The 8 bits 100 MS/s Pipeline ADC for the INNOTEP Project – TWEPP-09

This paper describes the Analog to Digital Converter developed for the front end electronic of the IN2P3 INNOTEP project by the “pole microelectronique Rhone-Auvergne”. (Collaboration between LPC Clermont-Ferrand and IPNL Lyon). This ADC is a 4 stages 2.5 bits per stage pipe line with open loops track and holds and amplifiers. It runs at 100MSamples/s and has 8 bits resolution. The stages used two lines, the gain line and the comparison line, with most operators running in current. The main idea of this current line is to make a first step toward an all in current structure. Currently, this ADC is designed with a 0,35μm SiGe technology

Contribution of HEP electronics techniques to the medical imaging field

présenté par P.-E. Vert, proceedings sous forme de CD Imagerie Médical

Health benefits of physical activity related to an urban riverside regeneration

The promotion of physical activity through better urban design is one pathway by which health and well-being improvements can be achieved. This study aimed to quantify health and health-related economic impacts associated with physical activity in an urban riverside park regeneration project in Barcelona, Spain. We used data from Barcelona local authorities and meta-analysis assessing physical activity and health outcomes to develop and apply the “Blue Active Tool”. We estimated park user health impacts in terms of all-cause mortality, morbidity (ischemic heart disease; ischemic stroke; type 2 diabetes; cancers of the colon and breast; and dementia), disability-adjusted life years (DALYs) and health-related economic impacts. We estimated that 5753 adult users visited the riverside park daily and performed different types of physical activity (walking for leisure or to/from work, cycling, and running). Related to the physical activity conducted on the riverside park, we estimated an annual reduction of 7.3 deaths (95% CI: 5.4; 10.2), and 6.2 cases of diseases (95% CI: 2.0; 11.6). This corresponds to 11.9 DALYs (95% CI: 3.4; 20.5) and an annual health-economic impact of 23.4 million euros (95% CI: 17.2 million; 32.8 million). The urban regeneration intervention of this riverside park provides health and health-related economic benefits to the population using the infrastructure

Informe del seguimiento científico de la acción piloto RAI/AP-30/2004: Efectividad de rejillas separadoras para la mejora de la selectividad de los artes de arrastre en Mallorca (Illes Balears)

