A pipeline approach with spatial information for segmenting multiple sclerosis lesions on brain magnetic resonance imaging

Background: Conventional magnetic resonance imaging (MRI) techniques are highly sensitive to detect multiple sclerosis (MS) plaques, enabling a quantitative assessment of inflammatory activity and lesion load. In quantitative analyses of focal lesions, manual or semi-automated segmentations have been widely used to compute the total number of lesions and the total lesion volume. These techniques, however, are both challenging and time-consuming, being also prone to intra-observer and inter-observer variability.Aim: To develop an automated approach to segment brain tissues and MS lesions from brain MRI images. The goal is to reduce the user interaction and to provide an objective tool that eliminates the inter- and intra-observer variability.Methods: Based on the recent methods developed by Souplet et al. and de Boer et al., we propose a novel pipeline which includes the following steps: bias correction, skull stripping, atlas registration, tissue classification, and lesion segmentation. After the initial pre-processing steps, a MRI scan is automatically segmented into 4 classes: white matter (WM), grey matter (GM), cerebrospinal fluid (CSF) and partial volume. An expectation maximisation method which fits a multivariate Gaussian mixture model to T1-w, T2-w and PD-w images is used for this purpose. Based on the obtained tissue masks and using the estimated GM mean and variance, we apply an intensity threshold to the FLAIR image, which provides the lesion segmentation. With the aim of improving this initial result, spatial information coming from the neighbouring tissue labels is used to refine the final lesion segmentation.Results:The experimental evaluation was performed using real data sets of 1.5T and the corresponding ground truth annotations provided by expert radiologists. The following values were obtained: 64% of true positive (TP) fraction, 80% of false positive (FP) fraction, and an average surface distance of 7.89 mm. The results of our approach were quantitatively compared to our implementations of the works of Souplet et al. and de Boer et al., obtaining higher TP and lower FP values.Conclusion: Promising MS lesion segmentation results have been obtained in terms of TP. However, the high number of FP which is still a well-known problem of all the automated MS lesion segmentation approaches has to be improved in order to use them for the standard clinical practice. Our future work will focus on tackling this issue.

Urban Governance und nachhaltige Quartiere: Ein Beitrag zur Förderung einer dauerhaft nachhaltigen Stadtentwicklung

