Saskatchewan is the only province in Canada to have routinely tested the antimicrobial susceptibility of all provincially reported human cases of campylobacteriosis. From 1999 to 2006, 1378 human Campylobacter species infections were tested for susceptibility at the Saskatchewan Disease Control Laboratory using the Canadian Integrated Program for Antimicrobial Resistance Surveillance panel and minimum inhibitory concentration (MIC) breakpoints. Of these, 1200 were C. jejuni, 129 were C. coli, with the remaining made up of C. lari, C. laridis, C. upsaliensis and undifferentiated Campylobacter species. Campylobacter coli had significantly higher prevalences of ciprofloxacin resistance (CIPr), erythromycin resistance (ERYr), combined CIPr-ERYr resistance and multidrug resistance (to three or greater drug classes) than C. jejuni. Logistic regression models indicated that CIPr in C. jejuni decreased from 1999 to 2004 and subsequently increased in 2005 and 2006. The risk of CIPr was significantly increased in the winter months (January to March) compared to other seasons. A comparison of logistic regression and Cox proportional hazard survival models found that the latter were better able to detect significant temporal trends in CIPr and tetracycline resistance by directly modeling MICs, but that these trends were more difficult to interpret. Scan statistics detected significant spatial clusters of CIPr C. jejuni infections in urban centers (Saskatoon and Regina) and temporal clusters in the winter months; the space-time permutation model did not detect any space-time clusters. Bernoulli scan tests were computationally the fastest for cluster detection, compared to ordinal MIC and multinomial antibiogram models. eBURST analysis of antibiogram patterns showed a marked distinction between case and non-case isolates from the scan statistic clusters. Multilevel logistic regression models detected significant individual and regional contextual risk factors for infection with CIPr C. jejuni. Patients infected in the winter, that were between the ages of 40-45 years of age, that lived in urban regions and that lived in regions of moderately high poultry density had higher risks of a resistant infection. These results advance the epidemiologic knowledge of CIPr C. jejuni in Saskatchewan and provide novel analytical methods for antimicrobial resistance surveillance data in Canada. / Saskatchewan Disease Control Laboratory (Saskatchewan Ministry of Health); Laboratory for Foodborne Zoonoses (Public Health Agency of Canada); Centre for Foodborne, Environmental and Zoonotic Infectious Diseases (Public Health Agency of Canada); Ontario Veterinary College Blake Graham Fellowship

Cette thèse se place dans le cadre de l'étude in silico, c'est-à-dire assistée par ordinateur, des liens qui unissent la séquence d'une protéine à la (ou aux) structure(s) tri-dimensionnelle(s) qu'elle adopte. Le décryptage de ces liens présente de nombreuses applications dans divers domaines et constitue sans doute l'une des problématiques les plus fascinantes de la recherche en biologie moléculaire.<p><p>Le premier aspect de notre travail concerne le développement de potentiels statistiques dérivés de bases de données de protéines dont les structures sont connues. Ces potentiels présentent plusieurs avantages: ils peuvent être aisément adaptés à des représentations structurales simplifiées, et permettent de définir un nombre limité de fonctions énergétiques qui incarnent l'ensemble complexe d'interactions gouvernant la structure et la stabilité des protéines, et qui incluent également certaines contributions entropiques. Cependant, leur signification physique reste assez nébuleuse, car l'impact des diverses hypothèses nécessaires à leur dérivation est loin d'être clairement établi. Nous nous sommes attachés à l'étude de certaines limitations des ces potentiels: leur dépendance en la taille des protéines incluses dans la base de données, la non-additivité des termes de potentiels, et l'importance souvent négligée de l'environnement protéique spécifique ressenti par chaque résidu. Nous avons ainsi mis en évidence que l'influence de la taille des protéines de la base de