All-in-one whole exome sequencing strategy with simultaneous copy number variant,single nucleotide variant and absence-of-heterozygosity analysis in fetuses with structural ultrasound anomalies: A 1-year experience

Objective

We performed a 1-year evaluation of a novel strategy of simultaneously analyzing single nucleotide variants (SNVs), copy number variants (CNVs) and copy-number-neutral Absence-of-Heterozygosity from Whole Exome Sequencing (WES) data for prenatal diagnosis of fetuses with ultrasound (US) anomalies and a non-causative QF-PCR result.

Methods

After invasive diagnostics, whole exome parent-offspring trio-sequencing with exome-wide CNV analysis was performed in pregnancies with fetal US anomalies and a non-causative QF-PCR result (WES-CNV). On request, additional SNV-analysis, restricted to (the) requested gene panel(s) only (with the option of whole exome SNV-analysis afterward) was performed simultaneously (WES-CNV/SNV) or as rapid SNV-re-analysis, following a normal CNV analysis.

Results

In total, 415 prenatal samples were included. Following a non-causative QF-PCR result, WES-CNV analysis was initially requested for 74.3% of the chorionic villus (CV) samples and 45% of the amniotic fluid (AF) samples. In case WES-CNV analysis did not reveal a causative aberration, SNV-re-analysis was requested in 41.7% of the CV samples and 17.5% of the AF samples. All initial analyses could be finished within 2 weeks after sampling. For SNV-re-analysis during pregnancy, turn-around-times (TATs) varied between one and 8 days.

Conclusion

We show a highly efficient all-in-one WES-based strategy, with short TATs, and the option of rapid SNV-re-analysis after a normal CNV result.     

Use of a Hydrogen Peroxide Nebulizer for Viral Disinfection of Emergency Ambulance and Hospital Waiting Room

Food and Environmental Virology - Disinfection of hospital facilities and ambulances is an important issue for breaking the chain of transmission of viral pathogens. Hydrogen peroxide has provided...     

Multiple Determinants of Anuran Richness and Occurrence in an Agricultural Region in South-Eastern Brazil

In agricultural landscapes, studies that identify factors driving species richness and occupancy are important because they can guide farmers to use conservation practices that minimize species loss. In this context, anurans are threatened by habitat loss because they depend on the characteristics of both local water bodies and adjacent landscapes. We used a model selection approach to evaluate the influence of local and landscape variables in determining anuran species richness and occurrence in 40 freshwater bodies in a heavily deforested region of semideciduous Atlantic Forest in southeastern Brazil. Our aim was to develop recommendations for conservation of anuran communities in rural areas. Pond hydroperiod and area were the most important variables for explaining anuran species richness and occupancy, with greatest species richness being found in water bodies with intermediate hydroperiod and area. Other important variables that reflected individual species occupancies were the number of vegetation types and pond isolation. In addition, recent studies evidenced that water bodies near forest fragments have higher anuran abundance or diversity. In conclusion, we suggest the maintenance of semi-permanent ponds, isolated from large rivers or reservoirs and near forest fragments, as an effective strategy to conserve anuran fauna in agricultural landscapes of southeastern Brazil. Brazilian government requires the maintenance of forests as legal reserve in each farm, and farmers need to maintain ponds as drinking water for cattle or crop irrigation. For this reason, the guidelines suggested in the present study can be easily adopted, without additional costs to rural productivity.     

Biodecoloration of Reactive Black 5 by the methylotrophic yeast Candida boidinii MM 4035

Azo dyes are extensively used in textile dyeing and other industries. Effluents of dying industries are specially colored and could cause severe damage to the environment. The anaerobic treatment of textile dying effluents is nowadays the preferred option, but it could generate carcinogenic aromatic amines. Recently, yeasts have become a promising alternative, combining unicellular growth with oxidative mechanisms. This work reports the characterization of the first methylotrophic yeast with dye decolorizing ability, Candida boidinii MM 4035 and some insights into its decoloration mechanism. The analysis of two selected media revealed a possible two stages mechanism of Reactive Black 5 decoloration. In glucose poor media, decoloration is incomplete and only the first stage proceeds, leading to the accumulation of a purple compound. In media with higher glucose concentrations, the yeast is able to decolorize totally an initial concentration of 200 mg/L. The entire process is co-metabolic, being largely dependent on glucose concentration but being able to proceed with several nitrogen sources. Manganese dependent peroxidase but not laccase activity could be detected during decoloration. Aromatic amines do not accumulate in culture media, supporting an oxidative decoloration mechanism of unknown ecophysiological relevance.     

An interactive simulation and visualization tool for flood analysis usable for practitioners

Developing strategies to mitigate or to adapt to the threats of floods is an important topic in the context of climate changes. Many of the world’s cities are endangered due to rising ocean levels and changing precipitation patterns. It is therefore crucial to develop analytical tools that allow us to evaluate the threats of floods and to investigate the influence of mitigation and adaptation measures, such as stronger dikes, adaptive spatial planning, and flood disaster plans. Up until the present, analytical tools have only been accessible to domain experts, as the involved simulation processes are complex and rely on computational and data-intensive models. Outputs of these analytical tools are presented to practitioners (i.e., policy analysts and political decision-makers) on maps or in graphical user interfaces. In practice, this output is only used in limited measure because practitioners often have different information requirements or do not trust the direct outcome. Nonetheless, literature indicates that a closer collaboration between domain experts and practitioners can ensure that the information requirements of practitioners are better aligned with the opportunities and limitations of analytical tools. The objective of our work is to present a step forward in the effort to make analytical tools in flood management accessible for practitioners to support this collaboration between domain experts and practitioners. Our system allows the user to interactively control the simulation process (addition of water sources or influence of rainfall), while a realistic visualization allows the user to mentally map the results onto the real world. We have developed several novel algorithms to present and interact with flood data. We explain the technologies, discuss their necessity alongside test cases, and introduce a user study to analyze the reactions of practitioners to our system. We conclude that, despite the complexity of flood simulation models and the size of the involved data sets, our system is accessible for practitioners of flood management so that they can carry out flood simulations together with domain experts in interactive work sessions. Therefore, this work has the potential to significantly change the decision-making process and may become an important asset in choosing sustainable flood mitigations and adaptation strategies.     

