An assurance-based model to holistically assess the information security posture

EXECUTIVE SUMMARY : Evaluating Information Security Posture within an organization is becoming a very complex task. Currently, the evaluation and assessment of Information Security are commonly performed using frameworks, methodologies and standards which often consider the various aspects of security independently. Unfortunately this is ineffective because it does not take into consideration the necessity of having a global and systemic multidimensional approach to Information Security evaluation. At the same time the overall security level is globally considered to be only as strong as its weakest link. This thesis proposes a model aiming to holistically assess all dimensions of security in order to minimize the likelihood that a given threat will exploit the weakest link. A formalized structure taking into account all security elements is presented; this is based on a methodological evaluation framework in which Information Security is evaluated from a global perspective. This dissertation is divided into three parts. Part One: Information Security Evaluation issues consists of four chapters. Chapter 1 is an introduction to the purpose of this research purpose and the Model that will be proposed. In this chapter we raise some questions with respect to "traditional evaluation methods" as well as identifying the principal elements to be addressed in this direction. Then we introduce the baseline attributes of our model and set out the expected result of evaluations according to our model. Chapter 2 is focused on the definition of Information Security to be used as a reference point for our evaluation model. The inherent concepts of the contents of a holistic and baseline Information Security Program are defined. Based on this, the most common roots-of-trust in Information Security are identified. Chapter 3 focuses on an analysis of the difference and the relationship between the concepts of Information Risk and Security Management. Comparing these two concepts allows us to identify the most relevant elements to be included within our evaluation model, while clearing situating these two notions within a defined framework is of the utmost importance for the results that will be obtained from the evaluation process. Chapter 4 sets out our evaluation model and the way it addresses issues relating to the evaluation of Information Security. Within this Chapter the underlying concepts of assurance and trust are discussed. Based on these two concepts, the structure of the model is developed in order to provide an assurance related platform as well as three evaluation attributes: "assurance structure", "quality issues", and "requirements achievement". Issues relating to each of these evaluation attributes are analysed with reference to sources such as methodologies, standards and published research papers. Then the operation of the model is discussed. Assurance levels, quality levels and maturity levels are defined in order to perform the evaluation according to the model. Part Two: Implementation of the Information Security Assurance Assessment Model (ISAAM) according to the Information Security Domains consists of four chapters. This is the section where our evaluation model is put into a welldefined context with respect to the four pre-defined Information Security dimensions: the Organizational dimension, Functional dimension, Human dimension, and Legal dimension. Each Information Security dimension is discussed in a separate chapter. For each dimension, the following two-phase evaluation path is followed. The first phase concerns the identification of the elements which will constitute the basis of the evaluation: ? Identification of the key elements within the dimension; ? Identification of the Focus Areas for each dimension, consisting of the security issues identified for each dimension; ? Identification of the Specific Factors for each dimension, consisting of the security measures or control addressing the security issues identified for each dimension. The second phase concerns the evaluation of each Information Security dimension by: ? The implementation of the evaluation model, based on the elements identified for each dimension within the first phase, by identifying the security tasks, processes, procedures, and actions that should have been performed by the organization to reach the desired level of protection; ? The maturity model for each dimension as a basis for reliance on security. For each dimension we propose a generic maturity model that could be used by every organization in order to define its own security requirements. Part three of this dissertation contains the Final Remarks, Supporting Resources and Annexes. With reference to the objectives of our thesis, the Final Remarks briefly analyse whether these objectives were achieved and suggest directions for future related research. Supporting resources comprise the bibliographic resources that were used to elaborate and justify our approach. Annexes include all the relevant topics identified within the literature to illustrate certain aspects of our approach. Our Information Security evaluation model is based on and integrates different Information Security best practices, standards, methodologies and research expertise which can be combined in order to define an reliable categorization of Information Security. After the definition of terms and requirements, an evaluation process should be performed in order to obtain evidence that the Information Security within the organization in question is adequately managed. We have specifically integrated into our model the most useful elements of these sources of information in order to provide a generic model able to be implemented in all kinds of organizations. The value added by our evaluation model is that it is easy to implement and operate and answers concrete needs in terms of reliance upon an efficient and dynamic evaluation tool through a coherent evaluation system. On that basis, our model could be implemented internally within organizations, allowing them to govern better their Information Security. RÉSUMÉ : Contexte général de la thèse L'évaluation de la sécurité en général, et plus particulièrement, celle de la sécurité de l'information, est devenue pour les organisations non seulement une mission cruciale à réaliser, mais aussi de plus en plus complexe. A l'heure actuelle, cette évaluation se base principalement sur des méthodologies, des bonnes pratiques, des normes ou des standards qui appréhendent séparément les différents aspects qui composent la sécurité de l'information. Nous pensons que cette manière d'évaluer la sécurité est inefficiente, car elle ne tient pas compte de l'interaction des différentes dimensions et composantes de la sécurité entre elles, bien qu'il soit admis depuis longtemps que le niveau de sécurité globale d'une organisation est toujours celui du maillon le plus faible de la chaîne sécuritaire. Nous avons identifié le besoin d'une approche globale, intégrée, systémique et multidimensionnelle de l'évaluation de la sécurité de l'information. En effet, et c'est le point de départ de notre thèse, nous démontrons que seule une prise en compte globale de la sécurité permettra de répondre aux exigences de sécurité optimale ainsi qu'aux besoins de protection spécifiques d'une organisation. Ainsi, notre