Breast cancer is the most common cancer in women and research efforts to unravel the underlying mechanisms that drive carcinogenesis are continuous. The emergence of high-throughput sequencing techniques and their constant advancement, in combination with large scale studies of genomic and transcriptomic data, allowed the identification of important genetic changes that take place in the breast cancer genome, including somatic mutations, copy number aberrations and genomic rearrangements.The overall aim of this thesis is to explore the presence of genetic changes that take place in the breast cancer transcriptome and their possible contribution to carcinogenesis. The aim of the first research study was the identification of expressed gene fusions in breast cancer and the study of their association with other genomic events. For achieving this, transcriptome sequencing and Single Nucleotide Polymorphism arrays data for a cohort of 55 tumors and 10 normal breast tissues were combined. Gene fusions were detected in the majority of the samples, with evident differences between breast cancer subtypes, where HER2+ samples had significantly more fusions than the other subtypes. The genome-wide analysis uncovered localization of fusion genes in specific chromosomes like 17, 8 or 20. Additionally, a positive correlation between the number of gene fusions and the number of amplifications was observed, including the association between fusions on chromosome 17 and the amplifications in HER2+ samples, which can be attributed to the highly rearranged genomes of these subtypes. Finally, the absence of highly recurrent fusions across this cohort adds to the notion that gene fusions in breast cancer are most likely private events, with the majority being “passenger” events. In the second research study, the aim was to identify a connection between viral infections and breast cancer by devising five different computational methods for the analysis of both transcriptome and exome data in a cohort of 58 breast tumors. Despite being able to detect viral sequences in our testing dataset, no significantly high numbers of viral sequences were detected in our samples. Specifically, viral sequences (~2-30 reads) were extracted belonging to viruses EBV, HHV6 and Merkel cell polyomavirus. Such low levels of viral expression direct against a viral etiology for breast cancer but one should not exclude possible cases of integrated but silent viruses.In the third research project, we analyzed in silico the transcriptional profiles of human endogenous retroviruses in breast cancer. Despite being scattered across the genome in large numbers, a number of ERVs are actively transcribed, consisting of a small percentage of the total mapped reads. Alongside protein coding genes and lncRNAs, they show distinct expression profiles across the different breast cancer subtypes with luminal and basal-like samples clear separating from each other. Additionally, distinct profiles between ER+ and ER- samples were observed. Tumor specific ERV loci show an association with the immune status of the tumors, indicating that ERVs are reactivated in tumors and could play a role in the activation of the immune response cascade.The results presented in this thesis exhibit only in a small fragment the diversity and heterogeneity of the breast cancer transcriptome. The strength of the sequencing techniques allows the in depth detection of different genomic events. Gene fusions should be considered as part of the breast cancer transcriptome but their low recurrence across samples indicates for a role as passenger events. Under the light of existing results, viral infections do not play a significant role in breast cancer. On the other hand, human endogenous retroviruses, despite originating from exogenous viruses, seems to exhibit transcriptional profiles similar to those of normal genes, indicating that they are part of the genome’s transcriptional machinery. / Doctorat en Sciences biomédicales et pharmaceutiques (Médecine) / info:eu-repo/semantics/nonPublished

The paper analyses the degree of output persistence in GDP in order to empirically discriminate between the Solow growth model, the perfect competition endogenous growth model, the imperfect competition endogenous growth model, and the subcase of a multiple equilibria model of endogenous growth for the case of Austria. We find that a temporary shock in the growth rate of output induces a permanent and larger effect on the level of GDP. This leads us to refute the Solow growth model and the perfect competition model. We find strong empirical support for the imperfect competition growth model, but cannot fully rule out the possibility of multiple equilibria growth rates. / Series: Department of Economics Working Paper Series

This dissertation addresses the modeling and solution of mixed-integer linear multistage stochastic programming problems involving both endogenous and exogenous uncertain parameters. We propose a composite scenario tree that captures both types of uncertainty, and we exploit its unique structure to derive new theoretical properties that can drastically reduce the number of non-anticipativity constraints (NACs). Since the reduced model is often still intractable, we discuss two special solution approaches. The first is a sequential scenario decomposition heuristic in which we sequentially solve endogenous MILP subproblems to determine the binary investment decisions, fix these decisions to satisfy the first-period and exogenous NACs, and then solve the resulting model to obtain a feasible solution. The second approach is Lagrangean decomposition. We present numerical results for a process network planning problem and an oilfield development planning problem. The results clearly demonstrate the efficiency of the special solution methods over solving the reduced model directly. To further generalize this work, we also propose a graph-theory algorithm for non-anticipativity constraint reduction in problems with arbitrary scenario sets. Finally, in a break from the rest of the thesis, we present the basics of stochastic programming for non-expert users.

