Computational neuroanatomy and co-expression of genes in the adult mouse brain, analysis tools for the Allen Brain Atlas

We review quantitative methods and software developed to analyze genome-scale, brain-wide spatially-mapped gene-expression data. We expose new methods based on the underlying high-dimensional geometry of voxel space and gene space, and on simulations of the distribution of co-expression networks of a given size. We apply them to the Allen Atlas of the adult mouse brain, and to the co-expression network of a set of genes related to nicotine addiction retrieved from the NicSNP database. The computational methods are implemented in {\ttfamily{BrainGeneExpressionAnalysis}}, a Matlab toolbox available for download.Comment: 25 pages, 8 figures, accepted in Quantitative Biology (2012) 000

Objets d'analyse pour l'étude des réseaux de parenté: Une application aux familles de la grande bourgeoisie juive parisienne, XIXe-XXe siècles

International audienceThis article introduces a number of helpful concepts for studying kinship networks: the matrimonial network, its components and bi-components, network segmentation according to exogenous or endogenous criteria, restricted matrimonial networks derived from particular matrimonial censuses, the frames of these restricted networks, the constellations that compose these frames, etc. It emphasizes the usefulness, for the analysis of alliance patterns, of the “nucleus” of a kinship network (its maximal matrimonial bicomponent), a homogenous and densely interconnected network object. Matrimonial constellations, that is, sets of individuals selected by some genealogically based criteria, are also shown to be particularly interesting units of observation. Genealogical data concerning upper-class, bourgeois Jewish families in finance and industry installed in Paris at the end of the 19th century is used to illustrate the various theoretical objects described. The authors draw a number of conclusions regarding the marriage behaviour of this population. Observing the emergence of uterine (and maternal) configurations from 1880 onwards, they caution that this should not be understood as the introduction of a new alliance form as such, but as resulting from the disappearance of previously dominant agnatic unions. Identifying the most prestigious dynasties is shown to be particularly useful, revealing distinctive marriage patterns characterized by an intense circulation among the most privileged patrilines, less advantaged families being much less densely interconnected.Cet article expose un certain nombre de concepts utiles pour l'étude des réseaux de parenté : le réseau matrimonial, les composantes et bi-composantes, la segmentation du réseau matrimonial selon des critères exogènes ou endogènes, les réseaux matrimoniaux restreints issus de recensements ciblés auprès du corpus, les armatures de ces réseaux restreints, les constellations qui composent ces armatures... Il insiste notamment sur l'intérêt de l'"amande" du réseau (bicomposante matrimoniale maximale), objet réticulaire homogène et fortement interconnectée, pour l'analyse des structures d'alliance. De même les constellations, ensembles d'individus rassemblés selon un critère de proximité de nature généalogique, apparaissent comme une unité d'observation des données particulièrement féconde. Un corpus d'observation composé des familles de la haute bourgeoisie juive financière et industrielle installée à Paris à la fin du XIXe siècle est utilisé pour l'illustration des différents objets théoriques passés en revue. Quelques conclusions sur les comportements d'alliance de cette population ont d'ailleurs pu être tirées. Ainsi on observe une émergence de figures utérines (et maternelles) à partir de 1880 qui ne doit cependant pas être lue comme l'introduction d'une nouvelle forme d'alliance en tant que telle mais plutôt comme le résultat de l'effacement des unions agnatiques, largement dominantes auparavant. Le « marquage » des dynasties les plus prestigieuses apparaît comme un critère de segmentation particulièrement opératoire. Il met au jour des pratiques matrimoniales spécifiques, caractérisées par des échanges intenses entre les patrilignes les plus huppés, les familles les moins privilégiées témoignant d'un degré d'interconnection bien moindre

La parenté radiographiée. Un nouveau logiciel pour l'analyse des réseaux matrimoniaux

International audienceKinship under the Microscope : A New Software for the Analysis of Matrimonial Networks. — Marriage choices can not be treated as isolated phenomena. They draw their meaning from how they are distributed and combined so as to form complex patterns whose study requires the use of computerized tools. While computers have been used in the study of kinship for over forty years, an instrument capable of making a complete matrimonial census of a kinship network has been lacking. The software Puck (Program for the Use and Computation of Kinship Data) fills this gap. This article presents the main applications of this software, and discusses the theoretical issues and methodological choices that went into its development.Les choix matrimoniaux ne sauraient être traités comme des éléments isolés. Ils n'acquièrent leur signification que par la manière dont ils se distribuent et se combinent pour former des agencements complexes dont l'étude est difficilement envisageable sans recours à un traitement informatique. Si l'ordinateur a été introduit il y a une quarantaine d'années dans les études de la parenté, on manquait encore d'un instrument rendant possible un recensement matrimonial complet d'un réseau de parenté. Le logiciel Puck (Program for the Use and Computation of Kinship Data) remédie à ce manque. Cet article présente les principales applications de ce logiciel, en précisant les enjeux théoriques et les choix méthodologiques qui ont présidé à son élaboration

