Abstract Prognostic features of colorectal cancer (CRC) are important for determining the optimal treatment for an individual patient. This study was carried out to evaluate the significance of the prognostic significance of inflammatory cell reaction and tumour budding at the invasive front of the tumour in CRC patients, to study the pattern of alterations in the serum cytokine levels of CRC patients compared to healthy controls, and to evaluate whether the patterns of the cytokine levels alter according to the stage of disease. Study material consists of a series of CRC patients operated in Oulu University Hospital (N=466, studies I-II, and N=148, study III). The intensities of inflammatory cell reaction and tumour budding were estimated and the association of these features with survival was analysed (I-II). Preoperative serum samples were collected from patients and age- and sex-matched controls, and concentrations of 13 cytokines and chemokines were analysed (III). Inflammatory cell reaction and tumour budding at the tumour invasive margin were independent prognostic markers in CRC. In patients with stage I-II disease, high-grade inflammation was associated with better 5-year survival (87.6%) than low-grade inflammation (47.0%). Tumour budding was present in 24.0% of cases and predicted worse 5-year survival (15.4% in contrast to 63.5%). Serum levels of PDGF, IL-6, IL-7, and IL-8 were higher, and levels of MCP-1 were lower in CRC patients compared to controls. A pattern of five most predictive cytokines reached an excellent capacity in discriminating patients from healthy controls and reached an AUC of 0.890 in the ROC analysis. High-stage CRC was associated with increased levels of IL-6, IL-8 and IL-1ra, and metastasised disease was accompanied by an orientation to Th2 cytokine milieu. According to this study, patients with CRC can be stratified into different prognostic groups by assessing inflammatory cell reaction and tumour budding at the invasive front of the tumour. Evaluation of these features may give additional information for making treatment decisions. Serum cytokine profile was shown to change during cancer progression and seems promising in separating CRC patients from healthy controls, but its clinical value is yet to be confirmed. / Tiivistelmä Kasvaimen ennusteeseen vaikuttavien tekijöiden tunteminen on tärkeää syöpäpotilaan yksilöllisen hoidon suunnittelussa. Tässä tutkimuksessa selvitettiin kasvaimen tulehdusreaktion ja kasvaimen reunan silmuilevan kasvutavan merkitystä kolorektaalisyöpäpotilaiden ennusteeseen. Lisäksi tutkimuksessa mitattiin tulehdusreaktion välittäjäaineiden, seerumin sytokiinien, pitoisuuksia potilailla ja verrokeilla sekä näiden pitoisuuksien vaihtelua suhteessa syövän levinneisyyteen. Tutkimusaineisto koostui Oulun yliopistollisessa sairaalassa leikatuista kolorektaalisyöpäpotilaista (N=466, tutkimukset I–II, N=148, tutkimus III). Kasvainnäytteistä tutkittiin kasvaimen tulehdusreaktion ja silmuilevan kasvutavan voimakkuutta ja arvioitiin näitä piirteitä suhteessa potilaiden elinaikatietoihin (tutkimukset I–II). Potilaiden ja verrokkihenkilöiden seeruminäytteistä mitattiin 13 sytokiinin pitoisuudet (tutkimus III). Kasvaimen tulehdusreaktio ja silmuileva kasvutapa osoittautuivat itsenäisiksi ennustetekijöiksi. Potilailla oli parempi 5-vuotisennuste (87.6 %), jos kasvaimen tulehdusreaktio oli voimakas verrattuna tapauksiin, joissa tulehdusreaktio oli heikko (47.0 %). 24 %:ssa kasvaimista kasvutapa oli silmuileva, ja näillä 5-vuotisennuste oli huonompi kuin ei-silmuilevissa (15.4 % vs. 63.5 %). Potilailla todettiin korkeammat seerumin PDGF, IL-6, IL-7, ja IL-8 -pitoisuudet ja matalammat MCP-1 -pitoisuudet kuin verrokeilla. Mittaamalla viiden ennustearvoltaan merkitsevimmän sytokiinin pitoisuudet voitiin potilaat luotettavasti erottaa verrokeista ROC-analyysin avulla, kun ROC-käyrän alle jäävä pinta-ala oli 0.890 %. Pidemmälle levinneissä taudeissa todettiin korkeampia IL-6, IL-8 ja IL-1ra -pitoisuuksia, ja etäpesäkkeisissä taudeissa sytokiinipitoisuudet muuttuivat Th2 -profiilin suuntaiseksi. Tutkimuksen mukaan kasvaimen tulehdusreaktion ja silmuilevan kasvutavan arvioinnilla kolorektaalisyöpäpotilaat voidaan jakaa ennusteellisiin ryhmiin, mitä on mahdollista hyödyntää hoidon suunnittelussa. Seerumin sytokiiniprofiilin osoitettiin muuttuvan taudin edetessä, ja sytokiinien pitoisuudet poikkeavat kolorektaalisyöpäpotilailla verrattuna terveiltä verrokeilta mitattuihin arvoihin.