The main focus of this thesis was to gain a better understanding about the dynamics of risk perception and its influence on people’s evacuation behavior. Another major focus was to improve our knowledge regarding geo-spatial and temporal variations of risk perception and hurricane evacuation behavior. A longitudinal dataset of more than eight hundred households were collected following two major hurricane events, Ivan and Katrina. The longitudinal survey data was geocoded and a geo-spatial database was integrated to it. The geospatial database was composed of distance, elevation and hazard parameters with respect to the respondent’s household location. A set of Bivariate Probit (BP) model suggests that geospatial variables have had significant influences in explaining hurricane risk perception and evacuation behavior during both hurricanes. The findings also indicated that people made their evacuation decision in coherence with their risk perception. In addition, people updated their hurricane evacuation decision in a subsequent similar event.

This thesis examines the effect of the government expenditure structure on the economic growth. The objective is to determine which components of public expenditures are growth enhancing and which growth retarding. The theoretical model is set into the endogenous growth framework and describes the growth mechanism of productive and unproductive government expenditures. The growth impact of public spending composition is analysed for 18 European countries from 1996 to 2012. The empirical part is based on the panel data analysis. The empirical findings suggest that reallocating public resources towards education and health can promote growth. Whereas, higher expenditures on spending and defence are likely to be growth-retarding.

Endogenous neural stem/progenitor cells therapy is one of the most advanced clinical trial worldwide. Generally, drug is given to the targeted area through the traditional strategies such as intraventricular or intravenous delivery method. However, those methods always come with undesired side-effects such as over-dose of drug and offensive injection are not applicable to the large-scale clinical application. In this study, the clinical feasibility of blended biosynthesized cellulose duraplasty was studied. Our results showed that physical properties of BBC can be controlled through the optimized fabrication process. In addition, the time length of Middle cerebral artery occlusion rat model was tested through the 60 vs 90 mins occlusion time behavioral assessments of rat and the data indicated that 60 mins length can induce significant motor functional impairment. Finally, the EGF & EPO-loaded BBC duraplasty was implanted over the removed area and the ELISA test revealed that BBC duraplasty can release and delivery the growth factors to the targeted area (subvertical zone) at least 3 days after implantation. In summary, our BBC duraplasty is showing the potential prospection to be a clinical-applicable duraplasty to replace the traditional commercial duraplasty in the future stroke recovery therapy.

Introduction: Viruses, extracellular vesicles (EVs) and endogenous retroviruses (ERVs) are types of sub-micron particles which are known to be released from a vast range of cell types, across many species. There are many medically relevant sub-micron particles which can enter healthy cells and enable the intercellular delivery of functional host-derived and foreign products, through their enclosed lipid layers. While multiple particle subsets have been identified, many of the properties, behaviors and biochemical functions have not been fully described and have yet to be characterized. Materials and Methods: CD4⁺ naïve T-cells were isolated from female C57BL6/N mice and stimulated with varying concentrations of PMA/I. In addition to concentration, the length of PMA/I activation was assessed. Supernatants and cells were harvested, filtered, and stained to be subsequently analyzed by Nanoscale Flow Cytometry, Nanoparticle Tracking Analysis and Flow Cytometry. Particle populations were quantified and sorted by size, by NTA. Labelling dye CFSE was used in conjunction with fluorescently conjugated CD81 and CD9 antibodies to separate EVs, including exosomes, from background signal. Naïve T-cell purity, viability and levels of activation were assessed by flow cytometry using CD3, CD4 and CD62L antibodies and viability staining. Results: Increasing PMA concentration led to a global increase in particles by T-cells and a specific increase in smaller particle production and were demonstrated to be significant by Welch’s T-test, when compared to non-activated and DMSO controls (p<0.0001). In addition to concentration, activation length also correlated with increases in total particle counts and a specific increase in the secretion of smaller particles in comparison to non-activated and DMSO controls (p<0.0001). Labelling techniques by NFC revealed an increased presence of CFSE-CD81 positive and CFSE-CD9 positive particles secreted by T-cells, treated for 24 hours, compared to the 0- and 12-hour timepoints. Conclusion: This work demonstrates preliminary steps and outlines methods to begin assessing discrete particle populations and subsets secreted by murine naïve T-cells. Being able to identify patterns of particle secretions by naïve T-cells, especially under immune-stimulated conditions, may be the solution to uncovering the necessary information on EV physiology, that is required to understand the roles EVs play in pathology and how these conserved pathways may lead conditions to become exacerbated. This knowledge is essential to uncovering the roles EVs play in pathophysiology, and in the development of novel rapid diagnostic tests, to screen for cancers, infections, autoimmune disorders, and numerous other pathological conditions.