Seit den 1990er Jahren werden zunehmend nachhaltige Quartiere realisiert. Dabei besteht häufig eine beachtliche Diskrepanz zwischen den Zielen, die von den beteiligten Akteuren angestrebt werden, deren Umsetzung (Realisierungsphase) und deren Erhalt auf Dauer (Nutzungsphase). Es stellt sich folglich die Frage, auf welche Weise die Projektqualität im Sinne einer nachhaltigen Quartiersentwicklung verbessert werden kann. Diese Projekte sind jedoch enorm komplex aufgrund der großen Interdisziplinarität und Interdependenz ihrer Ziele sowie der vielschichtigen Akteursstrukturen. Sie stellen daher be-sonders hohe Anforderungen an die Projektsteuerung. Das konkrete Ziel dieser Arbeit besteht darin, die Bedeutung einer Prozesssteuerung im Sinne von Urban Governance zur Realisierung und zum Erhalt nachhaltiger Quartiere zu untersuchen. Damit soll einen Beitrag zur Förderung einer nachhalti-gen Stadtentwicklung geleistet werden. Die Arbeit stützt sich auf ein umfassendes theoretisches Fundament zum Thema Governance, wobei die relevanten Elemente für den Kontext nachhaltiger Quartiere herausgearbeitet werden. Die Hypothesen prüfen die Bedeutung der Schlüsselcharakteristika von Urban Governance (Kooperation, Partizipation, Verhandlungen) für die Projektqualität während der Realisierungs- und Nutzungsphase. Eine erste empirische Untersuchung wurde an zwanzig europäischen nachhaltigen Modellquartieren vorgenommen. Stärken und Schwächen aus der Perspektive der Nachhaltigkeit werden analysiert, deren Ursachen identifiziert und Handlungsoptio-nen aufgezeigt. Die Erkenntnisse zeigen die Notwendigkeit einer Verbesserung der Projektsteuerung während der Realisierungs- und der Nutzungsphase. Auf der Grundlage dieser Erkenntnisse wird ein umfassender Ansatz zur empirischen Untersuchung von Urban Governance im Kontext nachhaltiger Quartiere entwickelt. Dieser beruht auf dem akteurzentrierten Institutionalismus und den Merkmalen der Urban Governance. Anhand dieses Ansatzes wird mithilfe von Experteninterviews der Realisierungsprozess des nach-haltigen Quartiers Kronsberg (Hannover) analysiert. Betrachtet werden dabei die beteiligten Akteure und ihre Handlungso-rientierungen, die verwendeten Schlüsselinstrumente sowie aufgetretene Divergenzen zwischen Akteuren und deren Auswirkungen auf die Projekt- und Prozessqualität. Eine Vertiefung relevanter Themenfelder wird anhand der Fallstudie Neu-Oerlikon (Zürich) vorgenommen. Diese empirische Arbeit zeigt, dass eine Prozesssteuerung im Sinne von Urban Governance im Vergleich zu einer klassis-chen hierarchischen Steuerung eine notwendige aber nicht hinreichende Bedingung zur Verbesserung der Projektqualität nachhaltiger Quartiere darstellt. An konkreten Beispielen wird herausgearbeitet, dass der Mehrwert einer solchen Steuerung nur unter bestimmten Voraussetzungen erzielt werden kann: In manchen Situationen ist die Steuerungsform Kooperation und die Interaktionsform Verhandlung in ihrer Wirksamkeit zur Sicherung der Projektqualität begrenzt und hierarchische Interventionen sind notwendig. Nicht ein bestimmtes Steuerungsmodell per se ist geeignet, sondern es kommt auf den Ein-zelfall an: auf die Akteursstruktur, die individuellen und institutionellen Handlungsorientierungen der Akteure und deren Ver-haltensweisen, die Rahmenbedingungen und die Ausgestaltung des Urban Governance-Prozesses. Wenn die Spielregeln dieses Prozesses von den Akteuren nicht wirklich angenommen und gelebt werden, dominieren individuelle und institutio-nelle Akteursinteressen zu Lasten der Projektqualität. Ferner zeigen die Untersuchungen, dass die Partizipation der zukünftigen Quartiersnutzer in der Praxis häufig unzureichend ist. Dies führt zu Einbußen in der Projektqualität. Entscheidend ist auf jeden Fall, dass mindestens ein Akteur, in der Regel die öffentliche Hand, präsent ist, der die Definition anspruchsvoller Nachhaltigkeitsstandards, deren Umsetzung und deren Erhalt sichert sowie die notwendigen Rahmenbedingungen dafür schafft. Diese Arbeit belegt darüber hinaus, dass der Erhalt der Projektqualität während der Nutzungsphase (Faktor Zeit) bisher un-zureichend beachtet und in die Projektplanung einbezogen wird. Gerade dieser Aspekt bestimmt aber, ob das Quartier auch auf Dauer dem Nachhaltigkeitsanspruch gerecht werden kann! Tatsächlich handelt es sich um einen fortlaufenden Prozess, der nicht mit der Einweihung des Quartiers abgeschlossen ist. Vor diesem Hintergrund werden relevante Handlungsfelder beschrieben und die Notwendigkeit der langfristigen Fortsetzung einer Steuerung im Sinne von Urban Governance bzw. der Herausbildung einer Urban Governance-Kultur aufgezeigt. Aus den empirischen Erhebungen werden Erfolgs- und Risikofaktoren für Urban Governance-Prozesse während der Realisierungs- und der Nutzungsphase abgeleitet. Ferner werden bisher vernachlässigte Handlungsfelder (langfristiges Umwelt-management, ökologische Finanzierungsformen, urbane Landwirtschaft, Umweltkommunikation, etc.) eruiert. Die Berücksichtigung dieser Erkenntnisse ist unerlässlich für eine Verbesserung der Projektqualität nachhaltiger Quartiere. ---------------------------------------------- Gouvernance urbaine et quartiers durables: Entre intensions et mise en oeuvre --- Résumé --- Depuis les années 90, la thématique des quartiers durables a gagné en importance, même si leur développement s'est avéré difficile. Le décalage entre les objectifs, leur mise en oeuvre et le projet tel qu'il est vécu par ses habitants est souvent important et nécessite d'être réduit. Un quartier durable est par nature un projet complexe, aux objectifs ambitieux situé à la croisée de multiples champs disciplinaires, mobilisant de nombreux acteurs aux intérêts divergents. De plus, chaque projet, du fait des ses spécificités, requiert un pilotage adapté. L'objectif principal de la recherche vise à analyser la nature du pilotage du processus de conception, de réalisation et d'exploitation des quartiers durables. Ses résultats ont pour ambition de contribuer à optimiser et promouvoir le développement urbain durable. Le fondement théorique de la recherche se base sur le concept de gouvernance urbaine, adapté au contexte particulier de la gouvernance des quartiers durables. La gouvernance urbaine, au sens où nous l'entendons, est un mode de pilotage basé sur la coopération entre les acteurs publics et privés. Les hypothèses centrales du travail testent la portée et les limites des caractéristiques-clefs de la gouvernance urbaine (coopération, participation, négociation), ainsi que l'importance de la notion de pérennité pour la qualité du projet. Dans un premier temps, nous avons analysé vingt quartiers durables modèles européens et identifié leurs atouts et leurs faiblesses en termes de durabilité, ainsi que leurs divers modes de pilotage. Les enseignements tirés de ces exemples révèlent la nécessité d'améliorer le pilotage des projets. Dans un deuxième temps, nous avons élaboré une grille d'analyse fine fondée sur l'approche institutionnelle des acteurs et les caractéristiques-clefs de la gouvernance urbaine. En nous appuyant sur cette grille, nous avons analysé le processus de conception et de réalisation du quartier durable de « Kronsberg » (Hanovre) à l'aide des éléments suivants : les acteurs (avec leurs intérêts et objectifs propres), les instruments d'aménagement du territoire, les modes de pilotage, les zones de divergence et de convergence entre les acteurs, ainsi que leurs impacts sur le processus et le projet. Dans un troisième temps, les