Introdução: No mundo especula-se que 15 a 20 milhões tenham infecção crônica pelo HDV. No Brasil, a área endêmica de hepatite Delta corresponde aos estados da Amazônia Ocidental, incluindo Rondônia. Hepatite Delta é a mais grave e com mais rápida evolução para cirrose dentre as hepatites virais. Poucos estudos avaliaram os aspectos epidemiológicos, clínicos e laboratoriais de uma coorte de pacientes em nosso país e no mundo. Objetivos: Em uma coorte de pacientes acompanhados em um serviço de referência: 1. Avaliar as características demográficas, epidemiológicas e clínicas; 2. Avaliar a frequência de doença hepática avançada; 3. Avaliar as características da população atendida com idade <=18 anos; 4. Avaliar a acurácia de escores não invasivos (razão AST/ALT, APRI e FIB-4) na determinação dos diferentes graus de fibrose. Métodos: Trata-se de um estudo transversal, descritivo, de uma coorte de pacientes retrospectivamente identificadas no ambulatório especializado em hepatites virais, pertencente ao Centro de Pesquisa em Medicina Tropical do Estado de Rondônia (CEPEM), situado na cidade de Porto Velho, com diagnóstico de infecção pelo HDV. Foram incluídos todos os pacientes com diagnóstico dessa infecção por sorologia (ELISA) ou por biologia molecular (HDV-RNA reagente), matriculados e atendidos neste serviço entre novembro de 1996 a março de 2015. Resultados: Dentre 4.101 pacientes diagnosticado com HBV, 224 (5,5%) apresentavam coinfecção com o HDV, e 205 foram incluídos nas análises. Dentre eles, 132 (64,4%) eram do sexo masculino, com idade média de 35,1 anos. O contato familiar foi o fator de exposição para infecção pelo VHB/VHD mais frequente. A determinação do genótipo do HDV foi obtida em 78 pacientes, destes 74 (94,9%) eram genótipo III e 4 (5,1%) genótipo I. Noventa e dois (44,9%) pacientes apresentavam evidência de doença hepática avançada. Dentre os pacientes incluídos 22 (10,7%) tinham idade <= 18 anos, sendo que 6 (27,3%) apresentavam sinais e sintomas de doença hepática avançada ou fulminante à primeira consulta. Métodos não invasivos foram calculados e comparados à biópsia hepática em 50 pacientes. A razão AST/ALT não teve valor significativo para avaliar fibrose em nenhum dos estágios. APRI e FIB-4 tiveram melhor desempenho para avaliar fibrose significativa (>=F2), com acurácia de 86 e 80, respectivamente. Conclusões: 1. O HDV representa importante agravo de saúde pública em Rondônia com frequência expressiva entre pessoas do sexo masculino e população indígena; 2. A presença da infecção pelo HDV esteve associada a expressivo número de complicações hepáticas e foi frequente causa de óbito na população analisada, particularmente entre adultos jovens; 3. Entre pacientes com idade <= 18 anos a hepatite delta esteve associada a significante morbidade e mortalidade e a falta de adesão dessa população pareceu contribuir para esse tipo de desfecho; 4. A utilização dos métodos não invasivos (APRI e FIB-4) foi capaz de identificar pacientes com fibrose significativa entre indivíduos infectados com HDV na Amazônia brasileira, podendo, apesar de todas as limitações destes métodos servir como alternativa para avaliação de fibrose hepática significativa, na ausência de outros métodos mais efetivos / Introduction: In the world, it is speculated that 15 to 20 million people have chronic HDV infection. In Brazil, the endemic area of hepatitis Delta corresponds to the states of the Western Amazon, including Rondônia. Hepatitis Delta is the most serious and most rapidly evolving cirrhosis among viral hepatitis. Few studies have evaluated the epidemiological, clinical, and laboratory aspects of a cohort of patients in our country and around the world. Objectives: In a cohort of patients followed at a referral service: 1. Evaluate demographic, epidemiological and clinical characteristics; 2. Assess the frequency of advanced liver disease; 3. Evaluate the characteristics of the population served with age <=18 years; 4. To evaluate the accuracy of non-invasive scores (AST/ALT ratio, APRI and FIB-4) in determining the different degrees of fibrosis. Methods: This is a cross-sectional, descriptive study of a cohort of patients retrospectively identified in the ambulatory specialized in viral hepatitis, belonging to the Research Center of Tropical Medicine of Rondônia State (CEPEM), located in the city of Porto Velho. All patients diagnosed with this serological method (ELISA) or molecular biology (HDV-RNA), enrolled in this service between November 1996 and March 2015, were included. Results: Out of 4,101 patients diagnosed with infection by HBV, 224 (5.5%) had coinfection with the hepatitis delta virus, and 205 were included in the analyzes. Among them, 132 (64.4%) were males, with a mean age at the time of enrollment of 35.1 years. Family contact was the most frequent exposure factor for HBV/HDV infection. It was identified seventy-eight patients (94.9%) of genotype III and four (5.1%) of genotype I. Ninety-two (44.9%) patients had evidence of advanced liver disease. Among the patients included, 22 (10.7%) were aged <= 18 years, and 6 (27.3%) had signs and symptoms of advanced or fulminant liver disease at the first visit. Noninvasive methods were calculated and compared to liver biopsy in 50 patients. The AST/ALT ratio had no significant value for evaluating fibrosis in any of the stages. APRI