Für die Beschichtung von Bauelementen im Bereich der Elektronik erlangt das Beschichtungsverfahren der Atomlagenabscheidung zunehmend an Bedeutung. Dieses Verfahren überzeugt hier durch seine Fähigkeit sehr homogene Schichten mit einer Dicke von wenigen nm auch auf Strukturen mit hohen Aspektverhältnissen zu erzeugen. Diese Arbeit beschäftigt sich mit der Atomlagenabscheidung von Aluminiumoxid unter Verwendung der Präkursoren Trimethylaluminium und Wasser. Hauptaufgabe dieser Arbeit ist die Modellierung eines experimentellen Prozessaufbaus mit kommerzieller Simulationssoftware. Anhand der Simulationsergebnisse können Aussagen zur Optimierung des ALD-Prozesses getroffen werden. Die durchgeführten Untersuchungen zeigen, dass für die Simulation eines ALD-Prozesses sehr lange Rechenzeiten erforderlich sind. Insbesondere konnte ein tieferes Verständnis der automatischen Zeitschrittweitenregulierung der Software bei transienten Simulationen gewonnen werden. Die Dauer der Spülschritte wurde durch die Simulationsergebnisse als ausreichend bestätigt. Des Weiteren kann die Verwendung der zur Anlage gehörigen Gasdusche anhand der Simulationsergebnisse nicht empfohlen werden.

Since the rediscovery of carbon nanotubes (CNTs) due to the publication of Sumio Iijima's article Helical microtubules of graphitic carbon in the magazine Nature in 1991 the interest in carbon nanotubes has rapidly increased. This bachelor thesis also deals with this popular material with the aim to functionalize CNTs for further uses in the microelectronic industry. A promising approach is the functionalization of the CNTs with metal nanoparticles or metal films. To achieve this, one can perform an atomic layer deposition (ALD) on CNTs. In the present work the Trimethylaluminum (TMA) ALD is the chosen process for the functionalization of the CNTs, which will be studied here. Since the available knowledge on the CNT-functionalization by gas phase reactions is very limited, a theoretical study of possible reaction pathways is necessary. Those studies are carried out with two modern quantumchemical programs, Turbomole and DMol³, which are described together with an introduction into Density Functional Theory, as well as an introduction of CNTs and the ALD process. A basic model of a CNT with a Single Vacancy defect, which had been selected according to the demands of the studies, is introduced. Because the TMA ALD process requires hydroxyl groups as its starting point, not only is the performance of a TMA ALD cycle on a CNT studied, but also reactions which result in the CNTs owning of hydroxyl groups. Consequently, this bachelor thesis will focus on two di erent aspects: The performance of one TMA ALD cycle and the study of possible educts for the TMA ALD process. This study of the educts includes possible structures which can be formed when a CNT comes into contact with air.