thèse propose un nouveau paradigme d'évaluation de la sécurité afin de satisfaire aux besoins d'efficacité et d'efficience d'une organisation donnée. Nous proposons alors un modèle qui vise à évaluer d'une manière holistique toutes les dimensions de la sécurité, afin de minimiser la probabilité qu'une menace potentielle puisse exploiter des vulnérabilités et engendrer des dommages directs ou indirects. Ce modèle se base sur une structure formalisée qui prend en compte tous les éléments d'un système ou programme de sécurité. Ainsi, nous proposons un cadre méthodologique d'évaluation qui considère la sécurité de l'information à partir d'une perspective globale. Structure de la thèse et thèmes abordés Notre document est structuré en trois parties. La première intitulée : « La problématique de l'évaluation de la sécurité de l'information » est composée de quatre chapitres. Le chapitre 1 introduit l'objet de la recherche ainsi que les concepts de base du modèle d'évaluation proposé. La maniéré traditionnelle de l'évaluation de la sécurité fait l'objet d'une analyse critique pour identifier les éléments principaux et invariants à prendre en compte dans notre approche holistique. Les éléments de base de notre modèle d'évaluation ainsi que son fonctionnement attendu sont ensuite présentés pour pouvoir tracer les résultats attendus de ce modèle. Le chapitre 2 se focalise sur la définition de la notion de Sécurité de l'Information. Il ne s'agit pas d'une redéfinition de la notion de la sécurité, mais d'une mise en perspectives des dimensions, critères, indicateurs à utiliser comme base de référence, afin de déterminer l'objet de l'évaluation qui sera utilisé tout au long de notre travail. Les concepts inhérents de ce qui constitue le caractère holistique de la sécurité ainsi que les éléments constitutifs d'un niveau de référence de sécurité sont définis en conséquence. Ceci permet d'identifier ceux que nous avons dénommés « les racines de confiance ». Le chapitre 3 présente et analyse la différence et les relations qui existent entre les processus de la Gestion des Risques et de la Gestion de la Sécurité, afin d'identifier les éléments constitutifs du cadre de protection à inclure dans notre modèle d'évaluation. Le chapitre 4 est consacré à la présentation de notre modèle d'évaluation Information Security Assurance Assessment Model (ISAAM) et la manière dont il répond aux exigences de l'évaluation telle que nous les avons préalablement présentées. Dans ce chapitre les concepts sous-jacents relatifs aux notions d'assurance et de confiance sont analysés. En se basant sur ces deux concepts, la structure du modèle d'évaluation est développée pour obtenir une plateforme qui offre un certain niveau de garantie en s'appuyant sur trois attributs d'évaluation, à savoir : « la structure de confiance », « la qualité du processus », et « la réalisation des exigences et des objectifs ». Les problématiques liées à chacun de ces attributs d'évaluation sont analysées en se basant sur l'état de l'art de la recherche et de la littérature, sur les différentes méthodes existantes ainsi que sur les normes et les standards les plus courants dans le domaine de la sécurité. Sur cette base, trois différents niveaux d'évaluation sont construits, à savoir : le niveau d'assurance, le niveau de qualité et le niveau de maturité qui constituent la base de l'évaluation de l'état global de la sécurité d'une organisation. La deuxième partie: « L'application du Modèle d'évaluation de l'assurance de la sécurité de l'information par domaine de sécurité » est elle aussi composée de quatre chapitres. Le modèle d'évaluation déjà construit et analysé est, dans cette partie, mis dans un contexte spécifique selon les quatre dimensions prédéfinies de sécurité qui sont: la dimension Organisationnelle, la dimension Fonctionnelle, la dimension Humaine, et la dimension Légale. Chacune de ces dimensions et son évaluation spécifique fait l'objet d'un chapitre distinct. Pour chacune des dimensions, une évaluation en deux phases est construite comme suit. La première phase concerne l'identification des éléments qui constituent la base de l'évaluation: ? Identification des éléments clés de l'évaluation ; ? Identification des « Focus Area » pour chaque dimension qui représentent les problématiques se trouvant dans la dimension ; ? Identification des « Specific Factors » pour chaque Focus Area qui représentent les mesures de sécurité et de contrôle qui contribuent à résoudre ou à diminuer les impacts des risques. La deuxième phase concerne l'évaluation de chaque dimension précédemment présentées. Elle est constituée d'une part, de l'implémentation du modèle général d'évaluation à la dimension concernée en : ? Se basant sur les éléments spécifiés lors de la première phase ; ? Identifiant les taches sécuritaires spécifiques, les processus, les procédures qui auraient dû être effectués pour atteindre le niveau de protection souhaité. D'autre part, l'évaluation de chaque dimension est complétée par la proposition d'un modèle de maturité spécifique à chaque dimension, qui est à considérer comme une base de référence pour le niveau global de sécurité. Pour chaque dimension nous proposons un modèle de maturité générique qui peut être utilisé par chaque organisation, afin de spécifier ses propres exigences en matière de sécurité. Cela constitue une innovation dans le domaine de l'évaluation, que nous justifions pour chaque dimension et dont nous mettons systématiquement en avant la plus value apportée. La troisième partie de notre document est relative à la validation globale de notre proposition et contient en guise de conclusion, une mise en perspective critique de notre travail et des remarques finales. Cette dernière partie est complétée par une bibliographie et des annexes. Notre modèle d'évaluation de la sécurité intègre et se base sur de nombreuses sources d'expertise, telles que les bonnes pratiques, les normes, les standards, les méthodes et l'expertise de la recherche scientifique du domaine. Notre proposition constructive répond à un véritable problème non encore résolu, auquel doivent faire face toutes les organisations, indépendamment de la taille et du profil. Cela permettrait à ces dernières de spécifier leurs exigences particulières en matière du niveau de sécurité à satisfaire, d'instancier un processus d'évaluation spécifique à leurs besoins afin qu'elles puissent s'assurer que leur sécurité de l'information soit gérée d'une manière appropriée, offrant ainsi un certain niveau de confiance dans le degré de protection fourni. Nous avons intégré dans notre modèle le meilleur du savoir faire, de l'expérience et de l'expertise disponible actuellement au niveau international, dans le but de fournir un modèle d'évaluation simple, générique et applicable à un grand nombre d'organisations publiques ou privées. La valeur ajoutée de notre modèle d'évaluation réside précisément dans le fait qu'il est suffisamment générique et facile à implémenter tout en apportant des réponses sur les besoins concrets des organisations. Ainsi notre proposition constitue un outil d'évaluation fiable, efficient et dynamique découlant d'une approche d'évaluation cohérente. De ce fait, notre système d'évaluation peut être implémenté à l'interne par l'entreprise elle-même, sans recourir à des ressources supplémentaires et lui donne également ainsi la possibilité de mieux gouverner sa sécurité de l'information.

