Ce travail vise à la mise en œuvre d'une plateforme de simulation basée sur SystemC-AMS. Elle permet de traiter un système complexe et hétérogène. Nous validons cette approche sur une application de réseau de capteurs (communication entre véhicule). Pour ce faire un niveau d'abstraction élevé a été adopté et une modélisation en bande de base des blocs RF a été développée. Non seulement les aspects relatifs à l'émetteur/récepteur ont été traités, mais également le canal radio.Si les actuels flots de conceptions permettent d'estimer la consommation des blocs numériques d'un SoC, une méthodologie d'estimation de la consommation des blocs analogiques et RF n'est toujours pas disponible. Nous proposons une méthodologie descendante basée sur le facteur de mérite et les paramètres systèmes pour estimer la consommation instantané de ces blocs. Ainsi des estimations de la consommation globale des nœuds et du réseau sont fournies par la plateforme.Nous avons fourni une bibliothèque implémentée en SystemC-AMS pour différents blocs d'un réseau de capteurs (nœud et canal radio). Les résultats montrent la faisabilité d'une simulation complexe mixte analogique, numérique et RF. Par ailleurs, ils montrent le gain considérable apporté par la simulation au niveau système en SystemC-AMS de modèles comportementaux d'un réseau de capteurs. La plateforme développée dans ce travail ouvre diverses perspectives sur de nombreux et importants aspects de la simulation système des réseaux de capteurs. Parmi ces aspects, le choix et l'optimisation des algorithmes de routage, les protocoles MAC, les algorithmes de traitement du signal sous une contrainte de consommation d'énergie. / This work aims at implementing a simulation platform based on SystemC-AMS. It can handle a complex and heterogeneous system on chip (SoC). An application of wireless sensor network (WSN): inter-vehicle communication is used to validate this approach. To realize this application, a high level of abstraction was adopted and a baseband modeling of RF blocks has been developed. Besides, not only aspects related to the RF transceiver, but also the radio channel were studied.The current design flows enable the estimation of power consumption of digital blocks, however a high-level methodology for power consumption estimation of analog and RF blocks is still not available. We propose a Top-Down methodology based on the figure of merit (FoM) and system parameters to estimate the instantaneous power consumption of these blocks. Thus, estimates of overall consumption of nodes and the WSN are provided by the platform.We delivered a library implemented in SystemC-AMS for different blocks of a WSN such as node and radio channel. The results show the feasibility to simulate complex, RF and analog mixed SoC. In addition, they show the significant gain in terms of simulation time provided by the system-level simulation using SystemC-AMS and behavioural models of WSN.The platform developed in this work opens a variety of perspectives on many important aspects of system-level simulation of WSN. These aspects include the choice and optimization of routing algorithms, MAC protocols, signal processing algorithms, as a function of power consumption which is the main constraint of WSN.

In comparison with other Muslim Arabic countries, Tunisia have attained a unique and successful progress when it comes to women’s rights and gender equality. According to researchers, the progress of women’s rights in Tunisia is due to a policy of top down State feminism that the country has adapted since the independence from the French colonialism 1956. Researchers have mainly focused on investigating the diverse factors that contributed to this progress and on tracing the causal mechanism behind the unique women’s legal rights in Tunisia. Nevertheless, there are few studies that carefully examined gender norms in Tunisian society and its relation to the adopted top down State feminism. The goal of this thesis is to analyse how gender norm are described in Tunisians legal texts and compare it to how young educated citizens in Tunisia relate to gender norms, as well to see if there are any eventual potential progress regarding gender equality in the future in Tunisia. This thesis is based on text analysis of law texts and qualitative group interviews. This thesis has no high explanatory ambitions, but it seeks to illustrate the various potential explanations for the differences and similarities between how gender norms are constructed in law texts and among young educated citizens in Tunisia. Also, this thesis seeks to obtain an