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

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

High prevalence of closely-related Acinetobacter baumannii in pets according to a multicentre study in veterinary clinics, Reunion Island

Our objective was to study the carriage of Acinetobacter baumannii (AB) in pets in Reunion Island (RI), a French territory in Indian Ocean. Overall, 138 pets were sampled (rectum, mouth, wounds if applicable) in 9 veterinary clinics (VC). The prevalence of AB carriage was 6.5% (95%CI; 2.4, 10.6) and 9 carriers were identified from 4 VC. Hospitalization in a VC and antimicrobial treatment administered within the 15 preceding days were significantly associated with AB carriage (P<0.01 and P<0.05, respectively). Despite the VC in which animals have been sampled were located all around RI, most isolates (8/9) were closely-related (>90% similarity by pulsed-field gel electrophoresis). Additional studies are needed to improve the understanding about interactions between the different reservoirs of AB in RI

Curvature tensors on distorted Killing horizons and their algebraic classification

We consider generic static spacetimes with Killing horizons and study properties of curvature tensors in the horizon limit. It is determined that the Weyl, Ricci, Riemann and Einstein tensors are algebraically special and mutually aligned on the horizon. It is also pointed out that results obtained in the tetrad adjusted to a static observer in general differ from those obtained in a free-falling frame. This is connected to the fact that a static observer becomes null on the horizon. It is also shown that finiteness of the Kretschmann scalar on the horizon is compatible with the divergence of the Weyl component $\Psi_{3}$ or $\Psi_{4}$ in the freely falling frame. Furthermore finiteness of $\Psi_{4}$ is compatible with divergence of curvature invariants constructed from second derivatives of the Riemann tensor. We call the objects with finite Krestschmann scalar but infinite $\Psi_{4}$ ``truly naked black holes''. In the (ultra)extremal versions of these objects the structure of the Einstein tensor on the horizon changes due to extra terms as compared to the usual horizons, the null energy condition being violated at some portions of the horizon surface. The demand to rule out such divergencies leads to the constancy of the factor that governs the leading term in the asymptotics of the lapse function and in this sense represents a formal analog of the zeroth law of mechanics of non-extremal black holes. In doing so, all extra terms in the Einstein tensor automatically vanish.Comment: 21 pages, To appear in Class. Quant. Gra

Survival and ice nucleation activity of bacteria as aerosols in a cloud simulation chamber

The residence time of bacterial cells in the atmosphere is predictable by numerical models. However, estimations of their aerial dispersion as living entities are limited by a lack of information concerning survival rates and behavior in relation to atmospheric water. Here we investigate the viability and ice nucleation (IN) activity of typical atmospheric ice nucleation active bacteria (Pseudomonas syringae and P. fluorescens) when airborne in a cloud simulation chamber (AIDA, Karlsruhe, Germany). Cell suspensions were sprayed into the chamber and aerosol samples were collected by impingement at designated times over a total duration of up to 18 h, and at some occasions after dissipation of a cloud formed by depressurization. Aerosol concentration was monitored simultaneously by online instruments. The cultivability of airborne cells decreased exponentially over time with a half-life time of 250 ±30 min (about 3.5 to 4.5 h). In contrast, IN activity remained unchanged for several hours after aerosolization, demonstrating that IN activity was maintained after cell death. Interestingly, the relative abundance of IN active cells still airborne in the chamber was strongly decreased after cloud formation and dissipation. This illustrates the preferential precipitation of IN active cells by wet processes. Our results indicate that from 10⁶ cells aerosolized from a surface, one would survive the average duration of its atmospheric journey estimated at 3.4 days. Statistically, this corresponds to the emission of 1 cell that achieves dissemination every ~33 min m¯² of cultivated crops fields, a strong source of airborne bacteria. Based on the observed survival rates, depending on wind speed, the trajectory endpoint could be situated several hundreds to thousands of kilometers from the emission source. These results should improve the representation of the aerial dissemination of bacteria in numeric models