BioCloud Search EnGene: Surfing Biological Data on the Cloud

The massive production and spread of biomedical data around the web introduces new challenges related to identify computational approaches for providing quality search and browsing of web resources. This papers presents BioCloud Search EnGene (BSE), a cloud application that facilitates searching and integration of the many layers of biological information offered by public large-scale genomic repositories. Grounding on the concept of dataspace, BSE is built on top of a cloud platform that severely curtails issues associated with scalability and performance. Like popular online gene portals, BSE adopts a gene-centric approach: researchers can find their information of interest by means of a simple “Google-like” query interface that accepts standard gene identification as keywords. We present BSE architecture and functionality and discuss how our strategies contribute to successfully tackle big data problems in querying gene-based web resources. BSE is publically available at: http://biocloud-unica.appspot.com/

Xerostomia induced by radiotherapy: an overview of the physiopathology, clinical evidence, and management of the oral damage

Background: The irradiation of head and neck cancer (HNC) often causes damage to the salivary glands. The resulting salivary gland hypofunction and xerostomia seriously reduce the patient\u2019s quality of life. Purpose: To analyze the literature of actual management strategies for radiation-induced hypofunction and xerostomia in HNC patients. Methods: MEDLINE/PubMed and the Cochrane Library databases were electronically evaluated for articles published from January 1, 1970, to June 30, 2013. Two reviewers independently screened and included papers according to the predefined selection criteria. Results: Sixty-one articles met the inclusion criteria. The systematic review of the literature suggests that the most suitable methods for managing the clinical and pathophysiological consequences of HNC radiotherapy might be the pharmacological approach, for example, through the use of cholinergic agonists when residual secretory capacity is still present, and the use of salivary substitutes. In addition, a modified diet and the patient\u2019s motivation to enhance oral hygiene can lead to a significant improvement. Conclusion: Radiation-induced xerostomia could be considered a multifactorial disease. It could depend on the type of cancer treatment and the cumulative radiation dose to the gland tissue. A preventive approach and the correct treatment of the particular radiotherapeutic patient can help to improve the condition of xerostomia

Factors influencing the relationship between fluoride in drinking water and dental fluorosis: a ten-year systematic review and meta-analysis

The relationship between naturally fluoridated groundwater and dental fluorosis has received large attention from researchers around the world. Despite recognition that several factors influence this relationship, there is a lack of systematic studies analyzing the heterogeneity of these results. To fill such a gap, this study performs a systematic review and meta-analysis to understand which factors influence this relationship and how. Selected studies were sampled between 2007 and 2017 from Web of Science, PubMed, Google Scholar and Scopus using keywords and Boolean operators. Results of the systematic review show that dental fluorosis affects individuals of all ages, with the highest prevalence below 11, while the impact of other factors (gender, environmental conditions, diet and dental caries) was inconclusive. Meta-regression analysis, based on information collected through systematic review, indicates that both fluoride in drinking water and temperature influence dental fluorosis significantly and that these studies might be affected by publication bias. Findings show that fluoride negatively affects people's health in less developed countries. The conclusions discuss policy tools and technological innovations that could reduce fluoride levels below that of the WHO (<1.5 mg/L)

Determination of Pesticide Residues in IV Range Artichoke (Cynara cardunculus L.) and Its Industrial Wastes

Fourth-range products are those types of fresh fruit and vegetables that are ready for raw consumption or after cooking, and belong to organic or integrated cultivations. These products are subject to mild post-harvesting processing procedures (selection, sorting, husking, cutting, and washing), and are afterwards packaged in packets or closed food plates, with an average shelf life of 5–10 days. Artichokes are stripped of the leaves, stems and outer bracts, and the remaining heads are washed with acidifying solutions. The A LC-MS/MS analytical method was developed and validated following SANTE guidelines for the detection of 220 pesticides. This work evaluated the distribution of pesticide residues among the fraction of artichokes obtained during the industrial processing, and the residues of their wastes left on the field were also investigated. The results showed quantifiable residues of one herbicide (pendimethalin) and four fungicides (azoxystrobin, propyzamide, tebuconazole, and pyraclostrobin). Pendimethalin was found in all samples, with the higher values in leaves 0.046 ± 8.2 mg/kg and in field waste 0.30 ± 6.7 mg/kg. Azoxystrobin was the most concentrated in the outer bracts (0.18 ± 2.9 mg/kg). The outer bracts showed the highest number of residues. The industrial waste showed a significant decrease in the number of residues and their concentration