idea about how these differences and similarities can be understood. This was done with the help of the data collected from the group interviews and also using theories about State feminism and the relation between the state and gender norms. The analysis of law texts shows that the Tunisian state draws a rigorous line between the public and the private sphere. The Tunisian state expresses a progressive view regarding gender norms on the public sphere but a conservative one when it comes to the private sphere. The interviewees’ views regarding gender norms in the public and the private sphere can be divided into two main categories depending on how they argument for their point of view: “Progressive” and “Conservative”. Thus, differences and similarities between how gender norms are expressed in law texts and by the participants in this study and how those can be understood, depends on which ideologies and mindsets the participants have concerning gender norms. Thus, the cultural and religious heritage as well as the social current circumstances can be assumed to be one of the most crucial factors that affects the progress of gender norms and equality in the public sphere likewise the private sphere in the case of Tunisia. / Jämfört med andra arabiska muslimska länder har Tunisien genomgått en märkbar och annorlunda utveckling vad gäller jämställdhet och kvinnors rättigheter. Enligt forskning på området berodde detta huvudsakligen på en top down State feminism policy som landet har anammat sedan självständigheten från den franska kolonialismen 1956. Forskare har mest fokuserat på att undersöka de olika faktorer som ledde till denna framgång och den kausala mekanismen bakom kvinnors unika juridiska rättigheter i Tunisien. Det är dock få forskare som har ägnat sig åt att studera genusnormer i det tunisiska samhället och dess relation till denna top-down State Feminism. Syftet med denna uppsats är att analysera hur lagtexter I Tunisien skildrar genusnormer och jämföra det med hur unga utbildade tunisier förhåller sig till genusnormer samt att se om det verkar finnas en potential för en framtida förändring vad gäller jämställdhet i Tunisien. Denna uppsats är baserad på textanalys av lagtexter samt kvalitativa gruppintervjuer med unga universitetsutbildade i Tunisien. Uppsatsen har inga höga förklarande ambitioner men ämnar snarare att, med hjälp av intervjumaterialet samt teorier kring State feminism och relationen mellan staten och genusnormer, kasta ljus på de potentiella förklaringarna till hur eventuella skillnader och likheter mellan lagtexters och ungas syn på genusnormer kan förstås. Analysen av lagtexter visar att staten i Tunisien drar en strikt linje mellan den offentliga och privata sfären. Staten uttrycker en progressiv syn på genusnormer i den offentliga sfären men en konservativ syn i den privata. Hur deltagare i denna studie ser på genusnormer i den offentliga och den privata sfären kan egentligen delas i två kategorier beroende på hur de argumenterade för sina synpunkter: ”Progressiva” och ”Konservativa”. Således beror vilka eventuella skillnader och likheter som finns mellan gennusnormer som uttrycks i lagtexter och bland unga i denna studie samt de potentiella förklaringarna till dessa skillnader och likheter, på vilket tankesättet deltagarna tillhör. Det kulturella och religiösa arvet samt samhällets omständigheter och behov kan antas dock vara bland de mest betydelsefulla faktorerna för genusnormers utveckling och jämställdhet både inom lagen och i samhället i just fallet Tunisien.

Raman spectroscopy is among the most widely employed methods to investigate the properties of materials in several fields of study. Evolution in materials science allowed us to fabricate suitable substrates, at the nanoscale, capable to enhance the electromagnetic field of the signals coming from the samples which at this range turn out to be in most cases singles or a few molecules. This particular variation of the classical technique is called SERS (Surface Enanched Raman Spectroscopy). In this work, the enhancement of the electromagnetic field is obtained by manipulation of the optical properties of metals with respect to their size. By using electroless deposition (bottom up technique), gold and silver nanoparticles were deposited in nanostructured patterns obtained on silicon wafers by means of electron beam lithography (top down technique). Rhodamine 6G in aqueous solution at extremely low concentration (10-8 M) was absorbed on the resultant dimers and the collection of the Raman spectra demonstrated the high efficiency of the substrates.

