Pseudolikelihood inference for Gibbsian T-tessellations ... and point processes

Recently a new class of planar tessellations, named T-tessellations, was introduced. Splits, merges and a third local modification named flip where shown to be sufficient for exploring the space of T-tessellations. Based on these local transformations and by analogy with point process theory, tools Campbell measures and a general simulation algorithm of Metropolis-Hastings-Green type were translated for random T-tessellations.The current report is concerned with parametric inference for Gibbs models of T-tessellations. The estimation criterion referred to as the pseudolikelihood is derived from Campbell measures of random T-tessellations and the Kullback-Leibler divergence. A detailed algorithm for approximating the pseudolikelihood maximum is provided. A simulation study seems to show that bias and variability of the pseudolikelihood maximum decrease when the tessellated domain grows in size.In the last part of the report, it is shown that an analogous approach based on the Campbell measure and the KL divergence when applied to point processes leads to the well-known pseudo-likelihood introduced by Besag. More surprisingly, the binomial regression method recently proposed by Baddeley and his co-authors for computing the pseudolikelihood maximum can be derived using the same approach starting from a slight modification of the Campbell measure

Visibilité et prévisibilité : cartographie de la part cachée d'un paysage urbain: Etude comparée de quatre indicateurs qualifiant le champ visuel en milieu urbain

International audienceAccording to permeability theory, surroundings' configuration, and more precisely, the existence of occlusions in our enclosure may invite us to explore our environment. This article aims to analyze, in a systematic and reproducible way, the ratio of mystery in one's surrounding visualscape. To assess this property in each place, we recall three indicators relative to the boundary previsibility (entropy), the weight of visual heap (drift), and the occlusions ratio (occlusivity). We also introduce a fourth indicator which weights each occlusion (anticipation). At last, we refer to some convex partition technics of urban open spaces.Pour la théorie de la perméabilité, la configuration des lieux et plus précisément la présence d'occlusions dans notre environnement visuel immédiat, peuvent nous inciter à son exploration. L'étude présentée dans cet article a pour but d'analyser de manière systématique et reproductible la part d'inconnu, d'incertitude de l'environnement urbain immédiat d'un piéton. Pour évaluer cette propriété du visualscape en tout point, nous rappelons trois indicateurs permettant de quantifier la prévisibilité de la forme ambiante (entropie), le poids des masses visuelles (drift) et la part d'occlusions (occlusivité) avant d'en proposer un quatrième relativisant le poids de chaque occlusion (l'anticipation). Nous concluons cette analyse par une référence aux techniques de partitionnement convexe de l'espace ouvert

Evidence that the Pomeron transforms as a non-conserved vector current

The detailed dependences of central meson production on the azimuthal angle phi, t and the meson J^P are shown to be consistent with the hypothesis that the soft Pomeron transforms as a non-conserved vector current. Further tests are proposed. This opens the way for a quantitative description of q-qbar and glueball production in p p -> p M p.Comment: 12 pages, latex, 4 figure

Genome-wide transcriptome analysis of hydrogen production in the cyanobacterium Synechocystis: Towards the identification of new players

International audienceWe report the development of new tools and methods for facile integration and meaningful representation of high throughput data generated by genome-wide analyses of the model cyanobacterium Synechocystis PCC6803, for future genetic engineering aiming at increasing its level of hydrogen photoproduction. These robust tools comprise new oligonucleotide DNA microarrays to monitor the transcriptomic responses of all 3725 genes of Synechocystis, and the SVGMapping method and custom-made templates to represent the metabolic reprogramming for improved hydrogen production. We show, for the first time, that the AbrB2 repressor of the hydrogenase-encoding operon, also regulates metal transport and protection against oxidative stress, as well as numerous plasmid genes, which have been overlooked so far. This report will stimulate the construction and global analysis of hydrogen production mutants with the prospect of developing powerful cell factories for the sustainable production of hydrogen, as well as investigations of the probable role of plasmids in this process

Slowdown of surface diffusion during early stages of bacterial colonization

We study the surface diffusion of the model cyanobacterium Synechocystis sp. PCC6803 during the incipient stages of cell contact with a glass surface in the dilute regime. We observe a twitching motility with alternating immobile tumble and mobile run periods, resulting in a normal diffusion described by a continuous-time random walk with a coefficient of diffusion D. Surprisingly, D is found to decrease with time down to a plateau. This is observed only when the cyanobacterial cells are able to produce released extracellular polysaccharides, as shown by a comparative study between the wild-type strain and various polysaccharides-depleted mutants. The analysis of the trajectories taken by the bacterial cells shows that the temporal characteristics of their intermittent motion depend on the instantaneous fraction of visited sites during diffusion. This describes quantitatively the time dependence of D, related to the progressive surface coverage by the polysaccharides. The observed slowdown of the surface diffusion may constitute a basic precursor mechanism for microcolony formation and provides clues for controlling biofilm formation

The challenge of studying TiO2 nanoparticle bioaccumulation at environmental concentrations: Crucial use of a stable isotope tracer

