Thinking like a director: Film editing paterns for virtual cinematographic storytelling

International audienceThis paper introduces Film Editing Patterns (FEP), a language to formalize film editing practices and stylistic choices found in movies. FEP constructs are constraints, expressed over one or more shots from a movie sequence that characterize changes in cinematographic visual properties such as shot sizes, camera angles, or layout of actors on the screen. We present the vocabulary of the FEP language, introduce its usage in analyzing styles from annotated film data, and describe how it can support users in the creative design of film sequences in 3D. More specifically, (i) we define the FEP language, (ii) we present an application to craft filmic sequences from 3D animated scenes that uses FEPs as a high level mean to select cameras and perform cuts between cameras that follow best practices in cinema and (iii) we evaluate the benefits of FEPs by performing user experiments in which professional filmmakers and amateurs had to create cinematographic sequences. The evaluation suggests that users generally appreciate the idea of FEPs, and that it can effectively help novice and medium experienced users in crafting film sequences with little training

Essentiality of mmpL3 and impact of its silencing on Mycobacterium tuberculosis gene expression

MmpL3 is an inner membrane transporter of Mycobacterium tuberculosis responsible for the export of trehalose momomycolate, a precursor of the mycobacterial outer membrane component trehalose dimycolate (TDM), as well as mycolic acids bound to arabinogalactan. MmpL3 represents an emerging target for tuberculosis therapy. In this paper, we describe the construction and characterization of an mmpL3 knockdown strain of M. tuberculosis. Downregulation of mmpL3 led to a stop in bacterial division and rapid cell death, preceded by the accumulation of TDM precursors. MmpL3 was also shown to be essential for growth in monocyte-derived human macrophages. Using RNA-seq we also found that MmpL3 depletion caused up-regulation of 47 genes and down-regulation of 23 genes (at least 3-fold change and false discovery rate <= 1%). Several genes related to osmoprotection and metal homeostasis were induced, while several genes related to energy production and mycolic acids biosynthesis were repressed suggesting that inability to synthesize a correct outer membrane leads to changes in cellular permeability and a metabolic downshift

2D shallow water GPU parallelized scheme for high resolution real-field flood simulations

In this paper a parallelization of a Shallow Water numerical scheme suitable for Graphics Processor Unit (GPU) architectures under the NVIDIATM's Compute Unified Device Architecture (CUDA) framework is presented. In order to provide robust, fast and accurate simulations of real flood events, the system features a state-of-the-art Finite Volume explicit discretization technique which is well balanced, second order accurate and based on positive depth reconstruction. The CUDA parallelization led to speedups of two orders of magnitude with respect to a single-core CPU. The code, already validated against several severe benchmark tests, was here applied to two real-world cases. To capture all the main characteristics of the flow at different scales and to describe road and railway embankments without the introduction of 1D relationships, a high-resolution mesh size (2-5 meters) was adopted. Since the ratio between physical and computational time is always high, the numerical scheme herein presented can be embedded in real-time simulation tools, which can provide accurate and fast predictions useful also for flood management of occurring flood events. © 2014 Taylor & Francis Group, London

Global transcriptional responce to Vancomycin in Mycobacterium tuberculosis

In order to gain additional understanding of the physiological mechanisms used by bacteria to maintain surface homeostasis and to identify potential targets for new antibacterial drugs, we analysed the variation of the Mycobacterium tuberculosis transcriptional profile in response to inhibitory and subinhibitory concentrations of vancomycin. Our analysis identified 153 genes differentially regulated after exposing bacteria to a concentration of the drug ten times higher than the MIC, and 141 genes differentially expressed when bacteria were growing in a concentration of the drug eightfold lower than the MIC. Hierarchical clustering analysis indicated that the response to these different conditions is different, although with some overlap. This approach allowed us to identify several genes whose products could be involved in the protection from antibiotic stress targeting the envelope and help to confer the basal level of M. tuberculosis resistance to antibacterial drugs, such as Rv2623 (UspA-like), Rv0116c, PE20-PPE31, PspA and proteins related to toxin-antitoxin systems. Moreover, we also demonstrated that the alternative sigma factor sigma(E) confers basal resistance to vancomycin, once again underlining its importance in the physiology of the mycobacterial surface stress response

Efficient non-uniform grid for GPU-parallel shallow water equations models

A GPU parallelized finite volume scheme which solves the two dimensional Shallow Water Equations with multi-resolution is presented. Different levels of resolution are introduced by means of a novel type of grid called Block-Uniform Quadtree (BUQ), which is able to exploit the computational capability of GPUs with negligible overheads, allowing at the same time to reproduce small scale effects. The model has been tested by simulating floods propagation on a 38 km long reach of the Parma River (Italy) with a remarkable reduction of computational times and allocated memory, if compared with a Cartesian high-resolution grid

A non-uniform efficient grid type for GPU-parallel Shallow Water Equations models