Combining digital elevation model analysis and run-out modeling to characterize hazard posed by a potentially unstable rock slope at Turtle Mountain, Alberta, Canada

Turtle Mountain in Alberta, Canada has become an important field laboratory for testing different techniques related to the characterization and monitoring of large slope mass movements as the stability of large portions of the eastern face of the mountain is still questionable. In order to better quantify the volumes potentially unstable and the most probable failure mechanisms and potential consequences, structural analysis and runout modeling were preformed. The structural features of the eastern face were investigated using a high resolution digital elevation model (HRDEM). According to displacement datasets and structural observations, potential failure mechanisms affecting different portions of the mountain have been assessed. The volumes of the different potentially unstable blocks have been calculated using the Sloping Local Base Level (SLBL) method. Based on the volume estimation, two and three dimensional dynamic runout analyses have been performed. Calibration of this analysis is based on the experience from the adjacent Frank Slide and other similar rock avalanches. The results will be used to improve the contingency plans within the hazard area.

BRAIN DAMAGE IN METHYLMALONIC ACIDURIA: 2-METHYLCITRATE LEADS TO AMMONIA INCREASE AND APOPTOSIS

A 3D in vitro model of rat organotypic brain cell cultures in aggregates was used to investigate neurotoxicity mechanisms in methylmalonic aciduria. 1 mM methylmalonate (MMA), 2-methylcitrate (2-MCA) or propionate (PA) were repeatedly added to the culture media at two different time points of the cultures. In cultures treated with 2-MCA, we observed a significant increase of lactate in the medium, consistent with a possible inhibition of Krebs cycle and respiratory chain, as described earlier in the literature. Interestingly, we further observed that 2-MCA induced an important increase in ammonia production with concomitant decrease of glutamine concentrations, which suggests an inhibition of the astrocytic enzyme glutamine synthetase. These previously unreported findings may uncover a pathogenic mechanism in this disease with deleterious effects on early stages of brain development. By immunohistochemistry we could show that 2-MCA substantially increased the number of apoptotic cells. On the cellular level, 2-MCA had a toxic effect (cell swelling and cell death) on glial cells, but not on neurons. Surprisingly, MMA seemed to have a growth stimulating effect on the cultures. We can conclude that 2-MCA was the most toxic metabolite in our model for methylmalonic aciduria inducing ammonia accumulation and massive apoptosis in brain cells.