Indiana University-Purdue University Indianapolis (IUPUI) / Proteoforms are distinct protein molecule forms created by variations in genes, gene expression, and other biological processes. Many proteoforms contain multiple primary structural alterations, including amino acid substitutions, terminal truncations, and posttranslational modifications. These primary structural alterations play a crucial role in determining protein functions: proteoforms from the same protein with different alterations may exhibit different functional behaviors. Because top-down mass spectrometry directly analyzes intact proteoforms and provides complete sequence information of proteoforms, it has become the method of choice for the identification of complex proteoforms. Although instruments and experimental protocols for top-down mass spectrometry have been advancing rapidly in the past several years, many computational problems in this area remain unsolved, and the development of software tools for analyzing such data is still at its very early stage. In this dissertation, we propose several novel algorithms for challenging computational problems in proteoform identification by top-down mass spectrometry. First, we present two approximate spectrum-based protein sequence filtering algorithms that quickly find a small number of candidate proteins from a large proteome database for a query mass spectrum. Second, we describe mass graph-based alignment algorithms that efficiently identify proteoforms with variable post-translational modifications and/or terminal truncations. Third, we propose a Markov chain Monte Carlo method for estimating the statistical signi ficance of identified proteoform spectrum matches. They are the first efficient algorithms that take into account three types of alterations: variable post-translational modifications, unexpected alterations, and terminal truncations in proteoform identification. As a result, they are more sensitive and powerful than other existing methods that consider only one or two of the three types of alterations. All the proposed algorithms have been incorporated into TopMG, a complete software pipeline for complex proteoform identification. Experimental results showed that TopMG significantly increases the number of identifications than other existing methods in proteome-level top-down mass spectrometry studies. TopMG will facilitate the applications of top-down mass spectrometry in many areas, such as the identification and quantification of clinically relevant proteoforms and the discovery of new proteoform biomarkers. / 2019-06-21

No description available.

Proceeding from a specification, one develops an abstract mathematical model of a system, or portion of a system. This model of a system is validated to insure that the specification is interpreted accurately and to explore different algorithms for implementing the system behavior. We use the words "portion of a system," because only rarely are systems designed wholly using a purely top-down approach. Commonly, the design approach is a mixture of top-down and bottom-up. But even in this mixed approach, top-down techniques are critical to the development of new, advanced system features and improving the performance of existing system components. An example of this style of design tools and environments is Ptolemy II. Ptolemy II is a high-level modeling tool created at UC-Berkeley. It supports heterogeneous and homogeneous modeling, simulation, and design of concurrent systems. High-level modeling of such embedded systems as digital electronics, hardware, and software can be effectively represented. The bottom-up design approach exploits design reuse to achieve the productivity necessary to build complex systems. Historically, chip design companies have always reused designs in going from one product generation to another, but the efficiency of bottom-up design is enhanced by the use of IP (Intellectual Property) cores that a company can buy from an outside source. Design libraries are useful for system design and are an example of IP cores. A sound methodology to translate Ptolemy models to SystemC models would have a very beneficial effect on the CAD/EDA industry. Ptolemy II is written in Java and its high-level designs, or abstract graph models, are represented as XML documents. Ptolemy's major emphasis is on the methodology for defining and producing embedded software together with the system in which it is embedded. SystemC is written in C++, and its industrial use is gaining momentum due to its ability to represent functionality, communication, software, and hardware at various levels of abstraction. SystemC produces synthesizable code. A methodology to convert Ptolemy models to synthesizable SystemC code would be the technical epitome of a hybrid between top-down and bottom-up design styles and methodologies. Such a methodology would enable system designers to obtain fast design exploration, efficient IP-reuse, and validation. Ptolemy has various components and models of computation. A model of computation dictates how components interact between other components. SystemC has its own models of computation and design libraries. XML and Perl are both powerful tools by themselves, and we use these tools in this research to create a sound methodology for translating Ptolemy models (high-level of abstraction) to synthesizable SystemC code (low-level of abstraction), i.e.: code which can serve as input to hardware tools. / Ph. D.

