KplE1 est l’un des dix prophages présents sur le chromosome de la souche Escherichia coli K12. Nous avons montré in vivo que ce prophage est compétant pour s’exciser du chromosome bactérien bien qu’il soit incapable de former des particules virales et de lyser son hôte. Au laboratoire, nous avons identifié les protéines IntS (intégrase) et TorI (RDF), codées sur le prophage KplE1, et la protéine IHF (NBP) de l’hôte comme seules impliquées dans le mécanisme de recombinaison spécifique de site (RSS). Nous avons cartographié sur les régions attL et attR, les sites de fixations des protéines de recombinaison permettant l’assemblage de l’intasome, le complexe nucléoprotéique compétant pour la RSS. L’ensemble de ces sites ainsi que les gènes intS et torI qui chevauchent respectivement les régions attL et attR, ont permis de définir un module de recombinaison de type KplE1. Ce module est très conservé et se retrouve chez des phages infectant différentes souches d’E. coli et de shigella. Le modèle en terme de RSS est celui décrit pour les bactériophages de type λ. Cependant, le nombre et l’organisation des sites de recombinaison suggèrent que l’architecture de l’intasome de type KplE1 diffère de celle de λ. Nos résultats renforcent ainsi l’idée que l’assemblage de l’intasome est spécifique du module de RSS considéré même si, in fine, la réaction catalysée demeure similaire.En ce qui concerne l’expression des gènes intS et torI, le fait que ces gènes soient localisés à chacune des extrémités du prophage, rend ainsi impossible leur couplage transcriptionnel à partir d’un promoteur commun au moment de la commutation lyse/lysogénie, tel qu’il est connu pour les phages lambdoïdes. De part son orientation atypique sur attL, la présence de sites de fixations des protéines IntS et TorI au niveau du promoteur du gène intS, nous ont logiquement amené à étudier sa régulation. Nous avons ainsi montré que le gène intS est négativement régulé par son propre produit ainsi que par la protéine RDF TorI. Nos résultats in vivo et in vitro indiquent que l’efficacité de la réaction de recombinaison excisive est intimement liée à la quantité d’intégrase présente, pouvant alors justifier la raison d’être de ce contrôle strict de l’expression du gène intS. En parallèle, une approche in silico a révélé que cette orientation atypique du gène codant pour l’intégrase est largement répandue sur les génomes des prophages, nous amenant à généraliser ce mécanisme atypique de régulation négative de l’intégrase. / KplE1 is one of the 10 prophage region present on the Escherichia coli K12 chromosome. We showed in vivo that this prophage is fully competent to excise from the bacterial chromosome, although it is unable to form viral particles and lyse its host. In the laboratory, we have identified Ints (integrase) and TorI (RDF) proteins, encoded on the KplE1 prophage, and the host protein IHF (NBP) only involved in the mechanism of site-specific recombination (SSR). We have mapped on attL and attR regions, the binding sites of recombinant proteins for the assembly of the intasome, the nucleoprotein complex competent for SSR. All of these sites as well as intS and torI genes that overlap respectively attL and attR regions, have permit to define a KplE1 recombination module. This module is highly conserved and is found among phages infecting different E. coli and shigella strains. The model in terms of RSS is that described for λ bacteriophage. However, the number and organization of recombination sites suggests that the architecture of the KplE1 intasome differs from that of λ. Our findings reinforce the idea that the intasome assembly is specific to the SSR module considered even if ultimately the catalyzed reaction is similar.Regarding the intS and torI gene expressions, the fact that these genes are located at each end of the prophage, prevented the transcriptional coupling of these genes from a common promoter when the lysis/lysogeny switch occurs. Because of its atypical orientation on attL, and the presence of IntS and TorI protein binding sites that overlap its promoter region, we have logically studied the regulation of the intS gene. We have shown that intS is negatively regulated by both IntS and TorI proteins. Our in vivo and in vitro results suggest that the efficiency of the excision recombination reaction is closely related to the amount of this integrase, which can justify the strict control of the intS gene expression. In parallel, an in silico approach has revealed that the atypical orientation of the integrase gene is widespread in prophage genomes, leading us to generalize this atypical mechanism of negative regulation of integrase

