Electrode level Monte Carlo model of radiation damage effects on astronomical CCDs

Current optical space telescopes rely upon silicon Charge Coupled Devices (CCDs) to detect and image the incoming photons. The performance of a CCD detector depends on its ability to transfer electrons through the silicon efficiently, so that the signal from every pixel may be read out through a single amplifier. This process of electron transfer is highly susceptible to the effects of solar proton damage (or non-ionizing radiation damage). This is because charged particles passing through the CCD displace silicon atoms, introducing energy levels into the semi-conductor bandgap which act as localized electron traps. The reduction in Charge Transfer Efficiency (CTE) leads to signal loss and image smearing. The European Space Agency's astrometric Gaia mission will make extensive use of CCDs to create the most complete and accurate stereoscopic map to date of the Milky Way. In the context of the Gaia mission CTE is referred to with the complementary quantity Charge Transfer Inefficiency (CTI = 1-CTE). CTI is an extremely important issue that threatens Gaia's performances. We present here a detailed Monte Carlo model which has been developed to simulate the operation of a damaged CCD at the pixel electrode level. This model implements a new approach to both the charge density distribution within a pixel and the charge capture and release probabilities, which allows the reproduction of CTI effects on a variety of measurements for a large signal level range in particular for signals of the order of a few electrons. A running version of the model as well as a brief documentation and a few examples are readily available at http://www.strw.leidenuniv.nl/~prodhomme/cemga.php as part of the CEMGA java package (CTI Effects Models for Gaia).Comment: Accepted by MNRAS on 13 February 2011. 15 pages, 7 figures and 5 table

Innate Intracellular Antiviral Responses Restrict the Amplification of Defective Virus Genomes of Parainfluenza Virus 5.

During the replication of parainfluenza virus 5 (PIV5), copyback defective virus genomes (DVGs) are erroneously produced and are packaged into "infectious" virus particles. Copyback DVGs are the primary inducers of innate intracellular responses, including the interferon (IFN) response. While DVGs can interfere with the replication of nondefective (ND) virus genomes and activate the IFN-induction cascade before ND PIV5 can block the production of IFN, we demonstrate that the converse is also true, i.e., high levels of ND virus can block the ability of DVGs to activate the IFN-induction cascade. By following the replication and amplification of DVGs in A549 cells that are deficient in a variety of innate intracellular antiviral responses, we show that DVGs induce an uncharacterized IFN-independent innate response(s) that limits their replication. High-throughput sequencing was used to characterize the molecular structure of copyback DVGs. While there appears to be no sequence-specific break or rejoining points for the generation of copyback DVGs, our findings suggest there are region, size, and/or structural preferences selected for during for their amplification.IMPORTANCE Copyback defective virus genomes (DVGs) are powerful inducers of innate immune responses both in vitro and in vivo They impact the outcome of natural infections, may help drive virus-host coevolution, and promote virus persistence. Due to their potent interfering and immunostimulatory properties, DVGs may also be used therapeutically as antivirals and vaccine adjuvants. However, little is known of the host cell restrictions which limit their amplification. We show here that the generation of copyback DVGs readily occurs during parainfluenza virus 5 (PIV5) replication, but that their subsequent amplification is restricted by the induction of innate intracellular responses. Molecular characterization of PIV5 copyback DVGs suggests that while there are no genome sequence-specific breaks or rejoin points for the generation of copyback DVGs, genome region, size, and structural preferences are selected for during their evolution and amplification

Searching for "monogenic diabetes" in dogs using a candidate gene approach

BACKGROUND: Canine diabetes is a common endocrine disorder with an estimated breed-related prevalence ranging from 0.005% to 1.5% in pet dogs. Increased prevalence in some breeds suggests that diabetes in dogs is influenced by genetic factors and similarities between canine and human diabetes phenotypes suggest that the same genes might be associated with disease susceptibility in both species. Between 1-5% of human diabetes cases result from mutations in a single gene, including maturity onset diabetes of the adult (MODY) and neonatal diabetes mellitus (NDM). It is not clear whether monogenic forms of diabetes exist within some dog breeds. Identification of forms of canine monogenic diabetes could help to resolve the heterogeneity of the condition and lead to development of breed-specific genetic tests for diabetes susceptibility. RESULTS: Seventeen dog breeds were screened for single nucleotide polymorphisms (SNPs) in eighteen genes that have been associated with human MODY/NDM. Six SNP associations were found from five genes, with one gene (ZFP57) being associated in two different breeds. CONCLUSIONS: Some of the genes that have been associated with susceptibility to MODY and NDM in humans appear to also be associated with canine diabetes, although the limited number of associations identified in this study indicates canine diabetes is a heterogeneous condition and is most likely to be a polygenic trait in most dog breeds. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/2052-6687-1-8) contains supplementary material, which is available to authorized users

The chain rule implies Tsirelson's bound: an approach from generalized mutual information