données sur les potentiels de distance entre résidus est spécifique à chaque paire d'acides aminés, peut être relativement importante, et résulte essentiellement de la répartition inhomogène des résidus hydrophobes et hydrophiles entre le coeur et la surface des protéines. Ces résultats ont guidé la mise au point de fonctions correctives qui permettent de tenir compte de cette influence lors de la dérivation des potentiels. Par ailleurs, la définition d'une procédure générale de dérivation de potentiels et de termes de couplage a rendu possible la création d'une fonction énergétique qui tient compte simultanément de plusieurs descripteurs de séquence et de structure (la nature des résidus, leurs conformations, leurs accessibilités au solvant, ainsi que les distances qui les séparent dans l'espace et le long de la séquence). Cette fonction énergétique présente des performances nettement améliorées par rapport aux potentiels originaux, et par rapport à d'autres potentiels décrits dans la littérature.<p><p>Le deuxième aspect de notre travail concerne l'application de programmes basés sur des potentiels statistiques à l'étude de protéines qui adoptent des structures alternatives. La permutation de domaines est un phénomène qui affecte diverses protéines et qui implique la génération d'un oligomère suite à l'échange de fragments structuraux entre monomères identiques. Nos résultats suggèrent que la présence de "faiblesses structurales", c'est-à-dire de régions qui ne sont pas optimales vis-à-vis de la stabilité de la structure native ou qui présentent une préférence marquée pour une conformation non-native en absence d'interactions tertiaires, est intimement liée aux mécanismes de permutation. Nous avons également mis en évidence l'importance des interactions de type cation-{pi}, qui sont fréquemment observées dans certaines zones clés de la permutation. Finalement, nous avons sélectionné un ensemble de mutations susceptibles de modifier sensiblement la propension de diverses protéines à permuter. L'étude expérimentale de ces mutations devrait permettre de valider, ou de raffiner, les hypothèses que nous avons proposées quant au rôle joué par les faiblesses structurales et les interactions de type cation-{pi}. Nous avons également analysé une autre protéine soumise à d'importants réarrangements conformationnels: l'{alpha}1-antitrypsine. Dans le cas de cette protéine, les modifications structurales sont indispensables à l'exécution de l'activité biologique normale, mais peuvent sous certaines conditions mener à la formation de polymères insolubles et au développement de maladies. Afin de contribuer à une meilleure compréhension des mécanismes responsables de la polymérisation, nous avons cherché à concevoir rationnellement des protéines mutantes qui présentent une propension à polymériser contrôlée. Des tests expérimentaux ont été réalisés par le groupe australien du Professeur S.P. Bottomley, et ont permis de valider nos prédictions de manière assez remarquable.<p><p><p><p>The work presented in this thesis concerns the computational study of the relationships between the sequence of a protein and its three-dimensional structure(s). The unravelling of these relationships has many applications in different domains and is probably one of the most fascinating issues in molecular biology.<p><p>The first part of our work is devoted to the development of statistical potentials derived from databases of known protein structures. These potentials allow to define a limited number of energetic functions embodying the complex ensemble of interactions that rule protein folding and stability (including some entropic contributions), and can be easily adapted to simplified representations of protein structures. However, their physical meaning remains unclear since several hypotheses and approximations are necessary, whose impact is far from clearly understood. We studied some of the limitations of these potentials: their dependence on the size of the proteins included in the database, the non-additivity of the different potential terms, and the importance of the specific environment of each residue. Our results show that residue-based distance potentials