RESUMEN: Del 28 de Octubre al 28 de Noviembre de 2005, se han realizado 21 pescas de arrastre de fondo, entre 113 y 796 m de profundidad, en caladeros del Sur de Mallorca (Islas Baleares, Mediterráneo occidental), a bordo del B/P Moralti Nou. Se ha utilizado un arte de arrastre de doble manga, con rejillas selectivas flexibles de 15 y 20 mm de separación entre barras, que ocupan ~75% de la superficie, montadas por delante del copo, con una inclinación de ~40º. Se trata de un estudio pionero en el Mediterráneo, que ha permitido evaluar, en condiciones comerciales, la eficacia de este tipo de red y estimar los rendimientos comerciales, la composición de la captura y los parámetros y curvas de selección con ambas rejillas, para las principales especies explotadas en la pesquería de arrastre en el área de estudio. Tanto la red como las rejillas no han presentado ninguna dificultad adicional a las maniobras de pesca comerciales. No se han observado diferencias en los rendimientos comerciales obtenidos con ambas rejillas, pero si en los porcentajes de retención de las principales especies, con valores mayores con rejilla de 15 mm que con rejilla de 20 mm, que dejan escapar ejemplares menores y mayores, respectivamente. La talla de primera captura estimada con rejilla de 20 mm ha sido mayor que con rejilla de 15 mm. Las rejillas separadoras no han mostrado tanta eficacia en la mejora de la selectividad de los artes de arrastre en el area de estudio como previamente había mostrado la malla cuadrada de 40 mm en el copo. Las rejillas permiten escapar ejemplares de mayor tamaño que el copo de malla cuadrada, si bien el porcentaje de ejemplares que escapan a través de la rejilla es menor, por lo que sus curvas de selección presentan rangos de selección mayores y tallas de primera captura menores que el copo de malla cuadrada. Además, se ha observado efecto de saturación en las rejillas entre 100 y 200 m de profundidad. Por todo lo anterior, las rejillas no se han mostrado tan eficaces como la malla cuadrada en el copo. Por ello, un cambio del tipo de malla en el copo (de rómbica a cuadrada de 40 mm) podría ser una mejor medida de gestión para mejorar la selectividad de los artes de arrastre en las Islas Baleares, que la introducción de rejillas.INFORME DEL SEGUIMENT CIENTÍFIC DE L’ACCIÓ PILOT RAI/AP-30/2004: EECTIVITAT DE GRAELLES SEPARADORES PER A LA MILLORA DE LA SELECTIVITAT DELS ARTS D’ARROSSEGAMENT A MALLORCA (ILLES BALEARS).- Del 28 d’Octubre al 28 de Novembre de 2005, s’han realitzat 21 pesques d’arrossegament de fons, entre 113 y 796 m de fondària, als caladors del Sud de Mallorca (Illes Balears, Mediterrània occidental), a bord del V/P Moralti Nou. S’ha utilitzat un art d’arrossegament de doble màniga, amb graelles selectives flexibles de 15 i 20 mm de separació entre barres, que ocupen ~75% de la superfície, muntades davant del cop, amb una inclinació de ~40º. Es tracta d’un estudi pioner a la Mediterrània, que ha permès avaluar, en condicions comercials, l’eficàcia d’aquest tipus de xarxa i estimar els rendiments comercials, la composició de la captura i els paràmetres i corbes de selecció d’ambdues graelles, per a les principals espècies explotades en la pesquera d’arrossegament a l’àrea d’estudi. Tant la xarxa com les graelles no han presentat capa dificultat addicional a les maniobres de pesca comercials. No s’han observat diferències en els rendiments comercials obtinguts amb les dues graelles, però sí en els percentatges de retenció de les principals espècies, amb valors majors amb graella de 15 mm que amb graella de 20 mm, que deixen escapar exemplars menors i majors, respectivament. La talla de primera captura estimada amb graella de 20 mm ha sigut major que amb graella de 15 mm. Les graelles separadores no han mostrat tanta eficàcia en la millora de la selectivitat dels arts d’arrossegament a l’àrea d’estudi com prèviament havia mostrat la malla quadrada de 40 mm en el cop. Les graelles permeten escapar exemplars de major mida que el cop de malla quadrada, tot i que el percentatge d’exemplars que escapen a través de la graella és menor, per la qual cosa les corbes de selecció presenten rangs de selecció majors i talles de primera captura menors que el cop de malla quadrada. A més a més, s’ha observat efecte de saturació en les graelles entre 100 i 200 m de profunditat. Per tot l’anterior, les graelles no s’han mostrat tan eficaces com la malla quadrada en el cop. Por això, un canvi del tipus de malla en el cop (de ròmbica a quadrada de 40 mm) podria ser una millor mesura de gestió per a millorar la selectivitat dels arts d’arrossegament a les Illes Balears que la introducció de graelles.SCIENTIFIC REPORT OF THE PILOT SURVEY RAI/AP-30/2004: EFFICIENCY OF SORTING GRIDS FOR THE IMPROVEMENT OF SELECTIVITY IN THE TRAWL FISHERY DEVELOPED OFF MAJORCA (BALEARIC ISLANDS).- From October 28th to November 28th 2005, 21 bottom trawls have been developed, between 113 and 796 m depth, on fishing grounds off South of Majorca (Balearic Islands, western Mediterranean), on board F/V Moralti Nou. A doubled extension piece trawl net has been used, with flexible sorting grids of 15 and 20 mm between bars, occupying ~75% of their surface, mounted in front of the codend, with an angle of ~40º. It is one of the first attempts in the Mediterranean Sea, which has allowed to assess, under commercial conditions, the efficiency of this kind of net and to estimate the commercial yields, the catch composition and the selection curves and parameters with both grids, for the main species exploited in the trawl fishery developed in the study area. Neither the net not the grids have showed any additional difficulty to the fishing commercial manoeuvres. No differences have been observed in the commercial yields with both grids. By contrast, differences in the percentage of retention for the main species were observed, with higher values with 15 mm than with 20 mm grid, allowing to escape smaller and larger individuals, respectively. The length of first capture estimated with 20 mm grid has been larger than with 15 mm grid. The sorting grids are not so efficient to improve trawl selectivity in the study area as the 40 mm square mesh in the codend previously showed. The sorting grids allow the escapement of larger individuals than the square mesh codend, but they have a lower percentage of escapement. For this reason, their selection curves show selection ranges wider and lengths of first capture lower than the square mesh codend. Moreover, a saturation effect of the sorting grids has been observed between 100 and 200 m depth. In conclusion, the sorting grids have not shown so effective as the square mesh in the codend. For this reason, a change of the mesh shape in the codend (from 40 mm diamond to square) could be a better management measure than the introduction of sorting grids to improve the selectivity of bottom trawls in the Balearic Islands

