Integration of olfactory information in a spatial representation enabling accurate arm choice in the radial arm maze

The aim of the present study was to determine whether and how rats can use local olfactory cues for spatial orientation. Rats were trained in an eight-arm radial maze under different conditions as defined by the presence or absence of supplementary olfactory cues marking each arm, the availability of distant visuospatial information, and the illumination of the maze (light or darkness). The different visual conditions were designed to dissociate among the effects of light per se and those of visuospatial cues, on the use of olfactory cues for accurate arm choice. Different procedures with modifications of the arrangement of olfactory cues were used to determine if rats formed a representation of the spatial configuration of the olfactory cues and if they could rely on such a representation for accurate arm choice in the radial maze. The present study demonstrated that the use of olfactory cues to direct arm choice in the radial arm maze was critically dependent on the illumination conditions and implied two different modes of processing of olfactory information according to the presence or the absence of light. Olfactory cues were used in an explicit manner and enabled accurate arm choice only in the absence of light. Rats, however, had an implicit memory of the location of the olfactory cues and formed a representation of the spatial position of these cues, whatever the lighting conditions. They did not memorize the spatial configuration of the olfactory cues per se but needed these cues to be linked to the external spatial frame of reference.

From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways

Background: Single nucleotide polymorphisms (SNPs) are the most frequent type of sequence variation between individuals, and represent a promising tool for finding genetic determinants of complex diseases and understanding the differences in drug response. In this regard, it is of particular interest to study the effect of non-synonymous SNPs in the context of biological networks such as cell signalling pathways. UniProt provides curated information about the functional and phenotypic effects of sequence variation, including SNPs, as well as on mutations of protein sequences. However, no strategy has been developed to integrate this information with biological networks, with the ultimate goal of studying the impact of the functional effect of SNPs in the structure and dynamics of biological networks. Results: First, we identified the different challenges posed by the integration of the phenotypic effect of sequence variants and mutations with biological networks. Second, we developed a strategy for the combination of data extracted from public resources, such as UniProt, NCBI dbSNP, Reactome and BioModels. We generated attribute files containing phenotypic and genotypic annotations to the nodes of biological networks, which can be imported into network visualization tools such as Cytoscape. These resources allow the mapping and visualization of mutations and natural variations of human proteins and their phenotypic effect on biological networks (e.g. signalling pathways, protein-protein interaction networks, dynamic models). Finally, an example on the use of the sequence variation data in the dynamics of a network model is presented. Conclusion: In this paper we present a general strategy for the integration of pathway and sequence variation data for visualization, analysis and modelling purposes, including the study of the functional impact of protein sequence variations on the dynamics of signalling pathways. This is of particular interest when the SNP or mutation is known to be associated to disease. We expect that this approach will help in the study of the functional impact of disease-associated SNPs on the behaviour of cell signalling pathways, which ultimately will lead to a better understanding of the mechanisms underlying complex diseases.

@neurIST infrastructure for advanced disease management through integration of heterogeneous data, computing, and complex processing services

The increasing volume of data describing humandisease processes and the growing complexity of understanding, managing, and sharing such data presents a huge challenge for clinicians and medical researchers. This paper presents the@neurIST system, which provides an infrastructure for biomedical research while aiding clinical care, by bringing together heterogeneous data and complex processing and computing services. Although @neurIST targets the investigation and treatment of cerebral aneurysms, the system’s architecture is generic enough that it could be adapted to the treatment of other diseases.Innovations in @neurIST include confining the patient data pertaining to aneurysms inside a single environment that offers cliniciansthe tools to analyze and interpret patient data and make use of knowledge-based guidance in planning their treatment. Medicalresearchers gain access to a critical mass of aneurysm related data due to the system’s ability to federate distributed informationsources. A semantically mediated grid infrastructure ensures that both clinicians and researchers are able to seamlessly access andwork on data that is distributed across multiple sites in a secure way in addition to providing computing resources on demand forperforming computationally intensive simulations for treatment planning and research.

Man Made Black Holes and Big Bangs: Diffusion and Integration of Scientific Information into Everyday Thinking

Drawing on Social Representations Theory, this study investigates focalisation and anchoring during the diffusion of information concerning the Large Hadron Collider (LHC), the particle accelerator at the European Organisation for Nuclear Research (CERN). We hypothesised that people focus on striking elements of the message, abandoning others, that the nature of the initial information affects diffusion of information, and that information is anchored in prior attitudes toward CERN and science. A serial reproduction experiment with two generations and four chains of reproduction diffusing controversial versus descriptive information about the LHC shows a reduction of information through generations, the persistence of terminology regarding the controversy and a decrease of other elements for participants exposed to polemical information. Concerning anchoring, positive attitudes toward CERN and science increase the use of expert terminology unrelated to the controversy. This research highlights the relevance of a social representational approach in the public understanding of science.

Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.

In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10(-9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10(-4)-2.2 × 10(-7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.

Activation of a HIF1alpha-PPARgamma axis underlies the integration of glycolytic and lipid anabolic pathways in pathologic cardiac hypertrophy.

Development of cardiac hypertrophy and progression to heart failure entails profound changes in myocardial metabolism, characterized by a switch from fatty acid utilization to glycolysis and lipid accumulation. We report that hypoxia-inducible factor (HIF)1alpha and PPARgamma, key mediators of glycolysis and lipid anabolism, respectively, are jointly upregulated in hypertrophic cardiomyopathy and cooperate to mediate key changes in cardiac metabolism. In response to pathologic stress, HIF1alpha activates glycolytic genes and PPARgamma, whose product, in turn, activates fatty acid uptake and glycerolipid biosynthesis genes. These changes result in increased glycolytic flux and glucose-to-lipid conversion via the glycerol-3-phosphate pathway, apoptosis, and contractile dysfunction. Ventricular deletion of Hif1alpha in mice prevents hypertrophy-induced PPARgamma activation, the consequent metabolic reprogramming, and contractile dysfunction. We propose a model in which activation of the HIF1alpha-PPARgamma axis by pathologic stress underlies key changes in cell metabolism that are characteristic of and contribute to common forms of heart disease.

Integration of Pore Features into the Evaluation of Fingerprint Evidence

Fingerprint practitioners rely on level 3 features to make decisions in relation to the source of an unknown friction ridge skin impression. This research proposes to assess the strength of evidence associated with pores when shown in (dis)agreement between a mark and a reference print. Based upon an algorithm designed to automatically detect pores, a metric is defined in order to compare different impressions. From this metric, the weight of the findings is quantified using a likelihood ratio. The results obtained on four configurations and 54 donors show the significant contribution of the pore features and translate into statistical terms what latent fingerprint examiners have developed holistically through experience. The system provides LRs that are indicative of the true state under both the prosecution and the defense propositions. Not only such a system brings transparency regarding the weight to assign to such features, but also forces a discussion in relation to the risks of such a model to mislead.

Integration of ground-penetrating radar and microgravimetric methods to map shallow caves

Ground-penetrating radar (GPR) and microgravimetric surveys have been conducted in the southern Jura mountains of western Switzerland in order to map subsurface karstic features. The study site, La Grande Rolaz cave, is an extensive system in which many portions have been mapped. By using small station spacing and careful processing for the geophysical data, and by modeling these data with topographic information from within the cave, accurate interpretations have been achieved. The constraints on the interpreted geologic models are better when combining the geophysical methods than when using only one of the methods, despite the general limitations of two-dimensional (2D) profiling. For example, microgravimetry can complement GPR methods for accurately delineating a shallow cave section approximately 10 X 10 mt in size. Conversely, GPR methods can be complementary in determining cavity depths and in verifying the presence of off-line features and numerous areas of small cavities and fractures, which may be difficult to resolve in microgravimetric data.

Electroluminiscence and optical amplification in silicon nanostructures: towards the integration of electronics and photonics

This line of research of my group intends to establish a Silicon technological platform in the field of photonics allowing the development of a wide set of applications. Particularly, what is still lacking in Silicon Photonics is an efficient and integrable light source such an LED or laser. Nanocrystals in silicon oxide or nitride matrices have been recently demonstrated as competitive materials for both active components (electrically and optically driven light emitters and optical amplifiers) and passive ones (waveguides and modulators). The final goal is the achievement of a complete integration of electronic and optical functions in the same CMOS chip. The first part of this paper will introduce the structural and optical properties of LEDs fabricated from silicon nanostructures. The second will treat the interaction of such nanocrystals with rare-earth elements (Er), which lead to an efficient hybrid system emitting in the third window of optical fibers. I will present the fabrication and assessment of optical waveguide amplifiers at 1.54 ¿m for which we have been able to demonstrate recently optical gain in waveguides made from sputtered silicon suboxide materials.