are affected by the size of the database proteins, and that this effect can be quite strong, is residue-specific, and seems to result mostly from the inhomogeneous partition of hydrophobic and hydrophilic residues between the surface and the core of proteins. On the basis of these observations, we defined a set of corrective functions in order to take protein size into account while deriving the potentials. On the other hand, we developed a general procedure of derivation of potentials and coupling terms and consequently created an energetic function describing the correlations between several sequence and structure descriptors (the nature of each residue, the conformation of its main chain, its solvent accessibility, and the distances that separate it from other residues, in space and along the sequence). This energetic function presents a strongly improved predictive power, in comparison with the original potentials and with other potentials described in the literature.<p><p>The second part describes the application of different programs, based on statistical potentials, to the study of proteins that adopt alternative structures. Domain swapping involves the exchange of a structural element between identical proteins, and leads to the generation of an oligomeric unit. We showed that the presence of “structural weaknesses”, regions that are not optimal with respect to the folding mechanisms or to the stability of the native structure, seems to be intimately linked with the swapping mechanisms. In addition, cation-{pi} interactions were frequently detected in some key locations and might also play an important role. Finally, we designed a set of mutations that are likely to affect the swapping propensities of different proteins. The experimental study of these mutations should allow to validate, or refine, our hypotheses concerning the importance of structural weaknesses and cation-{pi} interactions. We also analysed another protein that undergoes large conformational changes: {alpha}1-antitrypsin. In this case, the structural modifications are necessary to the proper execution of the biological activity. However, under certain circumstances, they lead to the formation of insoluble polymers and the development of diseases. With the aim of reaching a better understanding of the mechanisms that are responsible for this polymerisation, we tried to design mutant proteins that display a controlled polymerisation propensity. An experimental study of these mutants was conducted by the group of Prof. S.P. Bottomley, and remarkably confirmed our predictions.<p> / Doctorat en sciences appliquées / info:eu-repo/semantics/nonPublished

在傳統的迴歸模型架構下，統計推論的進行需要假設誤差項之間相互獨立，且來自於常態分配。當理論模型假設條件無法達成的時候，排列檢定（permutation tests）這種無母數的統計方法通常會是可行的替代方法。 在以往的文獻中，應用於複迴歸模型（multiple regression）之係數排列檢定方法主要以樞紐統計量（pivotal quantity）作為檢定統計量，進而探討不同排列檢定方式的差異。本文除了採用t統計量這一個樞紐統計量作為檢定統計量的排列檢定方式外，亦納入以非樞紐統計量的迴歸係數估計量b22所建構而成的排列檢定方式，藉由蒙地卡羅模擬方法，比較以此兩類檢定方式之型一誤差（type I error）機率以及檢定力（power），並觀察其可行性以及適用時機。模擬結果顯示，在解釋變數間不相關且誤差分配較不偏斜的情形下，Freedman and Lane (1983)、Levin and Robbins (1983)、Kennedy (1995)之排列方法在樣本數大時適用b2統計量，且其檢定力較使用t2統計量高，但差異程度不大；若解釋變數間呈現高度相關，則不論誤差的偏斜狀態，Freedman and Lane (1983)、Kennedy (1995) 之排列方法於樣本數大時適用b2統計量，其檢定力結果也較使用t2統計量高，而且兩者的差異程度比起解釋變數間不相關時更加明顯。整體而言，使用t2統計量適用的場合較廣；相反的，使用b2的模擬結果則常需視樣本數大小以及解釋變數間相關性而定。 / In traditional linear models, error term are usually assumed to be independently, identically, normally distributed with mean zero and a constant variance. When the assumptions cannot meet, permutation tests can be an alternative method. Several permutation tests have been proposed to test the significance of a partial regression coefficient in a multiple regression model. t=b⁄(se(b)), an asymptotically pivotal quantity, is usually preferred and suggested as the test statistic. In this study, we take not only t statistics, but also the estimates of the partial regression coefficient as our test statistics. Their performance are compared in terms of the probability of committing a type I error and the power through the use of Monte Carlo simulation method. Situations where estimates of the partial regression coefficients may outperform t statistics are discussed.