A GPU-parallel numerical model for the solution of the 2D Shallow Water Equations, based on a novel type of grid called Block-Uniform Quadtree (BUQ), is presented. BUQ grids are based on a data structure which allows to exploit the computational capability of GPUs with minimum overheads, while discretizing the domain with non-uniform resolution. Different cases have been simulated in order to assess the efficiency of the BUQ grids. Theoretical and laboratory tests demonstrate that speed-ups of up to one order of magnitude can be achieved in comparison with uniform Cartesian grids. In the simulation of a hypothetical flood event induced by a levee breach in a real 83 km long river reach, with maximum resolution of 5 m, a ratio of physical to computational time of about 12 was obtained, opening scenarios of quasi real-time 2D simulations in large domains, still retaining a high resolution where necessary

Microarray analysis during adipogenesis identifies new genes altered by antiretroviral drugs

OBJECTIVE: To elucidate the pathogenesis of HAART-associated lipodystrophy, by investigating the effects of antiretroviral drugs on adipocyte differentiation and gene expression profile. DESIGN AND METHODS: Analysis of gene expression profile by DNA microarrays and quantitative RT-PCR of 3T3-L1 preadipocytes treated with the nucleoside reverse transcriptase inhibitors (NRTI) lamivudine, zidovudine, stavudine, and zalcitabine, and with the protease inhibitors (PI) indinavir, saquinavir, and lopinavir during maturation into adipocytes. RESULTS: Under standard adipogenic differentiation protocols, PI significantly inhibited adipocyte differentiation, as demonstrated by cell viability assay and Oil Red O staining and quantification, whereas NRTI had mild effects on adipogenesis. Gene expression profile analysis showed that treatment with NRTI modulated the expression of transcription factors, such as Aebp1, Pou5f1 and Phf6, which could play a key role in the determination of the adipocyte phenotype. PI also modulated gene expression toward inhibition of adipocyte differentiation, with up-regulation of the Wnt signaling gene Wnt10a and down-regulation of the expression of genes encoding master adipogenic transcription factors (e.g., C/EBPalpha and PPARgamma), oestrogen receptor beta, and adipocyte-specific markers (e.g., Adiponectin, Leptin, Mrap, Cd36, S100A8). CONCLUSIONS: This study identifies new genes modulated by PI and NRTI in differentiating adipocytes. Abnormal expression of these genes, which include master adipogenic transcription factors and genes involved in lipid metabolism and cell cycle control, could contribute to the understanding of the pathogenesis of HAART-associated lipodystrophy

Electrospun scaffolds of self-assembling peptides with poly(ethylene oxide) for bone tissue engineering

Structural, mechanical and biochemical properties have to be considered when searching for suitable extracellular matrix substitutes. Fibrous structures of synthetic or natural polymers have received increasing interest as three-dimensional scaffolds for tissue engineering applications as they can be easily produced by electrospinning with different topographical features by changing the process parameters. On the other hand, the nanobiotechnology approach suggests mimicking molecular architectures in nature through self-assembly. In particular, self-assembling peptide-based biomaterials have been successfully used as scaffolds for cell growth. In order to amalgamate these two strategies nanofibrous electrospun scaffolds of hybrid polymer were designed and obtained by mixing poly(ethylene oxide) and self-assembling peptides in aqueous solution. The results of in vitro osteoblast adhesion and proliferation assays on the electrospun scaffolds obtained using different self-assembling peptide sequences are discussed

Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak

BACKGROUND: Next generation sequencing (NGS) is being increasingly used for the detection and characterization of pathogens during outbreaks. This technology allows rapid sequencing of pathogen full genomes, useful not only for accurate genotyping and molecular epidemiology, but also for identification of drug resistance and virulence traits. METHODS: In this study, an approach based on whole genome sequencing by NGS, comparative genomics, and gene function prediction was set up and retrospectively applied for the investigation of two N. meningitidis serogroup C isolates collected from a cluster of meningococcal disease, characterized by a high fatality rate. RESULTS: According to conventional molecular typing methods, all the isolates had the same typing results and were classified as outbreak isolates within the same N. meningitidis sequence type ST-11, while full genome sequencing demonstrated subtle genetic differences between the isolates. Looking for these specific regions by means of 9 PCR and cycle sequencing assays in other 7 isolates allowed distinguishing outbreak cases from unrelated cases. Comparative genomics and gene function prediction analyses between outbreak isolates and a set of reference N. meningitidis genomes led to the identification of differences in gene content that could be relevant for pathogenesis. Most genetic changes occurred in the capsule locus and were consistent with recombination and horizontal acquisition of a set of genes involved in capsule biosynthesis. CONCLUSIONS: This study showed the added value given by whole genome sequencing by NGS over conventional sequence-based typing methods in the investigation of an outbreak. Routine application of this technology in clinical microbiology will significantly improve methods for molecular epidemiology and surveillance of infectious disease and provide a bulk of data useful to improve our understanding of pathogens biology