Incineration with energy recovery is the main disposal strategy for waste that cannot be reused or recycled, and a well-established source of energy in Europe, especially in Sweden where 2.2 Mtonnes of waste including domestic and imported municipal solid waste (MSW) and waste wood (WW) were combusted during 2015. However, owing to its inherent heterogeneous composition, inclusion of such waste in Waste-to-energy (WtE) technologies is challenging. These heterogeneities may lead to operationally-related issues in the WtE facilities and contribute to toxic emissions, which can be reduced by waste pre-treatment technologies.    This thesis examines the variations in the composition of MSW and WW streams used as a fuel supply in WtE facilities after undergoing waste pre-treatment technologies, and the effect of fuel composition on its combustion behaviour and formation of persistent organic pollutants (POPs) such as polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs). The overall objective is to contribute to a more thorough understanding of the selection of waste pre-treatment technologies to mitigate harmful emissions into the atmosphere when waste fuels are combusted in WtE facilities.    This thesis describes the high variability of contaminants in domestic and imported WW and suggests adaptation of WW pre-treatment techniques to produce fuels with a low potential for generating pollutants. A comparison of mechanical solid waste pre-treatments revealed that screening and shredding is more efficient than extrusion for reducing emissions of pollutants such as PCDDs and PCDFs in combustion. The evaluation of the combustion behaviour of MSW-based fuels showed a three-stage oxidative decomposition, and an acceleration of the decomposition of the MSW compared to the lignocellulosic materials, which may be attributed to the presence of food waste and plastics in the MSW. Combustion tests of fuel blends containing WW and MSW-based fuels with different food waste content suggested that WW, not food waste content, is the key factor for the formation of PCDDs, PCDFs, and polychlorinated biphenyls (PCB), benzenes (PCBzs) and phenols (PCPhs). Torrefaction may be a suitable technology for improving the properties of waste as a fuel e.g. due to its low PCDD and PCDF emissions. / Förbränning med energiåtervinning är det huvudsakliga sättet att ta hand om avfall som inte kan återanvändas eller återvinnas. Det är en väletablerad energikälla i Europa och särskilt i Sverige där 2,2 miljoner ton avfall, däribland inhemskt och importerat hushållsavfall och returträ, förbrändes under 2015. På grund av den heterogena sammansättningen hos hushållsavfall och returträ är förbränning av dessa material i anläggningar med energiåtervinning (så kallade WtE-anläggningar) förknippade med en del driftsrelaterade utmaningar. Det kan även ge upphov till miljöfarliga utsläpp, som dock kan reduceras genom förbehandling av avfallet. I denna avhandling har variationer i sammansättningen hos hushållsavfall och returträ som förbränns i WtE-anläggningar undersökts. Effekten av bränslemixens sammansättning och ev förbehandling på bränslets förbränningsegenskaper samt bildning av långlivade organiska föroreningar (så kallade POPar) såsom polyklorerade dibenso-p-dioxiner och polyklorerade dibensofuraner vid förbränning har utvärderats. Det övergripande målet är att bidra till en djupare förståelse av hur valet av förbehandlingsteknik för avfall kan bidra till att minska skadliga utsläpp till luft när avfallsbränslen förbränns i WtE-anläggningar. Denna avhandling beskriver den stora variabiliteten av metall- och materialföroreningar i inhemskt och importerat returträ och föreslår förbehandlingstekniker för att producera bränslen med låg potential att generera föroreningar. En jämförelse av mekaniska förbehandlingstekniker visade att mekanisk sönderdelning och separering (krossning och siktning) är mer effektivt än s.k. högtrycks-pressning för att minska utsläppen av föroreningar som dioxiner och furaner vid förbränning. Utvärderingen av bränslemixar innehållande hushållsavfall uppvisade en oxidativ nedbrytning i tre steg vid förbränning, och en accelererad nedbrytning av avfallsmaterialet jämfört med vedmaterialet i bränslet, troligen som effekt av innehållet av matavfall och plast i hushållsavfallet. Förbränningsförsök med bränsleblandningar av returträ och hushållsavfall med olika innehåll av matavfall visade att mängden returträ, och inte mängden matavfall, är den viktigaste faktorn för bildning av dioxiner, furaner, klorbifenyler, klorbensener, och klorfenoler. Torrefiering kan vara en lämplig teknik för att förbättra avfallets bränsleegenskaper, t.ex. på grund av dess låga emissioner.