Tato práce se zabývá problematikou urychlování genetických algoritmů a hned v úvodu nastiňuje možnosti využití genetických algoritmů v praxi. V první kapitole je detailně rozebrán princip fungování genetického algoritmu. Tato kapitola se dále zabývá možnostmi zákódování problému, který je použit pro běh genetického algoritmu. Konkrétně je vzpomenuto binární zakódování jedince, celočíselné zakódování jedince, neceločíselné zakódování jedince a permutační zakódování jedince. Pro každý typ zakódování jsou dále představeny genetické operátory mutace, křížení a selekce. Důraz je kladen na permutační genetické operátory OX a PMX. Další kapitola se zabývá možnostmi paralelizace genetického algoritmu. Další kapitola představuje nový standard jménem OpenCL, který umožňuje snadnou paralelizaci výpočtú s využitím různých typů procesorů v ten samý čas. OpenCL taktéž zjednodušuje programování pro grafické karty. Další kapitola navrhuje možnost, jak urychlit výpočet genetického algoritmu s využitím grafické karty a jazyka OpenCL. Pro urychlení byl zvolen permutační genetický algoritmus "problém N-dam", který je náročný na paměť grafické karty. Tato kapitola rozebírá technické specifikace grafické karty, které jsou nevyhnutelné k určení maximální velikosti šachovnice. V kapitole je analyzována správná práce s pamětí grafické karty, která je nevyhnutelná k dosažení urychlení zvoleného genetického algoritmu. Jsou zde taky nastíněny dva generátory náhodných čísel, které jsou součástí testů. Následující kapitola detailně popisuje fungování navržené paralelizace genetického algoritmu. Jsou zde porovnány dvě metody evaluace jedince a je popsán způsob testování a vyhodnocování výsledků. Předposlední kapitola porovnává časovou náročnost generátorů náhodných čísel. Bylo zjištěno, že generátor HybridTaus je o 20 rychlejší o proti generátoru XORshift na GPU. Na CPU byl naopak rychlejší generátor XORshift. Generátor XORshift je na GPU 20 krát rychlejší a generátor HybridTaus je dokonce až 80 krát rychlejší. Dále byly porovnány evaluační funkce. Bylo zjištěno, že GPU běh je 800 krát rychlejší oproti běhu na CPU. Paměťově náročná evaluační metoda byla schopná dosáhnout jenom dvojnásobné zrychlení. Kapitola dále porovnává funkce křížení. PMX dosáhlo zrychlení maximálně o 100 a i to v případech, které nejsou atraktivní pro řešení problému N-dam (N>20). V případe OX je možné dosáhnout zrychlení až o 1100. Také v tomto případě jsou atraktivní hodnoty pouze do 500. Testy, které vyhodnocují běh celého GA, ukázaly, že GPU verze je zhruba dvojnásobně rychlejší. Malé zrychlení bylo způsobeno operátorem selekce a funkcí křížení.

[ES] Los viroides, genomas mínimos de RNA circular no codificante, monocatenarios y muy estructurados, parasitan factores celulares de las plantas para replicarse autónomamente, establecer infecciones sistémicas y usualmente causar enfermedades. Los de la familia Avsunviroidae se replican y acumulan en cloroplastos por un mecanismo de círculo rodante simétrico. Una RNA polimerasa cloroplástica produce concatémeros lineales de polaridad complementaria que son reducidos a monómeros por las ribozimas de cabeza de martillo (HHR) del concatémero. Producen extremos 5'-hidroxilo y 2',3'-fosfodiéster cíclico, que la isoforma cloroplástica de la tRNA ligasa convierte en enlaces 5',3'-fosfodiéster intramoleculares, generando viroides circulares de polaridad complementaria que pueden entrar en otra ronda de transcripción, simétrica a ésta. En esta Tesis se han analizado las secuencias y estructuras viroidales esenciales para su circularización, usando como modelo el viroide latente de berenjena (ELVd), que induce infecciones asintomáticas en berenjena. Expresamos en Escherichia coli precursores del ELVd(+) lineales flanqueados por dos copias de su HHR. Su procesamiento genera monómeros con los extremos adecuados para la ligación por la tRNA ligasa de la berenjena, que es coexpresada. Mutaciones puntuales y deleciones en el sitio nativo de ligación sugieren que solo el dominio HHR es esencial