and FIB-4 had better performance to evaluate significant fibrosis (>=F2), with the accuracy of 86 and 80 respectively. Conclusions: 1. The hepatitis delta virus represents an important public health problem in the State of Rondônia, affecting both adults and children, with significant frequency among males and the indigenous population; 2. The presence of HDV infection was associated with a significant number of hepatic complications and was a frequent cause of death in the analyzed population, particularly among young adults; 3. Among patients aged <= 18 years, delta hepatitis was associated with significant morbidity and mortality and the lack of adherence of this population to follow-up seemed to contribute to this type of outcome; 4. The use of the non-invasive APRI and FIB-4 methods were able to identify patients with significant fibrosis among individuals infected with HDV in the Brazilian Amazon, although all limitations of these methods may serve as an alternative for the evaluation of significant hepatic fibrosis in the absence of other more effective methods

For this project, a Software-In-the-Loop (SIL) simulation tool is used at Scania (“VTAB” – Virtual Truck and Bus), which simulates the submodels of the mechanical vehicle components together with the real control units. The simulation tool contains the following submodels: Engine model, Drivetrain model, Drive cycle model, Restbus model, and Driver model. The simulated human driver submodel in the restbus model outputs two pedal control signals to the control unit, namely the gas and brake pedals. With these two pedal signals, the control unit decides the modes of mechanical vehicle components. This driver model needs to be reworked to obtain a better velocity following performance. Two controllers, fuzzy PI anti-windup and backward calculation, are implemented in the driver model and compared by the velocity tracking accuracy and the pedal switching frequency. In the comparison and analysis section, two different cycles and two weights of payload are simulated. The simulation results demonstrate that both controllers can improve the driver model’s velocity tracing accuracy. Further, the fuzzy PI anti-windup controller is better when considering pedal signals fluctuation frequency and implementation complexity. / För detta projekt används ett simuleringsverktyg Software-In-the-Loop (SIL) på Scania (“VTAB” - Virtual Truck and Bus), vilket simulerar submodellerna för de mekaniska fordonskomponenterna tillsammans med de verkliga styrenheterna. Simuleringsverktyget innehåller följande submodeller: Motormodell, Drivmotormodell, Drivcykelmodell, Restbusmodell och Drivermodell. Den simulerade submodellen för mänsklig förare i restbussmodellen kommer att sända två pedalsstyrsignaler till styrenheten, nämligen gas och broms. Med dessa två pedalsignaler kan styrenheten avgöra lägen av mekaniska fordonskomponenter. Denna drivrutinmodell måste omarbetas för att få en bättre hastighetsspårnings presentationsförmåga. Två styrenheter, fuzzy PI anti-windup och bakåtberäkning, implementeras i förarmodell och jämförs respektive med hastighetsspårningsnoggrannhet och pedalväxelfrekvens. I jämförelseoch analysavsnittet simuleras två olika cyklar och två nyttolast. Simuleringsresultaten visar att båda kontrollerna kan förbättra förarmodellens hastighetsspårningskapacitet. Vidare är fuzzy PI-anti-windup-kontroller bättre när man tar hänsyn till pedalsignalernas fluktueringsfrekvens och implementeringskomplexitet

<p>HDV antigenomic RNA is processed in two distinct pathways; it can be cleaved at the polyA site and polyadenylated to become mRNA for the delta antigens, or the RNA can be cleaved by the antigenomic ribozyme to become full-length antigenomic RNA that is used for synthesis of genomic HDV RNA. The polyA site is located just 33 nucleotides upstream of the ribozyme cleavage site. If processing occurs primarily at the upstream polyA site, there may not be enough full-length antigenomic RNA to support replication. On the other hand, ribozyme cleavage downstream of the polyA site could inhibit polyadenylation by interfering with polyadenylation complex assembly. Thus, it appears that HDV may need a mechanism to control RNA processing so that both products can be generated in the proper amounts during the infection cycle. </p><p>A model has been proposed in which the choice between ribozyme cleavage and polyadenylation is determined by alternative RNA secondary structures formed by the polyA sequence (Wadkins and Been 2002). One of the hypothetical structures, AltP2, is a pairing between part of the upstream polyA sequence and the 3' end of the ribozyme sequence. For this model, the same upstream sequence that forms AltP2 could also form a stem loop, P(-1), within the leader, by pairing with sequences located farther upstream. A processing choice is possible because AltP2 is predicted to inhibit ribozyme cleavage and favor polyadenylation resulting in mRNA production, whereas P(-1) would inhibit polyadenylation and favor ribozyme cleavage resulting in full-length replication product. </p><p>The P(-1) vs. AltP2 model was tested using an antigenomic HDV ribozyme construct with the 60-nucleotide sequence upstream of the ribozyme cleavage site. This leader sequence contains the proposed polyA sequence elements. In vitro analysis of this construct revealed that the kinetic profile of ribozyme self-cleavage was altered in two ways. Relative to the ribozyme without upstream sequences, the fraction of precursor RNA that cleaved decreased to about 50%, but the active ribozyme fraction cleaved faster. Native gel electrophoresis revealed that the active and inactive precursor RNAs adopted persistent alternative structures, and structure mapping with Ribonuclease T1 and RNase H provided evidence for structures resembling P(-1) and AltP2.