hypothèses centrales ont été testées sur le quartier de « Neu-Oerlikon » (Zurich) afin d'approfondir et d'élargir les enseignements tirés de celui de « Kronsberg ». Les résultats des analyses mettent en évidence le fait qu'un pilotage de projet selon le modèle de la gouvernance urbaine est certes une condition nécessaire mais non suffisante pour améliorer la qualité du projet. De plus, la valeur ajoutée de la gouvernance urbaine n'est valable qu'à certaines conditions. En effet, la coopération et la négociation peuvent même, dans certaines situations, réduire la qualité du projet ! Le principal enseignement de la recherche révèle qu'il n'y a pas de mode de pilotage idéal, mais que la qualité d'un projet dépend d'une multitude de facteurs, tels que les constellations d'acteurs, leurs intérêts personnels et institutionnels, les conditions cadres et les « règles du jeu » de la gouvernance urbaine. Si les « règles du jeu » en particulier ne sont pas réellement appropriées par l'ensemble des acteurs, les intérêts et les comportements personnels ou institutionnels prédominent au détriment de la qualité du projet. De même, si la participation des futurs usagers à l'élaboration du projet de quartier durable n'est pas assurée, tant la qualité du projet que sa pérennité en pâtissent. Nous avons également constaté que la présence d'un acteur (en règle générale les autorités publiques) qui veille à la définition d'objectifs ambitieux en matière de développement durable et à leur application constitue un apport essentiel à la qualité du projet. En outre, la recherche met en évidence les carences dans le suivi et le maintien à long terme des qualités de durabilité de la phase d'exploitation des projets de quartiers durables analysés. Dans la phase d'exploitation, le degré de coopération diminue généralement et les modes de fonctionnement et de pilotage sectoriels se mettent en place au détriment de la qualité du projet. Cela confirme la nécessité de poursuivre le processus de pilotage selon le modèle de la gouvernance urbaine au-delà de la phase de réalisation des projets. La recherche précise les enjeux des champs d'action de la phase d'exploitation (domaine encore peu étudié) et démontre la pertinence du mode de pilotage préconisé. Enfin, les analyses permettent d'identifier des facteurs de réussite et de risque susceptibles d'influencer les systèmes de gouvernance urbaine, ainsi que les enjeux des domaines de la durabilité encore négligés (agriculture urbaine, gestion environnementale dans la durée, comportement des usagers, financement équitable, etc.). La prise en compte de ces enseignements est essentielle à l'amélioration de la gestion de futurs projets de quartiers durables. ---------------------------------------------- Urban Governance and Sustainable Neighbourhoods: A Contribution to a Lasting Sustainable Development --- Abstract --- Since the 1990s, sustainable neighbourhoods have become an increasingly important topic. However, their development has proven to be difficult. There is an often considerable gap, which must be reduced, between the initial goals, the way they are implemented and how the project is finally inhabited. A sustainable neighbourhood is inherently a complex project, with ambitious goals that lie at the intersection of multiple disciplines, involving numerous stakeholders with diverging interests. Moreover, each project, due to its specific characteristics, requires an adapted steering. The main goal of this research is to analyse the nature of the steering process during the planning, realisation and use of sustainable neighbourhoods. The results aim to contribute to the promotion of sustainable urban development. The theoretical foundation of this research is based on the concept of urban governance, adapted to the particular context of sustainable neighbourhoods. Urban governance is understood in this work, as a mode of project steering based on the cooperation between public and private stakeholders. The central hypotheses of this work test the importance and the limits of the key characteristics of urban governance (cooperation, participation, negotiation) as well as the importance of continuity for the project quality. To begin with, we surveyed and analysed twenty exemplary European sustainable neighbourhoods and identified their strengths and weaknesses in terms of sustainability, as well as their diverse steering modes. The lessons learned from these examples reveal the need to improve the projects' steering. Secondly we elaborated a detailed framework for analysis founded on stakeholder-centred institutionalism and the key characteristics of urban governance. By systematically applying this framework, we analysed the planning and implementation process of the sustainable neighbourhood "Kronsberg" (Hannover). Our focus was on the following dimensions: the stakeholders (with their particular interests and goals), the instruments of spatial planning, the steering modes, the points of divergence and convergence amongst the stakeholders, as well as their impacts on the process and on the project. The final step was to test the core hypotheses on the neighbourhood "Neu-Oerlikon" (Zürich) in order to broaden the lessons learned from "Kronsberg". The results of the analysis highlight the fact that an urban governance type project steering is certainly a necessary but insufficient condition to improve the project quality. Moreover, the added value of urban governance is only valid under certain conditions. In fact, cooperation and negotiation can even in certain situations reduce the project's quality! The main lesson of this research is that there is not an ideal steering mode, but rather that the quality of the project depends on numerous factors, such as the stakeholder constellation, their individual and institutional interests, the general conditions and the "rules of the game" of urban governance. If these "rules of the game" are not really appropriated by all stakeholders, individual and institutional interests and behaviours predominate at the expense of the project's quality. Likewise, if the future users' participation in the project development is insufficient, both the project's quality and its continuity suffer. We have also observed that the presence of a stakeholder (in general the public authorities) who ensures the definition of ambitious goals in terms of sustainable development and their implementation is crucial for the project's quality. Furthermore, this research highlights the deficiencies in the follow-up and long-term preservation of the sustainability qualities in the neighbourhood projects which we have analysed. In the use phase, the degree of cooperation generally diminishes. Attitudes and project management become more sectorial at the expense of the project's quality. This confirms the need to continue the steering process according to the principles of urban governance beyond the project's implementation phase. This research specifies the challenges that affect the use phase (a still neglected area) and shows the relevance of the recommended steering mode. Finally, the analyses also identify the success and risk factors that may influence urban-governance systems, as well as the challenges of still neglected fields of sustainability (urban agriculture, long-term environmental management, user behaviour, fair funding, etc.). Taking into account these outcomes is essential to improve the management of future sustainable-neighbourhood projects.