para la circularización. La conservación de la secuencia y estructura de la HHR con las del sustrato natural del enzima (los tRNAs) nos hacen proponer que la HHR del ELVd secuestra la ligasa mimetizando las características generales del bucle anticodón de los tRNAs. Este sistema de expresión permite también producir RNAs recombinantes, insertándolos en una posición particular del RNA del ELVd. Las quimeras son procesadas por las HHRs flanqueantes y sus extremos ligados por la tRNA ligasa. El andamiaje viroidal circular, compacto y posiblemente asociado a la ligasa, permite aumentar la vida media del RNA de interés y su acumulación en la bacteria. En esta Tesis adaptamos el sistema para producir RNAs de doble cadena (dsRNAs) que desencadenen interferencia por RNA (RNAi), un mecanismo de defensa y regulación génica eucariota basado en la complementariedad de bases entre RNAs. dsRNAs complementarios a genes endógenos reducen los niveles de sus transcritos y generan fenotipos de pérdida de función. Los insectos pueden tomar dsRNAs del ambiente, internalizarlos en sus células y distribuirlos sistémicamente, haciendo al RNAi una estrategia prometedora para el control de plagas. Para producir dsRNAs, separamos las repeticiones invertidas del gen diana que genera la horquilla con el cDNA de un intrón autocatalítico del grupo I de Tetrahymena thermophila, aumentando la estabilidad de los plásmidos de expresión. El intrón es eliminado tras la transcripción, resultando en una molécula viroidal de la que protruye el dsRNA de interés. Flanquear las repeticiones invertidas con una copia adicional permutada del intrón permite separar el ELVd del producto final, un dsRNA circular cerrado en ambos lados por pequeños bucles. Ambas moléculas poseen actividad reguladora: las quimeras viroide-dsRNA con homología al gen de la unión septada suave 1 del gusano de la raíz del maíz (Diabrotica virgifera virgifera) exhiben actividad insecticida oral contra las larvas similar a la de horquillas sintetizadas in vitro, y los dsRNAs circulares sin andamiaje viroidal homólogos al gen de la ATPasa vacuolar (subunidad A) y la proteína ribosomal S13 silencian eficientemente estos genes en adultos de la mosca del Mediterráneo (Ceratitis capitata); este caso es de especial relevancia al ser la primera demostración del RNAi para el control de esta plaga. En conclusión, a pesar de su limitada relevancia agrícola, el ELVd es útil para investigar la biología molecular de la familia Avsunviroidae y una poderosa herramienta biotecnológica en combinación con el sistema de expresión en E. coli. / [CA] Els viroides, genomes mínims d'RNA circular no codificant, monocatenaris i molt estructurats, parasiten factors cel·lulars de les plantes per a replicar-se autònomament, establir infeccions sistèmiques i usualment causar malalties. Els de la família Avsunviroidae es repliquen i acumulen en cloroplasts per un mecanisme de cercle rodant simètric. Una RNA polimerasa cloroplàstica produeix concatèmers lineals de polaritat complementària que són reduïts a monòmers per els ribozims de cap de martell (HHR) del concatèmer. Produeixen extrems 5'-hidroxil i 2',3'-fosfodièster cíclic, que la isoforma cloroplàstica de la tRNA lligasa converteix en enllaços 5',3'-fosfodièster intramoleculars, generant viroides circulars de polaritat complementària que poden entrar en una nova ronda de transcripció, simètrica a la primera. En aquesta Tesi s'han analitzat les seqüències i estructures viroidals essencials per a la seua circularització, emprant com a model el viroide latent d'albergínia (ELVd), que indueix infeccions asimptomàtiques en albergínia. Expressem en Escherichia coli precursors de l'ELVd(+) lineals flanquejats per dos còpies del seu HHR. El seu processament produeix monòmers amb els extrems apropiats per a la lligació mediada per la tRNA ligasa de l'albergínia, que és coexpressada. Mutacions puntuals i delecions en el lloc nadiu de lligació suggereixen que només el domini HHR és essencial per a la circularització. La