We propose a framework for managing changes in Long term Composed Services (LCSs). The key components of the proposed framework include a Web Service Change Management Language (SCML), change enactment, and change optimization. The SCML is a formal language to specify top-down changes. It is built upon a formal model which consists of a Web service ontology and a LCS schema. The Web service ontology gives a semantic description on the important features of a service, including functionality, quality, and context. The LCS schema gives a high-level overview of a LCS's key features. A top-down change is specified as the modification of a LCS schema in the first place. Change enactment is the process of reacting to a top-down change. It consists of two subcomponents, including change reaction and change verification. The change reaction component implements the proposed change operators by modifying a LCS schema and the membership of Web services. The change verification component ensures that the correctness of a LCS is maintained during the process of change reaction. We propose a set of algorithms for the processes of change reaction and verification. The change optimization component selects the Web services that participate in a LCS to ensure that the change has been reacted to in the best way. We propose a two-phase optimization process to select services using both service reputation and service quality. We present a change management system that implements the proposed approaches. We also conduct a set of simulations to assess the performance. / Ph. D.

The red imported fire ant, Solenopsis invicta, is an abundant and aggressive component of early-successional communities in the southeastern United States. After disturbance, it rapidly invades new habitats, and once there, it has strong competitive and predatory effects on the existing arthropod community. In upland coastal plain pine forests at the Savannah River Site in South Carolina, I conducted two studies of fire ant ecology. In my first study (chapter 1), I investigated the way in which fire ants colonize early-successional road and powerline cuts through forests, and I tested whether some of these linear habitats provided better fire ant habitat than others. I found that fire ant mound density (#/ha) was similar in narrow dirt roads and in wider roads with the same intermediate level of mowing disturbance, and that density was lower in wide powerline cuts where the vegetation is only removed every five years. Furthermore, mound density was greatest near the edges of cleared roads and powerline cuts and was also greater on the northern sides of roads and powerline cuts where there was less shading from the adjacent forest. Results from this study suggest that allowing increased shading from adjacent forest vegetation, especially along northern roadside edges, would limit the suitability of road and powerline cuts as fire ant habitat, thereby slowing invasion. In my second study (chapter 2), I examined the impact of fire ants on arthropod and plant species in early-successional forest gaps. In a tritrophic system, I tested whether the top-down effect of insect herbivore consumption by fire ants was strong enough to cascade through two trophic levels and improve plant growth and fitness. I compared this potential effect to that of other arthropod predators in the community. I found that fire ants controlled the level of tissue damage to plant leaves by herbivores, but that the damage was not severe enough to influence plant growth or fitness. Fire ants had stronger negative interactions with insect herbivores than other predators in the community, and for this reason, fire ants can be considered keystone predators. This project provides further evidence that fire ants successfully invade even small patches of early-successional habitat that exist within larger matrices of uninhabitable, late-successional forest, and that once there, they have a dramatic effect on the arthropod community. Restricting the amount of early-successional habitat within southeastern forests, either as permanent road and powerline cuts or as temporary gaps, would limit the potential for strong and detrimental effects by the invasive fire ant. / Master of Science