Shock waves are generally characterized by a sharp change of the pressure, which causes subsequent changes in properties of the surrounding in which it spreads. In medical applications, it is an acoustic shock wave which is used for the treatment of concrements for more than 25 years. This success naturally led to considerations about the possibility of using shock waves in other areas of medicine. One of the main directions of the research is the possibility of the damage to tumor tissue. In contrast to concrements the tumor tissue is not different from surrounding tissues by its acoustic attributes, so the normal lithotryptor is not appropriate for this application. Therefore, there has been developed a new source of shock waves, which is based on the principle of multichannel discharge on the composite anode. The experiments demonstrated the effect of the new source on the acoustically homogeneous tissue of the thigh muscle at a depth of rabbit in vivo. Then there was observed the damage to tumor tissue in vivo in rats. Finally, there was observed the damage to tumor tissue in vivo in rats in the combination with cisplatin and Photosan. It was found that the new source of shock waves can cause the damage to the acoustically homogeneous tissue in vivo in depth. It also can damage the tumor...

Introduction: Human papillomavirus (HPV) is changing the prevalence, survival and treatment paradigms in oropharyngeal squamous cell carcinoma (OPSCC). Improved survival of patients with HPV positive compared to HPV negative OPSCC has led to trials of treatment de-escalation. Current HPV detection methods are imprecise, therefore standardised assessment of transcriptionally active HPV in OPSCC is required. Furthermore, the differences in immune characteristics and/or the hypoxia response/effects could explain observed differences in prognosis between HPV positive and negative OPSCC. Rigorous HPV detection and subsequent biomarker evaluation should provide additional information required before introduction of treatment de-escalation in broad patient groupings. Methods: The study cohort was 218 patients with OPSCC who received radiotherapy with curative intent. HPV status was determined on pre-treatment, formalin-fixed paraffin-embedded blocks using: 1) polymerase chain reaction (PCR); 2) in-situ hybridisation (ISH) and 3) immuno-histochemistry (IHC). QuantiGene multiplex assay was designed to detect mRNA of reference sequences of the common high-risk HPV types (16, 18, 33, 35, 45, 52 and 58). HPV detection methods were compared with mRNA quantification. Multimarker IHC of immune cell markers using chromogenic and fluorescent staining was performed, analysed and compared with single marker IHC using automated multispectral image analysis. A validated multiplex IHC method was used for a) chromogenic (CD3, CD4, CD8, and FoxP3) and b) fluorescent (CD8, CD68 and PD1/PD-L1) evaluation in tumour and stroma compartments. Single marker IHC was used to investigate tumour hypoxia markers (HIF-1α and CA-IX) in HPV positive and negative OPSCC. Results: p16 IHC and ISH were the most sensitive and specific, respectively, for classifying HPV status. The combination of the three tests had the highest positive/negative predictive values compared with QuantiGene mRNA detection. Multiplex validation showed that, for serial sections up to 6 μm apart, there were highly significant correlations (P<0.0001) between single and multiplex counts for both chromogenic and fluorescent IHC. Overall there was less variation in cell counts with fluorescent staining when compared to chromogenic staining. Multiplex IHC of TILs in HPV positive and negative OPSCC showed higher infiltration in both tumour and stromal areas of CD3+CD4+ and CD3+CD8+ T cells but not CD4+FoxP3 Tregs in HPV positive compared with HPV negative OPSCC. Only CD3+CD8+ stromal and not tumour area infiltration was associated with increased survival (P=0.02). PD-L1 expression was higher in HPV negative OPSCC and this was related to macrophage (CD68) expression of PD-L1. In HPV negative tumours infiltration with CD68+PD-L1 was associated with a good prognosis. HPV negative patients had higher expression of HIF-1α but not CA-IX. High expression of both markers was associated with a poor prognosis irrespective of HPV status. Conclusions: There are other prognostic factors operating in the larger subdivision of HPV positive and negative OPSCC. Precise HPV detection and inclusion of other prognostic factors is required before treatment de-escalation is used. Expression of immune inhibitory factors (PD1/PD-L1) alone without contextualisation with immune cell density is insufficient for patient prognostication and potential selection for therapy using immune checkpoint inhibitors. Hypoxia modification of radiotherapy should be explored in both HPV positive and negative OPSCC.

