Vectors fields defined on surfaces constitute relevant and useful representations but are rarely used. One reason might be that comparing vector fields across two surfaces of the same genus is not trivial: it requires to transport the vector fields from the original surfaces onto a common domain. In this paper, we propose a framework grounded on differential geometry to achieve this task. The proposed framework enables the computation of statistics on vector fields. We demonstrate its interest in practice with an application on real neuroimaging data. We provide a quantitative assessment of the reproducibility of curvature directions that describe the complex geometry of cortical folding patterns. The proposed framework is general and can be applied to different types of vector fields and surfaces, allowing for a large number of high potential applications in medical imaging.

We present an automatic translation of a skeletal semantics written in big-step style into an equivalent structural operational semantics. This translation is implemented on top of the Necro tool, which lets us automatically generate an OCaml interpreter for the small step semantics and a Coq mechanization of both semantics. We prove the framework correct in two ways: we provide a paper proof of the core of the transformation, and we generate Coq certification scripts alongside the transformation. We illustrate the approach using a simple imperative language and show how it scales to larger languages.

MI-LXC is a framework to simulate an internet-like infrastructure on top of LXC to practice cybersecurity on a realistic environment. MI-LXC follows the infrastructure-as-code paradigm to program the topology of the system and the provisioning of the different hosts. This construction is highly customizable, allowing to create hosts ranging from webservers to graphical desktops. Provisioning of similar subsets of features on different hosts is attained through a template mechanism. MI-LXC currently provides 28 hosts in 11 AS, allowing to simulate BGP routing, DNS, SMTP, HTTP, Certification authorities as well as attacks against these protocols. In this article, we present the MI-LXC framework, the generated infrastructure and some labs on top of it. MI-LXC is a free software (AGPL).

Opportunistic networking allows mobile devices to communicate without any fixed infrastructure, using the store-carry-and-forward principle, based on D2D (device to device) transmissions. Although smartphones may appear as perfect candidates to implement opportunistic networking protocols and algorithms, it turns out that their ability to support D2D transmissions is quite constrained, which hinders the deployment of opportunistic applications at a large scale. Acknowledging this fact we present Ligo, a device that is meant to behave as a peripheral device of a smartphone, providing this smartphone with the opportunistic networking services it cannot implement natively. The hardware components of Ligo are detailed in this paper, as well as the different software elements that enable the communication in the opportunistic network and the interaction with the smartphone.

Riemannian BCI based on EEG covariance have won many data competitions and achieved very high classification results on BCI datasets. To increase the accuracy of BCI systems, we propose an approach grounded on Riemannian geometry that extends this framework to functional connectivity measures. This paper describes the approach submitted to the Clinical BCI Challenge-WCCI2020 and that ranked 1ston the task 1 of the competition.

With new emerging technologies, such as satellites and drones, archaeologists collect data over large areas. However, it becomes difficult to process such data in time. Archaeological data also have many different formats (images, texts, sensor data) and can be structured, semi-structured and unstructured. Such variety makes data difficult to collect, store, manage, search and analyze effectively. A few approaches have been proposed, but none of them covers the full data lifecycle nor provides an efficient data management system. Hence, we propose the use of a data lake to provide centralized data stores to host heterogeneous data, as well as tools for data quality checking, cleaning, transformation and analysis. In this paper, we propose a generic, flexible and complete data lake architecture. Our metadata management system exploits goldMEDAL, which is the most generic metadata model currently available. Finally, we detail the concrete implementation of this architecture dedicated to an archaeological project.

Conflict-Free Replicated Data Types (CRDTs) are distributed data types that support optimistic replication: replicas can be updated locally, and updates propagate asynchronously among replicas, so consistency is eventually obtained. This ability to tolerate asynchronous communication makes them ideal candidates to serve as software building blocks in opportunistic networks (OppNets), that is, mobile networks in which the dissemination of information can only depend on unpredicted transient radio contacts between pairs of nodes. In this paper we investigate the problem of implementing CRDTs in an Opp-Net, and we propose a delta-state-based algorithm to solve this problem. Experimental results confirm that this algorithm ensures the synchronization of CRDT replicas in an OppNet, and that it outperforms a pure state-based synchronization algorithm when dealing with container CRDTs.