</p><p>Sequence changes in the 5' leader designed to alter the relative stability of P(-1) and AltP2 increased or decreased the extent of ribozyme cleavage in a predictable way, but disrupting AltP2 did not completely restore ribozyme activity. The analysis of deletion and base change variants supported a second alternative pairing, AltP4, formed by the pyrimidine-rich sequence immediately 5' of the ribozyme cleavage site and a purine-rich sequence from the 5' side of P4. A similar approach was used to test if the effect of disrupting both AltP2 and AltP4 might be additive, and the results suggested that ribozyme precursors with 5' leader sequences could fold into multiple inactive conformations, which can include, but may not be limited to, AltP2, AltP4, or a combination of both.</p><p>Luciferase expression constructs with HDV polyA and ribozyme sequences were used to investigate the effects of RNA structure and ribozyme cleavage on polyadenylation in cells. One hypothesis was that P(-1) could inhibit polyadenylation by making the polyA sequence elements less accessible to polyA factors, but sequence changes designed to alter the stability of the stem loop had no effect on polyadenylation. The model also predicts that the ribozyme sequence downstream of the polyA site could affect polyadenylation, possibly in two different ways. Ribozyme cleavage could interfere with polyadenylation by uncoupling transcription from processing, however, the ribozyme sequence might also influence polyadenylation in a manner independent of the ribozyme cleavage activity. As such, the AltP2 structure could potentially have a positive effect on polyadenylation either by inhibiting ribozyme cleavage or by making the polyA signal sequences more accessible to the polyA factors. To distinguish between the effects of ribozyme cleavage and alternative RNA structures, luciferase expression levels from constructs with an HDV polyA sequence followed by the active wild-type ribozyme or the inactive C76u version of the ribozyme were compared. For the wild-type HDV polyA sequence, the active ribozyme reduced expression, whereas the inactive ribozyme control had no effect on expression. However, for the modified leader sequences, which were efficiently polyadenylated in the absence of ribozyme, there were changes in expression that appeared to be independent of ribozyme cleavage. Based on these findings, two alternative models are proposed. One model predicts that protein factors might affect antigenomic RNA processing, and the other model suggests that additional alternative structures, such as AltP4, might influence the choice between ribozyme cleavage and polyadenylation.</p> / Dissertation

L’ARN est sans aucun doute la molécule biologique la plus versatile qui soit. Tout comme l’ADN, il peut contenir et transmettre de l’information génétique. Tout comme les protéines, il peut accomplir une multitude de fonctions biologiques. De plus, son rôle le plus connu demeure celui d’intermédiaire entre l’ADN et les protéines. L’ARN est donc au cœur d’un bon nombre de processus biologiques. Ceci lui confère un immense potentiel thérapeutique qui jusqu’à présent demeure largement inexploité. Pour accomplir ses fonctions, l’ARN doit adopter une structure tridimensionnelle précise qui est dépendante à la fois de sa séquence et de son environnement. Ainsi, en modifiant la structure d’un ARN, il est possible d’en moduler sa fonction. C’est l’objectif global des travaux présentés dans cette thèse. Pour y parvenir, de courts oligonucléotides antisens (OA) ont été utilisés. Cette stratégie revêt plusieurs avantages. Comme les OA s’apparient à leur cible en formant des paires de bases Watson-Crick, ils offrent une grande spécificité et leur design est facile. De plus, en se fiant aux données structurales et aux logiciels de prédictions de structures des ARN, on peut aisément identifier les régions à cibler avec les OA. Enfin, cette technique est versatile puisqu’on peut cibler différents motifs d’ARN. La première cible a été le ribozyme du virus de l’hépatite D. Cet ARN, qui catalyse une réaction d’auto-coupure, a été modifié afin que son activité devienne dépendante à la liaison d’OA. Plusieurs modules ont ainsi été créés et combinés afin d’obtenir des ribozymes qui répondaient à la présence d’un ou plusieurs OA. En insérant ces interrupteurs moléculaires dans les régions non traduites d’un ARNm, nous avons ainsi modulé l’expression de ce gène avec les OA. Cet outil a des applications intéressantes pour la régulation de gènes en biologie synthétique. Un autre motif ciblé a été le G-quadruplex (G4). Cette structure non canonique exerce de nombreuses fonctions biologiques et représente donc une cible thérapeutique intéressante. Lorsque présent dans la région 5’ non traduite d’un ARNm, le G4 mène généralement à une diminution de la traduction. En