Internal arsenite bioassay calibration using multiple reporter cell lines

Bioassays with bioreporter bacteria are usually calibrated with analyte solutions of known concentrations that are analysed along with the samples of interest. This is done as bioreporter output (the intensity of light, fluorescence or colour) does not only depend on the target concentration, but also on the incubation time and physiological activity of the cells in the assay. Comparing the bioreporter output with standardized colour tables in the field seems rather difficult and error-prone. A new approach to control assay variations and improve application ease could be an internal calibration based on the use of multiple bioreporter cell lines with drastically different reporter protein outputs at a given analyte concentration. To test this concept, different Escherichia coli-based bioreporter strains expressing either cytochrome c peroxidase (CCP, or CCP mutants) or β-galactosidase upon induction with arsenite were constructed. The reporter strains differed either in the catalytic activity of the reporter protein (for CCP) or in the rates of reporter protein synthesis (for β-galactosidase), which, indeed, resulted in output signals with different intensities at the same arsenite concentration. Hence, it was possible to use combinations of these cell lines to define arsenite concentration ranges at which none, one or more cell lines gave qualitative (yes/no) visible signals that were relatively independent of incubation time or bioreporter activity. The discriminated concentration ranges would fit very well with the current permissive (e.g. World Health Organization) levels of arsenite in drinking water (10 µg l−1).

Paper 5: Surveillance of multiple congenital anomalies: implementation of a computer algorithm in European registers for classification of cases.

