Coupling a distributed grid based hydrological model and MM5 meteorological model for flooding alert mapping

International audienceThe increased number of extreme rainfall events seems to be one of the common feature of climate change signal all over the world (Easterlin et al., 2000; Meehl et al., 2000). In the last few years a large number of floods caused by extreme meteorological events has been observed over the river basins of Mediterranean area and they mainly affected small basins (few hundreds until few thousands of square kilometres of drainage area) . A strategic goal of applied meteorology is now to try to predict with high spatial resolution the segments of drainage network where floods may occur. A possible way to reach this aim is the coupling of meteorological mesoscale model with high resolution hydrological model. In this work few case studies of observed floods in the Italian Mediterranean area will be presented. It is shown how a distributed hydrological model, using the precipitation fields predicted by MM5 meteorological model, is able to highlight the area where the major floods may occur

ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest.

Next-generation sequencing technology (NGS) enables the discovery of nearly all genetic variants present in a genome. A subset of these variants, however, may have poor sequencing quality due to limitations in NGS or variant callers. In genetic studies that analyze a large number of sequenced individuals, it is critical to detect and remove those variants with poor quality as they may cause spurious findings. In this paper, we present ForestQC, a statistical tool for performing quality control on variants identified from NGS data by combining a traditional filtering approach and a machine learning approach. Our software uses the information on sequencing quality, such as sequencing depth, genotyping quality, and GC contents, to predict whether a particular variant is likely to be false-positive. To evaluate ForestQC, we applied it to two whole-genome sequencing datasets where one dataset consists of related individuals from families while the other consists of unrelated individuals. Results indicate that ForestQC outperforms widely used methods for performing quality control on variants such as VQSR of GATK by considerably improving the quality of variants to be included in the analysis. ForestQC is also very efficient, and hence can be applied to large sequencing datasets. We conclude that combining a machine learning algorithm trained with sequencing quality information and the filtering approach is a practical approach to perform quality control on genetic variants from sequencing data

Thermally driven circulation in a region of complex topography: comparison of wind-profiling radar measurements and MM5 numerical predictions

The diurnal variation of regional wind patterns in the complex terrain of Central Italy was investigated for summer fair-weather conditions and winter time periods using a radar wind profiler. The profiler is located on a site where interaction between the complex topography and land-surface produces a variety of thermally and dynamically driven wind systems. The observational data set, collected for a period of one year, was used first to describe the diurnal evolution of thermal driven winds, second to validate the Mesoscale Model 5 (MM5) that is a three-dimensional numerical model. This type of analysis was focused on the near-surface wind observation, since thermally driven winds occur in the lower atmosphere. According to the valley wind theory expectations, the site – located on the left sidewall of the valley (looking up valley) – experiences a clockwise turning with time. Same characteristics in the behavior were established in both the experimental and numerical results. <P style="line-height: 20px;"> Because the thermally driven flows can have some depth and may be influenced mainly by model errors, as a third step the analysis focuses on a subset of cases to explore four different MM5 Planetary Boundary Layer (PBL) parameterizations. The reason is to test how the results are sensitive to the selected PBL parameterization, and to identify the better parameterization if it is possible. For this purpose we analysed the MM5 output for the whole PBL levels. The chosen PBL parameterizations are: 1) Gayno-Seaman; 2) Medium-Range Forecast; 3) Mellor-Yamada scheme as used in the ETA model; and 4) Blackadar

Immunosuppressive effect and global dysregulation of blood transcriptome in response to psychosocial stress in vervet monkeys (Chlorocebus sabaeus).

Psychosocial stressors - life events that challenge social support and relationships - represent powerful risk factors for human disease; included amongst these events are relocation, isolation and displacement. To evaluate the impact of a controlled psychosocial stressor on physiology and underlying molecular pathways, we longitudinally studied the influence of a 28-day period of quarantine on biomarkers of immune signalling, microbial translocation, glycaemic health and blood transcriptome in the wild-born vervet monkey. This event caused a coordinated, mostly transient, reduction of circulating levels of nine immune signalling molecules. These were paralleled by a massive dysregulation of blood transcriptome, including genes implicated in chronic pathologies and immune functions. Immune and inflammatory functions were enriched among the genes downregulated in response to stress. An upregulation of genes involved in blood coagulation, platelet activation was characteristic of the rapid response to stress induction. Stress also decreased neutrophils and increased CD4 + T cell proportions in blood. This model of psychosocial stress, characterised by an immune dysregulation at the transcriptomic, molecular and cellular levels, creates opportunities to uncover the underlying mechanisms of stress-related diseases with an immune component, including cardiovascular diseases and susceptibility to infections

Retinal nerve fibre layer thinning is associated with drug resistance in epilepsy.