Bioleaching of Valuable Elements from Red Mud: A Study on the Potential of Non-Enriched Biomass

Red mud (RM) is the main residue produced by the alkaline extraction of alumina (Al2O3) from bauxite, and it contains valuable metals such as iron (Fe), aluminium (Al), titanium (Ti), magnesium (Mg), manganese (Mn), rare earth elements, etc. This research aimed to investigate the biologically induced leaching of some valuable elements from raw RM without preliminary biomass enrichment and inoculum, simultaneously reducing RM polluting potential and extracting metals for their subsequent recovery within a circular economy-based approach. In addition to the missing inoculum, such an approach is challenging since high RM alkalinity and pH, as well as the absence of any sulphides, constrain the use of the most common biohydrometallurgical techniques. Red Muds from two European locations were tested (RM-I and RM-II, respectively). Bioleaching tests were performed at different temperatures (T = 22 &amp; DEG;C and 28 &amp; DEG;C; and also 15 &amp; DEG;C for RM-II) and solid-to-liquid ratios (S/L = 2%, 5%). A sudden drop in pH from alkaline to constant neutral/acidic values was observed in almost all tests, and such results were attributed to biological activity since abiotic tests did not show any pH decrease. The best results in terms of extraction were achieved with RM-II, in particular for Al, Mg and Mn (17%, 42% and 47%, respectively). At 2% S/L, the highest temperature allowed for a better metal release, while at 5% S/L, the highest extraction of Al, Mg and Ti was observed at 22 &amp; DEG;C. As expected, iron was less available to leach at the achieved pH values, as it was mostly present as hematite in both RMs. Finally, the first microbiological characterisation of the autochthonous biomass selected during the bioleaching treatment of RM was provided

When data sharing gets close to 100%. What human paleogenetics can teach the open science movement

This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on ancient human DNA published between 1988 and 2013. The estimated sharing rate was not far from totality (97.6% ± 2.1%) and substantially higher than observed in other fields of genetic research (evolutionary, medical and forensic genetics). Both a questionnaire-based survey and the examination of Journals’ editorial policies suggest that this high sharing rate cannot be simply explained by the need to comply with stakeholders requests. Most data were made available through body text, but the use of primary databases increased in coincidence with the introduction of complete mitochondrial and next-generation sequencing methods. Our study highlights three important aspects. First, our results imply that researchers’ awareness of the importance of openness and transparency for scientific progress may complement stakeholders’ policies in achieving very high sharing rates. Second, widespread data sharing does not necessarily coincide with a prevalent use of practices which maximize data findability, accessibility, useability and preservation. A detailed look at the different ways in which data are released can be very useful to detect failures to adopt the best sharing modalities and understand how to correct them. Third and finally, the case of human paleogenetics tells us that a widespread awareness of the importance of Open Science may be important to build reliable scientific practices even in the presence of complex experimental challenges

Cooking Particulate Matter: A Systematic Review on Nanoparticle Exposure in the Indoor Cooking Environment

Background: Cooking and fuel combustion in the indoor environment are major sources of respirable suspended particulate matter (RSPM), which is an excellent carrier of potentially harmful absorbed inorganic and organic compounds. Chronic exposure to RSPM can lead to acute pulmonary illness, asthma, cardiovascular disease, and lung cancer in people involved in cooking. Despite this, questions remain about the harmfulness of different particulate matter (PM) sources generated during cooking, and the factors influencing PM physico-chemical properties. The most reliable methods for sampling and analyzing cooking emissions remain only partially understood. Objectives: This review aims to comprehensively assess the risks of PM generated during cooking, considering the main sources of PM, PM chemical composition, and strategies for PM physico-chemical analysis. We present the first systematic analysis of PM sources and chemical composition related to cooking. We highlight significant differences between studies using different experimental conditions, with a lack of a standard methodology. Methods: Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement rules and the Patient, Intervention, Comparison, and Outcome (PICO) strategy for scientific research, three different scientific databases (PubMed, Scopus, and Web of Science) were screened to find scientific articles that measure, collect, and analyze the chemical composition of nanometer-and micrometer-sized PM generated during cooking activities under different conditions. Data are summarized to assess risk, evaluating the main sources and factors influencing PM generation, their chemical composition, and how they have been collected and analyzed in changing experimental conditions. Results: From 2474 search results, there were 55 studies that met our criteria. Overall, the main variable sources of PM in cooking activities relate to the stove and fuel type. The concentration and chemical–physical properties of PM are also strongly influenced by the food and food additive type, food processing type, cooking duration, temperature, and utensils. The most important factor influencing indoor PM concentration is ventilation. The PM generated during cooking activities is composed mainly of elemental carbon (EC) and its derivatives, and the porous structure of PM with high surface-to-volume ratio is a perfect carrier of inorganic and organic matter. Conclusions: This review reveals a growing interest in PM exposure during cooking activities and highlights significant variability in the chemical–physical properties of particles, and thus variable exposure risks. Precise risk characterization improves possible preventive strategies to reduce the risk of indoor pollutant exposure. However, comprehensive PM analysis needs proper sampling and analysis methods which consider all factors influencing the physico-chemical properties of PM in an additive and synergistic way. Our analysis highlights the need for method standardization in PM environmental analyses, to ensure accuracy and allow deeper comparisons between future studies

Leaves and fruits preparations of Pistacia lentiscus L.: A review on the ethnopharmacological uses and implications in inflammation and infection

There is an increasing interest in revisiting plants for drug discovery, proving scientifically their role as remedies. The aim of this review was to give an overview of the ethnopharmacological uses of Pistacia lentiscus L. (PlL) leaves and fruits, expanding the search for the scientific discovery of their chemistry, anti-inflammatory, antioxidative and antimicrobial activities. PlL is a wild-growing shrub rich in terpenoids and polyphenols, the oil and extracts of which have been widely used against inflammation and infections, and as wound healing agents. The more recurrent components in PlL essential oil (EO) are represented by α-pinene, terpinene, caryophyllene, limonene and myrcene, with high variability in concentration depending on the Mediterranean country. The anti-inflammatory activity of the oil mainly occurs due to the inhibition of pro-inflammatory cytokines and the arachidonic acid cascade. Interestingly, the capacity against COX-2 and LOX indicates PlL EO as a dual inhibitory compound. The high content of polyphenols enriching the extracts provide explanations for the known biological properties of the plant. The protective effect against reactive oxygen species is of wide interest. In particular, their anthocyanins content greatly clarifies their antioxidative capacity. Further, the antimicrobial activity of PlL oil and extracts includes the inhibition of Staphylococcus aureus, Escherichia coli, periodontal bacteria and Candida spp. In conclusion, the relevant scientific properties indicate PlL as a nutraceutical and also as a therapeutic agent against a wide range of diseases based on inflammation and infections

A pilot study of occupational exposure to ultrafine particles during 3D printing in research laboratories

Introduction3D printing is increasingly present in research environments, and could pose health risks to users due to air pollution and particulate emissions. We evaluated the nanoparticulate emissions of two different 3D printers, utilizing either fused filament fabrication with polylactic acid, or stereolithography (SLA) with light curing resin. MethodsNanoparticulate emissions were evaluated in two different research environments, both by environmental measurements in the laboratory and by personal sampling. ResultsThe SLA printer had higher nanoparticulate emissions, with an average concentration of 4,091 parts/cm(3), versus 2,203 particles/cm(3) for the fused filament fabrication printer. The collected particulate matter had variable morphology and elemental composition with a preponderance of carbon, sulfur and oxygen, the main byproducts. DiscussionOur study implies that when considering the health risks of particulate emissions from 3D printing in research laboratories, attention should be given to the materials used and the type of 3D printer