utilisant des OA qui empêchent la formation du G4, nous avons été en mesure d’augmenter la traduction du gène ciblé. De plus, il a été possible de développer des OA qui favorisent la formation d’un G4 dans le but de diminuer l’expression de la cible. Finalement, dans le dernier chapitre de cette thèse, il est démontré que les G4 présents dans les microARN primaires influencent leur maturation en microARN matures. Des OA ciblant ces G4 ont été utilisés afin de favoriser la maturation de microARN suppresseurs de tumeurs, ce qui présente un potentiel thérapeutique intéressant. En bref, les travaux présentés dans cette thèse démontrent clairement que les OA sont un outil de choix pour cibler et modifier la structure de motifs d’ARN spécifiques. / Abstract : RNA is a versatile biological molecule. Like DNA, it can contain and transmit genetic information. Like proteins, it can accomplish multiple biological functions. Also, its most known role remains that of intermediary between DNA and proteins. RNA is thus a key player in many biological processes. This gives it an immense therapeutic potential which remains largely untapped. To fulfill its functions, RNA must adopt a precise threedimensional structure that is dependent on both its sequence and its environment. Thus, by modifying the structure of an RNA, it is possible to modulate its function. This is the overall objective of the work presented in this thesis. To achieve this, small antisense oligonucleotides (ASO) have been used. This strategy has several advantages. As ASO bind their target with Watson-Crick base pairs, they offer great specificity and their design is easy. Moreover, reliance on structural data and RNA structure prediction softwares makes it easy to identify the regions to be targeted with ASO. Finally, this technique is versatile since it is possible to target different RNA motifs. The first target was the HDV self-cleaving motif. This RNA, which catalyzes a self-cleaving reaction, has been modified so that its activity became dependent on the binding of ASO. Several modules were thus created and combined in order to obtain ribozymes which responded to the presence of one or more ASO. By inserting these molecular switches into an mRNA’s UTR, the expression of this gene was modulated with the ASO. This has interesting applications for the regulation of genes in synthetic biology. Another target motif was the G-quadruplex (G4). This non-canonical structure exerts many biological functions and therefore represents an interesting therapeutic target. When present in the mRNA’s 5’UTR, G4 generally lead to a decrease in translation. Using ASO that prevent G4 formation, we were able to increase the translation of the target gene. In addition, it has been possible to develop ASO which promote the formation of a G4 in order to decrease the expression of the target. Finally, in the last chapter of this thesis, it is demonstrated that the G4 present in the primary microRNAs influence their maturation in mature microRNAs. ASO targeting these G4 have been used in order to promote the maturation of tumor suppressor microRNAs, which has an interesting therapeutic potential. The work presented in this thesis clearly demonstrates that ASO are ideal for targeting and altering the structure of specific RNA motifs.

The efficiency of the transport sector is under close examination due to multiple different reasons. Among them are the environmental aspects of emission reduction along with the need to maintain a tight time schedule. Heavy trucks have a significant negative impact on the environment and are sensitive to external factors. Planning green routes is a way to minimize the emissions from heavy trucks by reducing the fuel consumption without sacrificing travel time. This thesis will investigate suspected parameters relevance to the fuel consumption of heavy trucks and their effect on the fuel consumption on heavy trucks. To achieve this, two independent literature searches were conducted, the first to find the relevance and the second to understand the effect. Then a comparison was made with the NVDB to see if the suspected parameters were represented by the attributes in the database. The result of the first literature search varied and the speed and congestion parameter showed the strongest relevance to the fuel consumption of the heavy truck. The second literature search found past research that stated that the fuel consumption of heavy trucks were affected by the parameters, gradient, speed, road curvature, road roughness, congestion, road elements and weather. The result of the investigation of attributes in the NVDB is displayed with respect to green routing. The relevance measure in the first literature search was assumed to be higher if the number of relevant articles were high. The results of the second literature search were discussed with respect to green routing. This was followed by suggesting eventual improvements in the NVDB and improvements in the method used in this thesis. Furthermore, the parameters usage and implementation in GIS were discussed. It was concluded that all parameters found in the second literature search except weather were appropriate for green routing. Other parameters could also have an effect on the fuel consumption of heavy trucks but further research is necessary to investigate this.