Microstructure and indentation mechanical properties of YSZ nanostructured coatings obtained by suspension plasma spraying

[EN] A commercial nanosuspension of yttria-stabilised zirconia (YSZ) was successfully deposited on austenitic stainless steel substrate by suspension plasma spraying technique (SPS). A SG-100 torch with internal radial injection was used for the spraying. The pneumatic system transported the feed suspension from the containers to the plasma torch. In order to study the effect of the spraying parameters, a factorial model was used to design the experiments, changing both spraying translation speed and suspension flow rate. The coating microstructure was characterised by FEG-SEM. All coatings displayed a two-zone microstructure formed by nanometre-sized particles surrounded by fully molten areas. Moreover, crystalline phases were determined by XRD and Raman spectroscopy. Mechanical properties were also determined using nanoindentation technique. Nanoindentation tests showed a bimodal distribution of the mechanical properties (hardness and Young's modulus) which is related to the two zones (molten and partially molten) present in the coatings. (C) 2012 Elsevier B.V. All rights reserved.This work has been supported by the Spanish Ministry of Science and Innovation (project MAT2009-14144-C03) and the Research Promotion Plan of the Universitat Jaume I, action 2.1 (ref. E-2011-05) and action 3.1 (ref. PREDOC/2009/10). The authors are grateful to Leszek Łatka for his help in plasma spray experiments.Carpio, P.; Rayón Encinas, E.; Pawlowski, L.; Cattini, A.; Benavente Martínez, R.; Bannier, E.; Salvador Moya, MD.... (2013). Microstructure and indentation mechanical properties of YSZ nanostructured coatings obtained by suspension plasma spraying. Surface and Coatings Technology. 220:237-243. https://doi.org/10.1016/j.surfcoat.2012.09.047S23724322

Modeling recursive RNA interference.

An important application of the RNA interference (RNAi) pathway is its use as a small RNA-based regulatory system commonly exploited to suppress expression of target genes to test their function in vivo. In several published experiments, RNAi has been used to inactivate components of the RNAi pathway itself, a procedure termed recursive RNAi in this report. The theoretical basis of recursive RNAi is unclear since the procedure could potentially be self-defeating, and in practice the effectiveness of recursive RNAi in published experiments is highly variable. A mathematical model for recursive RNAi was developed and used to investigate the range of conditions under which the procedure should be effective. The model predicts that the effectiveness of recursive RNAi is strongly dependent on the efficacy of RNAi at knocking down target gene expression. This efficacy is known to vary highly between different cell types, and comparison of the model predictions to published experimental data suggests that variation in RNAi efficacy may be the main cause of discrepancies between published recursive RNAi experiments in different organisms. The model suggests potential ways to optimize the effectiveness of recursive RNAi both for screening of RNAi components as well as for improved temporal control of gene expression in switch off-switch on experiments

A new pairwise kernel for biological network inference with support vector machines

International audienceBACKGROUND: Much recent work in bioinformatics has focused on the inference of various types of biological networks, representing gene regulation, metabolic processes, protein-protein interactions, etc. A common setting involves inferring network edges in a supervised fashion from a set of high-confidence edges, possibly characterized by multiple, heterogeneous data sets (protein sequence, gene expression, etc.). RESULTS: Here, we distinguish between two modes of inference in this setting: direct inference based upon similarities between nodes joined by an edge, and indirect inference based upon similarities between one pair of nodes and another pair of nodes. We propose a supervised approach for the direct case by translating it into a distance metric learning problem. A relaxation of the resulting convex optimization problem leads to the support vector machine (SVM) algorithm with a particular kernel for pairs, which we call the metric learning pairwise kernel. This new kernel for pairs can easily be used by most SVM implementations to solve problems of supervised classification and inference of pairwise relationships from heterogeneous data. We demonstrate, using several real biological networks and genomic datasets, that this approach often improves upon the state-of-the-art SVM for indirect inference with another pairwise kernel, and that the combination of both kernels always improves upon each individual kernel. CONCLUSION: The metric learning pairwise kernel is a new formulation to infer pairwise relationships with SVM, which provides state-of-the-art results for the inference of several biological networks from heterogeneous genomic data