Virtual Research Integration Collaboration: Procedural report

The aim of the project is to build a framework for the integration of basic science and clinical research to manage research lifecycles and allow for integration of scientific approaches throughout these lifecycles into the everyday work practice of the consortia that manage translational clinical research. The project will take the CORE VRE and embed it into a National centre for surgical excellence, the Royal National Orthopaedic Hospital (RNOH). The VRE will integrate both with the institutional systems and research life cycle, and with the national systems such as the National Health Service (NHS). It is our aim to integrate the CORE VRE with myExperiment to provide a set of services at RNOH to cover the four main areas of the research cycle, namely: the monitoring and governance of trials (experiment research administration); the trial protocols (experiment workflows); the publishing, dissemination and discussion on the results of trials in a repository; and the discovery of information from the repository and other resources. For this community, there are three tightly coupled areas of focus: research, clinical practice, and education (in the form of continuing professional development and training of the next generation of surgeons). In this project, our user community will be heavily involved in co-designing and codeployment of the tool set, and in particular the front end of the workbench will be user focused. The tools will need to be available to staff anywhere with the organisation, as clinicians need to be able to enter the data during clinics and directors of research need to be able to monitor the trials. This will bring with it a number of inter-operability issues, as we move data between the VRE, the hospital systems (NHS) and the institutional systems. To aid the understanding of the how the system will be used, we outline a typical ‘research cycle’ that includes the practice of a clinical specialist in orthopaedics (who may also be a Higher surgical trainee) and a basic scientist. The purpose of this is to identify time essential information provision and interaction with pervasive technologies. For new researchers one of the most difficult tasks is to learn good practice or find related experiments to learn how to instantiate the protocols; in many organisations it is often easier to repeat an experiment than to find the results of a similar previous experiment. In this abstracted model of the research lifecycle, we have split up the cycle into four main research activities. In each of these activities the different issues and stakeholders are addressed. The wider community nationally is represented by the Musculoskeletal network of Greater London, NHS, e-science, Surgical and VRE communities. It is through the Musculoskeletal network of Greater London that we will be able to co-ordinate knowledge and demonstrations to advise the community and for continuity. This project will impact on the wider academic community in the UK, initially through dissemination via organisations such as BriteNet (Tissue Engineering), The British Orthopaedic Association, British Orthopaedic Research Society, and the British Elbow and Shoulder Society as the groups tied into the consortia development

Performance of NO, NO2 low cost sensors and three calibration approaches within a real world application

Low cost sensors for measuring atmospheric pollutants are experiencing an increase in popularity worldwide among practitioners, academia and environmental agencies, and a large amount of data by these devices are being delivered to the public. Notwithstanding their behaviour, performance and reliability are not yet fully investigated and understood. In the present study we investigate the medium term performance of a set of NO and NO2 electrochemical sensors in Switzerland using three different regression algorithms within a field calibration approach. In order to mimic a realistic application of these devices, the sensors were initially co-located at a rural regulatory monitoring site for a 4-month calibration period, and subsequently deployed for 4 months at two distant regulatory urban sites in traffic and urban background conditions, where the performance of the calibration algorithms was explored. The applied algorithms were Multivariate Linear Regression, Support Vector Regression and Random Forest; these were tested, along with the sensors, in terms of generalisability, selectivity, drift, uncertainty, bias, noise and suitability for spatial mapping intra-urban pollution gradients with hourly resolution. Results from the deployment at the urban sites show a better performance of the non-linear algorithms (Support Vector Regression and Random Forest) achieving RMSE R2 between 0.74 and 0.95 and MAE between 2 and 4\u11d\u20acppb. The combined use of both NO and NO2 sensor output in the estimate of each pollutant showed some contribution by NO sensor to NO2 estimate and vice-versa. All algorithms exhibited a drift ranging between 5 and 10\u11d\u20acppb for Random Forest and 15\u11d\u20acppb for Multivariate Linear Regression at the end of the deployment. The lowest concentration correctly estimated, with a 25\u11d\u20ac% relative expanded uncertainty, resulted in ca. 15\u201320\u11d\u20acppb and was provided by the non-linear algorithms. As an assessment for the suitability of the tested sensors for a targeted application, the probability of resolving hourly concentration difference in cities was investigated. It was found that NO concentration differences of 5\u201310\u11d\u20acppb (8\u201310 for NO2) can reliably be detected (90\u11d\u20ac% confidence), depending on the air pollution level. The findings of this study, although derived from a specific sensor type and sensor model, are based on a flexible methodology and have extensive potential for exploring the performance of other low cost sensors, that are different in their target pollutant and sensing technology

La parenté radiographiée

RésuméLes choix matrimoniaux ne sauraient être traités comme des éléments isolés. Ils n’acquièrent leur signification que par la manière dont ils se distribuent et se combinent pour former des agencements complexes dont l’étude est difficilement envisageable sans recours à un traitement informatique. Si l’ordinateur a été introduit il y a une quarantaine d’années dans les études de la parenté, on manquait encore d’un instrument rendant possible un recensement matrimonial complet d’un réseau de parenté. Le logiciel Puck (Program for the Use and Computation of Kinship Data) remédie à ce manque. Cet article présente les principales applications de ce logiciel, en précisant les enjeux théoriques et les choix méthodologiques qui ont présidé à son élaboration.Kinship under the Microscope : A New Software for the Analysis of Matrimonial NetworksMarriage choices can not be treated as isolated phenomena. They draw their meaning from how they are distributed and combined so as to form complex patterns whose study requires the use of computerized tools. While computers have been used in the study of kinship for over forty years, an instrument capable of making a complete matrimonial census of a kinship network has been lacking. The software Puck (Program for the Use and Computation of Kinship Data) fills this gap. This article presents the main applications of this software, and discusses the theoretical issues and methodological choices that went into its development

Successor-Invariant First-Order Logic on Classes of Bounded Degree

We study the expressive power of successor-invariant first-order logic, which is an extension of first-order logic where the usage of an additional successor relation on the structure is allowed, as long as the validity of formulas is independent on the choice of a particular successor. We show that when the degree is bounded, successor-invariant first-order logic is no more expressive than first-order logic