Tumour necrosis factor-stimulated gene-6 (TSG-6) is a protein expressed in a wide range of cell types and tissues, predominantly in response to inflammatory stimuli. The expression of TSG-6 is believed to be associated with the protection of tissues from the damaging effects of inflammation. In animal models treatment with TSG-6 protein has been found to reduce inflammatory damage in myocardial infarction, corneal injury and arthritis. Endogenous TSG-6 production has been suggested to play a protective role in inflammatory arthritis and has been implicated in bone homeostasis. The expression of TSG-6 is also essential in the process of cumulus matrix formation that occurs around the oocyte in the periovulatory period and is necessary for successful ovulation and fertilisation. In many cases the mechanism underlying a particular TSG-6 function is not fully understood. TSG-6 has numerous binding partners including the serum glycoprotein inter-alpha-inhibitor (IαI), the growth factor bone morphogenetic protein-2 (BMP-2) and the extracellular matrix protein fibronectin, as well as glycosaminoglycans (GAGs) such as hyaluronan and heparan sulphate (HS). The TSG-6 protein is mostly composed of contiguous Link and CUB domains, with the majority of ligand binding sites identified within the Link module. The CUB domain of TSG-6 has been less extensively studied. Here biophysical techniques have been used to investigate the TSG-6 interactome including both the Link module and CUB domain. Intrinsic fluorescence spectroscopy was used to establish the metal-ion binding properties of the CUB domain, which was established to have a high affinity Ca2+-binding site. Using surface plasmon resonance (SPR), a novel metal-ion dependent interaction was found for the CUB domain of TSG-6 and the heavy chains (HCs) of IαI. Investigation using mutants of both the CUB domain of TSG-6 and HC of IαI established that the metal-ion binding sites within each protein are involved in the interaction. SPR analysis was also used to define the affinities and binding sites for TSG-6 interactions with fibronectin and BMP-2. High affinity interactions between TSG-6 ligands were also revealed (e.g. BMP-2 and HC, fibronectin and HC) and their binding sites defined. The discovery of the novel interactions between these TSG-6 ligands suggests crosstalk within the TSG-6 interactome, with the potential for ternary complex formation or indeed hierarchical orders of binding. Thus work was undertaken to develop a passivated lipid bilayer platform for use with surface sensitive techniques. This platform was used to investigate the hierarchy of protein and GAG interactions using quartz crystal microbalance with dissipation monitoring (QCM-D) and dual polarisation interferometry (DPI). The investigation revealed a novel role for the Link module of TSG-6 in heparin condensation, potentially via protein dimerisation and/or oligomerisation which could affect heparin/HS functions within the extracellular matrix (ECM). Thus the biophysical analysis of TSG-6 presented here has identified novel interactions and functions of TSG-6 which may provide mechanisms for the protective functioning of TSG-6 in inflammation and its ECM structuring role in ovulation.

This work is a revision of the article "Die Kalkulation kalkulierbarer Mutationen” by the same author. In some chapters errors have been corrected in the mathematical representation. Chapters 6 and 7 have been re-edited. In this work, corrected excerpts from "Tumour Physics" and from "Evolution and mutation Physics" are used. To the agencies concerned should be noted.

Impact of NKR-P1 polymorphism on Ly49 receptors expression in hybrid mouse strains (C57BL/6 x Balb/c, F10-12) Abstract Natural killer (NK) cells constitute the subpopulation of large granular lymphocytes which mediate spontaneous immune response against infected, transformed or allogeneic cells and thus represent an important component of the innate immunity. NK cells express a wide repertoir of surface receptors which can be either activating or inhibitory and which mediate NK cell recognition and regulation of cytolytic activity. NKR-P1 and Ly49 receptor families belong to the most important murine NK receptors. Both NKR-P1 and Ly49 families are members of C-type lectin-like superfamily of receptors encoded by natural killer gene complex (NKC) on chromosome 6 and include both activating and inhibitory members. The aim of this diploma thesis was to elucidate the impact of Nkr-p1c gene divergence on Ly49 receptors expression and to find out whether the Ly49 and Nkr-p1 gene clusters (which are localized on opposite ends of NKC) are inherited independently or whether the NKC domain is inherited as a complex. The second research interest was to illustrate the influence of the above mentioned divergence on cytotoxic activity of NK cells and tumor growth. In this study, inbred mouse strains C57BL/6 and Balb/c...

Background: There is need for judicious use of immunosuppression in patients with active lupus nephritis (LN), however this is guided by renal biopsy which is invasive and not freely available in most centres. Novel urinary biomarkers such as monocyte chemoattractant protein-1 (MCP-1) and tumour necrosis factor-like weak inducer of apoptosis (TWEAK) are secreted in the kidney and may be useful for predicting histological class, monitoring flares and assessing response to therapy. We assessed the utility of urinary MCP-1 (uMCP-1) and TWEAK (uTWEAK) in predicting renal histological findings, disease flares and treatment response 6 months following initiation of treatment for LN in newly biopsied patients. Methods: We recruited consenting patients with active LN confirmed on kidney biopsy. Relevant baseline demographic, biochemical and histological information was collected from the patients. ELISA methods were used to assess uMCP-1 and uTWEAK at baseline and at 6 months after completion of induction therapy. Results: There were 14 females and 6 male patients with a mean age of 29.8 ± 10.7 years, 60% were of mixed ancestry, 70% had proliferative LN. There was no association between uMCP-1 and uTWEAK and histological features (LN class, activity index, chronicity index and interstitial fibrosis). At 6 months, 6 patients were lost to follow-up and of the remaining 14, 12 (85%) attained remission (partial remission (n = 7) or complete remission (n = 5)). Both biomarkers were elevated in patients with active disease and significantly declined amongst those attaining remission, p = 0.018 and p = 0.015 respectively. However, for those not attaining remission, no association was found for both biomarkers (p >0.05). Conclusion: Our study did not show correlation between uMCP-1 and uTWEAK with histological features of LN. However, both biomarkers were elevated in patients with active disease and correlated with the remission status at the end of induction phase of treatment.

Shock waves have been used in medicine for more than 30 year. At the beginning was mainly use for lithotripsy, but today is also applied in other fields of medicine, such as orthopedics, rheumatology and others. Single shock wave is one shock that usually is repeated every 1-1.5 seconds. By contrast tandem shock waves are two shocks consecutively (ideal interval between shocks is from 8 to 15 microseconds), that are repeated. In this work we investigated the clinical use of single and tandem shock waves that are generated entirely new source. It is based on the principle of multichannel discharge. It was found that a single shock wave can destroy the union between bone and bone cement, this effect could be used in orthopedics. Single and tandem shock wave can damage the tumor in vivo, but the principle damage is different. Tandem shockwave is able to cause damage in a depth of acoustically homogeneous medium and enhances the effect of chemotherapy. It would therefore be possible to used single and tandem shock waves in oncology either alone, or their combination with other chemicals. Functional sample of clinically usable applicator of shock waves with a new source was made for these applications. Powered by TCPDF (www.tcpdf.org)

In der vorliegenden prospektiven Studie wurde der postoperative Krankheitsverlauf von 93 Hündinnen mit Mammatumoren untersucht. Ziel der Studie war es, eine präoperative Einschätzung der Dignität der Tumoren und der Prognose für die Hündin anhand der Relaxin-Plasmakonzentration zu gewinnen. In einer humanmedizinischen Studie konnte gezeigt werden, dass an Brustkrebs erkrankte Frauen mit einer hohen Relaxin-Plasmakonzentration häufiger an einem malignen Tumor erkrankt sind, der Tumor häufiger bereits metastasiert hatte und die Frauen früher starben. Der Kastrationsstatus (p = 0,132), eine hormonelle Läufigkeitsunterdrückung (p = 0,960), vorausgegangene Graviditäten (p = 0,780) und das Auftreten von Pseudograviditäten (p = 0,138) bei den an Mammatumoren erkrankten Hündinnen hatten keinen Einfluss auf die präoperativ bestimmte Relaxin-Plasmakonzentration. An Mammatumoren erkrankte Hündinnen und gesunde Kontrolltiere hatten keine unterschiedlichen Relaxin-Plasmakonzentrationen (p = 0,813). Die Relaxin-Plasma-konzentrationen von Hündinnen mit einer Herzerkrankung aus der Patientengruppe waren identisch mit denen der herzgesunden Hündinnen aus der Kontrollgruppe (p = 0,328). Innerhalb der Patientengruppe war es hinsichtlich der gemessenen Relaxin-Plasmakonzentration unerheblich, ob die Hündinnen einerseits an einem solitären oder an multiplen Mammatumoren erkrankt waren (p = 0,470), oder ob andererseits bei ihnen einseitig oder beidseitig Mammatumoren feststellbar waren (p = 0,371). Weder die Tumorgröße (p = 0,518) noch eine Ulzeration (p = 0,746) wirkten sich auf die Relaxin-Plasmakonzentration aus. Das Vorliegen von Nahmetastasen (p = 0,131) oder eines malignen Mammatumors (p = 0,240) führte zu keiner erhöhten Relaxin-Plasmakonzentration. Entsprechend war auch das Stadium der Erkrankung ohne Einfluss auf das gemessene Relaxin (p = 0,829). Im Rahmen der Verlaufsuntersuchung gab es keinen Unterschied zwischen den präoperativ und den sechs Monate postoperativ bestimmten Relaxin-Plasmakonzentrationen (p = 0,983). Weder eine Rezidivierung des Mammatumors (p = 0,084) noch eine Metastasierung des Tumors in die Lunge sechs Monate postoperativ (p = 0,200) waren anhand der präoperativ bestimmten Relaxin-Plasmakonzentrationen vorhersehbar. Auch lieferte Relaxin keinen Hinweis auf einen Tod infolge der Mammatumoren (p = 0,205). In dieser Arbeit konnte nach Auswertung der vorliegenden Daten kein Hinweis auf die Verwendbarkeit der Relaxin-Plasmakonzentration als prognostischer Marker für an Mammatumoren erkrankte Hündinnen gefunden werden. Es konnte, wie in vorherigen Studien, bestätigt werden, dass Hündinnen mit Tumoren kleiner 3 cm (p = 0,001) und Hündinnen im Stadium I der Erkrankung (p = 0,009, p = 0,022) eine signifikant niedrigere Wahrscheinlichkeit haben innerhalb des ersten Jahres postoperativ an den Folgen des Mammatumors zu versterben als Hündinnen mit größeren Tumoren oder in einem höheren Stadium der Erkrankung. Hündinnen, die an einem ulzerierenden Mammatumor erkrankt waren (p = 0,002) oder bei denen histopathologisch nachweisbare Metastasen in den regionären Lymphknoten vorlagen (p = 0,001), hatten eine signifikant niedrigere Wahrscheinlichkeit das erste postoperative Jahr zu überleben. Die Tiere, bei denen sechs Monate postoperativ Metastasen in der Lunge festgestellt werden konnten (p = 0,001) oder bei denen es zu einer Rezidivierung des Mammatumors kam (p = 0,001), hatten eine sehr hohe Wahrscheinlichkeit innerhalb des ersten postoperativen Jahres zu versterben.

Segmentation of magnetic resonance images is an important part of planning radiotherapy treat-ments for patients with brain tumours but due to the number of images contained within a scan and the level of detail required, manual segmentation is a time consuming task. Convolutional neural networks have been proposed as tools for automated segmentation and shown promising results. However, the data sets used for training these deep learning models are often imbalanced and contain data that does not contribute to the performance of the model. By carefully selecting which data to train on, there is potential to both speed up the training and increase the network’s ability to detect tumours. This thesis implements the method of importance sampling for training a convolutional neural network for patch-based segmentation of three dimensional multimodal magnetic resonance images of the brain and compares it with the standard way of sampling in terms of network performance and training time. Training is done for two different patch sizes. Features of the most frequently sampled volumes are also analysed. Importance sampling is found to speed up training in terms of number of epochs and also yield models with improved performance. Analysis of the sampling trends indicate that when patches are large, small tumours are somewhat frequently trained on, however more investigation is needed to confirm what features may influence the sampling frequency of a patch. / Segmentering av magnetröntgenbilder är en viktig del i planeringen av strålbehandling av patienter med hjärntumörer. Det höga antalet bilder och den nödvändiga precisionsnivån gör dock manuellsegmentering till en tidskrävande uppgift. Faltningsnätverk har därför föreslagits som ett verktyg förautomatiserad segmentering och visat lovande resultat. Datamängderna som används för att träna dessa djupinlärningsmodeller är ofta obalanserade och innehåller data som inte bidrar till modellensprestanda. Det finns därför potential att både skynda på träningen och förbättra nätverkets förmåga att segmentera tumörer genom att noggrant välja vilken data som används för träning. Denna uppsats implementerar importance sampling för att träna ett faltningsnätverk för patch-baserad segmentering av tredimensionella multimodala magnetröntgenbilder av hjärnan. Modellensträningstid och prestanda jämförs mot ett nätverk tränat med standardmetoden. Detta görs förtvå olika storlekar på patches. Egenskaperna hos de mest valda volymerna analyseras också. Importance sampling uppvisar en snabbare träningsprocess med avseende på antal epoker och resulterar också i modeller med högre prestanda. Analys av de oftast valda volymerna indikerar att under träning med stora patches förekommer små tumörer i en något högre utsträckning. Vidareundersökningar är dock nödvändiga för att bekräfta vilka aspekter som påverkar hur ofta en volym används.