conservació de la seqüència i estructura del HHR amb les del substrat natural de l'enzim (els tRNAs) ens fan proposar que el HHR de l'ELVd segresta la lligasa mimetitzant les característiques generals del bucle anticodó dels tRNAs. Aquest sistema d'expressió també permet produir RNAs recombinants, inserint-los en una posició particular de l'RNA de l'ELVd. Les quimeres són processades pels HHR flanquejants i els seus extrems lligats per la tRNA lligasa. L'RNA viroïdal circular, compacte i possiblement associat a la lligasa, permet augmentar la vida mitjana de l'RNA d'interés i la seua acumulació en els bacteris. En aquesta Tesi adaptem el sistema per a produir RNAs de doble cadena (dsRNAs) que desencadenen interferència per RNA (RNAi), un mecanisme de defensa i regulació gènica eucariota basat en la complementarietat de bases entre RNAs. dsRNAs complementaris a gens endògens redueixen els nivells dels seus transcrits i generen fenotips de pèrdua de funció. Els insectes poden prendre dsRNAs de l'ambient, internalitzar-los en les seues cèl·lules i distribuir-los sistèmicament, fent a l'RNAi una estratègia prometedora en el control de plagues. Per a produir dsRNAs, separem les repeticions invertides del gen diana que genera la forqueta amb el cDNA d'un intró autocatalític del grup I de Tetrahymena thermophila, augmentant l'estabilitat dels plasmidis d'expressió. L'intró és eliminat després de la transcripció, resultant en una molècula viroïdal de la qual protrueix el dsRNA d'interés. Flanquejar les repeticions invertides amb una còpia addicional permutada de l'intró permet separar l'ELVd del producte final, un dsRNA circular tancat als dos costats per xicotets bucles. Els dos tipus de molècules posseeixen activitat reguladora: les quimeres viroide-dsRNA amb homologia al gen de la unió septada suau 1 del cuc de l'arrel de la dacsa (Diabrotica virgifera virgifera) exhibeixen activitat insecticida oral contra les larves similar a la de forquetes sintetitzades in vitro, i els dsRNAs circulars sense l'RNA viroïdal homòlegs al gen de la ATPasa vacuolar (subunitat A) i la proteïna ribosomal S13 silencien eficientment aquests gens en adults de la mosca del Mediterrani (Ceratitis capitata); aquest cas és d'especial rellevància perquè és la primera demostració de l'RNAi per al control d'aquesta plaga. En conclusió, malgrat la seua limitada rellevància agrícola l'ELVd és útil per a investigar la biologia molecular de la família Avsunviroidae i una poderosa ferramenta biotecnològica en combinació amb el sistema d'expressió en E. coli. / [EN] Viroids, minimal genomes of non-coding circular RNA, single-stranded and highly structured, parasitize plant cellular factors to replicate autonomously, establish systemic infections, and typically cause disease. Those of the family Avsunviroidae replicate and accumulate in chloroplasts by a symmetrical rolling circle mechanism. A chloroplast RNA polymerase produces linear concatemers of complementary polarity that are reduced to monomers by the hammerhead ribozymes (HHR) of the concatemer. They produce 5'-hydroxyl and 2',3'-cyclic phosphodiester ends, which the chloroplastic isoform of tRNA ligase converts to intramolecular 5',3'-phosphodiester bonds, generating circular viroids of complementary polarity that can enter another round of transcription, symmetric to the first one. In this Thesis, the viroid sequences and structures essential for its circularization have been analyzed, using as a model the eggplant latent viroid (ELVd), which induces asymptomatic infections in eggplant. We expressed in Escherichia coli linear ELVd(+) precursors flanked by two copies of its HHR. Its processing generates monomers with suitable ends for ligation by the eggplant tRNA ligase, which is co-expressed. Point mutations and deletions at the wild-type ligation site suggest that only the HHR domain is essential for circularization. The conservation of the sequence and structure of the HHR with those of the natural substrate of the enzyme (the tRNAs) lead us to