Making web applications run in a decentralized though collaborative way, with connectivity disruptions, is a challenging task. Opportunistic networking offers a way to be independent from a fixed infrastructure and cope with intermittent connectivity by leveraging both the mobility of nodes and their transient radio contacts. This paper presents an environment that facilitates the development of web applications deployed in opportunistic networks built out of smartphones. In order to overcome the technology hindrance regarding smartphones’ ad hoc communication capabilities, our contribution externalizes opportunistic networking to a dedicated device. On top of this support for smartphones, we propose an implementation of a programming model called foglet that allows web browsers to share consistent data structures. This implementation helps achieving decentralized applications distributed across mobile web browsers without relying on any network infrastructure.

MOTIVATION: Simulation-based inference can bypass the limitations of statistical methods based on analytical approximations, but software allowing simulation of structured population genetic data without the classical n-coalescent approximations (such as those following from assuming large population size) are scarce or slow. RESULTS: We present GSpace, a simulator for genomic data, based on a generation-by-generation coalescence algorithm taking into account small population size, recombination and isolation by distance. AVAILABILITY AND IMPLEMENTATION: Freely available at site web INRAe (http://www1.montpellier.inra.fr/CBGP/software/gspace/download.html).

Abstract We present a novel temporally coherent stylized rendering technique working entirely at the compositing stage. We first generate a distribution of 3D anchor points using an implicit grid based on the local object positions stored in a G‐buffer, hence following object motion. We then draw splats in screen space anchored to these points so as to be motion coherent. To increase the perceived flatness of the style, we adjust the anchor points density using a fractalization mechanism. Sudden changes are prevented by controlling the anchor points opacity and introducing a new order‐independent blending function. We demonstrate the versatility of our method by showing a large variety of styles thanks to the freedom offered by the splats content and their attributes that can be controlled by any G‐buffer.

Abstract Motivated by recent findings in the field of visual perception, we present a novel approach for enhancing shape depiction and perception of surface details. We propose a shading‐based technique that relies on locally adjusting the direction of light to account for the different components of materials. Our approach ensures congruence between shape and shading flows, leading to an effective enhancement of the perception of shape and details while impairing neither the lighting nor the appearance of materials. It is formulated in a general way allowing its use for multiple scales enhancement in real‐time on the GPU, as well as in global illumination contexts. We also provide artists with fine control over the enhancement at each scale.

Mycobacterium tuberculosis complex (MTC) CRISPR locus diversity has long been studied solely investigating the presence/absence of a known set of spacers. Unveiling the genetic mechanisms of its evolution requires a more exhaustive reconstruction in a large amount of representative strains. In this article, we point out and resolve, with a new pipeline, the problem of CRISPR reconstruction based directly on short read sequences in M. tuberculosis. We first show that the process we set up, that we coin as "CRISPRbuilder-TB" (https://github.com/cguyeux/CRISPRbuilder-TB), allows an efficient reconstruction of simulated or real CRISPRs, even when including complex evolutionary steps like the insertions of mobile elements. Compared to more generalist tools, the whole process is much more precise and robust, and requires only minimal manual investigation. Second, we show that more than 1/3 of the currently complete genomes available for this complex in the public databases contain largely erroneous CRISPR loci. Third, we highlight how both the classical experimental in vitro approach and the basic in silico spoligotyping provided by existing analytic tools miss a whole diversity of this locus in MTC, by not capturing duplications, spacer and direct repeats variants, and IS6110 insertion locations. This description is extended in a second article that describes MTC-CRISPR diversity and suggests general rules for its evolution. This work opens perspectives for an in-depth exploration of M. tuberculosis CRISPR loci diversity and of mechanisms involved in its evolution and its functionality, as well as its adaptation to other CRISPR locus-harboring bacterial species.

The relationship between different levels of integration is a key feature for understanding the genotype-phenotype map. Here, we describe a novel method of integrated data analysis that incorporates protein abundance data into constraint-based modeling to elucidate the biological mechanisms underlying phenotypic variation. Specifically, we studied yeast genetic diversity at three levels of phenotypic complexity in a population of yeast obtained by pairwise crosses of eleven strains belonging to two species, Saccharomyces cerevisiae and S. uvarum. The data included protein abundances, integrated traits (life-history/fermentation) and computational estimates of metabolic fluxes. Results highlighted that the negative correlation between production traits such as population carrying capacity (K) and traits associated with growth and fermentation rates (Jmax) is explained by a differential usage of energy production pathways: a high K was associated with high TCA fluxes, while a high Jmax was associated with high glycolytic fluxes. Enrichment analysis of protein sets confirmed our results. This powerful approach allowed us to identify the molecular and metabolic bases of integrated trait variation, and therefore has a broad applicability domain.