As hepatites virais estão entre as mais importantes pandemias mundiais da atualidade. Existem várias causas de hepatite, entre elas, o vírus da hepatite B (HBV), o vírus da hepatite C (HCV) e o vírus da Hepatite Delta (HDV). Da mesma forma, o vírus GB-C (GBV-C) é importante na coinfecção com outros vírus, como o HIV. Nesse estudo, várias regiões da América do Sul foram analisadas. Na Colômbia, os estados do Amazonas e Magdalena foram encontradas como regiões hiperendêmicas para HBV. O genótipo F3 (75%) foi o mais prevalente. Determinou-se que o subgenótipo F3 é o mais antigo dos subgenótipos F. No estado de Chocó, encontrou-se o subgenótipo A1 (52,1%) como o mais prevalente. Surpreendentemente, nesse mesmo estado foram encontrados nove casos autóctones de infecção pelo genótipo E (39,1%). Para o HCV, em Bogotá, encontrou-se o subtipo 1b (82,8%) como o mais prevalente. Da mesma forma, estimou-se que esse subtipo foi introduzido por volta de 1950 e se propagou exponencialmente entre 1970 a 1990. O HDV foi identificado em casos de hepatite fulminante do estado de Amazonas, todos classificados como genótipo 3. Se determinou que o HDV/3 se espalhou exponencialmente a partir de 1950 a 1970 na América do Sul e depois desta época, esta infecção deixou de aumentar, provavelmente devido a introdução de vacinação contra o HBV. GBV-C foi procurado em doadores de sangue colombianos infectados com HCV e/ou HBV de Bogotá e em povos indígenas com infecção pelo HBV no Amazonas. A análise filogenética revelou a presença do genótipo 2a como o mais prevalente entre os doadores de sangue e o 3 nos povos indígenas estudados. A presença do genótipo 3 na população indígena foi previamente relatada na região de Santa Marta, na Colômbia e nos povos indígenas da Venezuela e da Bolívia. No Chile, foi realizado um estudo com 21 pacientes cronicamente infectados pelo HBV sem tratamento antiviral prévio. Todas as sequências obtidas eram do subgenótipo F1b e se agrupavam em quatro diferentes grupos, sugerindo que diferentes linhagens desse subgenótipo estão circulando no Chile. No Brasil, no estado de Rondônia, para o HCV, encontramos o subtipo 1b (50,0%) como o mais frequente. Esse foi o primeiro relato sobre os genótipos do HCV neste estado. Para o HBV, o subgenótipo A1 (37,0%) foi o mais frequente. Os resultados do estado de Rondônia são consistentes com outros estudos no Brasil, mostrando a presença de vários genótipos do HBV, refletindo a origem mista da população Brasileira. Estudando o estado do Maranhão, avaliamos a frequência da infecção pelo HBV e seus genótipos. Foram encontradas 4 sequencias genótipo A1 que agruparam com outras sequências reportadas do Brasil. Em outro estudo, caracterizamos os subgenótipos do HBV em 68 pacientes com hepatite crônica B em Pernambuco, encontrando 78,7% de presença do subgenótipo A1. Finalmente, em um estudo realizado com amostras da cidade de São Paulo, encontramos um caso de HBV genótipo C em um brasileiro nativo, sendo essa a primeira sequência completa do genoma de HBV/C2 notificados no Brasil / Viral hepatitis are among the major pandemics in the world nowadays. There are many causes of hepatitis, including hepatitis B virus (HBV), hepatitis C virus (HCV) and hepatitis delta virus (HDV). Similarly, GB virus C (GBV-C) is a relevant agent in co-infection with HIV. In this study, several regions of South America were studied. In Colombia, the states of Amazonas and Magdalena were identified as highly endemic areas for HBV. Genotype F3 (75%) was the most prevalent. It was determined that subgenotype F3 is the oldest among all F subgenotypes. In the state of Chocó, subgenotype A1 (52.1%) was the most prevalent. Surprisingly, nine indigenous cases of infection by genotype E (39.1%) were found in this state. For HCV, in Bogotá, subtype 1b (82.8%) was the most frequent. Likewise, it was estimated that this subtype was introduced around 1950 and spread exponentially from 1970 to 1990. HDV has been identified in cases of fulminant hepatitis in the state of Amazonas, all of them classified as genotype 3. It was determined that the HDV/3 spread exponentially from 1950 to 1970 in South America and after this time, this infection stopped to increase, probably due to introduction of vaccination against HBV. GBV-C was sought in Colombian blood donors infected with HCV and/or HBV in Bogotá and indigenous peoples with HBV infection in the Amazon. The phylogenetic analysis revealed the presence of genotype 3 as the most prevalent among blood donors and in three studied indigenous people. The presence of genotype 3 in the indigenous population has been previously reported in the region of Santa Marta, Colombia, and in the indigenous peoples of Venezuela and Bolivia. In Chile, a study was carried out with 21 patients chronically infected with HBV without any prior antiviral treatment. All sequences obtained belonged to subgenotype F1b and clustered into four different groups, suggesting that different strains that are circulating in Chile. In Brazil, the state of Rondônia, we found HCV subtype 1b (50.0%) as the most frequent. This was the first report on HCV genotypes in this state. For HBV, subgenotype A1 (37.0%) was the most frequent. The results of the state of Rondônia are consistent with other studies carried out in Brazil, showing the presence of several HBV genotypes, reflecting the mixed origin of the Brazilian population. Studying the state of Maranhão, we evaluated the frequency of HBV infection and its genotypes and we found 4 genotype A1 sequences that grouped with other sequences reported in Brazil. In another study, we characterized HBV subgenotypes in 68 patients with chronic hepatitis B in Pernambuco and we found subgenotype A1 in 78.7% cases. Finally, in a study of samples from São Paulo, we found a case of HBV genotype C in a native Brazilian patient and this is the first complete genome sequence of HBV/C2 reported in Brazil