BACKGROUND: Surveillance of multiple congenital anomalies is considered to be more sensitive for the detection of new teratogens than surveillance of all or isolated congenital anomalies. Current literature proposes the manual review of all cases for classification into isolated or multiple congenital anomalies. METHODS: Multiple anomalies were defined as two or more major congenital anomalies, excluding sequences and syndromes. A computer algorithm for classification of major congenital anomaly cases in the EUROCAT database according to International Classification of Diseases (ICD)v10 codes was programmed, further developed, and implemented for 1 year's data (2004) from 25 registries. The group of cases classified with potential multiple congenital anomalies were manually reviewed by three geneticists to reach a final agreement of classification as "multiple congenital anomaly" cases. RESULTS: A total of 17,733 cases with major congenital anomalies were reported giving an overall prevalence of major congenital anomalies at 2.17%. The computer algorithm classified 10.5% of all cases as "potentially multiple congenital anomalies". After manual review of these cases, 7% were agreed to have true multiple congenital anomalies. Furthermore, the algorithm classified 15% of all cases as having chromosomal anomalies, 2% as monogenic syndromes, and 76% as isolated congenital anomalies. The proportion of multiple anomalies varies by congenital anomaly subgroup with up to 35% of cases with bilateral renal agenesis. CONCLUSIONS: The implementation of the EUROCAT computer algorithm is a feasible, efficient, and transparent way to improve classification of congenital anomalies for surveillance and research.

Magnetoencephalography demonstrates multiple asynchronous generators during human sleep spindles.

Sleep spindles are approximately 1 s bursts of 10-16 Hz activity that occur during stage 2 sleep. Spindles are highly synchronous across the cortex and thalamus in animals, and across the scalp in humans, implying correspondingly widespread and synchronized cortical generators. However, prior studies have noted occasional dissociations of the magnetoencephalogram (MEG) from the EEG during spindles, although detailed studies of this phenomenon have been lacking. We systematically compared high-density MEG and EEG recordings during naturally occurring spindles in healthy humans. As expected, EEG was highly coherent across the scalp, with consistent topography across spindles. In contrast, the simultaneously recorded MEG was not synchronous, but varied strongly in amplitude and phase across locations and spindles. Overall, average coherence between pairs of EEG sensors was approximately 0.7, whereas MEG coherence was approximately 0.3 during spindles. Whereas 2 principle components explained approximately 50% of EEG spindle variance, >15 were required for MEG. Each PCA component for MEG typically involved several widely distributed locations, which were relatively coherent with each other. These results show that, in contrast to current models based on animal experiments, multiple asynchronous neural generators are active during normal human sleep spindles and are visible to MEG. It is possible that these multiple sources may overlap sufficiently in different EEG sensors to appear synchronous. Alternatively, EEG recordings may reflect diffusely distributed synchronous generators that are less visible to MEG. An intriguing possibility is that MEG preferentially records from the focal core thalamocortical system during spindles, and EEG from the distributed matrix system.

Corporate responsibility in the postnational constellation : a multiple-case study

In my thesis I present the findings of a multiple-case study on the CSR approach of three multinational companies, applying Basu and Palazzo's (2008) CSR-character as a process model of sensemaking, Suchman's (1995) framework on legitimation strategies, and Habermas (1996) concept of deliberative democracy. The theoretical framework is based on the assumption of a postnational constellation (Habermas, 2001) which sends multinational companies onto a process of sensemaking (Weick, 1995) with regards to their responsibilities in a globalizing world. The major reason is that mainstream CSR-concepts are based on the assumption of a liberal market economy embedded in a nation state that do not fit the changing conditions for legitimation of corporate behavior in a globalizing world. For the purpose of this study, I primarily looked at two research questions: (i) How can the CSR approach of a multinational corporation be systematized empirically? (ii) What is the impact of the changing conditions in the postnational constellation on the CSR approach of the studied multinational corporations? For the analysis, I adopted a holistic approach (Patton, 1980), combining elements of a deductive and inductive theory building methodology (Eisenhardt, 1989b; Eisenhardt & Graebner, 2007; Glaser & Strauss, 1967; Van de Ven, 1992) and rigorous qualitative data analysis. Primary data was collected through 90 semi-structured interviews in two rounds with executives and managers in three multinational companies and their respective stakeholders. Raw data originating from interview tapes, field notes, and contact sheets was processed, stored, and managed using the software program QSR NVIVO 7. In the analysis, I applied qualitative methods to strengthen the interpretative part as well as quantitative methods to identify dominating dimensions and patterns. I found three different coping behaviors that provide insights into the corporate mindset. The results suggest that multinational corporations increasingly turn towards relational approaches of CSR to achieve moral legitimacy in formalized dialogical exchanges with their stakeholders since legitimacy can no longer be derived only from a national framework. I also looked at the degree to which they have reacted to the postnational constellation by the assumption of former state duties and the underlying reasoning. The findings indicate that CSR approaches become increasingly comprehensive through integrating political strategies that reflect the growing (self-) perception of multinational companies as political actors. Based on the results, I developed a model which relates the different dimensions of corporate responsibility to the discussion on deliberative democracy, global governance and social innovation to provide guidance for multinational companies in a postnational world. With my thesis, I contribute to management research by (i) delivering a comprehensive critique of the mainstream CSR-literature and (ii) filling the gap of thorough qualitative research on CSR in a globalizing world using the CSR-character as an empirical device, and (iii) to organizational studies by further advancing a deliberative view of the firm proposed by Scherer and Palazzo (2008).