Das grundlegende Verständnis von Selbstorganisationsprozessen auf molekularem Niveau ist von entscheidender Bedeutung für den Fortschritt der Nanotechnologie. In diesem Zusammenhang werden hier Untersuchungen derartiger Prozesse an der Grenzfläche zwischen einer flüssigen Phase (z.B. einer Lösung) und einer kristallinen Festkörperoberfläche durchgeführt. Die Konzentration der Lösung und die Polarität des Lösungsmittels sind von entscheidender Bedeutung für die Kontrolle der durch Selbstorganisation gebildeten Strukturen von Molekülen an den flüssig-fest Grenzflächen zu einem Graphitsubstrat (HOPG). Im Mittelpunkt der vorliegenden Arbeit stehen die Einflüsse dieser beiden Parameter auf die Anordnung der Moleküle. Zunächst wird die Polarität der Lösungsmittel diskutiert. Lösungsmittel mit verschiedenen Polaritäten wie Phenyloctan (unpolar), Fettsäuren (moderat polar) und Fettalkohole (stark polar) wurden verwendet um Trimesinsäure (TMA) zu lösen. TMA bildet keine geordnete Struktur aus wenn es aus Phenyloctan (PO) abgeschieden wird. Ein poröses Muster ("Chicken-wire"-Struktur) entsteht aus der Lösung von TMA in Octansäure, wohingegen aus der Lösung von TMA in Undecanol ein Linienmuster durch Koadsorption von TMA und Undecanol Molekülen gebildet wird. Als nächstes werden die Auswirkungen der Ultraschallbehandlung der Lösungen zur Kontrolle der Konzentration der Lösung und die daraus resultierende unterschiedliche molekulare Packungsdichte und Strukturen beschrieben. Eine selbstassemblierte Struktur aus Zick-Zack-Dimerketten wird bei der TMA-PO Lösung nur beobachtet, wenn die Lösung für 5 Stunden Ultraschall ausgesetzt wurde. Die hoher Packungsdichte in Form der "Flower"-Struktur wird für Lösungen von TMA in Octansäure gefunden, nachdem diese für lange Zeit mit Ultraschall behandelt wurden. Ein weiterer Aspekt der vorliegenden Arbeit ist die entdeckte Veresterungsreaktion an der TMA-undecanol/HOPG Grenzfläche. 1-undecyl Monoester von TMA wurde überraschender Weise an dieser Grenzfläche gefunden, nachdem die TMA-Undecanol Lösungen, für lange Zeit Ultraschall ausgesetzt wurden. Diese Monoestermoleküle bilden sich an der flüssig-fest Grenzfläche allein auf Grund der erhöhten Konzentration von TMA (ohne jegliche externe Katalysatoren). Der physikalische Hintergrund der Prozesse des Lösens und der Ultraschallbehandlung sind der Gegenstand weiterer Untersuchungen. Selbstassemblierte Abscheidung tritt auch bei Verwendung nur der reinen Lösungsmittel (Octansäure beziehungsweise Undecanol) auf, was zu verschiedenen Mustern führt, welche ebenfalls durch Ultraschallbehandlung kontrolliert eingestellt werden können.

Bladder cancer is a potentially curable malignancy; however in regards to the state of current therapy regimens, a plateau has been reached in both the non-muscle and muscle invasive types. To obtain effective treatment, and consequently a decreased mortality, it has become imperative to test and understand aspects affecting therapy response. The aim of this thesis is to illustrate a better understanding of clinical factors affecting therapy response using new drug combinations and new tumor markers alongside established risk criteria. In Paper I we reported the 5 year follow up from a multicenter, prospectively randomized study and we evaluated the 5-year outcomes of BCG alone compared to a combination of epirubicin and interferon-a2b in the treatment of patients with T1 bladder cancer. Treatment, tumor size and tumor status at second resection were independent variables associated with recurrence. Concomitant Cis was not predictive of failure of BCG therapy. Independent factor for treatment failure was remaining T1 stage at second resection. In Paper II &III we investigated the validity of emmprin, survivin and CCTα proteins as biomarkers for response and survival before neoadjuvant cisplatin chemotherapy. Bladder tumor specimens were obtained before therapy from a total of 250 patients with T1-T4 bladder cancer enrolled in 2 randomized trials comparing neoadjuvant chemotherapy before cystectomy with a surgery only arm. Protein expression was determined by immunohistochemistry (IHC). Patients in the chemotherapy cohort with negative emmprin and CCTα expression had significantly better overall survival (OS) than those with positive expression. In Paper IV primary end point was examining STMN1 as prognostic factor in bladder cancer.  Analysis was performed on three bladder cancer patient cohorts using IHC, western blot and a bladder cancer cell line. High levels of STMN1, expression correlated to shorter disease-specific survival and the growth and migration of the cells were significantly reduced when transfecting the cells with STMN1 siRNA. Conclusion Risk assessment and predictors of outcomes could help in individualized treatment and follow up.  Biomarkers will become more important for treatment choices in bladder cancer management.

