The macroscopic effects of microscopic heterogeneity

Over the past decade, advances in super-resolution microscopy and particle-based modeling have driven an intense interest in investigating spatial heterogeneity at the level of single molecules in cells. Remarkably, it is becoming clear that spatiotemporal correlations between just a few molecules can have profound effects on the signaling behavior of the entire cell. While such correlations are often explicitly imposed by molecular structures such as rafts, clusters, or scaffolds, they also arise intrinsically, due strictly to the small numbers of molecules involved, the finite speed of diffusion, and the effects of macromolecular crowding. In this chapter we review examples of both explicitly imposed and intrinsic correlations, focusing on the mechanisms by which microscopic heterogeneity is amplified to macroscopic effect.Comment: 20 pages, 5 figures. To appear in Advances in Chemical Physic

Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping

We have developed a computational framework for spatiotemporal integration of molecular and anatomical datasets in a virtual reality environment. Using two case studies involving gene expression data and pharmacokinetic data, respectively, we demonstrate how existing knowledge bases for molecular data can be semantically mapped onto a standardized anatomical context of human body. Our data mapping methodology uses ontological representations of heterogeneous biomedical datasets and an ontology reasoner to create complex semantic descriptions of biomedical processes. This framework provides a means to systematically combine an increasing amount of biomedical imaging and numerical data into spatiotemporally coherent graphical representations. Our work enables medical researchers with different expertise to simulate complex phenomena visually and to develop insights through the use of shared data, thus paving the way for pathological inference, developmental pattern discovery and biomedical hypothesis testing

Semantics-Space-Time Cube. A Conceptual Framework for Systematic Analysis of Texts in Space and Time

We propose an approach to analyzing data in which texts are associated with spatial and temporal references with the aim to understand how the text semantics vary over space and time. To represent the semantics, we apply probabilistic topic modeling. After extracting a set of topics and representing the texts by vectors of topic weights, we aggregate the data into a data cube with the dimensions corresponding to the set of topics, the set of spatial locations (e.g., regions), and the time divided into suitable intervals according to the scale of the planned analysis. Each cube cell corresponds to a combination (topic, location, time interval) and contains aggregate measures characterizing the subset of the texts concerning this topic and having the spatial and temporal references within these location and interval. Based on this structure, we systematically describe the space of analysis tasks on exploring the interrelationships among the three heterogeneous information facets, semantics, space, and time. We introduce the operations of projecting and slicing the cube, which are used to decompose complex tasks into simpler subtasks. We then present a design of a visual analytics system intended to support these subtasks. To reduce the complexity of the user interface, we apply the principles of structural, visual, and operational uniformity while respecting the specific properties of each facet. The aggregated data are represented in three parallel views corresponding to the three facets and providing different complementary perspectives on the data. The views have similar look-and-feel to the extent allowed by the facet specifics. Uniform interactive operations applicable to any view support establishing links between the facets. The uniformity principle is also applied in supporting the projecting and slicing operations on the data cube. We evaluate the feasibility and utility of the approach by applying it in two analysis scenarios using geolocated social media data for studying people's reactions to social and natural events of different spatial and temporal scales

Using mobility data as proxy for measuring urban vitality

In this paper, we propose a computational approach to Jane Jacobs\u27 concept of diversity and vitality, analyzing new forms of spatial data to obtain quantitative measurements of urban qualities frequently employed to evaluate places. We use smart card data collected from public transport to calculate a diversity value for each research unit. Diversity is composed of three dynamic attributes: intensity, variability, and consistency, each measuring different temporal variations of mobility flows. We then apply a regression model to establish the relationship between diversity and vitality, using Twitter data as a proxy for human activity in urban space. Final results (also validated using data sourced from OpenStreetMap) unveil which are the most vibrant areas in London

Multidimensional modeling and analysis of large and complex watercourse data: an OLAP-based solution

International audienceThis paper presents the application of Data Warehouse (DW) and On-Line Analytical Processing (OLAP) technologies to the field of water quality assessment. The European Water Framework Directive (DCE, 2000) underlined the necessity of having operational tools to help in the interpretation of the complex and abundant information regarding running waters and their functioning. Several studies have exemplified the interest in DWs for integrating large volumes of data and in OLAP tools for data exploration and analysis. Based on free software tools, we propose an extensible relational OLAP system for the analysis of physicochemical and hydrobiological watercourse data. This system includes: (i) two data cubes; (ii) an Extract, Transform and Load (ETL) tool for data integration; and (iii) tools for OLAP exploration. Many examples of OLAP analysis (thematic, temporal, spatiotemporal, and multiscale) are provided. We have extended an existing framework with complex aggregate functions that are used to define complex analysis indicators. Additional analysis dimensions are also introduced to allow their calculation and also for purposes of rendering information. Finally, we propose two strategies to address the problem of summarizing heterogeneous measurement units by: (i) transforming source data at the ETL tier, and (ii) introducing an additional analysis dimension at the OLAP server tier

Privacy in trajectory micro-data publishing : a survey

We survey the literature on the privacy of trajectory micro-data, i.e., spatiotemporal information about the mobility of individuals, whose collection is becoming increasingly simple and frequent thanks to emerging information and communication technologies. The focus of our review is on privacy-preserving data publishing (PPDP), i.e., the publication of databases of trajectory micro-data that preserve the privacy of the monitored individuals. We classify and present the literature of attacks against trajectory micro-data, as well as solutions proposed to date for protecting databases from such attacks. This paper serves as an introductory reading on a critical subject in an era of growing awareness about privacy risks connected to digital services, and provides insights into open problems and future directions for research.Comment: Accepted for publication at Transactions for Data Privac