight into the role of the D-PHI scaffold in combination with physiologically-relevant CMS in modulating VSMC proliferation and phenotype. The findings of this work can be used to tailor vascular tissue regeneration by regulating VSMC function in a directed manner.