Feature-based terrain editing from complex sketches

We present a new method for first person sketch-based editing of terrain models. As in usual artistic pictures, the input sketch depicts complex silhouettes with cusps and T-junctions, which typically correspond to non-planar curves in 3D. After analysing depth constraints in the sketch based on perceptual cues, our method best matches the sketched silhouettes with silhouettes or ridges of the input terrain. A deformation algorithm is then applied to the terrain, enabling it to exactly match the sketch from the given perspective view, while insuring that none of the user-defined silhouettes is hidden by another part of the terrain. We extend this sketch-based terrain editing framework to handle a collection of multi-view sketches. As our results show, this method enables users to easily personalize an existing terrain, while preserving its plausibility and style.This work was conducted during an internship of Flora Ponjou Tasse at Inria Rhône-Alpes in Grenoble. It was partly supported by the ERC advanced grant EXPRESSIVE.This is the accepted manuscript. The final version is available from Elsevier at http://www.sciencedirect.com/science/article/pii/S009784931400081

Photochemical Organocatalytic Functionalization of Pyridines via Pyridinyl Radicals

We report a photochemical method for the functionalization of pyridines with radicals derived from allylic C–H bonds. Overall, two substrates undergo C–H functionalization to form a new C(sp2)–C(sp3) bond. The chemistry harnesses the unique reactivity of pyridinyl radicals, generated upon single-electron reduction of pyridinium ions, which undergo effective coupling with allylic radicals. This novel mechanism enables distinct positional selectivity for pyridine functionalization that diverges from classical Minisci chemistry. Crucial was the identification of a dithiophosphoric acid that masters three catalytic tasks, sequentially acting as a Brønsted acid for pyridine protonation, a single electron transfer (SET) reductant for pyridinium ion reduction, and a hydrogen atom abstractor for the activation of allylic C(sp3)–H bonds. The resulting pyridinyl and allylic radicals then couple with high regioselectivit

Stress-strain behavior and geometrical properties of packings of elongated particles

We present a numerical analysis of the effect of particle elongation on the quasistatic behavior of sheared granular media by means of the Contact Dynamics method. The particle shapes are rounded-cap rectangles characterized by their elongation. The macroscopic and microstructural properties of several packings subjected to biaxial compression are analyzed as a function of particle elongation. We find that the shear strength is an increasing linear function of elongation. Performing an additive decomposition of the stress tensor based on a harmonic approximation of the angular dependence of branch vectors, contact normals and forces, we show that the increasing mobilization of friction force and the associated anisotropy are key effects of particle elongation. These effects are correlated with partial nematic ordering of the particles which tend to be oriented perpendicular to the major principal stress direction and form side-to-side contacts. However, the force transmission is found to be mainly guided by cap-to-side contacts, which represent the largest fraction of contacts for the most elongated particles. Another interesting finding is that, in contrast to shear strength, the solid fraction first increases with particle elongation, but declines as the particles become more elongated. It is also remarkable that the coordination number does not follow this trend so that the packings of more elongated particles are looser but more strongly connected.Comment: Submited to Physical Review

Analysis of a Putative Promoter in Mycobacteriophage JacoRen57

JacoRen57 is a cluster AB mycobacteriophage that infects Mycobacterium smegmatis mc²155. We recently reported on the characterization of a putative promoter in JacoRen57 using an mCherry reporter construct. This promoter is present in a gap upstream of a gene that is present in all AB phages. In all cases, these are forward genes immediately following a long series of reverse genes. The genes are most frequently identified as a RecA-like DNA recombinases but also as RepA by bioinformatics. To further analyze this putative promoter and gene product, NWC Molecular Genetics students cloned the RecA-like DNA recombinase into an E. coli expression vector with a TVMV removable N-terminal His-tag. They expressed and we purified the tagged protein and are using it to immunize Balb/c mice. We plan to use the antiserum to confirm RecA-like DNA recombinase expression patterns when JacoRen57 infects M. smegmatis

Force transmission in a packing of pentagonal particles

We perform a detailed analysis of the contact force network in a dense confined packing of pentagonal particles simulated by means of the contact dynamics method. The effect of particle shape is evidenced by comparing the data from pentagon packing and from a packing with identical characteristics except for the circular shape of the particles. A counterintuitive finding of this work is that, under steady shearing, the pentagon packing develops a lower structural anisotropy than the disk packing. We show that this weakness is compensated by a higher force anisotropy, leading to enhanced shear strength of the pentagon packing. We revisit "strong" and "weak" force networks in the pentagon packing, but our simulation data provide also evidence for a large class of "very weak" forces carried mainly by vertex-to-edge contacts. The strong force chains are mostly composed of edge-to-edge contacts with a marked zig-zag aspect and a decreasing exponential probability distribution as in a disk packing

ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS based metabolomics

We present ProbMetab, an R package which promotes substantial improvement in automatic probabilistic LC-MS based metabolome annotation. The inference engine core is based on a Bayesian model implemented to: (i) allow diverse source of experimental data and metadata to be systematically incorporated into the model with alternative ways to calculate the likelihood function and; (ii) allow sensitive selection of biologically meaningful biochemical reactions databases as Dirichlet-categorical prior distribution. Additionally, to ensure result interpretation by system biologists, we display the annotation in a network where observed mass peaks are connected if their candidate metabolites are substrate/product of known biochemical reactions. This graph can be overlaid with other graph-based analysis, such as partial correlation networks, in a visualization scheme exported to Cytoscape, with web and stand alone versions. ProbMetab was implemented in a modular fashion to fit together with established upstream (xcms, CAMERA, AStream, mzMatch.R, etc) and downstream R package tools (GeneNet, RCytoscape, DiffCorr, etc). ProbMetab, along with extensive documentation and case studies, is freely available under GNU license at: http://labpib.fmrp.usp.br/methods/probmetab/.Comment: Manuscript to be submitted very soon. 7 pages, 3 color figures. There is a companion material, the two case studies, which are going to be posted here together with the main text in next updated versio

A NEW SATELLITE IMAGERY STEREO PIPELINE DESIGNED FOR SCALABILITY, ROBUSTNESS AND PERFORMANCE

Abstract. This paper presents a new Multiview Stereo Pipeline (MVS), called CARS, dedicated to satellite imagery. This pipeline is intended for massive Digital Surface Model (DSM) production and has therefore been designed to maximize scalability robustness and performance. Those two properties have driven the design of the workflow as well as the choice of algorithms and parameter trends, making our pipeline unique with respect to existing solutions in literature. This paper intends to serve as a reference paper for the pipeline implementation, and therefore provides a detailed description of algorithms and workflow. It also demonstrates the pipeline robustness and stability in several use cases, and compares its accuracy with the state-of-the-art pipelines on a reference dataset. Document type: Articl

Simulation of laser-driven cratering experiments on aluminum

After a brief description of the physical principles involved in the cratering process, the authors present a specific methodology to simulate laser-driven cratering experiments performed with a long pulse duration (100 ns) and a small focal spot diameter (220 μ m). This methodology can be divided into two steps. First, the 2D-axisymmetrical pressure field generated by the laser on the target is determined from laser parameters. Second, this pressure is applied on the surface of the target in a Eulerian simulation. In order to validate this methodology, the authors simulate a laser shot on a thin aluminum target whose rear surface velocity is recorded by a VISAR (Velocity Interferometer System for Any Reflector). Once validated, they use the methodology to simulate laser-driven cratering experiments on semi-infinite aluminum targets. Numerical results are compared to experimental measurements of the craters. Although slight differences are pointed out and discussed, the proposed methodology is well adapted to simulate craterization laser shots

Open-access platform to synthesize knowledge of ape conservation across sites

Despite the large body of literature on ape conservation, much of the data needed for evidence-based conservation decision-making is still not readily accessible and standardized, rendering cross-site comparison difficult. To support knowledge synthesis and to complement the IUCN SSC Ape Populations, Environments and Surveys database, we created the A.P.E.S. Wiki (https://apeswiki.eva.mpg.de), an open-access platform providing site-level information on ape conservation status and context. The aim of this Wiki is to provide information and data about geographical ape locations, to curate information on individuals and organizations active in ape research and conservation, and to act as a tool to support collaboration between conservation practitioners, scientists, and other stakeholders. To illustrate the process and benefits of knowledge synthesis, we used the momentum of the update of the conservation action plan for western chimpanzees (Pan troglodytes verus) and began with this critically endangered taxon. First, we gathered information on 59 sites in West Africa from scientific publications, reports, and online sources. Information was compiled in a standardized format and can thus be summarized using a web scraping approach. We then asked experts working at those sites to review and complement the information (20 sites have been reviewed to date). We demonstrate the utility of the information available through the Wiki, for example, for studying species distribution. Importantly, as an open-access platform and based on the well-known wiki layout, the A.P.E.S. Wiki can contribute to direct and interactive information sharing and promote the efforts invested by the ape research and conservation community. The Section on Great Apes and the Section on Small Apes of the IUCN SSC Primate Specialist Group will guide and support the expansion of the platform to all small and great ape taxa. Similar collaborative efforts can contribute to extending knowledge synthesis to all nonhuman primate species