International audienceThe ecotoxicity of nanoparticles (NPs) is a growing area of research with many challenges ahead. To be relevant, laboratory experiments must be performed with well-controlled and environmentally realistic (i.e. low) exposure doses. Moreover, when focusing on the intensively manufactured titanium dioxide (TiO2) NPs, sample preparations and chemical analysis are critical steps to meaningfully assay NP?s bioaccumulation. To deal with these imperatives, we synthesized for the first time TiO2 NPs labeled with the stable isotope 47Ti. Thanks to the 47Ti labeling, we could detect the bioaccumulation of NPs in zebra mussels (Dreissena polymorpha) exposed for 1h at environmental concentrations via water (7 - 120 µg/L of 47TiO2 NPs) and via their food (4 ? 830 µg/L of 47TiO2 NPs mixed with 1?106 cells/mL of cyanobacteria) despite the high natural Ti background, which varied in individual mussels. The assimilation efficiency (AE) of TiO2 NPs by mussels from their diet was very low (AE= 3.0±2.7%) suggesting that NPs are mainly captured in mussel gut, with little penetration in their internal organs. Thus, our methodology is particularly relevant in predicting NP?s bioaccumulation and investigating the factors influencing their toxicokinetics in conditions mimicking real environments

A transcriptional-switch model for Slr1738-controlled gene expression in the cyanobacterium Synechocystis

<p>Abstract</p> <p>Background</p> <p>Protein-DNA interactions play a crucial role in the life of biological organisms in controlling transcription, regulation, as well as DNA recombination and repair. The deep understanding of these processes, which requires the atomic description of the interactions occurring between the proteins and their DNA partners is often limited by the absence of a 3D structure of such complexes.</p> <p>Results</p> <p>In this study, using a method combining sequence homology, structural analogy modeling and biochemical data, we first build the 3D structure of the complex between the poorly-characterized PerR-like regulator Slr1738 and its target DNA, which controls the defences against metal and oxidative stresses in <it>Synechocystis</it>. In a second step, we propose an expanded version of the Slr1738-DNA structure, which accommodates the DNA binding of Slr1738 multimers, a feature likely operating in the complex Slr1738-mediated regulation of stress responses. Finally, in agreement with experimental data we present a 3D-structure of the Slr1738-DNA complex resulting from the binding of multimers of the FUR-like regulator onto its target DNA that possesses internal repeats.</p> <p>Conclusion</p> <p>Using a combination of different types of data, we build and validate a relevant model of the tridimensional structure of a biologically important protein-DNA complex. Then, based on published observations, we propose more elaborated multimeric models that may be biologically important to understand molecular mechanisms.</p

How far is far enough? Towards an adaptive and " site-centric " modelling integrating co-visibility constraints for optimal land use

International audienceIn this article, we propose a renewed site-centric solution that allows us to characterize a specific region of interest by defining the extent of the surroundings that influence sunlight exposure. The proposed method is a mix of an adaptive refinement and a visual-based clipping technique. This method has been implemented in the SketchUp context and applied to three sites located next to the French historical thermal town of Aix-les-Bains

The cyanobacterial cell division factor Ftn6 contains an N-terminal DnaD-like domain

<p>Abstract</p> <p>Background</p> <p>DNA replication and cell cycle as well as their relationship have been extensively studied in the two model organisms <it>E. coli </it>and <it>B. subtilis</it>. By contrast, little is known about these processes in cyanobacteria, even though they are crucial to the biosphere, in utilizing solar energy to renew the oxygenic atmosphere and in producing the biomass for the food chain. Recent studies have allowed the identification of several cell division factors that are specifics to cyanobacteria. Among them, Ftn6 has been proposed to function in the recruitment of the crucial FtsZ proteins to the septum or the subsequent Z-ring assembly and possibly in chromosome segregation.</p> <p>Results</p> <p>In this study, we identified an as yet undescribed domain located in the conserved N-terminal region of Ftn6. This 77 amino-acids-long domain, designated here as FND (Ftn6 N-Terminal Domain), exhibits striking sequence and structural similarities with the DNA-interacting module, listed in the PFAM database as the DnaD-like domain (pfam04271). We took advantage of the sequence similarities between FND and the DnaD-like domains to construct a homology 3D-model of the Ftn6 FND domain from the model cyanobacterium <it>Synechocystis </it>PCC6803. Mapping of the conserved residues exposed onto the FND surface allowed us to identify a highly conserved area that could be engaged in Ftn6-specific interactions.</p> <p>Conclusion</p> <p>Overall, similarities between FND and DnaD-like domains as well as previously reported observations on Ftn6 suggest that FND may function as a DNA-interacting module thereby providing an as yet missing link between DNA replication and cell division in cyanobacteria. Consistently, we also showed that Ftn6 is involved in tolerance to DNA damages generated by UV rays.</p

Interview Chris McGregor

Photocopied interview of Chris McGregor. There are 2 pictures with this article. On the first page there is a photo of the Brotherhood of Breath rehearsing and on the second page a picture of Chris McGregor playing the piano