Local optima networks of hard combinatorial landscapes

Combinatorial optimization involves finding an optimal solution in a finite set of options; many everyday life problems are of this kind. However, the number of options grows exponentially with the size of the problem, such that an exhaustive search for the best solution is practically infeasible beyond a certain problem size. When efficient algorithms are not available, a practical approach to obtain an approximate solution to the problem at hand, is to start with an educated guess and gradually refine it until we have a good-enough solution. Roughly speaking, this is how local search heuristics work. These stochastic algorithms navigate the problem search space by iteratively turning the current solution into new candidate solutions, guiding the search towards better solutions. The search performance, therefore, depends on structural aspects of the search space, which in turn depend on the move operator being used to modify solutions. A common way to characterize the search space of a problem is through the study of its fitness landscape, a mathematical object comprising the space of all possible solutions, their value with respect to the optimization objective, and a relationship of neighborhood defined by the move operator. The landscape metaphor is used to explain the search dynamics as a sort of potential function. The concept is indeed similar to that of potential energy surfaces in physical chemistry. Borrowing ideas from that field, we propose to extend to combinatorial landscapes the notion of the inherent network formed by energy minima in energy landscapes. In our case, energy minima are the local optima of the combinatorial problem, and we explore several definitions for the network edges. At first, we perform an exhaustive sampling of local optima basins of attraction, and define weighted transitions between basins by accounting for all the possible ways of crossing the basins frontier via one random move. Then, we reduce the computational burden by only counting the chances of escaping a given basin via random kick moves that start at the local optimum. Finally, we approximate network edges from the search trajectory of simple search heuristics, mining the frequency and inter-arrival time with which the heuristic visits local optima. Through these methodologies, we build a weighted directed graph that provides a synthetic view of the whole landscape, and that we can characterize using the tools of complex networks science. We argue that the network characterization can advance our understanding of the structural and dynamical properties of hard combinatorial landscapes. We apply our approach to prototypical problems such as the Quadratic Assignment Problem, the NK model of rugged landscapes, and the Permutation Flow-shop Scheduling Problem. We show that some network metrics can differentiate problem classes, correlate with problem non-linearity, and predict problem hardness as measured from the performances of trajectory-based local search heuristics.

Focal degeneration of astrocytes in amyotrophic lateral sclerosis

Astrocytes emerge as key players in motor neuron degeneration in Amyotrophic Lateral Sclerosis (ALS). Whether astrocytes cause direct damage by releasing toxic factors or contribute indirectly through the loss of physiological functions is unclear. Here we identify in the hSOD1(G93A) transgenic mouse model of ALS a degenerative process of the astrocytes, restricted to those directly surrounding spinal motor neurons. This phenomenon manifests with an early onset and becomes significant concomitant with the loss of motor cells and the appearance of clinical symptoms. Contrary to wild-type astrocytes, mutant hSOD1-expressing astrocytes are highly vulnerable to glutamate and undergo cell death mediated by the metabotropic type-5 receptor (mGluR5). Blocking mGluR5 in vivo slows down astrocytic degeneration, delays the onset of the disease and slightly extends survival in hSOD1(G93A) transgenic mice. We propose that excitotoxicity in ALS affects both motor neurons and astrocytes, favouring their local interactive degeneration. This new mechanistic hypothesis has implications for therapeutic interventions.Cell Death and Differentiation advance online publication, 11 July 2008; doi:10.1038/cdd.2008.99.