<p>Breast cancer is one of the most common malignancies in women. Due to early detection and the use of screening programs approximately 60% of all new cases lack lymph node involvement. Today, a substantial proportion of these women will be offered adjuvant systemic chemotherapy. However, better proliferation markers are needed to predict patient outcome and to avoid overtreatment. </p><p>Cyclin A, cyclin E and Ki-67 are all markers for proliferation and involved in the regulation of the cell cycle. Overexpression has been associated with disease recurrence in several studies, but the results have not been consistent. However, none of these studies has investigated aberrant expression of cyclin E (the expression of cyclin E during phases of the cell cycle other than late G1 and early S-phase). Studies have shown that aberrant cyclin E might provide additional prognostic information compared to cyclin E alone.</p><p>The aims of this thesis were 1.to investigate the prognostic value of cyclin A, cyclin E and aberrant cyclin E in early breast cancer. 2.to validate the tissue microarray (TMA) technique for cyclin A and 3.to define the most optimal cut-off values for cyclin A and Ki-67.</p><p>We found that the agreement of TMA and large section results was good with kappa values 0.62-0.75 and that the reproducibility of the two readers’ results was good or even very good, with kappa values 0.71 – 0.87. </p><p>The optimal cut-off value for cyclin A average was 8% and for cyclin A maximum value 11%. The corresponding values for Ki-67 were 15 and 22%. </p><p>Neither cyclin E nor aberrant cyclin E was a prognostic factor in low-risk node negative breast cancer patients. </p><p>Finally, we conclude that cyclin A is a prognostic factor in node negative breast cancer (univariate analysis average value OR=2.9 95% CI 1.8-4.6; maximum value OR=3.7 95% CI 2.3-5.9).</p>

Breast cancer (BC) is one of the leading causes of cancer-related deaths in Canadian women. Aggressive BCs (e.g. triple-negative subtype; TN) present a clinical challenge as defined biomarkers, particularly those indicative of unique cancer-associated signaling pathways, are needed to improve prognostication and prediction of therapeutic response. Overexpression of Src and its substrates, Ezrin and Tks5, have been associated with poor prognosis in many cancers. We have previously shown that Ezrin regulates proteolytic-independent invasion, while others have shown that Tks5 is associated with proteolytic-dependent invasion. Thus, expression of Ezrin versus Tks5 in BC cases may represent different invasion modalities. Additionally, immunofluorescence (IF)-based technologies may provide a more quantitative and objective approach for analysis of biomarker expression and subcellular compartmentalization compared to immunohistochemistry (IHC). In this study, I hypothesize that expression and subcellular localization of Src, Ezrin and Tks5, have improved prognostic significance in BCs, compared to current clinico-pathological parameters. To assess this, I optimized an IF-based automated quantification analysis (AQUA) system to measure subcellular expression in a 63-patient BC cohort and tested associations with clinico-pathological data. This thesis presents that: 1) Expression of Src and Ezrin increased, but that of Tks5 decreased in breast tumours compared to normal breast. 2) Src and Ezrin localized to the apical regions of normal breast epithelia but shifted to the cytoplasm in breast tumours. Tks5 exhibited a granular basal expression in normal breast epithelia, and is weakly expressed in tumour cellular compartments. 3) In our 63-patient cohort, Src and Ezrin had significant correlations with multiple clinico-pathological parameters, including TN status and lymphovascular invasion. 4) Clinico-pathological associations with IF-based AQUA scoring are directly comparable to conventional manual IHC scoring. Our study supports the role of Src and Ezrin as potential prognostic biomarkers for BC. / Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2013-07-09 12:51:09.527