propose that the HHR of the ELVd hijacks the ligase, mimicking the general characteristics of the anticodon loop of the tRNAs. This expression system also allows the production of recombinant RNAs, inserting them into a particular position of the ELVd RNA. Chimeras are processed by flanking HHRs and their ends ligated by the tRNA ligase. The compact, circular viroidal scaffold, possibly associated with the ligase, allows increasing the half-life of the RNA of interest and its accumulation in the bacteria. In this Thesis we adapt the system to produce double-stranded RNAs (dsRNAs) that trigger RNA interference (RNAi), a eukaryotic gene regulation and defense mechanism based on base complementarity between RNAs. dsRNAs complementary to endogenous genes reduce the levels of their transcripts and generate loss-of-function phenotypes. Insects can take dsRNAs from the environment, internalize them into cells, and distribute them systemically, making RNAi a promising pest control strategy. To produce dsRNAs, we separated the inverted repeats of the target gene that generates the hairpin with the cDNA of a group-I autocatalytic intron from Tetrahymena thermophila, increasing the stability of the expression plasmids. The intron is removed after transcription, resulting in a viroidal molecule from which the dsRNA of interest protrudes. Flanking the inverted repeats with an additional copy of the intron in a permuted form allows the ELVd molecule to be separated from the final product, a circular dsRNA molecule capped on both sides by small loops. Both molecules have regulatory activity: the viroid-dsRNA chimeras with homology to the smooth septate junction 1 gene of the corn rootworm (Diabrotica virgifera virgifera) exhibit oral insecticidal activity against larvae similar to that of in vitro synthesized hairpins, and the circular dsRNAs without the viroid scaffold homologous to the vacuolar ATPase (subunit A) and ribosomal protein S13 genes efficiently silence those genes in adult Medfly (Ceratitis capitata); this case is of special relevance as it is the first demonstration of RNAi for the control of this pest. In conclusion, despite its limited agricultural relevance, the ELVd is useful for investigating the molecular biology of the Avsunviroidae family and a powerful biotechnological tool in combination with the E. coli expression system. / This work was supported by the Ministerio de Ciencia e Innovación (Spain; co-financed by the European Regional Development Fund) [BIO2017-83184-R] and [BIO2017‐ 91865‐EXP]; Universitat Politècnica de València [PAID-01-17]. We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI). / Ortolá Navarro, B. (2023). Heterologous expression of circular RNAs in Escherichia coli for analyzing the ligation process of chloroplastic viroids and producing double-stranded RNAs with insecticidal activity [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/192635

本論文主要是探討在二維度空間上二母體分佈是否一致。我們利用排列 (permutation)檢定方法來做比較, 並藉由費雪(Fisher)正確檢定方法的想法而提出重標記 (relabel)排列檢定方法或稱為費雪排列檢定法。 我們透過可交換性的特質證明它是正確 (exact) 的並且比 Syrjala (1996)所建議的排列檢定方法有更高的檢定力 (power)。 本論文另提出二個空間模型: spatial multinomial-relative-log-normal 模型 與 spatial Poisson-relative-log-normal 模型 來配適一般在漁業中常有的右斜長尾次數分佈並包含很多0 的空間資料。另外一般物種可能因天性或自然環境因素像食物、溫度等影響而有群聚行為發生, 這二個模型亦可描述出空間資料的群聚現象以做適當的推論。 / This thesis proposes the relabel (Fisher's) permutation test inspired by Fisher's exact test to compare between distributions of two (fishery) data sets locating on a two-dimensional lattice. We show that the permutation test given by Syrjala (1996} is not exact, but our relabel permutation test is exact and, additionally, more powerful. This thesis also studies two spatial models: the spatial multinomial-relative-log-normal model and the spatial Poisson-relative-log-normal model. Both models not only exhibit characteristics of skewness with a long right-hand tail and of high proportion of zero catches which usually appear in fishery data, but also have the ability to describe various types of aggregative behaviors.