Immunological mechanisms underlying infectious and chronic lung diseases

Le système respiratoire permet l'échange de gaz entre un organisme et son environnement. Pour fonctionner efficacement, il doit lutter contre les infections tout en maintenant une tolérance aux particules inoffensives. Les cytokines sont des petites protéines qui permettent la communication entre les différentes cellules et jouent un rôle important dans la régulation de l'homéostasie et de l'immunité des surfaces pulmonaires. Une production altérée des cytokines sous-tend beaucoup de maladies du système pulmonaire. Ainsi, la compréhension de la biologie fondamentale des cytokines pourrait contribuer à la mise au point de nouveaux traitements. Dans le cadre de cette thèse, nous avons étudié le rôle de deux cytokines, le TSLP (Thymic stromal lymphopoietin) et l'IL-17 (Interleukin 17) dans les réponses immunitaires bénéfiques et nuisibles en utilisant des modèles précliniques de souris des maladies pulmonaires. L'asthme est une maladie qui est caractérisée par la bronchoconstriction réversible, l'inflammation des voies respiratoires inférieures, l'hyperréactivité bronchique et le remodelage tissulaire. Le type d'inflammation affectant les voies respiratoires et la présence ou non d'allergie permettent d'établir les différents types d'asthme. La TSLP est une cytokine qui est principalement exprimée à des niveaux élevés dans les poumons de patients souffrant d'asthme allergique. En conséquence, la majeure partie de la recherche sur la TSLP a mis l'accent sur le rôle joué par celle- ci dans les réponses négatives conduisant au développement de l'asthme allergique. Dans cette thèse, nous montrons que la TSLP joue aussi un rôle bénéfique dans les réponses immunitaires pulmonaires. Nous avons découvert que la TSLP atténue la grippe en augmentant les réponses des lymphocytes T cytotoxiques contre le virus. Nous avons également étudié la fonction de la TSLP dans l'asthme non allergique. Contrairement à l'asthme allergique, nous avons constaté que la TSLP diminue les réponses inflammatoires dans l'asthme non allergique en réglant la production de l'IL-17, une cytokine qui favorise la maladie. Ainsi, nous démontrons les fonctions pleiotropes de la TSLP dans des contextes spécifiques de la maladie. Nos résultats ont des implications importantes pour le développement de thérapies ciblant la TSLP dans l'asthme. Dans la deuxième partie de la thèse, nous avons étudié les mécanismes pathogéniques qui sous-tendent le développement de la broncho-pneumopathie chronique obstructive (BPCO). La BPCO est une maladie chronique le plus largement associée aux fumeurs. Elle est caractérisée par une limitation progressive et irréversible du débit d'air et la destruction de la structure des poumons. L'augmentation globale de l'incidence de la maladie encourage grandement la compréhension des mécanismes pathogéniques et l'identification de nouvelles cibles thérapeutiques. Nous avons découvert que les micro-organismes trouvés dans les voies respiratoires aggravent la maladie en augmentant la production de l'IL-17. L'IL-17 est une cytokine inflammatoire qui est impliquée dans plusieurs maladies pulmonaires chroniques, dont la BPCO. Dans notre modèle animal de la maladie, nous avons neutralisé 1ÌL-17A en utilisant un anticorps spécifique et observé une reprise de la fonction pulmonaire. Dans cette étude, nous avons identifié 2 axes potentiels pour l'intervention thérapeutique contre la BPCO. Cibler les bactéries dans les voies respiratoires soit par l'utilisation d'antibiotiques ou l'utilisation de thérapies à base immunitaire qui antagonisent l'activité spécifiques de l'IL-17. Dans l'avenir, notre laboratoire va collaborer avec des cliniciens pour acquérir des échantillons humains et tester la pertinence de nos résultats dans la maladie humaine. -- L'interaction avec l'environnement extérieur est vitale pour le fonctionnement du système respiratoire. Par conséquent, ce dernier a adopté une multitude de réseaux effecteurs et régulateurs qui permettent de distinguer les particules inhalées comme «dangereuses» ou «inoffensives» et de réagir en conséquence. L'équilibre entre ces réseaux est essentielle pour lutter contre le «danger» déclenché par une infection ou des dommages, et finalement pour le retour à l'homéostasie. Le milieu de cytokine local contribue de manière significative à la mise au point de ces réponses. Ainsi, la caractérisation du rôle des cytokines dans l'état d'équilibre et la maladie a des implications claires pour les interventions thérapeutiques dans les maladies respiratoires aiguës et chroniques. Cette thèse a porté sur le rôle des cytokines, la lymphopoïétine stromale thymique (TSLP) et TIL-17A dans l'élaboration de réponses immunitaires pulmonaires. La TSLP est principalement produite par les cellules épithéliales et peut cibler une myriade de cellules immunitaires. Bien qu'elle ait été montrée être un puissant inducteur des réponses de type Th2, son rôle dans d'autres contextes inflammatoires est relativement inexploré. Dans le premier projet de cette thèse, nous avons découvert une nouvelle fonction de la TSLP dans l'immunité antivirale contre la grippe, une infection virale. Nous avons constaté que la TSLP a réglementé la réponse neutrophile au début de l'infection, en amplifiant l'immunité adaptative spécifique du virus. Mécaniquement, la TSLP a augmenté l'expression de l'IL-15 et du CD70 sur les cellules dendritiques recrutées dans les poumons suite à l'infection et a renforcé leur capacité de stimuler localement les lymphocytes T CD8+ spécifiques du virus. En outre, nous avons étudié la TSLP dans le cadre de divers phénotypes de l'asthme et également démontré l'impact pléiotropique qu'elle a sur les réponses immunitaires pulmonaires. En accord avec les rapports précédents, nous avons constaté que la TSLP a exacerbé l'inflammation atopique médiée par le Th2. En revanche la TSLP a réduit les réponses de l'IL-17A et l'inflammation neutrophile subséquente dans le modèle non atopique, ainsi que l'exacerbation du modèle atopique provoqué par une infection virale. Nos résultats démontrent une dichotomie dans le rôle de la TSLP dans la pathogenèse de l'asthme et soulignent la nécessité d'envisager plusieurs phénotypes d'asthme pour une évaluation approfondie de son potentiel thérapeutique dans cette maladie. Dans la seconde partie de cette thèse, nous avons caractérisé les mécanismes pathogènes qui sous-tendent la broncho-pneumopathie chronique obstructive (BPCO). La BPCO est une maladie hétérogène définie par une diminution progressive de la fonction pulmonaire. Bien que des déclencheurs environnementaux puissent aggraver la maladie, chez les personnes sensibles une maladie établie peut progresser à travers un cercle inflammatoire auto-entretenu. Nous avons cherché à définir les mécanismes sous-jacents à l'aide d'un modèle murin d'inflammation chronique, qui reproduit les caractéristiques pathologiques de la maladie humaine. Puisqu'ont été associés à la BPCO sévère des changements dans le microbiome des voies respiratoires, nous avons supposé que les signaux dérivés de certains microbes pourraient favoriser des voies inflammatoires chroniques de progression de la maladie. Nous avons observé que, en l'absence d un microbiome, la maladie s'est améliorée tel que démontré par une réduction de l'inflammation des voies respiratoires et une amélioration de la fonction pulmonaire. Cela a été lié spécifiquement à une production réduite d'IL-17A, une cytokine qui a été impliquée dans la maladie humaine. De plus la cinétique de production de 1IL- 17A dépendant du microbiote est corrélé à la sévérité de la maladie. Sur la base de ces données, la neutralisation de l'IL-17A a également eu un effet bénéfique sur l'évolution de la maladie. Le rôle significatif de 1TL-17A dans l'aggravation de la maladie a été couplé à sa capacité à engager un dialogue entre les voies inflammatoires innées et adaptatives. Il a influencé le recrutement et le phénotype des neutrophiles et des macrophages, ce qui a eu un impact direct et indirect sur la formation et la fonction des tissus lymphoïdes tertiaires associée à des stades sévères de la maladie. -- The interaction with the external environment is vital for the functioning of the respiratory system. Consequently, it has adopted a multitude of effector and regulatory networks that enable it to distinguish inhaled particles as 'dangerous' or 'innocuous' and respond accordingly. The balance between these networks is crucial to counteract the 'danger' triggered by infection or damage, and ultimately return to homeostasis. The local cytokine milieu contributes significantly to the fine- tuning of these responses. Thus, characterizing the role of cytokines in steady state and disease has clear implications for therapeutic interventions in acute and chronic respiratory disorders. This thesis focused on the role of the cytokines, thymic stromal lymphopoietin (TSLP) and IL-17A in shaping pulmonary immune responses. TSLP is primarily produced by barrier epithelial cells and can target a myriad of immune cells. Although it has been shown to be potent inducer of Th2 type responses, its role in other inflammatory settings is relatively unexplored. In the first project of this thesis, we discovered a novel function of TSLP in antiviral immunity to Influenza A infection. We found that while TSLP regulated the early neutrophilic response to infection, it amplified virus specific adaptive immunity. Mechanistically, TSLP enhanced the expression of IL-15 and CD70 on the lung recruited inflammatory dendritic cells and strengthened their ability to stimulate virus specific CD8+ T cell responses locally. In addition we investigated TSLP in the context of diverse asthma phenotypes and further demonstrated the pleiotropic impact it has on pulmonary immune responses. In concurrence with previous reports we found that TSLP exacerbated Th2 mediated atopic inflammation. In contrast TSLP curtailed IL-17A responses and subsequent neutrophilic inflammation in the non-atopic model as well as virus induced exacerbation of the atopic model. Our findings demonstrate a dichotomy in the role of TSLP in asthma pathogenesis and emphasize the need to consider multiple asthma phenotypes for a thorough evaluation of its therapeutic potential in this disease. In the next part of this thesis we characterized the pathogenic mechanisms underlying chronic obstructive pulmonary disease. COPD is a heterogeneous disease defined by a progressive decline in lung function. Although environmental triggers exacerbate the disease, in susceptible individuals the established disease can progress through a self-sustained inflammatory circle. We sought to delineate the underlying mechanisms by using a murine model of chronic inflammation, which reproduced key pathological features of the human disease. As changes in the airway microbiome have been linked to severe COPD, we speculated that microbial derived signals could facilitate the establishment of chronic inflammatory pathways that favour disease progression. We found that the absence of a microbiota ameliorated disease, exhibited by a reduction in airway inflammation and an improvement in lung function. This was linked specifically to an impaired production of IL-17A, a cytokine that has been implicated in human disease. Moreover the kinetics of microbiota-dependent IL-17A production correlated with the disease severity. Based on these data targeted neutralization of IL-17A also had a beneficiai effect on the disease outcome. The prominent role played by IL-I7A in driving the disease was coupled to its ability in engaging and mediating cross talk between pathogenic innate and adaptive immune pathways. It influenced the recruitment and phenotype of neutrophils and macrophages, as well as impacted upon the formation and function of tertiary lymphoid tissue associated with severe disease. Thus, temporal and spatial changes in cytokine production, their cellular targets and interaction with the local milieu determine the balance between immunity and pathology in the lung. Collectively our findings provide novel mechanistic insights in the complex role played by cytokines in orchestrating pulmonary immune responses and have clear implications for human disease.