Influence of multiple injections of human chorionic gonadotropin (hCG) on urine and serum endogenous steroids concentrations.

Since it is established that human chorionic gonadotropin (hCG) affects testosterone production and release in the human body, the use of this hormone as a performance enhancing drug has been prohibited by the World Anti-Doping Agency. Nowadays, the only validated biomarker of a hCG doping is its direct quantification in urine. However, this specific parameter is subjected to large inter-individual variability and its determination is directly dependent on the reliability of hCG immunoassays used. In order to counteract these weaknesses, new biomarkers need to be evidenced. To address this issue, a pilot clinical study was performed on 10 volunteers submitted to 3 subsequent hCG injections. Blood and urine samples were collected during two weeks in order to follow the physiological effects on related compounds such as the steroid profile or hormones involved in the hypothalamo-pituitary axis. The hCG pharmacokinetic observed in all subjects was, as expected, prone to important inter-individual variations. Using ROC plots, level of testosterone and testosterone on luteinizing hormone ratio in both blood and urine were found to be the most relevant biomarker of a hCG abuse, regardless of inter-individual variations. In conclusion, this study showed the crucial importance of reliable quantification methods to assess low differences in hormonal patterns. In regard to these results and to anti-doping requirements and constraints, blood together with urine matrix should be included in the anti-doping testing program. Together with a longitudinal follow-up approach it could constitute a new strategy to detect a hCG abuse, applicable to further forms of steroid or other forbidden drug manipulation.

Multiscale assessment of plant diversity in wooded pastures of the Jura mountains