This thesis deals with the multi-stage stochastic programming problems. In the first part, there are introduced two-stage and multi-stage stochastic programming problems. Next, two methods how to generate scenarios are described in detail - the moment method and paths-based methods. The second chapter describes the flower-girl problem, its various formulations and other extensions using ro- bustness and endogenous randomness. The practical part follows, where several different formulations of the flower-girl problem are solved. First, the problem when the florist sells roses with an unlimited life for one week is solved. Then this problem is reformulated as a two-stage problem and the results are compared. Then a formulation with a limited rose life of 2 days is presented. The greatest attention is paid to the problem with a limited rose life of 4 days - the basic formulation of the problem and several extended formulations are solved. 1

Les syncytines sont des gènes d'enveloppes rétrovirales (env) capturés qui sont essentiels pour l'établissement du placenta chez les mammifères. Il a été proposé que la diversité des syncytines capturées explique pourquoi le placenta est l'organe le plus variable chez les mammifères. Ici nous avons employé deux approches pour étudier le lien entre la capture d'env et l'émergence et la diversité des structures placentaires. D'abord, nous avons étudié la placentation des Hyaenidae, les seuls carnivores à présenter un placenta très invasif hémochorial, comme l'humain. Comme tous les carnivores, les hyènes expriment la syncytin-Car1 précédemment décrite, mais nous avons identifié une nouvelle env, capturée uniquement chez ces dernières, que nous avons nommée Hyena-Env2. Ce nouveau gène est présent au même locus chez toutes les hyènes, ayant été capturé pendant la radiation de la famille. Il est non-fusiogène mais a néanmoins été conservé pendant plus de 10 millions d'années et est exprimé à l'interface materno-fœtale du placenta, ce qui en fait un gène candidat pour expliquer le passage à la placentation hémochoriale qui a eu lieu chez les Hyaenidae. Ensuite, nous avons cherché des gènes syncytine dans le genre non-mammifère Mabuya, des lézards vivipares présentant un type rare de placenta très complexe et proche de celui des mammifères. Nous avons identifié une env qui a été capturée et conservée dans ce genre depuis sa radiation, il y a 25 millions d'années. Ce gène, que nous avons appelé syncytin-Mab1, est capable d'induire la fusion cellule-cellule et est exprimé dans une couche de cellules fusionnées à l'interface materno-fœtale du placenta, deux propriétés canoniques de syncytine. Nous avons aussi identifié le récepteur de syncytin-Mab1, MPZL1, et avons montré que leur interaction induit son activation et sa phosphorylation. L'activation de MPZL1 a été liée à la migration et à l'invasion cellulaire, indiquant que cette interaction env-récepteur pourrait jouer un rôle dans l'invasion placentaire du tissu maternel observée chez les Mabuya. Pour conclure, la caractérisation de ces deux nouvelles env indique que les gènes de type syncytine ont pu jouer un rôle à la fois dans l'émergence du placenta de Mabuya et dans la structure atypique du placenta des hyènes, supportant la notion que la capture d'env est une force évolutive majeure. / Syncytins are captured retroviral envelope genes (env) that are essential for the establishment of placental structures in mammals. The syncytins present in different mammalian families are highly diverse, resulting from distinct capture events, and it has been suggested that this might play a role in making the placenta the most diverse structure in mammals. Here we used two different approaches to investigate the links between env capture and emergence and diversity of placental structures. First, we investigated placentation in Hyaenidae, the only carnivorans that present a highly invasive hemochorial placenta, as is also found in humans. Hyenas express the previously identified syncytin-Car1 gene, as do all carnivorans, but we identified a new hyena-specific captured env that we named Hyena-Env2. This new gene is present at the same locus in all hyenas, having been captured during the radiation of this family. It is non-fusiogenic but still conserved over at least 10 million years of evolution and expressed at the materno-fetal interface in the hyena placenta, making it a candidate gene for explaining the endotheliochorial to hemochorial placental transition that occurred in Hyeanidae. Second, we searched for syncytin-like genes in the non-mammalian Mabuya lizards, which are viviparous and present a rare type of highly complex placenta that is very reminiscent of mammalian placentas. We identified an env gene that was captured and conserved in this genus since its radiation 25 million years ago. This gene, that we named syncytin-Mab1, is able to mediate cell-cell fusion in vitro and is expressed in a fused cell layer at the materno-fetal interface of the placenta in vivo, characteristic features of canonical mammalian syncytin genes. We also identified the cellular gene MPZL1 as the cognate receptor of syncytin-Mab1 and showed that their interaction induces activation and phosphorylation of the former. MPZL1 activation has been linked with cell migration and invasion, indicating that this env-receptor interaction could play a role in the placental invasion of maternal tissues observed in Mabuya. In conclusion, the characterization of these two novel env genes indicates that syncytin-like env might have played a role both in the emergence of the Mabuya placenta and the atypical placental structure of hyenas, reinforcing the notion that env capture is a major driving force in evolution.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第20447号 / 農博第2232号 / 新制||農||1050(附属図書館) / 学位論文||H29||N5068(農学部図書室) / 京都大学大学院農学研究科農学専攻 / (主査)教授 北島 宣, 教授 田尾 龍太郎, 教授 土井 元章 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM