A fast and robust patient specific Finite Element mesh registration technique: application to 60 clinical cases

Finite Element mesh generation remains an important issue for patient specific biomechanical modeling. While some techniques make automatic mesh generation possible, in most cases, manual mesh generation is preferred for better control over the sub-domain representation, element type, layout and refinement that it provides. Yet, this option is time consuming and not suited for intraoperative situations where model generation and computation time is critical. To overcome this problem we propose a fast and automatic mesh generation technique based on the elastic registration of a generic mesh to the specific target organ in conjunction with element regularity and quality correction. This Mesh-Match-and-Repair (MMRep) approach combines control over the mesh structure along with fast and robust meshing capabilities, even in situations where only partial organ geometry is available. The technique was successfully tested on a database of 5 pre-operatively acquired complete femora CT scans, 5 femoral heads partially digitized at intraoperative stage, and 50 CT volumes of patients' heads. The MMRep algorithm succeeded in all 60 cases, yielding for each patient a hex-dominant, Atlas based, Finite Element mesh with submillimetric surface representation accuracy, directly exploitable within a commercial FE software

Description and Optimization of Abstract Machines in a Dialect of Prolog

In order to achieve competitive performance, abstract machines for Prolog and related languages end up being large and intricate, and incorporate sophisticated optimizations, both at the design and at the implementation levels. At the same time, efficiency considerations make it necessary to use low-level languages in their implementation. This makes them laborious to code, optimize, and, especially, maintain and extend. Writing the abstract machine (and ancillary code) in a higher-level language can help tame this inherent complexity. We show how the semantics of most basic components of an efficient virtual machine for Prolog can be described using (a variant of) Prolog. These descriptions are then compiled to C and assembled to build a complete bytecode emulator. Thanks to the high level of the language used and its closeness to Prolog, the abstract machine description can be manipulated using standard Prolog compilation and optimization techniques with relative ease. We also show how, by applying program transformations selectively, we obtain abstract machine implementations whose performance can match and even exceed that of state-of-the-art, highly-tuned, hand-crafted emulators.Comment: 56 pages, 46 figures, 5 tables, To appear in Theory and Practice of Logic Programming (TPLP

A Synergistic Approach for Recovering Occlusion-Free Textured 3D Maps of Urban Facades from Heterogeneous Cartographic Data

In this paper we present a practical approach for generating an occlusion-free textured 3D map of urban facades by the synergistic use of terrestrial images, 3D point clouds and area-based information. Particularly in dense urban environments, the high presence of urban objects in front of the facades causes significant difficulties for several stages in computational building modeling. Major challenges lie on the one hand in extracting complete 3D facade quadrilateral delimitations and on the other hand in generating occlusion-free facade textures. For these reasons, we describe a straightforward approach for completing and recovering facade geometry and textures by exploiting the data complementarity of terrestrial multi-source imagery and area-based information

Image informatics strategies for deciphering neuronal network connectivity

Brain function relies on an intricate network of highly dynamic neuronal connections that rewires dramatically under the impulse of various external cues and pathological conditions. Among the neuronal structures that show morphologi- cal plasticity are neurites, synapses, dendritic spines and even nuclei. This structural remodelling is directly connected with functional changes such as intercellular com- munication and the associated calcium-bursting behaviour. In vitro cultured neu- ronal networks are valuable models for studying these morpho-functional changes. Owing to the automation and standardisation of both image acquisition and image analysis, it has become possible to extract statistically relevant readout from such networks. Here, we focus on the current state-of-the-art in image informatics that enables quantitative microscopic interrogation of neuronal networks. We describe the major correlates of neuronal connectivity and present workflows for analysing them. Finally, we provide an outlook on the challenges that remain to be addressed, and discuss how imaging algorithms can be extended beyond in vitro imaging studies

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa

Reconstruction of an in silico metabolic model of _Arabidopsis thaliana_ through database integration

The number of genome-scale metabolic models has been rising quickly in recent years, and the scope of their utilization encompasses a broad range of applications from metabolic engineering to biological discovery. However the reconstruction of such models remains an arduous process requiring a high level of human intervention. Their utilization is further hampered by the absence of standardized data and annotation formats and the lack of recognized quality and validation standards.

Plants provide a particularly rich range of perspectives for applications of metabolic modeling. We here report the first effort to the reconstruction of a genome-scale model of the metabolic network of the plant _Arabidopsis thaliana_, including over 2300 reactions and compounds. Our reconstruction was performed using a semi-automatic methodology based on the integration of two public genome-wide databases, significantly accelerating the process. Database entries were compared and integrated with each other, allowing us to resolve discrepancies and enhance the quality of the reconstruction. This process lead to the construction of three models based on different quality and validation standards, providing users with the possibility to choose the standard that is most appropriate for a given application. First, a _core metabolic model_ containing only consistent data provides a high quality model that was shown to be stoichiometrically consistent. Second, an _intermediate metabolic model_ attempts to fill gaps and provides better continuity. Third, a _complete metabolic model_ contains the full set of known metabolic reactions and compounds in _Arabidopsis thaliana_.

We provide an annotated SBML file of our core model to enable the maximum level of compatibility with existing tools and databases. We eventually discuss a series of principles to raise awareness of the need to develop coordinated efforts and common standards for the reconstruction of genome-scale metabolic models, with the aim of enabling their widespread diffusion, frequent update, maximum compatibility and convenience of use by the wider research community and industry

Intelligent systems in manufacturing: current developments and future prospects

Global competition and rapidly changing customer requirements are demanding increasing changes in manufacturing environments. Enterprises are required to constantly redesign their products and continuously reconfigure their manufacturing systems. Traditional approaches to manufacturing systems do not fully satisfy this new situation. Many authors have proposed that artificial intelligence will bring the flexibility and efficiency needed by manufacturing systems. This paper is a review of artificial intelligence techniques used in manufacturing systems. The paper first defines the components of a simplified intelligent manufacturing systems (IMS), the different Artificial Intelligence (AI) techniques to be considered and then shows how these AI techniques are used for the components of IMS

Spike sorting for large, dense electrode arrays

Developments in microfabrication technology have enabled the production of neural electrode arrays with hundreds of closely spaced recording sites, and electrodes with thousands of sites are under development. These probes in principle allow the simultaneous recording of very large numbers of neurons. However, use of this technology requires the development of techniques for decoding the spike times of the recorded neurons from the raw data captured from the probes. Here we present a set of tools to solve this problem, implemented in a suite of practical, user-friendly, open-source software. We validate these methods on data from the cortex, hippocampus and thalamus of rat, mouse, macaque and marmoset, demonstrating error rates as low as 5%

Multimedia delivery in the future internet

The term “Networked Media” implies that all kinds of media including text, image, 3D graphics, audio and video are produced, distributed, shared, managed and consumed on-line through various networks, like the Internet, Fiber, WiFi, WiMAX, GPRS, 3G and so on, in a convergent manner [1]. This white paper is the contribution of the Media Delivery Platform (MDP) cluster and aims to cover the Networked challenges of the Networked Media in the transition to the Future of the Internet. Internet has evolved and changed the way we work and live. End users of the Internet have been confronted with a bewildering range of media, services and applications and of technological innovations concerning media formats, wireless networks, terminal types and capabilities. And there is little evidence that the pace of this innovation is slowing. Today, over one billion of users access the Internet on regular basis, more than 100 million users have downloaded at least one (multi)media file and over 47 millions of them do so regularly, searching in more than 160 Exabytes1 of content. In the near future these numbers are expected to exponentially rise. It is expected that the Internet content will be increased by at least a factor of 6, rising to more than 990 Exabytes before 2012, fuelled mainly by the users themselves. Moreover, it is envisaged that in a near- to mid-term future, the Internet will provide the means to share and distribute (new) multimedia content and services with superior quality and striking flexibility, in a trusted and personalized way, improving citizens’ quality of life, working conditions, edutainment and safety. In this evolving environment, new transport protocols, new multimedia encoding schemes, cross-layer inthe network adaptation, machine-to-machine communication (including RFIDs), rich 3D content as well as community networks and the use of peer-to-peer (P2P) overlays are expected to generate new models of interaction and cooperation, and be able to support enhanced perceived quality-of-experience (PQoE) and innovative applications “on the move”, like virtual collaboration environments, personalised services/ media, virtual sport groups, on-line gaming, edutainment. In this context, the interaction with content combined with interactive/multimedia search capabilities across distributed repositories, opportunistic P2P networks and the dynamic adaptation to the characteristics of diverse mobile terminals are expected to contribute towards such a vision. Based on work that has taken place in a number of EC co-funded projects, in Framework Program 6 (FP6) and Framework Program 7 (FP7), a group of experts and technology visionaries have voluntarily contributed in this white paper aiming to describe the status, the state-of-the art, the challenges and the way ahead in the area of Content Aware media delivery platforms