Lipoxin A₄ prevents the progression of de novo and established endometriosis in a mouse model by attenuating prostaglandin E₂ production and estrogen signaling.

Endometriosis, a leading cause of pelvic pain and infertility, is characterized by ectopic growth of endometrial-like tissue and affects approximately 176 million women worldwide. The pathophysiology involves inflammatory and angiogenic mediators as well as estrogen-mediated signaling and novel, improved therapeutics targeting these pathways are necessary. The aim of this study was to investigate mechanisms leading to the establishment and progression of endometriosis as well as the effect of local treatment with Lipoxin A4 (LXA₄), an anti-inflammatory and pro-resolving lipid mediator that we have recently characterized as an estrogen receptor agonist. LXA₄ treatment significantly reduced endometriotic lesion size and downregulated the pro-inflammatory cytokines IL-1β and IL-6, as well as the angiogenic factor VEGF. LXA₄ also inhibited COX-2 expression in both endometriotic lesions and peritoneal fluid cells, resulting in attenuated peritoneal fluid Prostaglandin E₂ (PGE₂) levels. Besides its anti-inflammatory effects, LXA₄ differentially regulated the expression and activity of the matrix remodeling enzyme matrix metalloproteinase (MMP)-9 as well as modulating transforming growth factor (TGF)-β isoform expression within endometriotic lesions and in peritoneal fluid cells. We also report for first time that LXA₄ attenuated aromatase expression, estrogen signaling and estrogen-regulated genes implicated in cellular proliferation in a mouse model of disease. These effects were observed both when LXA₄ was administered prior to disease induction and during established disease. Collectively, our findings highlight potential targets for the treatment of endometriosis and suggest a pleotropic effect of LXA₄ on disease progression, by attenuating pro-inflammatory and angiogenic mediators, matrix remodeling enzymes, estrogen metabolism and signaling, as well as downstream proliferative pathways.

Local alignment refinement using structural assessment.