Résumé La diminution de la biodiversité, à toutes les échelles spatiales et sur l'ensemble de la planète, compte parmi les problèmes les plus préoccupants de notre époque. En terme de conservation, il est aujourd'hui primordial de mieux comprendre les mécanismes qui créent et maintiennent la biodiversité dans les écosystèmes naturels ou anthropiques. La présente étude a pour principal objectif d'améliorer notre compréhension des patrons de biodiversité végétale et des mécanismes sous jacents, dans un écosystème complexe, riche en espèces et à forte valeur patrimoniale, les pâturages boisés jurassiens. Structure et échelle spatiales sont progressivement reconnues comme des dimensions incontournables dans l'étude des patrons de biodiversité. De plus, ces deux éléments jouent un rôle central dans plusieurs théories écologiques. Toutefois, peu d'hypothèses issues de simulations ou d'études théoriques concernant le lien entre structure spatiale du paysage et biodiversité ont été testées de façon empirique. De même, l'influence des différentes composantes de l'échelle spatiale sur les patrons de biodiversité est méconnue. Cette étude vise donc à tester quelques-unes de ces hypothèses et à explorer les patrons spatiaux de biodiversité dans un contexte multi-échelle, pour différentes mesures de biodiversité (richesse et composition en espèces) à l'aide de données de terrain. Ces données ont été collectées selon un plan d'échantillonnage hiérarchique. Dans un premier temps, nous avons testé l'hypothèse élémentaire selon laquelle la richesse spécifique (le nombre d'espèces sur une surface donnée) est liée à l'hétérogénéité environnementale quelque soit l'échelle. Nous avons décomposé l'hétérogénéité environnementale en deux parties, la variabilité des conditions environnementales et sa configuration spatiale. Nous avons montré que, en général, la richesse spécifique augmentait avec l'hétérogénéité de l'environnement : elle augmentait avec le nombre de types d'habitats et diminuait avec l'agrégation spatiale de ces habitats. Ces effets ont été observés à toutes les échelles mais leur nature variait en fonction de l'échelle, suggérant une modification des mécanismes. Dans un deuxième temps, la structure spatiale de la composition en espèces a été décomposée en relation avec 20 variables environnementales et 11 traits d'espèces. Nous avons utilisé la technique de partition de la variation et un descripteur spatial, récemment développé, donnant accès à une large gamme d'échelles spatiales. Nos résultats ont montré que la structure spatiale de la composition en espèces végétales était principalement liée à la topographie, aux échelles les plus grossières, et à la disponibilité en lumière, aux échelles les plus fines. La fraction non-environnementale de la variation spatiale de la composition spécifique avait une relation complexe avec plusieurs traits d'espèces suggérant un lien avec des processus biologiques tels que la dispersion, dépendant de l'échelle spatiale. Dans un dernier temps, nous avons testé, à plusieurs échelles spatiales, les relations entre trois composantes de la biodiversité : la richesse spécifique totale d'un échantillon (diversité gamma), la richesse spécifique moyenne (diversité alpha), mesurée sur des sous-échantillons, et les différences de composition spécifique entre les sous-échantillons (diversité beta). Les relations deux à deux entre les diversités alpha, beta et gamma ne suivaient pas les relations attendues, tout du moins à certaines échelles spatiales. Plusieurs de ces relations étaient fortement dépendantes de l'échelle. Nos résultats ont mis en évidence l'importance du rapport d'échelle (rapport entre la taille de l'échantillon et du sous-échantillon) lors de l'étude des patrons spatiaux de biodiversité. Ainsi, cette étude offre un nouvel aperçu des patrons spatiaux de biodiversité végétale et des mécanismes potentiels permettant la coexistence des espèces. Nos résultats suggèrent que les patrons de biodiversité ne peuvent être expliqués par une seule théorie, mais plutôt par une combinaison de théories. Ils ont également mis en évidence le rôle essentiel joué par la structure spatiale dans la détermination de la biodiversité, quelque soit le composant de la biodiversité considéré. Enfin, cette étude souligne l'importance de prendre en compte plusieurs échelles spatiales et différents constituants de l'échelle spatiale pour toute étude relative à la diversité spécifique. Abstract The world-wide loss of biodiversity at all scales has become a matter of urgent concern, and improving our understanding of local drivers of biodiversity in natural and anthropogenic ecosystems is now crucial for conservation. The main objective of this study was to further our comprehension of the driving forces controlling biodiversity patterns in a complex and diverse ecosystem of high conservation value, wooded pastures. Spatial pattern and scale are central to several ecological theories, and it is increasingly recognized that they must be taken -into consideration when studying biodiversity patterns. However, few hypotheses developed from simulations or theoretical studies have been tested using field data, and the evolution of biodiversity patterns with different scale components remains largely unknown. We test several such hypotheses and explore spatial patterns of biodiversity in a multi-scale context and using different measures of biodiversity (species richness and composition), with field data. Data were collected using a hierarchical sampling design. We first tested the simple hypothesis that species richness, the number of species in a given area, is related to environmental heterogeneity at all scales. We decomposed environmental heterogeneity into two parts: the variability of environmental conditions and its spatial configuration. We showed that species richness generally increased with environmental heterogeneity: species richness increased with increasing number of habitat types and with decreasing spatial aggregation of those habitats. Effects occurred at all scales but the nature of the effect changed with scale, suggesting a change in underlying mechanisms. We then decomposed the spatial structure of species composition in relation to environmental variables and species traits using variation partitioning and a recently developed spatial descriptor, allowing us to capture a wide range of spatial scales. We showed that the spatial structure of plant species composition was related to topography at the coarsest scales and insolation at finer scales. The non-environmental fraction of the spatial variation in species composition had a complex relationship with several species traits, suggesting a scale-dependent link to biological processes, particularly dispersal. Finally, we tested, at different spatial scales, the relationships between different components of biodiversity: total sample species richness (gamma diversity), mean species .richness (alpha diversity), measured in nested subsamples, and differences in species composition between subsamples (beta diversity). The pairwise relationships between alpha, beta and gamma diversity did not follow the expected patterns, at least at certain scales. Our result indicated a strong scale-dependency of several relationships, and highlighted the importance of the scale ratio when studying biodiversity patterns. Thus, our results bring new insights on the spatial patterns of biodiversity and the possible mechanisms allowing species coexistence. They suggest that biodiversity patterns cannot be explained by any single theory proposed in the literature, but a combination of theories is sufficient. Spatial structure plays a crucial role for all components of biodiversity. Results emphasize the importance of considering multiple spatial scales and multiple scale components when studying species diversity.

Learning about Bayesian networks for forensic interpretation : An example based on the "the problem of multiple propositions"

Both, Bayesian networks and probabilistic evaluation are gaining more and more widespread use within many professional branches, including forensic science. Notwithstanding, they constitute subtle topics with definitional details that require careful study. While many sophisticated developments of probabilistic approaches to evaluation of forensic findings may readily be found in published literature, there remains a gap with respect to writings that focus on foundational aspects and on how these may be acquired by interested scientists new to these topics. This paper takes this as a starting point to report on the learning about Bayesian networks for likelihood ratio based, probabilistic inference procedures in a class of master students in forensic science. The presentation uses an example that relies on a casework scenario drawn from published literature, involving a questioned signature. A complicating aspect of that case study - proposed to students in a teaching scenario - is due to the need of considering multiple competing propositions, which is an outset that may not readily be approached within a likelihood ratio based framework without drawing attention to some additional technical details. Using generic Bayesian networks fragments from existing literature on the topic, course participants were able to track the probabilistic underpinnings of the proposed scenario correctly both in terms of likelihood ratios and of posterior probabilities. In addition, further study of the example by students allowed them to derive an alternative Bayesian network structure with a computational output that is equivalent to existing probabilistic solutions. This practical experience underlines the potential of Bayesian networks to support and clarify foundational principles of probabilistic procedures for forensic evaluation.