Integration of teacher education into the Swiss higher education system

The integration of specific institutions for teacher education into the higher education system represents a milestone in the Swiss educational policy and has broad implications. This thesis explores organizational and institutional change resulting from this policy reform, and attempts to assess structural change in terms of differentiation and convergence within the system of higher education. Key issues that are dealt with are, on the one hand, the adoption of a research function by the newly conceptualized institutions of teacher education, and on the other, the positioning of the new institutions within the higher education system. Drawing on actor-centred approaches to differentiation, this dissertation discusses system-level specificities of tertiarized teacher education and asks how this affects institutional configurations and actor constellations. On the basis of qualitative and quantitative empirical data, a comparative analysis has been carried out including case studies of four universities of teacher education as well as multivariate regression analysis of micro-level data on students' educational choices. The study finds that the process of system integration and adaption to the research function by the various institutions have unfolded differently depending on the institutional setting and the specific actor constellations. The new institutions have clearly made a strong push to position themselves as a new institutional type and to find their identity beyond the traditional binary divide which assigns the universities of teacher education to the college sector. Potential conflicts have been identified in divergent cognitive normative orientations and perceptions of researchers, teacher educators, policy-makers, teachers, and students as to the mission and role of the new type of higher education institution. - L'intégration dans le système d'enseignement supérieur d'institutions qui ont pour tâche spécifique de former des enseignants peut être considérée comme un événement majeur dans la politique éducative suisse, qui se trouve avoir des conséquences importantes à plusieurs niveaux. Cette thèse explore les changements organisationnels et institutionnels résultant de cette réforme politique, et elle se propose d'évaluer en termes de différentiation et de convergence les changements structurels intervenus dans le système d'éducation tertiaire. Les principaux aspects traités sont d'une part la nouvelle mission de recherche attribuée à ces institutions de formation pédagogique, et de l'autre la place par rapport aux autres institutions du système d'éducation tertiaire. Recourant à une approche centrée sur les acteurs pour étudier les processus de différen-tiation, la thèse met en lumière et en discussion les spécificités inhérentes au système tertiaire au sein duquel se joue la formation des enseignants nouvellement conçue et soulève la question des effets de cette nouvelle façon de former les enseignants sur les configurations institutionnelles et les constellations d'acteurs. Une analyse comparative a été réalisée sur la base de données qualitatives et quantitatives issues de quatre études de cas de hautes écoles pédagogiques et d'analyses de régression multiple de données de niveau micro concernant les choix de carrière des étudiants. Les résultats montrent à quel point le processus d'intégration dans le système et la nouvelle mission de recherche peuvent apparaître de manière différente selon le cadre institutionnel d'une école et la constellation spécifique des acteurs influents. A pu clairement être observée une forte aspiration des hautes écoles pédagogiques à se créer une identité au-delà de la structure binaire du système qui assigne la formation des enseignants au secteur des hautes écoles spéciali-sées. Des divergences apparaissent dans les conceptions et perceptions cognitives et normatives des cher-cheurs, formateurs, politiciens, enseignants et étudiants quant à la mission et au rôle de ce nouveau type de haute école. - Die Integration spezieller Institutionen für die Lehrerbildung ins Hochschulsystem stellt einen bedeutsamen Schritt mit weitreichenden Folgen in der Entwicklung des schweizerischen Bildungswesens dar. Diese Dissertation untersucht die mit der Neuerung verbundenen Veränderungen auf organisatorischer und institutioneller Ebene und versucht, die strukturelle Entwicklung unter den Gesichtspunkten von Differenzierung und Konvergenz innerhalb des tertiären Bildungssystems einzuordnen. Zentrale Themen sind dabei zum einen die Einführung von Forschung und Entwicklung als zusätzlichem Leistungsauftrag in der Lehrerbildung und zum andern die Positionierung der pädagogischen Hochschulen innerhalb des Hochschulsystems. Anhand akteurzentrierter Ansätze zur Differenzierung werden die Besonderheiten einer tertiarisierten Lehrerbildung hinsichtlich der Systemebenen diskutiert und Antworten auf die Frage gesucht, wie die Reform die institutionellen Konfigurationen und die Akteurkonstellationen beeinflusst. Auf der Grundlage qualitativer und quantitativer Daten wurde eine vergleichende Analyse durchgeführt, welche Fallstudien zu vier pädagogischen Hochschulen umfasst sowie Regressionsanalysen von Mikrodaten zur Studienwahl von Maturanden. Die Ergebnisse machen deutlich, dass sich der Prozess der Systemintegration und die Einführung von Forschung in die Lehrerbildung in Abhängigkeit von institutionellen Ordnungen und der jeweiligen Akteurkonstellation unterschiedlich gestalten. Es lässt sich bei den neu gegründeten pädagogischen Hochschulen ein starkes Bestreben feststellen, sich als neuen Hochschultypus zu positionieren und sich eine Identität zu schaffen jenseits der herkömmlichen binären Struktur, welche die pädagogischen Hochschulen dem Fachhochschul-Sektor zuordnet. Potentielle Konflikte zeichnen sich ab in den divergierenden kognitiven und normativen Orientierungen und Wahrnehmungen von Forschern, Ausbildern, Bildungspolitikern, Lehrern und Studierenden hinsichtlich des Auftrags und der Rolle dieses neuen Typs Hochschule.