As hepatites virais estão entre as mais importantes pandemias mundiais da atualidade. Existem várias causas de hepatite, entre elas, o vírus da hepatite B (HBV), o vírus da hepatite C (HCV) e o vírus da Hepatite Delta (HDV). Da mesma forma, o vírus GB-C (GBV-C) é importante na coinfecção com outros vírus, como o HIV. Nesse estudo, várias regiões da América do Sul foram analisadas. Na Colômbia, os estados do Amazonas e Magdalena foram encontradas como regiões hiperendêmicas para HBV. O genótipo F3 (75%) foi o mais prevalente. Determinou-se que o subgenótipo F3 é o mais antigo dos subgenótipos F. No estado de Chocó, encontrou-se o subgenótipo A1 (52,1%) como o mais prevalente. Surpreendentemente, nesse mesmo estado foram encontrados nove casos autóctones de infecção pelo genótipo E (39,1%). Para o HCV, em Bogotá, encontrou-se o subtipo 1b (82,8%) como o mais prevalente. Da mesma forma, estimou-se que esse subtipo foi introduzido por volta de 1950 e se propagou exponencialmente entre 1970 a 1990. O HDV foi identificado em casos de hepatite fulminante do estado de Amazonas, todos classificados como genótipo 3. Se determinou que o HDV/3 se espalhou exponencialmente a partir de 1950 a 1970 na América do Sul e depois desta época, esta infecção deixou de aumentar, provavelmente devido a introdução de vacinação contra o HBV. GBV-C foi procurado em doadores de sangue colombianos infectados com HCV e/ou HBV de Bogotá e em povos indígenas com infecção pelo HBV no Amazonas. A análise filogenética revelou a presença do genótipo 2a como o mais prevalente entre os doadores de sangue e o 3 nos povos indígenas estudados. A presença do genótipo 3 na população indígena foi previamente relatada na região de Santa Marta, na Colômbia e nos povos indígenas da Venezuela e da Bolívia. No Chile, foi realizado um estudo com 21 pacientes cronicamente infectados pelo HBV sem tratamento antiviral prévio. Todas as sequências obtidas eram do subgenótipo F1b e se agrupavam em quatro diferentes grupos, sugerindo que diferentes linhagens desse subgenótipo estão circulando no Chile. No Brasil, no estado de Rondônia, para o HCV, encontramos o subtipo 1b (50,0%) como o mais frequente. Esse foi o primeiro relato sobre os genótipos do HCV neste estado. Para o HBV, o subgenótipo A1 (37,0%) foi o mais frequente. Os resultados do estado de Rondônia são consistentes com outros estudos no Brasil, mostrando a presença de vários genótipos do HBV, refletindo a origem mista da população Brasileira. Estudando o estado do Maranhão, avaliamos a frequência da infecção pelo HBV e seus genótipos. Foram encontradas 4 sequencias genótipo A1 que agruparam com outras sequências reportadas do Brasil. Em outro estudo, caracterizamos os subgenótipos do HBV em 68 pacientes com hepatite crônica B em Pernambuco, encontrando 78,7% de presença do subgenótipo A1. Finalmente, em um estudo realizado com amostras da cidade de São Paulo, encontramos um caso de HBV genótipo C em um brasileiro nativo, sendo essa a primeira sequência completa do genoma de HBV/C2 notificados no Brasil / Viral hepatitis are among the major pandemics in the world nowadays. There are many causes of hepatitis, including hepatitis B virus (HBV), hepatitis C virus (HCV) and hepatitis delta virus (HDV). Similarly, GB virus C (GBV-C) is a relevant agent in co-infection with HIV. In this study, several regions of South America were studied. In Colombia, the states of Amazonas and Magdalena were identified as highly endemic areas for HBV. Genotype F3 (75%) was the most prevalent. It was determined that subgenotype F3 is the oldest among all F subgenotypes. In the state of Chocó, subgenotype A1 (52.1%) was the most prevalent. Surprisingly, nine indigenous cases of infection by genotype E (39.1%) were found in this state. For HCV, in Bogotá, subtype 1b (82.8%) was the most frequent. Likewise, it was estimated that this subtype was introduced around 1950 and spread exponentially from 1970 to 1990. HDV has been identified in cases of fulminant hepatitis in the state of Amazonas, all of them classified as genotype 3. It was determined that the HDV/3 spread exponentially from 1950 to 1970 in South America and after this time, this infection stopped to increase, probably due to introduction of vaccination against HBV. GBV-C was sought in Colombian blood donors infected with HCV and/or HBV in Bogotá and indigenous peoples with HBV infection in the Amazon. The phylogenetic analysis