An allele-specific, stochastic gene expression process controls the expression of multiple Ly49 family genes and generates a diverse, MHC-specific NK cell receptor repertoire.

Mouse NK cells express MHC class I-specific inhibitory Ly49 receptors. Since these receptors display distinct ligand specificities and are clonally distributed, their expression generates a diverse NK cell receptor repertoire specific for MHC class I molecules. We have previously found that the Dd (or Dk)-specific Ly49A receptor is usually expressed from a single allele. However, a small fraction of short-term NK cell clones expressed both Ly49A alleles, suggesting that the two Ly49A alleles are independently and randomly expressed. Here we show that the genes for two additional Ly49 receptors (Ly49C and Ly49G2) are also expressed in a (predominantly) mono-allelic fashion. Since single NK cells can co-express multiple Ly49 receptors, we also investigated whether mono-allelic expression from within the tightly linked Ly49 gene cluster is coordinate or independent. Our clonal analysis suggests that the expression of alleles of distinct Ly49 genes is not coordinate. Thus Ly49 alleles are apparently independently and randomly chosen for stable expression, a process that directly restricts the number of Ly49 receptors expressed per single NK cell. We propose that the Ly49 receptor repertoire specific for MHC class I is generated by an allele-specific, stochastic gene expression process that acts on the entire Ly49 gene cluster.

Familial occurrence of an association of multiple intestinal atresia and choanal atresia: a new syndrome?

We report on two familial cases from a non-consanguineous marriage, presenting multiple intestinal and choanal atresia. Massive hydramnios and dilatation of the bowel were observed at 29 weeks of gestation during routine ultrasound scan of a healthy mother. The fetal karyotype was normal and cystic fibrosis screening was negative. Regular scans were performed throughout the pregnancy. The child was born at 34 weeks gestation. Choanal atresia was diagnosed at birth and abdominal investigations showed multiple atresia interesting both the small bowel and the colon. Further interventions were necessary because of recurrent obstructions. During the following pregnancy, a dilatation of the fetal intestinal tract was detected by ultrasonography at 27 weeks of gestation. Pregnancy was interrupted. Post-mortem examination of the fetus confirmed the stenosis of long segments of the small intestine associated with areas of colonic atresia. In both cases, histology and distribution were consistent with those reported in hereditary multiple intestinal atresia (HMIA). An association between multiple intestinal and choanal atresia has never been reported. We suggest it could correspond to a new autosomal recessive entity for which cytogenetic investigations and high-resolution array CGH revealed no visible anomalies.

Genetic abnormalities and survival in multiple myeloma: the experience of the Intergroupe Francophone du Myélome.

Acquired genomic aberrations have been shown to significantly impact survival in several hematologic malignancies. We analyzed the prognostic value of the most frequent chromosomal changes in a large series of patients with newly diagnosed symptomatic myeloma prospectively enrolled in homogeneous therapeutic trials. All the 1064 patients enrolled in the IFM99 trials conducted by the Intergroupe Francophone du Myélome benefited from an interphase fluorescence in situ hybridization analysis performed on purified bone marrow plasma cells. They were systematically screened for the following genomic aberrations: del(13), t(11;14), t(4;14), hyperdiploidy, MYC translocations, and del(17p). Chromosomal changes were observed in 90% of the patients. The del(13), t(11;14), t(4;14), hyperdiploidy, MYC translocations, and del(17p) were present in 48%, 21%, 14%, 39%, 13%, and 11% of the patients, respectively. After a median follow-up of 41 months, univariate statistical analyses revealed that del(13), t(4;14), nonhyperdiploidy, and del(17p) negatively impacted both the event-free survival and the overall survival, whereas t(11;14) and MYC translocations did not influence the prognosis. Multivariate analyses on 513 patients annotated for all the parameters showed that only t(4;14) and del(17p) retained prognostic value for both the event-free and overall survivals. When compared with the currently used International Staging System, this prognostic model compares favorably. In myeloma, the genomic aberrations t(4;14) and del(17p), together with beta2-microglobulin level, are important independent predictors of survival. These findings have implications for the design of risk-adapted treatment strategies.