Retinal nerve fibre layer (RNFL) thickness is related to the axonal anterior visual pathway and is considered a marker of overall white matter 'integrity'. We hypothesised that RNFL changes would occur in people with epilepsy, independently of vigabatrin exposure, and be related to clinical characteristics of epilepsy

Non-linear stability in photogravitational non-planar restricted three body problem with oblate smaller primary

We have discussed non-linear stability in photogravitational non-planar restricted three body problem with oblate smaller primary. By photogravitational we mean that both primaries are radiating. We normalised the Hamiltonian using Lie transform as in Coppola and Rand (1989). We transformed the system into Birkhoff's normal form. Lie transforms reduce the system to an equivalent simpler system which is immediately solvable. Applying Arnold's theorem, we have found non-linear stability criteria. We conclude that $L_6$ is stable. We plotted graphs for $(\omega_1, D_2).$ They are rectangular hyperbola.Comment: Accepted for publication in Astrophysics & Space Scienc

Simulating the connections of ENSO and the rainfall regime of East Africa and the upper Blue Nile region using a climate model of the Tropics

We simulate the observed statistical relationship between ENSO and the rainfall regime of the upper Blue Nile using the tropical-band version of the regional climate model RegCM4 (or Reg-TB). An ensemble of nine simulations for the 28-year period 1982–2009 is completed to investigate the role of ENSO in modulating rainfall over the upper Blue Nile catchment. Reg-TB shows a good skill in simulating the climatology of temperature, outgoing long-wave radiation patterns as well as related atmospheric circulation features during the summer season (i.e. the rainy season over the Blue Nile catchment). The model also succeeds in reproducing the observed negative correlation between Pacific SST and rainfall anomalies over the Blue Nile catchment, and in particular the association of droughts over the Blue Nile with El Niño events that start in April–June. We thus propose that observations and model forecasts of Pacific SST during this season could be used in seasonal forecasting of summer rainfall over the upper Blue Nile region.Abdus Salam International Centre for Theoretical Physics. Earth System PhysicsAbdus Salam International Centre for Theoretical Physics. Sandwich Training Educational ProgrammeEuropean Union (DEWFORA Project

The Carina Project IX: on Hydrogen and helium burning variables

We present new multi-band (UBVI) time-series data of helium burning variables in the Carina dwarf spheroidal galaxy. The current sample includes 92 RR Lyrae-six of them are new identifications-and 20 Anomalous Cepheids, one of which is new identification. The analysis of the Bailey diagram shows that the luminosity amplitude of the first overtone component in double-mode variables is located along the long-period tail of regular first overtone variables, while the fundamental component is located along the short-period tale of regular fundamental variables. This evidence further supports the transitional nature of these objects. Moreover, the distribution of Carina double-mode variables in the Petersen diagram (P_1/P_0 vs P_0) is similar to metal-poor globulars (M15, M68), to the dwarf spheroidal Draco and to the Galactic Halo. This suggests that the Carina old stellar population is metal-poor and affected by a small spread in metallicity. We use trigonometric parallaxes for five field RR Lyrae stars to provide an independent estimate of the Carina distance using the observed reddening free Period--Wesenheit [PW, (BV)] relation. Theory and observations indicate that this diagnostic is independent of metallicity. We found a true distance modulus of \mu=20.01\pm0.02 (standard error of the mean) \pm0.05 (standard deviation) mag. We also provided independent estimates of the Carina true distance modulus using four predicted PW relations (BV, BI, VI, BVI) and we found: \mu=(20.08\pm0.007\pm0.07) mag, \mu=(20.06\pm0.006\pm0.06) mag, \mu=(20.07\pm0.008\pm0.08) mag and \mu=(20.06\pm0.006\pm0.06) mag. Finally, we identified more than 100 new SX Phoenicis stars that together with those already known in the literature (340) make Carina a fundamental laboratory to constrain the evolutionary and pulsation properties of these transitional variables.Comment: 44 pages, 13 tables, 13 figures, Accepted for publication in Ap

Current preventive policies and practices against Vaccine-Preventable Diseases and tuberculosis targeted for workers from hospitals of the Sardinia Region, Italy

Introduction. Health care Workers are exposed to infectious diseases more than the general population. Many of these infections are preventable by vaccination. The objective in this study is to investigate whether, how, and which vaccination underwent Sardinia Health Care Workers (HCWs) and the variability of policies in different Hospital Health Managements of the whole region. Methods. In March 2013, we enrolled the Hospital Health Management of all the 32 Sardinia hospitals. We investigate on immunity against vaccine-preventable diseases and education campaigns about recommended vaccinations for HCWs. Flu, hepatitis B, measles-mumps-rubella, varicella and tuberculosis were the objects of our research. Results. In most of the hospitals, influenza vaccination coverage among HCWs is less than 6%. Hepatitis B antibody assay was performed in all the respondent hospitals but only 14 had available data as collected electronically. Most of the hospitals did not perform serological tests for the evaluation of antibodies against Varicella, Measles, Mumps and Rubella in their HCWs. In 30 hospitals Mantoux test was replaced or integrated by "in vitro" test for health surveillance protocols. Conclusions. This method produced a large amount of data in small time and at a low cost. Sending back data to respective Hospital Health Management (HHM) we took a step towards greater awareness of the issue of biological risks of HCWs and of vaccine coverage