<p>Det nord-australiska pama-njunganspråket djambarrpuyŋu har studerats med avseende på finita egenskaper. Det går att påstå att det finns en finithetsdistinktion i djambarrpuyŋu eftersom det finns satser som kan uttrycka vissa egenskaper (t ex tempus, modus, aspekt och nominativt/ergativt subjekt) samtidigt som det finns satsliknande konstruktioner som inte kan uttrycka detta. Ett möjligt samband mellan finita kriterier i djambarrpuyŋu är förmåga att fungera som talhandling och förmåga att overt kunna uttrycka nominativt/ergativt subjekt, men detta behöver studeras närmare. Ett annat möjligt samband är att endast konstruktioner som kan uttrycka nominativt/ergativt subjekt har möjlighet att uttrycka TMA på något vis, dvs overt TMA-markering ses då som ett möjligt (men icke-obligatoriskt) finit kriterium medan nominativt/ergativt subjekt ses som ett nödvändigt kriterium.</p>

Breast cancer is one of the most common malignancies in women. Due to early detection and the use of screening programs approximately 60% of all new cases lack lymph node involvement. Today, a substantial proportion of these women will be offered adjuvant systemic chemotherapy. However, better proliferation markers are needed to predict patient outcome and to avoid overtreatment. Cyclin A, cyclin E and Ki-67 are all markers for proliferation and involved in the regulation of the cell cycle. Overexpression has been associated with disease recurrence in several studies, but the results have not been consistent. However, none of these studies has investigated aberrant expression of cyclin E (the expression of cyclin E during phases of the cell cycle other than late G1 and early S-phase). Studies have shown that aberrant cyclin E might provide additional prognostic information compared to cyclin E alone. The aims of this thesis were 1.to investigate the prognostic value of cyclin A, cyclin E and aberrant cyclin E in early breast cancer. 2.to validate the tissue microarray (TMA) technique for cyclin A and 3.to define the most optimal cut-off values for cyclin A and Ki-67. We found that the agreement of TMA and large section results was good with kappa values 0.62-0.75 and that the reproducibility of the two readers’ results was good or even very good, with kappa values 0.71 – 0.87. The optimal cut-off value for cyclin A average was 8% and for cyclin A maximum value 11%. The corresponding values for Ki-67 were 15 and 22%. Neither cyclin E nor aberrant cyclin E was a prognostic factor in low-risk node negative breast cancer patients. Finally, we conclude that cyclin A is a prognostic factor in node negative breast cancer (univariate analysis average value OR=2.9 95% CI 1.8-4.6; maximum value OR=3.7 95% CI 2.3-5.9).

In situ protein detection in human tissues using antibodies reveals the cellular protein localization, and affinity-based proteomic studies can help to discover proteins involved in the development of diseases. However, antibodies often suffer from cross-reactivity, and the lack of positive and negative tissue controls for uncharacterized proteins complicates the mapping of the proteome. The aim of this thesis is thus to improve the methodology for validating antibodies used for immunostaining on formalin-fixed paraffin-embedded tissues. Two of the papers include comparisons between mRNA-expression and immunostaining of corresponding protein. In paper I, ISH and IHC staining patterns were compared on consecutive TMA-slides. The study of well-characterized genes showed that ISH could be used for validation of antibodies. ISH was further used for antibody evaluation, and could validate four out of nine antibodies showing potentially interesting staining patterns. In paper III, transcriptomic data generated by RNA-sequencing were used to identify tissue specific expression in lymphohematopoietic tissues. An increased expression in one or more of these tissues compared to other tissue types was seen for 693 genes, and these were further compared to the staining patterns of corresponding proteins in tissues. Antibody labeling is necessary for many immunoassays. In paper II, two techniques for antibody-biotinylation were compared, aiming to find a stringent labeling method for antibodies used for immunostaining on TMAs. The ZBPA-method, binding specifically to Fc-part of antibodies, was found to be superior to the Lightning Link-biotinylation kit targeting amine groups, since labeling of amine groups on stabilizing proteins in the antibody buffer causes unspecific staining. The localization of the estrogen receptor beta (ERβ) in human normal and cancer tissues was studied in paper IV. Thorough evaluation of 13 antibodies using positive and negative control cell lines showed that only one antibody, PPZ0506, is specific for ERβ in all three immunoassays used. Contradictory to previously published data, tissue profiling using PPZ0506 showed that ERβ is expressed in a limited number of normal and cancer tissues. In conclusion, the present investigations present tools for validation of antibodies used for large-scale studies of protein expression in tissues.