revealed the presence of genotype 3 as the most prevalent among blood donors and in three studied indigenous people. The presence of genotype 3 in the indigenous population has been previously reported in the region of Santa Marta, Colombia, and in the indigenous peoples of Venezuela and Bolivia. In Chile, a study was carried out with 21 patients chronically infected with HBV without any prior antiviral treatment. All sequences obtained belonged to subgenotype F1b and clustered into four different groups, suggesting that different strains that are circulating in Chile. In Brazil, the state of Rondônia, we found HCV subtype 1b (50.0%) as the most frequent. This was the first report on HCV genotypes in this state. For HBV, subgenotype A1 (37.0%) was the most frequent. The results of the state of Rondônia are consistent with other studies carried out in Brazil, showing the presence of several HBV genotypes, reflecting the mixed origin of the Brazilian population. Studying the state of Maranhão, we evaluated the frequency of HBV infection and its genotypes and we found 4 genotype A1 sequences that grouped with other sequences reported in Brazil. In another study, we characterized HBV subgenotypes in 68 patients with chronic hepatitis B in Pernambuco and we found subgenotype A1 in 78.7% cases. Finally, in a study of samples from São Paulo, we found a case of HBV genotype C in a native Brazilian patient and this is the first complete genome sequence of HBV/C2 reported in Brazil

Le portage chronique du virus de l'hépatite B (HBV) en Afrique est très élevé, avoisinant parfois jusqu'à 30% dans certaines régions. Selon l'OMS, sur les 400 millions de personnes souffrant d'une infection chronique HBV, 70 à 140 millions vivent en Afrique avec un taux de décès annuel d'environ 250 000 cas par an. Les données concernant l'infection concomitante par le virus de l'hépatite D (HDV) virus satellite de l'HBV, sont rares car peu d'études ont été réalisées en Afrique. Malgré ce fort taux de prévalence, les données concernant la caractérisation moléculaire des souches HBV et HDV sont limitées ou inexistantes dans la plupart des pays d'Afrique Subsaharienne et en particulier dans région du Sahara, vaste zone multiethnique, de passage et de brassage de populations. Au cours de cette étude, nous avons voulu déterminer la prévalence et l'épidémiologie moléculaire des souches HBV et HDV circulant la région du Sahara (Niger et Mauritanie). Tout d'abord, nous avons étudié une cohorte de donneurs de sang du Niger porteurs de l'AgHBs. Nous avons trouvé que 80% des souches étudiées appartenaient au génotype E. De plus, nous avons identifié et caractérisé un nouveau recombinant HBV/D-HBV/E représentant près de 20% des souches étudiées. Les points de cassure se situaient dans des " points chauds " de recombinaison, régions impliquées dans les événements d'intégration du génome de l'HBV. Des analyses phylogénétiques extensives nous ont permis de le classer comme un nouveau sous génotype. Nous avons proposé HBV/D8. Nous avons par la suite, en collaboration avec des équipes locales, étudié la diversité génétique HBV en Mauritanie, pays voisin du Niger, au sein de différents groupes représentatifs de la population : femmes enceintes (n=1020), consultants (n=954), donneurs de sang (n=11110) et patients suivis pour une infection HBV chronique (n=300). Le taux de portage de l'AgHBs, était de 11 à 18 % selon les populations étudiées, classant la Mauritanie comme pays à haute endémie pour l'HBV. L'exposition à l'HBV était associée en analyse multivariée, au niveau d'éducation, à l'ethnie, à des antécédents de transfusion et à la profession chez les femmes enceintes et, chez les consultants, au sexe masculin. Sur le plan moléculaire, 3 génotypes différents circulaient en Mauritanie (n=240) : l'HBV/D (56,3%), l'HBV/E (34,6%) et l'HBV/A (8,8%). De façon intéressante, 30% des génotypes D circulant en Mauritanie étaient l'HBV/D8. Cette diversité de l'HBV peut être expliquée par la localisation géographique du Niger et de la Mauritanie comme zones de passage entre l'Afrique du Nord et l'Afrique Sub Saharienne où l'HDV/D et l'HBV/E respectivement sont prédominants. D'autre part, 14 à 33% des patients HBV positifs étaient également infectés par l'HDV. La présence d'anticorps anti-Delta était associée en analyse multivariée chez les consultants, à l'âge et au sexe masculin, et chez les donneurs de sang, à l'âge, au nombre de mariages, à la profession (militaire), à la résidence (région du désert) et à des antécédents d'hospitalisation. Sur le plan moléculaire, le génotype HDV-1 est largement majoritaire (90%) mais l'HDV-5 a aussi été isolé (10% des cas). En conclusion, ce travail souligne encore la forte prévalence des hépatites B et Delta au Niger et en Mauritanie. Nous avons aussi mis en évidence une diversité génétique importante des souches circulant et notamment la caractérisation d'un nouveau sous-génotype HBV/D8 hautement prévalent. Il convient d'évaluer la sévérité de la maladie hépatique liée à cette diversité génétique et à ce nouveau variant, notamment son implication éventuelle dans l'oncogenèse hépatique par des événements de recombinaison génétique.