Injuries and risk-taking behaviours in Portuguese adolescents: Highlights from the health behaviour in school-aged children survey

Aim

Injuries in adolescence are an important public health problem and a major cause of morbidity and mortality in this age group. This study aimed to determine the behaviour profile associated to risk of injury and the differences between genders, region and ethnic origin.

Methods

A cross-sectional study design of a nationally representative sample of 1581 adolescents of the Portuguese Health Behaviour in School-Aged Children study.

Results

An occurrence of one injury-related event in the previous year was reported by 21.4% of the respondents and 5.9% referred having more than one injury-related event. Boys reported higher frequency of those events when compared to girls, and non-Portuguese subjects referred higher frequency of events. Scoring higher in violence-related behaviour and psychosomatic complaints was associated to higher chances of referring more than one injury-related event.

Conclusion

Gender, social background and behaviour profile are factors that seem to influence the risk of injuries. This information should guide those involved in the planning of injuries prevention programs in youth.     

A method for simplifying the analysis of traffic accidents injury severity on two-lane highways using Bayesian networks

Introduction

This study describes a method for reducing the number of variables frequently considered in modeling the severity of traffic accidents. The method's efficiency is assessed by constructing Bayesian networks (BN).

Method

It is based on a two stage selection process. Several variable selection algorithms, commonly used in data mining, are applied in order to select subsets of variables. BNs are built using the selected subsets and their performance is compared with the original BN (with all the variables) using five indicators. The BNs that improve the indicators’ values are further analyzed for identifying the most significant variables (accident type, age, atmospheric factors, gender, lighting, number of injured, and occupant involved). A new BN is built using these variables, where the results of the indicators indicate, in most of the cases, a statistically significant improvement with respect to the original BN.

Conclusions

It is possible to reduce the number of variables used to model traffic accidents injury severity through BNs without reducing the performance of the model.

Impact on Industry

The study provides the safety analysts a methodology that could be used to minimize the number of variables used in order to determine efficiently the injury severity of traffic accidents without reducing the performance of the model.     

Mitochondrial and microsatellite assessment of population structure of South American sea lion (<Emphasis Type="Italic">Otaria flavescens</Emphasis>) in the Southwestern Atlantic Ocean

Several major breeding areas have been defined for the South American sea lion (Otaria flavescens) along the Atlantic Ocean including the Uruguayan and Patagonian coasts. Together with a documented and severe reduction in population sizes caused by commercial hunting in the last century, these areas show opposite population trends. While Patagonian populations are recovering since hunting ceased, Uruguayan populations are declining. In this context, population genetic structure and genetic diversity were studied for the first time with both nuclear (microsatellites) and mitochondrial (control region) markers together. Alternative scenarios were found for both markers. While mitochondrial marker showed geographically structured populations, the nuclear loci showed a lack of geographical structure. These opposite patterns in genetic structure could be explained by female phylopatry and high male dispersion. The reduction in population size caused by commercial hunting did not leave a detectable footprint of bottleneck at the genetic level.     

Saharan dust episodes and pregnancy

Desert dust is one of the natural contributors to atmospheric particulate matter worldwide. Although particulate pollution has been shown to adversely affect pregnancy, the available evidence on the impact of dust episodes on pregnancy is very scarce. The aim of this study was to evaluate the impact of Saharan dust episodes on pregnancy complications (preeclampsia and bacteriuria) and outcomes (birth weight and gestational age at delivery). This study was based on a cohort of births (N = 3565) that occurred in a major university hospital in Barcelona during 2003-2005. To determine Saharan dust episodes, we developed a two-stage approach based on meteorological evidence of the presence of Saharan dust cloud over the region and unusually high levels of particulate levels on the ground while taking account of traffic sources. The associations between the number of Saharan dust episodes during whole pregnancy as well as each pregnancy trimester and pregnancy complications and outcomes were analysed. There were 152 days (out of 838 days) with Saharan dust cloud over the region from which 45 days were determined as episodic days. We did not observe any statistically significant harmful effect of Saharan dust episodes on our included pregnancy complications and outcomes. However, we observed a small but statistically significant increase in gestational age at delivery in association with the number of episodic days during the third trimester and whole pregnancy (0.8 and 0.5 days respectively). Our findings were not suggestive for any adverse effect of Saharan dust episodes on our included pregnancy complications and outcomes.     

Actinides and decay products in selected produce and bioindicators in the vicinity of a uranium plant

Cypress needles collected at the edge of the Malvési uranium facility (SW France) exhibit enhanced activities of actinides and some decay products (uranium, americium, plutonium, (230)Th, (226)Ra) compared to a remote site. These enhanced activities resulted from the release of U via smokestacks and passive release from former artificial ponds located inside the nuclear site. Enhanced activities are also observed in selected produce (wheat, lettuce, fruits) sampled from the edge of the site. However, excess actinides measured in wheat grains in 2007 are inconsistent with the activities and the uranium ratio measured in the soils. This result suggests that the studied annual crops were contaminated mainly through the short-term release of airborne actinides, and that other transfer pathways, such as, uptake through the roots or adhesion of soil particles, were negligible.