Regulation of the integration of newly generated neurons in the adult hippocampus

Hippocampal adult neurogenesis results in the continuous formation of new neurons in the adult hippocampus, which participate to learning and memory. Manipulations increasing adult neurogenesis have a huge clinical potential in pathologies involving memory loss. Intringuingly, most of the newborn neurons die during their maturation. Thus, increasing newborn neuron survival during their maturation may be a powerful way to increase overall adult neurogenesis. The factors governing this neuronal death are yet poorly known. In my PhD project, we made the hypothesis that synaptogenesis and synaptic activity play a role in the survival of newborn hippocampal neurons. We studied three factors potentially involved in the regulation of the synaptic integration of adult-born neurons. First, we used propofol anesthesia to provoke a global increase in GABAergic activity of the network, and we evaluated the outcome on newborn neuron synaptic integration, morphological development and survival. Propofol anesthesia impaired the dendritic maturation and survival of adult-born neurons in an age-dependent manner. Next, we examined the development of astrocytic ensheathment on the synapses formed by newborn neurons, as we hypothesized that astrocytes are involved in their synaptic integration. Astrocytic processes ensheathed the synapses of newborn neurons very early in their development, and the processes modulated synaptic transmission on these cells. Finally, we studied the cell-autonomous effects of the overexpression of synaptic adhesion molecules on the development, synaptic integration and survival of newborn neurons, and we found that manipulating of a single adhesion molecule was sufficient to modify synaptogenesis and/or synapse function, and to modify newborn neuron survival. Together, these results suggest that the activity of the neuronal network, the modulation of glutamate transport by astrocytes, and the synapse formation and activity of the neuron itself may regulate the survival of newborn neurons. Thus, the survival of newborn neurons may depend on their ability to communicate with the network. This knowledge is crucial for finding ways to increase neurogenesis in patients. More generally, understanding how the neurogenic niche works and which factors are important for the generation, maturation and survival of neurons is fundamental to be able to maybe, one day, replace neurons in any region of the brain.

MAR-mediated integration of plasmid vectors for in vivo gene transfer and regulation.

BACKGROUND: The in vivo transfer of naked plasmid DNA into organs such as muscles is commonly used to assess the expression of prophylactic or therapeutic genes in animal disease models. RESULTS: In this study, we devised vectors allowing a tight regulation of transgene expression in mice from such non-viral vectors using a doxycycline-controlled network of activator and repressor proteins. Using these vectors, we demonstrate proper physiological response as consequence of the induced expression of two therapeutically relevant proteins, namely erythropoietin and utrophin. Kinetic studies showed that the induction of transgene expression was only transient, unless epigenetic regulatory elements termed Matrix Attachment Regions, or MAR, were inserted upstream of the regulated promoters. Using episomal plasmid rescue and quantitative PCR assays, we observed that similar amounts of plasmids remained in muscles after electrotransfer with or without MAR elements, but that a significant portion had integrated into the muscle fiber chromosomes. Interestingly, the MAR elements were found to promote plasmid genomic integration but to oppose silencing effects in vivo, thereby mediating long-term expression. CONCLUSIONS: This study thus elucidates some of the determinants of transient or sustained expression from the use of non-viral regulated vectors in vivo.

Integration of local-scale hydrological and regional-scale geophysical based on a nonlinear Bayesian sequential simulation approach

Significant progress has been made with regard to the quantitative integration of geophysical and hydrological data at the local scale. However, extending the corresponding approaches to the regional scale represents a major, and as-of-yet largely unresolved, challenge. To address this problem, we have developed a downscaling procedure based on a non-linear Bayesian sequential simulation approach. The basic objective of this algorithm is to estimate the value of the sparsely sampled hydraulic conductivity at non-sampled locations based on its relation to the electrical conductivity, which is available throughout the model space. The in situ relationship between the hydraulic and electrical conductivities is described through a non-parametric multivariate kernel density function. This method is then applied to the stochastic integration of low-resolution, re- gional-scale electrical resistivity tomography (ERT) data in combination with high-resolution, local-scale downhole measurements of the hydraulic and electrical conductivities. Finally, the overall viability of this downscaling approach is tested and verified by performing and comparing flow and transport simulation through the original and the downscaled hydraulic conductivity fields. Our results indicate that the proposed procedure does indeed allow for obtaining remarkably faithful estimates of the regional-scale hydraulic conductivity structure and correspondingly reliable predictions of the transport characteristics over relatively long distances.