Factors that could enable the development of a distribution system for hydrogen applied to heavy-duty vehicles in Sweden are studied in this thesis. Fuel cell and hydrogen technology could be a solution in an electrification mix to reduce the environmental impacts of heavy-duty vehicles (Neef, 2009). However, the distribution system for hydrogen in Sweden is limited, with only five hydrogen refueling stations geographically dispersed (Vätgas Sverige, n.d.). In addition, distribution options at the lowest-cost delivery mode are highly dependent on the hydrogen application, density of demand, quantity to be transported, and distance between the delivery point and the production (Bersani, et al., 2018) To determine what factors could be decisive to develop a distribution system, the technological innovation system framework has been applied in this study. The analysis is carried out with the framework’s system functions. Further, the analysis is based on literature on hydrogen that considers hindering factors and barriers, policy recommendations, lock-in effects, distribution and transportation, and centralized vs. de-centralized systems. Moreover, data has been collected through 11 semi-structured interviews with actors from different sectors, energy companies, truck manufacturers, and researchers, amongst others. The analysis concludes that cross-sectoral collaboration, pilot testing, and governmental support can be enabling factors for the development of a distribution system in Sweden. / Faktorer som kan möjliggöra utvecklingen av ett distributionssystem för vätgas applicerat för tunga fordon i Sverige studeras i den här studien. Tekniken för bränsleceller och vätgas kan vara en lösning i en elektrifieringsmix för att minska miljöpåverkan från tunga fordon (Neef,2009). Distributionssystemet för vätgas i Sverige är dock begränsat, med endast fem vätgastankstationer som är geografiskt spridda (Vätgas Sverige, n.d.). Dessutom är distributionsalternativen till lägst kostnad i hög grad beroende av väteapplikationen, efterfrågan, kvantitet som ska transporteras och avståndet mellan leveranspunkten och produktionen (Bersani, et al., 2018). För att avgöra vilka faktorer som kan vara avgörande för att utveckla ett distributionssystem har ramverket för teknisk innovation system tillämpats i den här studien. Analysen utförs med ramverkets systemfunktioner. Vidare baseras analysen på litteratur om väte som tar hänsyn till hindrande faktorer och barriärer, policyrekommendationer, lock-in-effekter, distribution och transport och centraliserade kontra decentraliserade system. Dessutom har data samlats ingenom 11 halvstrukturerade intervjuer med aktörer från olika sektorer, energibolag, lastbilstillverkare och forskare, bland annat. Utifrån analysen dras slutsatsen att sektorsövergripande samarbete, pilottestning och statligt stöd är faktorer som kan möjliggöra en utveckling av ett distributionssystem för vätgas i Sverige.

The interest in autonomous vehicles has never been higher and there are several components that need to function for a vehicle to be fully autonomous; one of which is the ability to perform a parking at the end of a mission. The objective of this thesis work is to develop and implement an automatic parking system (APS) for a heavy-duty vehicle (HDV). A delimitation in this thesis work is that the parking lot has a known structure and the HDV is a truck without any trailer and access to more computational power and sensors than today's commercial trucks. An automatic system for searching the parking lot has been developed which updates an occupancy grid map (OGM) based on measurements from GPS and LIDAR sensors mounted on the truck. Based on the OGM and the known structure of the parking lot, the state of the parking spots is determined and a path can be computed between the current and desired position. Based on a kinematic model of the HDV, a gain-scheduled linear quadratic (LQ) controller with feedforward action is developed. The controller's objective is to stabilize the lateral error dynamics of the system around a precomputed path. The LQ controller explicitly takes into account that there exist an input delay in the system. Due to minor complications with the precomputed path the LQ controller causes the steering wheel turn too rapidly which makes the backup driver nervous. To limit these rapid changes of the steering wheel a controller based on model predictive control (MPC) is developed with the goal of making the steering wheel behave more human-like. A constraint for maximum allowed changes of the controller output is added to the MPC formulation as well as physical restrictions and the resulting MPC controller is smoother and more human-like, but due to computational limitations the controller turns out less effective than desired. Development and testing of the two controllers are evaluated in three different environments of varying complexity; the simplest simulation environment contains a basic vehicle model and serves as a proof of concept environment, the second simulation environment uses a more realistic vehicle model and finally the controllers are evaluated on a full-scale HDV. Finally, system tests of the APS are performed and the HDV successfully parks with the LQ controller as well as the MPC controller. The concept of a self-parking HDV has been demonstrated even though more tuning and development needs to be done before the proposed APS can be used in a commercial HDV.