There is an emerging demand on techniques addressing the problem of efficiently archiving and (temporal) querying different versions of evolving semantic Web data. While systems archiving and/or temporal querying are still in their early days, we consider this a good time to discuss benchmarks for evaluating storage space efficiency for archives, retrieval functionality they serve, and the performance of various retrieval operations. To this end, we provide a blueprint on benchmarking archives of semantic data by defining a concise set of operators that cover the major aspects of querying of and interacting with such archives. Next, we introduce BEAR, which instantiates this blueprint to serve a concrete set of queries on the basis of real-world evolving data. Finally, we perform an empirical evaluation of current archiving techniques that is meant to serve as a first baseline of future developments on querying archives of evolving RDF data. (authors' abstract) / Series: Working Papers on Information Systems, Information Business and Operations

En större kunskap kring sammansättningen på bränsleblandningen som kommer in tillavfallsförbränningsanläggningarna kan ha en väsentlig positiv inverkan på driftekonomi,tillgänglighet, utsläppsnivåer och underhållsbehov av anläggningarna. I framtiden kommerdet troligen också att vara nödvändigt att kunna verifiera sammansättningen av t.ex. andelenfossilt kol i anläggningens bränsleblandning för att den skall kunna klassas i rätt skattenivå.Ett problem för att få denna bättre kunskap är att ett gram av avfallet ska utgöra en spegelbildav, och till fullo motsvara, en hel bunker på 1000-tals ton avfall. Metoder för provtagning,storleken på uttagna prover, neddelning och provberedning har stor inverkan på relevansen avanalysresultat som erhålls från laboratoriet. Även hanteringen av fraktioner som textil, metall,sten samt stora hårda plastbitar utgör problem då de är svåra att mala till den storlek somefterföljande analys kräver. Idag utesluts sådana fraktioner från provet trots att de kan habetydelse för att beskriva bränsleblandningens förbränningsegenskaper. Ytterligare ettproblem i sammanhanget är att anläggningsägarna inte alltid vet om hur mycket och vid vilkatillfällen som fraktioner har plockats bort.Mot denna bakgrund är det intressant att ta reda på vilka metoder som är lämpliga attapplicera på provtagning av fast heterogent avfallsbränsle ur avfallsbunker? Hur skall ejmalbart material hanteras på laboratoriet? Har den initiala provkvantiteten någon betydelse förkvaliteten på resultaten? Ännu en intressant fråga är hur mycket arbetsmetoden i fält och pålaboratoriet kan förenklas utan att resultaten påverkas negativt?Rapporten syftar till att sammanställa, utvärdera och komplettera metodik för provtagning,neddelning och provberedning för heterogena fasta avfallsbränslen. Syftet är även att ge ettförslag till en arbetsmetod för provtagning och analys av heterogent avfall. En empiriskundersökning har utförts i projektet för att se hur väl de metoder som nämns i teorin lämparsig för provtagning av heterogent avfallsbränsle ur avfallsbunker.Ett av de uttagna proverna var betydligt större än de övriga proverna då det fungerade som ettså kallat referensprov. Syftet med referensprovet var att undersöka relevansen ochjämförbarheten i resultaten hos de mindre proverna med det större provets resultat för atteventuellt föreslå en funktionell provkvantitet som skulle kunna ge ett representativt resultat.I det här projektet har det dock inte framkommit något som kunnat styrka att de störreproverna uppvisar ett resultat med högre kvalitet än de mindre proverna. Detta innebär attanläggningsägaren med fördel kan förenkla arbetsmetoden genom att ta ut mindre kvantiteterav varje prov. Det har dessutom i en analys av det totala provtagningsfelet visat sig attlaboratorieförfarandet bidrar med en ytterst liten del av det totala felet och att det ärprovtagningen som står för den största felkällan. Det betyder att även arbetsmetoden ilaboratoriet kan förenklas utan att mätosäkerhet ökar i någon större omfattning. Till exempelkan en mindre kvantitet användas för fortsatt partikelreducering och istället för att utföra ettstort antal värmevärdesbestämningar per prov räcker det att endast utföra två utan att förlora inoggrannhet.Genom användandet av mindre provkvantiteter underlättas hanteringen både vidanläggningen och på laboratoriet och arbetet kan förenklas och går därmed fortare att utförautan att resultatet påverkas negativt. Detta leder till lägre kostnader per provtagnings- ochanalystillfälle vilket i sin tur möjliggör att fler prov kan tas och/eller att prov kan utföras4oftare. Ett större antal provtagningar möjliggör en bättre vetskap av avfallets variation ochsammansättning över tiden. / Uppsatsnivå: D