Improved residue contact prediction using support vector machines and a large feature set

BACKGROUND: Predicting protein residue-residue contacts is an important 2D prediction task. It is useful for ab initio structure prediction and understanding protein folding. In spite of steady progress over the past decade, contact prediction remains still largely unsolved. RESULTS: Here we develop a new contact map predictor (SVMcon) that uses support vector machines to predict medium- and long-range contacts. SVMcon integrates profiles, secondary structure, relative solvent accessibility, contact potentials, and other useful features. On the same test data set, SVMcon's accuracy is 4% higher than the latest version of the CMAPpro contact map predictor. SVMcon recently participated in the seventh edition of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7) experiment and was evaluated along with seven other contact map predictors. SVMcon was ranked as one of the top predictors, yielding the second best coverage and accuracy for contacts with sequence separation >= 12 on 13 de novo domains. CONCLUSION: We describe SVMcon, a new contact map predictor that uses SVMs and a large set of informative features. SVMcon yields good performance on medium- to long-range contact predictions and can be modularly incorporated into a structure prediction pipeline

Considerations for management strategy evaluation for small pelagic fishes

Management strategy evaluation (MSE) is the state-of-the-art approach for testing and comparing management strategies in a way that accounts for multiple sources of uncertainty (e.g. monitoring, estimation, and implementation). Management strategy evaluation can help identify management strategies that are robust to uncertainty about the life history of the target species and its relationship to other species in the food web. Small pelagic fish (e.g. anchovy, herring and sardine) fulfil an important ecological role in marine food webs and present challenges to the use of MSE and other simulation-based evaluation approaches. This is due to considerable stochastic variation in their ecology and life history, which leads to substantial observation and process uncertainty. Here, we summarize the current state of MSE for small pelagic fishes worldwide. We leverage expert input from ecologists and modellers to draw attention to sources of process and observation uncertainty for small pelagic species, providing examples from geographical regions where these species are ecologically, economically and culturally important. Temporal variation in recruitment and other life-history rates, spatial structure and movement, and species interactions are key considerations for small pelagic fishes. We discuss tools for building these into the MSE process, with examples from existing fisheries. We argue that model complexity should be informed by management priorities and whether ecosystem information will be used to generate dynamics or to inform reference points. We recommend that our list of considerations be used in the initial phases of the MSE process for small pelagic fishes or to build complexity on existing single-species models.publishedVersio

The impact of cyclin-dependent kinase 5 depletion on poly(ADP-ribose) polymerase activity and responses to radiation

Cyclin-dependent kinase 5 (Cdk5) has been identified as a determinant of sensitivity to poly(ADP-ribose) polymerase (PARP) inhibitors. Here, the consequences of its depletion on cell survival, PARP activity, the recruitment of base excision repair (BER) proteins to DNA damage sites, and overall DNA single-strand break (SSB) repair were investigated using isogenic HeLa stably depleted (KD) and Control cell lines. Synthetic lethality achieved by disrupting PARP activity in Cdk5-deficient cells was confirmed, and the Cdk5KD cells were also found to be sensitive to the killing effects of ionizing radiation (IR) but not methyl methanesulfonate or neocarzinostatin. The recruitment profiles of GFP-PARP-1 and XRCC1-YFP to sites of micro-irradiated Cdk5KD cells were slower and reached lower maximum values, while the profile of GFP-PCNA recruitment was faster and attained higher maximum values compared to Control cells. Higher basal, IR, and hydrogen peroxide-induced polymer levels were observed in Cdk5KD compared to Control cells. Recruitment of GFP-PARP-1 in which serines 782, 785, and 786, potential Cdk5 phosphorylation targets, were mutated to alanines in micro-irradiated Control cells was also reduced. We hypothesize that Cdk5-dependent PARP-1 phosphorylation on one or more of these serines results in an attenuation of its ribosylating activity facilitating persistence at DNA damage sites. Despite these deficiencies, Cdk5KD cells are able to effectively repair SSBs probably via the long patch BER pathway, suggesting that the enhanced radiation sensitivity of Cdk5KD cells is due to a role of Cdk5 in other pathways or the altered polymer levels