In order to analyze an information theoretical derivation of Tsirelson's bound based on information causality, we introduce a generalized mutual information (GMI), defined as the optimal coding rate of a channel with classical inputs and general probabilistic outputs. In the case where the outputs are quantum, the GMI coincides with the quantum mutual information. In general, the GMI does not necessarily satisfy the chain rule. We prove that Tsirelson's bound can be derived by imposing the chain rule on the GMI. We formulate a principle, which we call the no-supersignalling condition, which states that the assistance of nonlocal correlations does not increase the capability of classical communication. We prove that this condition is equivalent to the no-signalling condition. As a result, we show that Tsirelson's bound is implied by the nonpositivity of the quantitative difference between information causality and no-supersignalling.Comment: 23 pages, 8 figures, Added Section 2 and Appendix B, result unchanged, Added reference

Site-selection model for optimal transplantation of eelgrass Zostera marina in the northeastern US

A site-selection model for eelgrass Zostera marina L. ecosystem restoration was developed in the northeastern US to select optimal areas for transplanting eelgrass. The site-selection model synthesizes available historic and literature-based information, reference data, and simple field measurements to identify and prioritize locations for large-scale eelgrass transplantation. Model development was based on the physical and biological characteristics associated with the most successful transplant sites in a mitigation project for the New Hampshire Port Authority. The site-selection process is divided into 3 phases: (1) the first phase uses available environmental information to formulate a preliminary transplant suitability index (PTSI) for pre-screening and eliminating unsuitable sites; (2) the second phase involves field measurements of light availability and bioturbation as well as survival and growth of test transplants at priority sites identified by the PTSI; (3) a transplant suitability index (TSI) score is calculated for each site based on the PTSI and the results of field assessments. The TSI is a multiplicative index that eliminates sites which receive ratings of zero and gives high scores to those sites with the greatest potential for successful transplantation. We applied the TSI post hoc to the New Hampshire Port Project¹s eelgrass transplant sites, and subsequently the site-selection model was used in an eelgrass restoration project in New Bedford Harbor, Massachusetts. After 2 yr of transplanting, the New Bedford Harbor effort has resulted in success at 62% of the sites planted using the site-selection model

Ignition of thermally sensitive explosives between a contact surface and a shock

The dynamics of ignition between a contact surface and a shock wave is investigated using a one-step reaction model with Arrhenius kinetics. Both large activation energy asymptotics and high-resolution finite activation energy numerical simulations are employed. Emphasis is on comparing and contrasting the solutions with those of the ignition process between a piston and a shock, considered previously. The large activation energy asymptotic solutions are found to be qualitatively different from the piston driven shock case, in that thermal runaway first occurs ahead of the contact surface, and both forward and backward moving reaction waves emerge. These waves take the form of quasi-steady weak detonations that may later transition into strong detonation waves. For the finite activation energies considered in the numerical simulations, the results are qualitatively different to the asymptotic predictions in that no backward weak detonation wave forms, and there is only a weak dependence of the evolutionary events on the acoustic impedance of the contact surface. The above conclusions are relevant to gas phase equation of state models. However, when a large polytropic index more representative of condensed phase explosives is used, the large activation energy asymptotic and finite activation energy numerical results are found to be in quantitative agreement

The millipedes of Barrow Island, Western Australia (Diplopoda)

Six species of millipedes are recorded from Barrow Island, including three species of pin-cushion millipedes of the order Polyxenida, Lophoturus madecassus (Marquet and Condé, 1950) (Lophoproctidae), Unixenus mjoebergi (Verhoeff, 1924) (Polyxenidae) and Phryssonotus novaehollandiae (Silvestri, 1923) (Synxenidae), a single species of the order Spirobolida, Speleostrophus nesiotes Hoffman, 1994 (Trigoniulidae), and two species of the order Polydesmida, Boreohesperus dubitalis Car and Harvey, 2013 (Paradoxosomatidae) and one species of the family Haplodesmidae (genus and species indet.). Lophoturus madecassus is circum-tropical in distribution, Unixenus mjoebergi and Phryssonotus novaehollandiae are found also on mainland Australia, but the other three species are endemic to the island. Speleostrophus nesiotes is a highly modified troglobiotic species, currently listed as threatened by the Western Australian government. It is unclear at present whether the haplodesmid specimen is a troglobite

Microstructural and compositional analysis of strontium-doped lead zirconate titanate thin films on gold-coated silicon substrates

This article discusses the results of transmission electron microscopy (TEM)-based characterization of strontium-doped lead zirconate titanate (PSZT) thin films. The thin films were deposited by radio frequency magnetron sputtering at 300°C on gold-coated silicon substrates, which used a 15 nm titanium adhesion layer between the 150 nm thick gold film and (100) silicon. The TEM analysis was carried out using a combination of high-resolution imaging, energy filtered imaging, energy dispersive X-ray (EDX) analysis, and hollow cone illumination. At the interface between the PSZT films and gold, an amorphous silicon-rich layer (about 4 nm thick) was observed, with the film composition remaining uniform otherwise. The films were found to be polycrystalline with a columnar structure perpendicular to the substrate. Interdiffusion between the bottom metal layers and silicon was observed and was confirmed using secondary ion mass spectrometry. This occurs due to the temperature of deposition (300°C) being close to the eutectic point of gold and silicon (363°C). The diffused regions in silicon were composed primarily of gold (analyzed by EDX) and were bounded by (111) silicon planes, highlighted by the triangular diffused regions observed in the two-dimensional TEM image