The Semantic Web, or the Web of Data, promotes common data formats for representing structured data and their links over the web. RDF is the defacto standard for semantic data where it provides a flexible semi-structured model for describing concepts and relationships. RDF datasets consist of entries (i.e, triples) that range from thousands to Billions. The astronomical growth of RDF data calls for scalable RDF management and query processing strategies. This dissertation addresses efficient query processing over web-scale RDF data. The first contribution is WORQ, an online, workload-driven, RDF query processing technique. Based on the query workload, reduced sets of intermediate results (or reductions, for short) that are common for specific join pattern(s) are computed in an online fashion. Also, we introduce an efficient solution for RDF queries with unbound properties. The second contribution is SPARTI, a scalable technique for computing the reductions offline. SPARTI utilizes a partitioning schema, termed SemVP, that enables efficient management of the reductions. SPARTI uses a budgeting mechanism with a cost model to determine the worthiness of partitioning. The third contribution is KC, an efficient RDF data management system for the cloud. KC uses generalized filtering that encompasses both exact and approximate set membership structures that are used for filtering irrelevant data. KC defines a set of common operations and introduces an efficient method for managing and constructing filters. The final contribution is semantic filtering where data can be reduced based on the spatial, temporal, or ontological aspects of a query. We present a set of encoding techniques and demonstrate how to use semantic filters to reduce irrelevant data in a distributed setting.

Anotações têm sido associadas a documentos em todas as gerações de sistemas hipermídia. Este trabalho explora o uso de anotações como hiperdocumentos de primeira classe baseados em sua semântica. Nesse contexto, anotações são entidades próprias, na forma de hipertexto, possuindo seus próprios atributos e operações. A Web Semântica é uma extensão da Web atual na qual é dado um significado bem definido à informação, permitindo que informações sejam compreensíveis não só por humanos, mas também por computadores. Este trabalho possui como objetivo prover um serviço aberto, o GroupNote, de suporte a anotações colaborativas como hiperdocumentos de primeira classe na Web Semântica. Para prover esse serviço foram realizadas a modelagem conceitual e a definição e implementação de uma API, a API GroupNote. Como um estudo de caso do serviço GroupNote foi construída a aplicação WebNote, uma ferramenta que permite que usuários tenham seu próprio repositório de anotações na Web. / Annotations have been associated with documents in all the generations of hypermedia systems. This work investigates annotations as first class hyperdocuments based on their semantics: annotations are entities (with their own attributes and operations) in the hypertext form. The Semantic Web is an extension of the current Web in which a well-defined meaning is given to information, allowing the information to be comprehensible not only by humans, but also by machines. This work aims at providing an open service, GroupNote, to support collaborative annotations as first class hyperdocuments in the Semantic Web. The provision of the GroupNote service demanded the conceptual modeling, the definition and implementation of its API. As a case study of the GroupNote service, the WebNote application was built as a tool that allows users to have your own repository of annotations in the Web.

The Semantic Web provides a framework for semantically annotating data on the web, and the Resource Description Framework (RDF) supports the integration of structured data represented in heterogeneous formats. Traditionally, the Semantic Web has focused primarily on more or less static data, but information on the web today is becoming increasingly dynamic. RDF Stream Processing (RSP) systems address this issue by adding support for streaming data and continuous query processing. To some extent, RSP systems can be used to perform complex event processing (CEP), where meaningful high-level events are generated based on low-level events from multiple sources; however, there are several challenges with respect to using RSP in this context. Event models designed to represent static event information lack several features required for CEP, and are typically not well suited for stream reasoning. The dynamic nature of streaming data also greatly complicates the development and validation of RSP queries. Therefore, reusing queries that have been prepared ahead of time is important to be able to support real-time decision-making. Additionally, there are limitations in existing RSP implementations in terms of both scalability and expressiveness, where some features required in CEP are not supported by any of the current systems. The goal of this thesis work has been to address some of these challenges and the main contributions of the thesis are: (1) an event model ontology targeted at supporting CEP; (2) a model for representing parameterized RSP queries as reusable templates; and (3) an architecture that allows RSP systems to be integrated for use in CEP. The proposed event model tackles issues specifically related to event modeling in CEP that have not been sufficiently covered by other event models, includes support for event encapsulation and event payloads, and can easily be extended to fit specific use-cases. The model for representing RSP query templates was designed as an extension to SPIN, a vocabulary that supports modeling of SPARQL queries as RDF. The extended model supports the current version of the RSP Query Language (RSP-QL) developed by the RDF Stream Processing Community Group, along with some of the most popular RSP query languages. Finally, the proposed architecture views RSP queries as individual event processing agents in a more general CEP framework. Additional event processing components can be integrated to provide support for operations that are not supported in RSP, or to provide more efficient processing for specific tasks. We demonstrate the architecture in implementations for scenarios related to traffic-incident monitoring, criminal-activity monitoring, and electronic healthcare monitoring.