L'apparition d'une protéinurie néphrotique constitue un effet secondaire aux thérapies ciblées anti-angiogéniques utilisées en oncologie (anti-VEGF ligand et les inhibiteurs de récepteurs tyrosine kinase). Dans ces travaux, nous avons étudié 29 patients traités par ces thérapies. 8 d'entre eux ont développé des lésions glomérulaires minimes ou hyalinose segmentaire et focale (LGM/HSF) majoritairement suite au traitement par les inhibiteurs des récepteurs tyrosine kinases (RTKIs) et 13 présentaient principalement des lésions de microangiopathie thrombotique (MAT) après thérapie anti-VEGF ligand. Dans cette étude, nous avons mis en évidence que c-mip est un acteur majeur du développement de protéinurie néphrotique consécutive aux traitements par les RTKIs. En effet, le Sorafenib (RTKI) induit l’expression de c-mip en inhibant l’activité de RelA et ce mécanisme serait impliqué dans le déclenchement des lésions LGM/HSF. Le rôle de c-mip dans la physiopathologie des podocytopathies acquises nous a conduit à générer un modèle murin d'invalidation de c-mip, conditionnelle et spécifique du podocyte. Les souris déficientes pour c-mip ont été étudiées dans deux modèles expérimentaux de protéinurie, induits par le LPS et le Sorafenib, respectivement. Dans les deux modèles, la protéinurie était significativement atténuée chez les souris déficientes avec préservation de l'architecture glomérulaire en comparaison des souris témoins. Le sorafenib a entraîné chez les souris témoins des lésions glomérulaires caractérisées par des rétractions du floculus, des thrombi intraglomérulaires et des lésions podocytaires. Ces résultats suggèrent que le sorafenib constitue un nouveau modèle murin d'induction d'une glomérulopathie expérimentale et que l'invalidation de c-mip spécifiquement dans le podocyte confèrerait une résistance au développement de protéinurie et de lésions rénales, suggérant que c-mip serait une cible thérapeutique potentielle. / Nephrotic proteinuria constitutes a serious side effect of anti-angiogenic therapies commonly used in oncology (anti-VEGF and tyrosine kinase receptorinhibitors, RTKI). In this work, we studied 29 patients treated by anti-angiogenic therapies. Eight of them developed minimal change nephrotic syndrome and focal and segmental glomerulosclerosis (MCNS/FSGS), mainly after RTKI treatment, and 13 underwent thrombotic microangiopathy lesions, mostly associated with anti-VEGF ligand therapy. C-mip overexpression was strongly related to the onset of nephrotic proteinuria after RTKI. Sorafenib (RTKI) induced c-mip expression by inhibiting RelA activity, ultimately leading to MCNS/FSGS. To confirm and clarify the pathophysiological role of c-mip in acquired podocytopathies, we generated a conditional, podocyte-specific c-mip knock-out mouse model. C-mip knockout mice were subjected to two experimental models of proteinuria, induced by LPS and Sorafenib, respectively. In each model, proteinuria was significantly decreased in cmip-invalidated mice, while glomerular architecture was preserved as compared to control mice. In the latter, Sorafenib led to glomerular tuft retractions, intraglomerular thrombi and podocyte lesions. This is suggested as the first experimental model of RTKI-induced glomerulopathy. Moreover, the podocyte specific knock out of c-mip confers resistance to proteinuria and renal injury, confirming c-mip as a potential therapeutic target in idiopathic nephrotic syndrome.