Homology modeling is the most commonly used technique to build a three-dimensional model for a protein sequence. It heavily relies on the quality of the sequence alignment between the protein to model and related proteins with a known three dimensional structure. Alignment quality can be assessed according to the physico-chemical properties of the three dimensional models it produces.In this work, we introduce fifteen predictors designed to evaluate the properties of the models obtained for various alignments. They consist of an energy value obtained from different force fields (CHARMM, ProsaII or ANOLEA) computed on residue selected around misaligned regions. These predictors were evaluated on ten challenging test cases. For each target, all possible ungapped alignments are generated and their corresponding models are computed and evaluated.The best predictor, retrieving the structural alignment for 9 out of 10 test cases, is based on the ANOLEA atomistic mean force potential and takes into account residues around misaligned secondary structure elements. The performance of the other predictors is significantly lower. This work shows that substantial improvement in local alignments can be obtained by careful assessment of the local structure of the resulting models.

Local shockwave-application prevents flap necrosis

Objective: Local shockwave-application (SW) has shown to improve healing of various tissues and decrease necrosis of flaps. Though, there is no data about the optimal time-point of SW-application with regard to induction of ischemia (i.e. flap elevation) and subsequent effect on flap survival. Therefore we compared 2 shock-wave protocols in a model of persistent ischemia and investigated underlying mechanisms. Methods: 18 C57BL/6-mice equipped with a skinfold chamber containing a musculocutaneous flap were assigned to 3 experimental groups: 1. One session of 500 SWimpulses at 0·15 mJ/mm2 applied 24 hrs before (preconditioning) or 2. Applied 30 min after flap elevation (treatment). 3. Untreated flaps (control). Tissue necrosis,microhemodynamics, inflammation, apoptosis and angiogenesis were assessed by intravital epi-fluorescence microscopy over 10 days. Results: SW significantly reduced flap necrosis independent from the application time-point (preconditioning: 29 ± 7%; treatment: 25 ± 7% vs. control: 47 ± 2%; d10, p<0·05). This was associated with an early increase of functional capillary density (preconditioning: 236 ± 39 cm/cm2; treatment: 211 ± 33 cm/cm2 vs. control: 141 ± 7 cm/cm2; day1, p<0·05). Arteriolar diameter, red blood cell velocity and blood flow were comparable between the 3 experimental groups. SW-application significantly decreased the ischemiainduced inflammatory response (apoptotic cell death and leukocyte-endothelial interaction: (p<0·05)). Sprouts indicating angiogenesis were observed from day 7 only after SW-application. Conclusions: SW protects ischemically challenged musculocutaneous tissue. Interestingly, postoperative SW-application is as efficient as preoperative SWapplication. The protective effect induced by mechanical stress might be based on an early recruitment of ''sleeping capillaries'' maintaining nutritive perfusion and an anti-inflammatory effect within the ischemically jeopardized tissue. SWapplication provides a non-invasive alternative to local thermic and systemic pre-treatment of endangered tissues.

A model for organ donation in switzerland, the latin organ donation programme (lodp); an ongoing successful regional initiative

Background: The 1st Swiss federal Transplant Law was finally enforced in July 2007 with the obligation to promote quality and efficiency in transplant procedures. The LODP was created to develop organ and tissue donation in the Latin area of Switzerland covering seventeen hospitals (29% of the population).Methods: Each of the partner hospitals designated at least one Local Donor Coordinator (LDC), member of the Intensive Care team, trained in the organ donation (OD) process. The principal tasks of the LDC's are the introduction of OD procedures, organisation of educational sessions for hospital staff and execution of the Donor Action programme. The LODP has been operational since July 2009, when training of the LDC's was completed, the web-site and hotline activated and the attendance of Transplant Procurement Coordinators (TPC) during the OD process organised.Results: National and regional guidelines are accessible on the LODP website. The Hospital Attitude Survey obtained a 57% return rate. Many of the staff requested training and sessions are now running in the partner hospitals. The Medical Record Revue revealed an increase in the conversion rate from 3.5% to 4.5%. During the 5 years before creation of LODP the average annual number of utilised donors was 31, an increase of 70%, has since been observed.Conclusion: This clear progression in utilised donors in the past two years can be attributed to the fact that partner hospitals benefit from the various support given (hotline, website and from TPC's). Despite the increase in OD within the LODP the Swiss donation rates remain low, on average 11.9 donors per million population. This successful model should be applied throughout Switzerland, but the crucial point is to obtain financial support.

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility.

The flexibility of different regions of HIV-1 protease was examined by using a database consisting of 73 X-ray structures that differ in terms of sequence, ligands or both. The root-mean-square differences of the backbone for the set of structures were shown to have the same variation with residue number as those obtained from molecular dynamics simulations, normal mode analyses and X-ray B-factors. This supports the idea that observed structural changes provide a measure of the inherent flexibility of the protein, although specific interactions between the protease and the ligand play a secondary role. The results suggest that the potential energy surface of the HIV-1 protease is characterized by many local minima with small energetic differences, some of which are sampled by the different X-ray structures of the HIV-1 protease complexes. Interdomain correlated motions were calculated from the structural fluctuations and the results were also in agreement with molecular dynamics simulations and normal mode analyses. Implications of the results for the drug-resistance engendered by mutations are discussed briefly.

