Controlled access under review : improving the governance of genomic data access

In parallel with massive genomic data production, data sharing practices have rapidly expanded over the last decade. To ensure authorized access to data, access review by data access committees (DACs) has been utilized as one potential solution. Here we discuss core elements to be integrated into the fabric of access review by both established and emerging DACs in order to foster fair, efficient, and responsible access to datasets. We particularly highlight the fact that the access review process could be adversely influenced by the potential conflicts of interest of data producers, particularly when they are directly involved in DACs management. Therefore, in structuring DACs and access procedures, possible data withholding by data producers should receive thorough attention

Estimating the potential impact of canine distemper virus on the Amur tiger population (Panthera tigris altaica) in Russia

Lethal infections with canine distemper virus (CDV) have recently been diagnosed in Amur tigers (Panthera tigris altaica), but long-term implications for the population are unknown. This study evaluates the potential impact of CDV on a key tiger population in Sikhote-Alin Biosphere Zapovednik (SABZ), and assesses how CDV might influence the extinction potential of other tiger populations of varying sizes. An individual-based stochastic, SIRD (susceptible-infected-recovered/dead) model was used to simulate infection through predation of infected domestic dogs, and/or wild carnivores, and direct tiger-to-tiger transmission. CDV prevalence and effective contact based on published and observed data was used to define plausible low- and high-risk infection scenarios. CDV infection increased the 50-year extinction probability of tigers in SABZ by 6.3% to 55.8% compared to a control population, depending on risk scenario. The most significant factors influencing model outcome were virus prevalence in the reservoir population(s) and its effective contact rate with tigers. Adjustment of the mortality rate had a proportional impact, while inclusion of epizootic infection waves had negligible additional impact. Small populations were found to be disproportionately vulnerable to extinction through CDV infection. The 50-year extinction risk in populations consisting of 25 individuals was 1.65 times greater when CDV was present than that of control populations. The effects of density dependence do not protect an endangered population from the impacts of a multi-host pathogen, such as CDV, where they coexist with an abundant reservoir presenting a persistent threat. Awareness of CDV is a critical component of a successful tiger conservation management policy

Heat flux identification using reduced model and the adjoint method. Application to a brake disk rotating at variable velocity

International audienceIn previous works [1], reduced models have been used for solving inverse problems, characterized by a complex geometry requiring a large number of nodes and / or an objective of online identification. The treated application was a brake disc in two-dimensional representation, in rotation at variable speed. The dissipated heat flux at the pad-disk interface had been identified by Beck's method. We present here a similar application using the adjoint method. The modal reduction is done by using special bases (called branch bases) that offer the advantage of dealing with nonlinear problems and / or unsteady parameters. Adjoint method provides particularly accurate results in this configuration

Population Estimate for the Bluenose-East Caribou Herd Using Post-calving Photography