A diversidade da Mata Atlântica está constantemente ameaçada devido à perda de habitats provocada pela destruição e alteração dos ambientes naturais. Este fato é muito preocupante, pois os remanescentes florestais da Mata Atlântica encontram-se, em sua maior parte, em pequenos fragmentos altamente perturbados, acarretando em perda de biodiversidade da fauna existente. Muitos estudos demonstraram que mamíferos e aves especialistas (e. g. insetívoros) são muito sensíveis à fragmentação ambiental, tendendo a desaparecer em áreas abertas. A perda destes animais pode alterar a densidade de artrópodes e as taxas de herbivoria, ocasionando um efeito cascata (top- down), que causará influência até na decomposição e ciclagem de nutrientes. Entretanto o estudo de como esse efeito top-down ocorre em diferentes coberturas de solo ainda não foi testado, desta forma, objetivou-se investigar como as taxas de decomposição são modificadas pela exclusão experimental de vertebrados em áreas com diferentes coberturas vegetais na mata Atlântica. Parcelas de exclusão de vertebrados e parcelas controle foram alocadas em áreas com coberturas vegetais de pastagem e floresta, para verificar como ocorre o efeito top-down na decomposição. Utilizaram-se três tipos de serapilheira diferentes, uma gramínea (Brachiaria decumbens), uma espécie pioneira (Tibouchina sellowiana) e uma mistura de folhas de diferentes espécies da floresta primária adjacente. A técnica dos litter bags foi utilizada para avaliar as diferentes taxas de decomposição e foram coletados em intervalos de 16, 36, 71, 181 e 247 dias. O resíduo vegetal foi limpo, seco e pesado para obtenção das massas remanescentes (%) e taxa de decomposição, após isso o material foi triturado e pesado em subamostras para analises de nutrientes e compostos orgânicos (nitrogênio, carbono, fósforo, lignina, celulose e polifenóis). A taxa de decomposição não diferiu entre os tratamentos controle e exclusão de vertebrados, desta forma, não foi possível observar o efeito top-down da exclusão de vertebrados neste estudo, provavelmente devido à elevada biodiversidade da fauna do solo na área onde o experimento foi realizado e sugere-se repeti-lo em uma área menor e mais desconectada, com a finalidade de simular como o efeito cascata ocorre em pequenos fragmentos da mata Atlântica. Além disso, a decomposição foi mais rápida nos litter bags localizados na floresta do que na pastagem e as folhas de gramínea tiveram maior perda de massa do que as folhas de floresta primária e T. sellowiana, possivelmente devido às interações entre nitrogênio, lignina e a relação C:N dos resíduos vegetais. / The diversity of Atlantic forest is constantly threatened due to habitat loss caused by the destruction and alteration of natural environments, and most of the biome is now in small and fragmented areas. This fact is of a great concern, because the remaining areas in Atlantic forest are in small highly disturbed fragments, resulting in loss of biodiversity of the existing fauna, like mammals and birds. Many studies have shown that specialist mammals and birds (e.g. insectivores) are very sensitive to environment fragmentation and tend to disappear in open areas. The loss of these animals is likely to cause an increase in the density of arthropods and rates of herbivory, causing a top-down effect that may even influence the cycling of nutrients. We aimed to investigate how decomposition rates are modified by the experimental exclusion of vertebrates in an area with different land coverage in the Atlantic forest. Vertebrate exclusion plots and control plots were allocated in areas with different land coverage (pasture and forest) to evaluate the top-down effects in decomposition. We used three different kinds of leaves, being one grass (Brachiaria decumbens), one very common primary specie of the area (Tibouchina sellowiana) and a mix of primary forest leaves. Litterbags were used to evaluate the decomposition rate and it was collected during intervals of 16, 36, 71, 181 and 247 days. The vegetal residue was cleaned, dried and weighted to obtain the remaining mass (%) and decomposition rate, after that, the material was milled and weighted in subsamples for analyses of nutritional quality (N, C, P, lignin, cellulose and polyphenols). The decomposition rate was not different for the control and vertebrate exclusion plots, as a result, it was not possible to show the top-down effect in decomposition, possibly because of the high soil biodiversity in the area where the experiment was done. It would be very important to remake this experiment in a smaller and more disconnected area, in order to show how this cascade effect occur in Atlantic forest´s smaller fragments. Furthermore, the decomposition was faster at the forest plots than at the pastureland plots and the grass leaf litter presented the higher decomposition rate than the primary forest leaves and T. sellowiana and it was possibly caused by the interaction between nitrogen, lignin and C:N ratio.