Le web sémantique est défini par un ensemble de méthodes et de technologies permettant à des agents logiciels de raisonner sur le contenu des ressources du Web. Cette vision du Web dépend de la construction des ontologies et de l'utilisation de métadonnées pour représenter ces ressources. L'objectif de notre travail de thèse est d'annoter sémantiquement des documents balisés et relatifs au même domaine. Ces documents peuvent comporter des parties bien structurées et d'autres textuelles. Nous supposons disposer d'une ontologie de domaine définie par des concepts, des relations entre ces concepts et des propriétés. Cette ontologie comporte une composante lexicale où chaque concept est accompagné de labels, d'un ensemble d'entités nommées (EN) et de termes du domaine. Nous avons défini une approche automatique SHIRI-Extract qui permet d'extraire des termes et des EN de manière indépendante du domaine et de les aligner aux concepts de l'ontologie. L'alignement utilise la composante lexicale ou le Web pour découvrir de nouveaux termes. Nous avons défini un modèle d'annotation représentant les résultats d'extraction et d'annotation. Les métadonnées de ce modèle distinguent les nœuds selon que les termes ou les EN agrégés dans un même nœud sont alignés avec un ou plusieurs concepts différents. Elles permettent également d'annoter la relation de voisinage entre les nœuds. Nous avons défini SHIRI-Annot, un ensemble de règles déclaratives pour annoter les nœuds et leurs relations. La base d'annotations RDF(S) construite peut être interrogée à l'aide de requêtes SPARQL. L'évaluation a porté sur une collection de documents portant sur des appels à participation à des conférences.

<p>Today, micro- and nano-electronic devices are becoming more complex and advanced as the dimensions are shrinking. It is therefore a very challenging task to develop new device technologies with performance that can be predicted. This thesis focuses on advanced measurement techniques and TCAD simulations in order to characterize and understand the device physics of advanced semiconductor devices. </p><p>TCAD simulations were made on a novel MOSFET device with asymmetric source and drain structures. The results showed that there exists an optimum range of implantation doses where the device has a significantly higher figure-of-merit regarding speed and voltage capability, compared to a symmetric MOSFET. Furthermore, both 2D and 3D simulations were used to develop a resistive model of the substrate noise coupling. </p><p>Of particular interest to this thesis is the random dopant fluctuation (RDF). The result of RDF can be characterized using very advance and reliable measurement techniques. In the thesis an ultra-high precision parametric mismatch measurement system was designed and implemented. The best ever reported performance on short-term repeatability of the measurements was demonstrated. A new bipolar parametric mismatch phenomenon was also revealed using the measurement system.</p><p>A complete simulation platform, called SiSPET (Simulated Statistical Parameter Extraction Tool), was developed and integrated into the framework of a commercial TCAD environment. A special program for randomization of the doping was developed and proven to provide RDF effects in agreement measurement. The SiSPET system was used to investigate how different device models were able to take RDF effects into account. The RDF effects were translated in to parameter fluctuations using the developed extraction routines. It was shown that the basic MOSFET fluctuation model could be improved by including the field dependenent mobility. However, if a precise description of the fluctuations is required an advanced compact-model, such as MOS Model 11 should be used.</p>

Today, micro- and nano-electronic devices are becoming more complex and advanced as the dimensions are shrinking. It is therefore a very challenging task to develop new device technologies with performance that can be predicted. This thesis focuses on advanced measurement techniques and TCAD simulations in order to characterize and understand the device physics of advanced semiconductor devices. TCAD simulations were made on a novel MOSFET device with asymmetric source and drain structures. The results showed that there exists an optimum range of implantation doses where the device has a significantly higher figure-of-merit regarding speed and voltage capability, compared to a symmetric MOSFET. Furthermore, both 2D and 3D simulations were used to develop a resistive model of the substrate noise coupling. Of particular interest to this thesis is the random dopant fluctuation (RDF). The result of RDF can be characterized using very advance and reliable measurement techniques. In the thesis an ultra-high precision parametric mismatch measurement system was designed and implemented. The best ever reported performance on short-term repeatability of the measurements was demonstrated. A new bipolar parametric mismatch phenomenon was also revealed using the measurement system. A complete simulation platform, called SiSPET (Simulated Statistical Parameter Extraction Tool), was developed and integrated into the framework of a commercial TCAD environment. A special program for randomization of the doping was developed and proven to provide RDF effects in agreement measurement. The SiSPET system was used to investigate how different device models were able to take RDF effects into account. The RDF effects were translated in to parameter fluctuations using the developed extraction routines. It was shown that the basic MOSFET fluctuation model could be improved by including the field dependenent mobility. However, if a precise description of the fluctuations is required an advanced compact-model, such as MOS Model 11 should be used.