Learning through Computer Model Improvisations

It has been convincingly argued that computer simulation modeling differs from traditional science. If we understand simulation modeling as a new way of doing science, the manner in which scientists learn about the world through models must also be considered differently. This article examines how researchers learn about environmental processes through computer simulation modeling. Suggesting a conceptual framework anchored in a performative philosophical approach, we examine two modeling projects undertaken by research teams in England, both aiming to inform flood risk management. One of the modeling teams operated in the research wing of a consultancy firm, the other were university scientists taking part in an interdisciplinary project experimenting with public engagement. We found that in the first context the use of standardized software was critical to the process of improvisation, the obstacles emerging in the process concerned data and were resolved through exploiting affordances for generating, organizing, and combining scientific information in new ways. In the second context, an environmental competency group, obstacles were related to the computer program and affordances emerged in the combination of experience-based knowledge with the scientists' skill enabling a reconfiguration of the mathematical structure of the model, allowing the group to learn about local flooding.

Computational modeling of resting-state activity demonstrates markers of normalcy in children with prenatal or perinatal stroke.

Children who sustain a prenatal or perinatal brain injury in the form of a stroke develop remarkably normal cognitive functions in certain areas, with a particular strength in language skills. A dominant explanation for this is that brain regions from the contralesional hemisphere "take over" their functions, whereas the damaged areas and other ipsilesional regions play much less of a role. However, it is difficult to tease apart whether changes in neural activity after early brain injury are due to damage caused by the lesion or by processes related to postinjury reorganization. We sought to differentiate between these two causes by investigating the functional connectivity (FC) of brain areas during the resting state in human children with early brain injury using a computational model. We simulated a large-scale network consisting of realistic models of local brain areas coupled through anatomical connectivity information of healthy and injured participants. We then compared the resulting simulated FC values of healthy and injured participants with the empirical ones. We found that the empirical connectivity values, especially of the damaged areas, correlated better with simulated values of a healthy brain than those of an injured brain. This result indicates that the structural damage caused by an early brain injury is unlikely to have an adverse and sustained impact on the functional connections, albeit during the resting state, of damaged areas. Therefore, these areas could continue to play a role in the development of near-normal function in certain domains such as language in these children.

Local Salmonella immunostimulation recruits vaccine-specific CD8 T cells and increases regression of bladder tumor.

NlmCategory="UNASSIGNED">The efficacy of antitumoral responses can be increased using combinatorial vaccine strategies. We recently showed that vaccination could be optimized by local administration of diverse molecular or bacterial agents to target and augment antitumoral CD8 T cells in the genital mucosa (GM) and increase regression of cervical cancer in an animal model. Non muscle-invasive bladder cancer is another disease that is easily amenable to local therapies. In contrast to data obtained in the GM, in this study we show that intravesical (IVES) instillation of synthetic toll-like receptor (TLR) agonists only modestly induced recruitment of CD8 T cells to the bladder. However, IVES administration of Ty21a, a live bacterial vaccine against typhoid fever, was much more effective and increased the number of total and vaccine-specific CD8 T cells in the bladder approximately 10 fold. Comparison of chemokines induced in the bladder by either CpG (a TLR-9 agonist) or Ty21a highlighted the preferential increase in complement component 5a, CXCL5, CXCL2, CCL8, and CCL5 by Ty21a, suggesting their involvement in the attraction of T cells to the bladder. IVES treatment with Ty21a after vaccination also significantly increased tumor regression compared to vaccination alone, resulting in 90% survival in an orthotopic murine model of bladder cancer expressing a prototype tumor antigen. Our data demonstrate that combining vaccination with local immunostimulation may be an effective treatment strategy for different types of cancer and also highlight the great potential of the Ty21a vaccine, which is routinely used worldwide, in such combinatorial therapies.

A multi-contrast MRI study of microstructural brain damage in patients with mild cognitive impairment.

OBJECTIVES: The aim of this study was to investigate pathological mechanisms underlying brain tissue alterations in mild cognitive impairment (MCI) using multi-contrast 3 T magnetic resonance imaging (MRI). METHODS: Forty-two MCI patients and 77 healthy controls (HC) underwent T1/T2* relaxometry as well as Magnetization Transfer (MT) MRI. Between-groups comparisons in MRI metrics were performed using permutation-based tests. Using MRI data, a generalized linear model (GLM) was computed to predict clinical performance and a support-vector machine (SVM) classification was used to classify MCI and HC subjects. RESULTS: Multi-parametric MRI data showed microstructural brain alterations in MCI patients vs HC that might be interpreted as: (i) a broad loss of myelin/cellular proteins and tissue microstructure in the hippocampus (p ≤ 0.01) and global white matter (p < 0.05); and (ii) iron accumulation in the pallidus nucleus (p ≤ 0.05). MRI metrics accurately predicted memory and executive performances in patients (p ≤ 0.005). SVM classification reached an accuracy of 75% to separate MCI and HC, and performed best using both volumes and T1/T2*/MT metrics. CONCLUSION: Multi-contrast MRI appears to be a promising approach to infer pathophysiological mechanisms leading to brain tissue alterations in MCI. Likewise, parametric MRI data provide powerful correlates of cognitive deficits and improve automatic disease classification based on morphometric features.