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The chromosome conformation capture (3C) method has been invaluable in studying chromatin interactions in a population of cells at a resolution surpassing that of light microscopy, for example in the detection of functional contacts between enhancers and promoters. Recent developments in sequencing-based chromosomal contact mapping (Hi-C, 5C and 4C-Seq) have allowed researchers to interrogate pairwise chromatin interactions on a wider scale, shedding light on the three-dimensional organization of chromosomes. These methods present significant technical and bioinformatic challenges to consider at the start of the project. Here, we describe two alternative methods for Hi-C, depending on the size of the genome, and discuss the major computational approaches to convert the raw sequencing data into meaningful models of how genomes are organized.

Part 6: Network Modeling; International audience; Mobile Adhoc Networks (MANET) are susceptible to jamming attacks which can inhibit data transmissions. There has been considerable work done in the detection of external jamming attacks. However, detection of insider jamming attack in MANET has not received enough attention. The presence of an insider node that has constantly monitored the network and is privy to the network secrets can acquire sufficient information to cause irreparable damage. In this paper we propose a framework for a novel reputation-based coalition game between multiple players in a MANET to prevent internal attacks caused by an erstwhile legitimate node. A grand coalition is formed which will make a strategic security defense decision by depending on the stored transmission rate and reputation for each individual node in the coalition. Our results show that the simulation of the reputation-based coalition game would help improve the network’s defense strategy while also reducing false positives that results from the incorrect classification of unfortunate legitimate nodes as insider jammers.

International audience; We study unlimited infinite churn in peer-to-peer overlay networks. Under this churn, arbitrary many peers may concurrently request to join or leave the overlay network; moreover these requests may never stop coming. We prove that unlimited adversarial churn, where processes may just exit the overlay network, is unsolvable. We focus on cooperative churn where exiting processes participate in the churn handling algorithm. We define the problem of unlimited infinite churn in this setting. We distinguish the fair version of the problem, where each request is eventually satisfied, from the unfair version that just guarantees progress. We focus on local solutions to the problem, and prove that a local solution to the Fair Infinite Unlimited Churn is impossible. We then present our algorithm UIUC that solves the Unfair Infinite Unlimited Churn Problem for a linearized peer-to-peer overlay network. We extend this solution to skip lists and skip graphs.

International audience; In this paper, we study the effect of smartphone camera exposure on the performance of optical camera communications (OCC) link. The exposure parameters of image sensor sensitivity (ISO), aperture and shutter speed are included. A static OCC link with a 8 × 8 red, green and blue (RGB) LED array employed as the transmitter and a smartphone camera as the receiver is demonstrated to verify the study. Signal-to-noise ratio (SNR) analysis at different ISO values, the effect of aperture and shutter speed on communication link quality is performed. While SNRs of 20.6 dB and 16.9 dB are measured at 1 m and 2 m transmission distance, respectively for a ISO value of 100, they are decreased to 17.4 dB and 13.32 dB for a ISO of 800. The bit error rate (BER) of a 1 m long OCC link with a camera's shutter speed of 1/6000 s is 1.3 × 10 −3 (i.e., below the forward error correction BER limit of 3.8 × 10 −3) and is dropped to 0.0125 at a shutter speed of 1/20 s. This study provides insight of the basic smartphone settings and the exposure adjustment for further complex OCC links.

International audience; This study presents an algebraic method to detect, count, and identify concomitant motions of parallel robots at the velocity level. The pose and orientation of moving platform of parallel manipulators (PMs) with f-DOF could be commonly described by f possible motion variables on the instantaneous motion space (IMS) and (6 − f) restriction motion variables on the instantaneous restriction space (IRS). However, in some situations, PMs moving platform may accompanied by a concomitant (parasitic) motions along the direction of restriction space. Therefore, the commonly understood one-to-one correspondence between joint space and task space mobility of non-redundant PMs would be compromised. This phenomenon occurred due to the fact that the alignment of screws can change the reciprocal screws while the given screw systems are still maintained. To demonstrate the proposed method, an amplitude-based concomitant motion comparison is performed on two widely utilized lower-mobility parallel mechanisms, 3RPS and 3PRS. The result has shown that for the selected mechanisms, concomitant motion is identical regardless of their difference in joint arrangements in each limbs.