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / Lectinas podem ser definidas como proteÃnas/glicoporteÃnas que reconhecem carboidratos de maneira especÃfica, mas nÃo participam do metabolismo dos mesmos e nÃo pertencem a nenhuma das principais classes de imunoglobulinas. As lectinas sÃo proteÃnas ubÃquas, estando presente em todos os organismos conhecidos. Em cÃlulas animais, lectinas tÃm sido encontradas no citoplasma, no nÃcleo e associadas a membranas das mais diversas organelas e nos mais variados tipos celulares. Tais lectinas animais podem ser classificadas em famÃlias distintas com base em suas caracterÃsticas fÃsico quÃmicas, funÃÃo e especialmente em sua identidade de estrutura primÃria e terciÃria. O objetivo deste trabalho foi purificar duas novas lectinas da esponja marinha Haliclona (Soestella) caerulea e caracterizar estruturalmente uma delas. EspÃcimes de H.caerulea foram coletados na praia do paracuru, CearÃ. Duas lectinas (H-1 e H-3) foram isoladas por tÃcnicas clÃssicas de quÃmica de proteÃnas. A estrutura primÃria de uma delas foi determinada por espectrometria de massas e RACE. A atividade tÃxica das lectinas foi avaliada frente à nÃuplios de Artemia e cepas das bactÃrias Escherichia coli e Staphylococus aureus. H-1 e H-3 apresentaram caracterÃsticas distinhas da lectina previamente isolada de H. caerulea. H-1 à uma proteÃna monomÃrica de aporoximadamente 40 kDa enquanto que H-3 à uma proteÃna trimÃrica com cadeias com massa aproximada de 9, 16 e 18 kDa. H-3 aglutina eritrÃcitos humanos do tipo A e B e foi inibida GalNAc e PSM, H-1 aglutina diversos grupos sanguineos e nÃo pÃde ser inibida por nenhum aÃÃcar testado. H-1 foi tÃxica a naÃplios de Artemia (LC50=6,4 μg.mL-1) e H-3 foi considerada nÃo tÃxica (LC50=414,2 μg.mL-1). H-3 à uma proteÃna azul, pois interage com um cromÃforo de 597 Da com absorÃÃo mÃxima a 620 nm. A estrutura primÃria de H-3 foi determinada e revelou-se Ãnica, nÃo sendo conhecida nenhuma lectina com estrutura similar. H-3 apresenta um glicano hÃbrido composto por Hex7NAcHex7DeoxiHex2. A cadeia α de H-3 sofre um processamento proteolÃtico complexo que ainda nÃo foi completamente elucidado. AlÃm disso, H-3 foi cristalizada, mas nÃo foi possÃvel a obtenÃÃo de um padraÃo de difraÃÃo que permita a resoluÃÃo da estrutura. Em suma, duas novas lectinas foram isoladas e fora observado pela primeira vez a interaÃÃo entre uma lectina e um cromÃforo natural. Pela primeira vez tambÃm, fora determinada a composiÃÃo glicÃdica de uma lectina de esponja. / Lectins are proteins/glycoproteins that recognize carbohydrate of a specific way, but not participate in the metabolism of the same and do not belong to any of major classes of immunoglobulins. Lectins are ubiquitous proteins, present in all known organisms. In animal cells, lectins have been found in the cytoplasm, in the nucleous and as membrane-associated proteins, in diverse organelles and cells. Animal lectins can be classified into distinct families based on their physicochemical characteristics, especially in their function and identity of primary and tertiary structure. The aim of this study was to purify, characterize structural and biologically new lectins from the marine sponge Haliclona (Soestella) caerulea. H. caerulea specimens were collected in Paracuru beach, CearÃ. Two lectins (H-1 and H-3) were isolated by classical techniques of protein chemistry. The primary structure of H-3 was determined by mass spectrometry and RACE. The toxic activity of lectins was evaluated against Artemia nauplii and Escherichia coli and Staphylococcus aureus strains. H-1 and H-3 showed distinct characteristics of the lectin previously isolated from H. caerulea. H-1 is a monomeric protein of 40 kDa whereas H-3 is a heterogeneus protein with chains of 9, 16 and 18 kDa. H-3 binds human erythrocytes of A and B type and was inhibited by GalNAc and PSM, H-1 binds different blood groups and could not be inhibited by any sugar tested. H-1 was toxic to Artemia nauplii (LC50 = 6.4 μg.mL-1) and H-3 was not considered toxic (LC50 = 414.2 μg.mL-1). H-3 is a blue protein that interacts with a chromophore of 597 Da of maximum absorbance at 620 nm. The primary structure of H-3 revealed a unique amino acid sequence no similar to any animal lectins known. H-3 has a hybrid glycan comprising by Hex7NAcHex7DeoxiHex2. The α-chain of H-3 undergoes complex proteolytic processing that not been fully elucidated. Moreover, H-3 was crystallized, but was not possible to obtain a diffraction pattern that permits solving the structure. In short, two new lectins were isolated and out first observed the interaction between a lectin and natural chromophore. Furthermore, for the first time given the composition glicidic out of a sponge lectin.