Astrophysical interpretation of the medium scale clustering in the ultra-high energy sky

We compare the clustering properties of the combined dataset of ultra-high energy cosmic rays events, reported by the AGASA, HiRes, Yakutsk and Sugar collaborations, with a catalogue of galaxies of the local universe (redshift z<~0.06). We find that the data reproduce particularly well the clustering properties of the nearby universe within z <~0.02. There is no statistically significant cross-correlation between data and structures, although intriguingly the nominal cross-correlation chance probability drops from ~50% to ~10% using the catalogue with a smaller horizon. Also, we discuss the impact on the robustness of the results of deflections in some galactic magnetic field models used in the literature. These results suggest a relevant role of magnetic fields (possibly extragalactic ones, too) and/or possibly some heavy nuclei fraction in the UHECRs. The importance of a confirmation of these hints by Auger data is emphasized.Comment: 10 pages, 7 figures; one reference adde

On leakage and seepage from geological carbon sequestration sites

Geologic carbon sequestration is one strategy for reducing the rate of increase of global atmospheric carbon dioxide (CO{sub 2} ) concentrations (IEA, 1997; Reichle, 2000). As used here, the term geologic carbon sequestration refers to the direct injection of supercritical CO{sub 2} deep into subsurface target formations. These target formations will typically be either depleted oil and gas reservoirs, or brine-filled permeable formations referred to here as brine formations. Injected CO{sub 2} will tend to be trapped by one or more of the following mechanisms: (1) permeability trapping, for example when buoyant supercritical CO{sub 2} rises until trapped by a confining caprock; (2) solubility trapping, for example when CO{sub 2} dissolves into the aqueous phase in water-saturated formations, or (3) mineralogic trapping, such as occurs when CO{sub 2} reacts to produce stable carbonate minerals. When CO{sub 2} is trapped in the subsurface by any of these mechanisms, it is effectively sequestered away from the atmosphere where it would otherwise act as a greenhouse gas. The purpose of this report is to summarize our work aimed at quantifying potential CO{sub 2} seepage due to leakage from geologic carbon sequestration sites. The approach we take is to present first the relevant properties of CO{sub 2} over the range of conditions from the deep subsurface to the vadose zone (Section 2), and then discuss conceptual models for how leakage might occur (Section 3). The discussion includes consideration of gas reservoir and natural gas storage analogs, along with some simple estimates of seepage based on assumed leakage rates. The conceptual model discussion provides the background for the modeling approach wherein we focus on simulating transport in the vadose zone, the last potential barrier to CO{sub 2} seepage (Section 4). Because of the potentially wide range of possible properties of actual future geologic sequestration sites, we carry out sensitivity analyses by means of numerical simulation and derive the trends in seepage flux and near-surface CO{sub 2} concentrations that will arise from variations in fundamental hydrogeological properties

Analysis of missense variants in the human genome reveals widespread gene-specific clustering and improves prediction of pathogenicity.

We used a machine learning approach to analyze the within-gene distribution of missense variants observed in hereditary conditions and cancer. When applied to 840 genes from the ClinVar database, this approach detected a significant non-random distribution of pathogenic and benign variants in 387 (46%) and 172 (20%) genes, respectively, revealing that variant clustering is widespread across the human exome. This clustering likely occurs as a consequence of mechanisms shaping pathogenicity at the protein level, as illustrated by the overlap of some clusters with known functional domains. We then took advantage of these findings to develop a pathogenicity predictor, MutScore, that integrates qualitative features of DNA substitutions with the new additional information derived from this positional clustering. Using a random forest approach, MutScore was able to identify pathogenic missense mutations with very high accuracy, outperforming existing predictive tools, especially for variants associated with autosomal-dominant disease and cancer. Thus, the within-gene clustering of pathogenic and benign DNA changes is an important and previously underappreciated feature of the human exome, which can be harnessed to improve the prediction of pathogenicity and disambiguation of DNA variants of uncertain significance

Implementation of an ecohealth approach for better management of leptospirosis in Kulon Progo District, Yogyakarta Special Province, Indonesia

Outbreaks of leptospirosis in Yogyakarta Special Province, Indonesia cause serious problems in humans and animals. With case fatality rates for the Kulon Progo District, Yogyakarta Special Province of 5.8% for 2011, 7.1% for 2012 and 33.3% for 2013 the PH importance has been clearly demonstrated. High mortalities in human due to renal failure can be observed whereas in animals a loss of production (i.e. due to abortions) is most prominent. The observed re-emergence of leptospirosis seems to be caused by multifactor components, and highly linked to environmental factors. However, observed cases of leptospirosis and related health impacts need to be better understood. Classical sector specific approaches have failed to be effective. Thus a more successful control and prevention requires alternative concepts such as EcoHealth to ensure transdisciplinary and participatory approaches across sectoral barriers. The objective of this study is to explore potential risk factors for leptospirosis in human and animals by using qualitative and quantitative tools for data collection. In-depth interviews (IDI) targeted on knowledge of zoonotic diseases particularly leptospirosis and behavior of people. Focus group discussions (FGD) were performed and included farmers, village officials, and stakeholders from Municipal Health Services and Livestock Services. The survey was carried out in between April to May 2013 in selected communities (N=9) of Kulon Progo with high (N=3), medium (N=3) and low cases (N=3) of human leptospirosis based on a recent serological survey. It is anticipated that the results from the FGD and IDI will provide additional information to the first phase of the project (Oct 2011 – May 2012) which focused on quantitative data collection such as prevalence surveys for leptospirosis in animals, questionnaires and spatial analysis using GIS including veterinarians, physicians, ecologists, demographist, social sciences, others stakeholders (government and public sector). Key results from both phases will be presented and synthesized. The synthesis from the qualitative and quantitative surveys will contribute to a better integrated understanding of disease emergence and the basis for a more effective addressing of public health policy concerns in order to better management the disease

Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes

Steroidal glycoalkaloids (SGAs) such as a-solanine found in solanaceous food plants—as, for example, potato—are antinutritional factors for humans. Comparative coexpression analysis between tomato and potato coupled with chemical profiling revealed an array of 10 genes that partake in SGA biosynthesis. We discovered that six of them exist as a cluster on chromosome 7, whereas an additional two are adjacent in a duplicated genomic region on chromosome 12. Following systematic functional analysis, we suggest a revised SGA biosynthetic pathway starting from cholesterol up to the tetrasaccharide moiety linked to the tomato SGA aglycone. Silencing GLYCOALKALOID METABOLISM 4 prevented accumulation of SGAs in potato tubers and tomato fruit. This may provide a means for removal of unsafe, antinutritional substances present in these widely used food crops