International audience; Orchestras of Digital Musical Instruments (DMIs) enable new musical collaboration possibilities, extending those of acoustic and electric orchestras. However the creation and development of these orchestras remain constrained. In fact, each new musical collaboration system or orchestra piece relies on a fixed number of musicians, a fixed set of instruments (often only one), and a fixed subset of possible modes of collaboration. In this paper, we describe a unified framework that enables the design of Digital Orchestras with potentially different DMIs and an expand-able set of collaboration modes. It relies on research done on analysis and classification of traditional and digital orchestras, on research in Collaborative Virtual Environments, and on interviews of musicians and composers. The BOEUF framework consists of a classification of modes of collaboration and a set of components for modelling digital orchestras. Integrating this framework into DMIs will enable advanced musical collaboration modes to be used in any digital orchestra, including spontaneous jam sessions.

Increases in arterial stiffness and pulse pressure are typical features of the arterial stiffness during aging and are associated with increased risk of cardiovascular complications. Cellular and molecular determinants of arterial stiffness have not been completely elucidated. Clinically, the carotid-femoral pulse wave velocity (PWV) is the gold standard parameter of arterial stiffness. A recent genome-wide scan of the Framingham Heart Study population has shown that arterial stiffness and mean and pulsatile components of blood pressure are heritable and map to separate the genetic loci in humans, suggesting that distinct genes may modulate these two phenotypes. This chapter details the recent knowledge on the influence of genetic determinants and telomere length on the development of age-related phenotypes. Recent genetic studies have revealed specific genes contributing to arterial stiffening. Available data on genome-wide association (GWA) have been initiated on PWV and have identified common genetic variation in specific loci or single-nucleotide polymorphisms (SNP) significantly associated with PWV. Telomere length at birth is strongly determined genetically and is the main determinant of leukocytes’ telomere length (LTL) later in life. Short LTL is associated with increased risk of stiffness and atherosclerosis of the carotid artery, atherosclerotic heart disease, and diminished survival in the elderly.

International audience; Toxoplasma gondii is a highly successful parasite that is thought to infect nearly one third of the world's population. Molecular epidemiology studies have illuminated the population structure of T. gondii strains world-wide and enabled insights into how the parasite is transmitted and the frequency of genetic exchange. Toxoplasma population genetics studies have shown that in North America and Europe, three genotypes have predominated whereas other diverse genotypes have propagated in other parts of the world, particularly in Central and South America. This chapter summarizes the techniques used to understand the population structure of T. gondii and how these techniques have also been helpful in understanding outbreaks of toxoplasmosis. As technology has advanced, more in-depth studies have facilitated our understanding of how differing genotypes can be linked to biological phenotypes including human disease.

This paper explores the sustainable manufacturing knowledge in the field of supply chain management in order to understand the best practices to diffuse sustainability across supply chain network. A systematic literature review was conducted, covering six databases by combinations of key-words between the periods of 1992 to November of 2013. A total of 92 peer-reviewed papers in English are reviewed. A lack of integration of the core SCM activities (purchasing, performance and collaboration) was found in the diffusion of environmental and social sustainability practices across supply chain. Thus, more studies are needed to cover the adoption of environmental and social practices into supply chain management activities and the process to diffuse them across the supply network. In addition, environmental issues have received more attention than social ones in both upstream and downstream supply chain management activities. Using the outputs of the literature review, a conceptual framework is proposed covered: 1) the interrelationship between the core upstream SCM activities (purchasing, suppliers´ performance assessment and collaboration with suppliers) and 2) the effect of internal cross function in upstream SCM activities.

Part 4: Enterprise Architecture; International audience; An executable model plays an important role on verifying the behavior and performance of an architecture. This paper summarizes the state of the art on the synthesis methods of the executable model for an architecture that is compliant with the Department of Defense Architecture Framework (DoDAF). To overcome the deficiencies of current executable modeling studies, a component data-focused method is proposed. Following the introduction of an executable modeling language named OPDL, the data elements of DoDAF Meta-model (DM2) required for building executable model is analyzed. The mapping relations between partial DM2 and OPDL elements are built. Finally, a process to create executable model is explained in detail.