再發事件資料常見於醫學、工業、財經、社會等等領域中，對再發資料分析研究時，我們往往無法確知再發事件發生的時間或是發生次數的分配。因此，本論文探討的是分析再發事件的無母數方法，包括Nelson提出的平均累積函數(mean cumulative function)估計量，及Wang、Chiang與Huang介紹的發生率(occurrence rate)之核函數(kernel function)估計量。 就平均累積函數估計量來說，藉由Nelson導出的變異數及自然(naive)變異數，可分別求得平均累積函數的區間估計。本文利用靴環法(bootstrap)計算出平均累積函數在不同時點的變異數，再與Nelson變異數及自然變異數比較，結果顯示Nelson變異數與靴環法算出的變異數較接近。因此，應依據Nelson變異數建構出事件發生累積次數之漸近信賴區間。 本論文亦介紹了兩個或多個母體的平均累積函數的比較方法，包含固定時點之比較與整條曲線之比較。在固定時點之下，比較方法分別為平均累積函數成對差異之漸近信賴區間及靴環信賴區間、變異數分析比較法，與排列檢定法；而整條曲線比較方法包含：類似 統計量、Lawless-Nadeau檢定。這些方法應用在本論文所採之實證資料時，所得到的檢定結論是一致的。 / Recurrent event data arise in many fields, such as medicine, industry, economics, social sciences and so on. When studying recurrent event data, we usually don’t know the exact joint or marginal distributions of the occurrence times or the number of events over time. So, in this article we talk about some nonparametric methods, such as the mean cumulative function (MCF) discussed by Nelson, and kernel estimation of the rate function introduced by Wang, Chiang and Huang. As to the estimator of MCF, we can compute the confidence interval by Nelson’s variance and naive variance. We use bootstrap method to compare the performance of Nelson variance of the estimated MCF and naive variance of the estimated MCF. The results show that Nelson variance is better than naive variance, so we should construct the confidence limits for the MCF by Nelson’s variance except when only grouped data are available. We also introduce methods for comparing MCFs, including pointwise comparison of MCFs and comparison of entire MCFs. Methods for pointwise comparing MCFs include approximate confidence limits for difference between two MCFs, analysis-of-variance comparison, permutation test, and bootstrap’s confidence limits for difference between two MCFs. Methods for comparing entire MCFs include a statistic like Hoetelling’s , and Lawless-Nadeau test. Finally, all approaches are employed to analyze a real data, and the conclusions concordance with each other.

This diploma’s thesis discourses the cryptographic systems and ciphers, whose function, usage and practical implementation are analysed. In the first chapter basic cryptographic terms, symmetric and asymetric cryptographic algorithms and are mentioned. Also usage and reliability are analysed. Following chapters mention substitution, transposition, block and stream ciphers, which are elementary for most cryptographic algorithms. There are also mentioned the modes, which the ciphers work in. In the fourth chapter are described the principles of some chosen cryptographic algorithms. The objective is to make clear the essence of the algorithms’ behavior. When describing some more difficult algorithms the block scheme is added. At the end of each algorithm’s description the example of practical usage is written. The chapter no. five discusses the hardware implementation. Hardware and software implementation is compared from the practical point of view. Several design instruments are described and different hardware design programming languages with their progress, advantages and disadvantages are mentioned. Chapter six discourses the hardware implementation design of chosen ciphers. Concretely the design of stream cipher with pseudo-random sequence generator is designed in VHDL and also in Matlab. As the second design was chosen the block cipher GOST, which was designed in VHDL too. Both designs were tested and verified and then the results were summarized.