Genetic and spatial analyses suggest that what was previously described as the Bluenose herd of barren-ground caribou (Rangifer tarandus groenlandicus) comprises three separate populations. Of these, the Bluenose-East caribou herd (BECH) has received little coverage in past surveys. Existing estimates of abundance suggested that current harvest rates of Bluenose-East caribou (~5000 animals/year) might be excessive. We used post-calving photography in June-July 2000 to estimate the size of the BECH. A maximum of 33 radio-collared caribou were available for location in June 2000. We located 30 of these caribou and photographed distinct groups containing 23 collared individuals. Excluding caribou assumed to belong to the neighboring Bluenose-West herd, we photographed a minimum of 84 412 adult and 4193 calf caribou. Using a simple mark-recapture model to account for caribou associated with collared individuals not photographed, we calculated an estimate of 104 000 ± 22 100 (95% CI 84 412 - 126 100) non-calf caribou. A recently published stochastic model produced a considerably higher and more variable estimate of 208 700 (95% CI 112 600 - 474 700). In March 2001, we deployed seven more radio collars in anticipation of repeating the census in 2001, but poor weather conditions precluded the formation of large aggregations. Present densities of Bluenose-East caribou seem high, and we recommend regular monitoring of body condition to assess the potential for a forage-induced population crash.Des analyses génétiques et spatiales suggèrent que ce que l'on a décrit précédemment comme le troupeau de caribous des toundras Bluenose (Rangifer tarandus groenlandicus) est en fait composé de trois populations distinctes. De ces trois hardes, le troupeau de caribous Bluenose de l'Est (TCBE) n'a pas reçu beaucoup d'attention au cours des relevés antérieurs. Les estimations d'abondance qui existent ont suggéré que le taux de prélèvement actuel de ce caribou (~ 5000 animaux/an) pourrait être excessif. On a eu recours à des clichés pris immédiatement après la mise bas en juin-juillet 2000 pour évaluer la taille du TCBE. En juin 2000, un maximum de 33 caribous munis de colliers émetteurs étaient disponibles pour la localisation. On en a repéré 30 et on a photographié des groupes distincts contenant 23 individus équipés de colliers émetteurs. Si l'on exclut les caribous qui feraient partie de la harde voisine Bluenose de l'Ouest, on a photographié un minimum de 84 412 adultes et 4193 veaux. En utilisant un simple modèle de marquage-recapture pour tenir compte des caribous reliés aux individus munis de colliers émetteurs non photographiés, on en arrive à une estimation du nombre de caribous excluant les veaux de 104 000 ± 22 100 (intervalle de confiance de 95 %: 84 412 - 126 000). Un modèle probabiliste publié récemment a donné une estimation nettement plus élevée et plus variable de 208 700 (intervalle de confiance de 95 %: 112 600 - 474 700). En mars 2001, on a eu recours à sept colliers émetteurs supplémentaires en prévision d'une reprise du recensement en 2001, mais le mauvais temps a empêché la formation de grands regroupements. Les densités actuelles du caribou Bluenose de l'Est semblent élevées, et on recommande une surveillance continue de l'état corporel afin d'évaluer le potentiel d'un effondrement de la population dû à un manque de fourrage

Damage-free single-mode transmission of deep-UV light in hollow-core PCF

Transmission of UV light with high beam quality and pointing stability is desirable for many experiments in atomic, molecular and optical physics. In particular, laser cooling and coherent manipulation of trapped ions with transitions in the UV require stable, single-mode light delivery. Transmitting even ~2 mW CW light at 280 nm through silica solid-core fibers has previously been found to cause transmission degradation after just a few hours due to optical damage. We show that photonic crystal fiber of the kagom\'e type can be used for effectively single-mode transmission with acceptable loss and bending sensitivity. No transmission degradation was observed even after >100 hours of operation with 15 mW CW input power. In addition it is shown that implementation of the fiber in a trapped ion experiment significantly increases the coherence times of the internal state transfer due to an increase in beam pointing stability

Energy and position resolution of a CdZnTe gamma-ray detector with orthogonal coplanar anodes

We report on the simulation, construction and performance of prototype CZT imaging detectors employing orthogonal coplanar anodes. These detectors employ a novel electrode geometry with non-collecting anode strips in 1D and collecting anode pixels, interconnected in rows, in the orthogonal dimensions. These detectors retain the spectroscopic and detection efficiency advantages of single carried charge sensing devices as well as the principal advantage of conventional strip detectors with orthogonal anode and cathode strips, i.e. an N X N array of imagin pixels are realized with only 2N electronic channels. Charge signals induced on the various electrodes of a prototype detector with 8 X 8 unit cells are in good agreement with the simulations. The position resolution is about 1 mm in the direction perpendicular to the pixel lines while it is of the order of 100 micrometers in the other direction. Energy resolutions of 0.9 percent at 662 keV, 2.6 percent at 122 keV and 5.7 percent at 60 keV have been obtained at room temperature