Computational tools for viral metagenomics and their application in clinical research

AbstractThere are 100 times more virions than eukaryotic cells in a healthy human body. The characterization of human-associated viral communities in a non-pathological state and the detection of viral pathogens in cases of infection are essential for medical care and epidemic surveillance. Viral metagenomics, the sequenced-based analysis of the complete collection of viral genomes directly isolated from an organism or an ecosystem, bypasses the “single-organism-level” point of view of clinical diagnostics and thus the need to isolate and culture the targeted organism. The first part of this review is dedicated to a presentation of past research in viral metagenomics with an emphasis on human-associated viral communities (eukaryotic viruses and bacteriophages). In the second part, we review more precisely the computational challenges posed by the analysis of viral metagenomes, and we illustrate the problem of sequences that do not have homologs in public databases and the possible approaches to characterize them

Walkability and street intersections in rural-urban fringes: a decision aiding evaluation procedure

We propose a decision-aiding evaluation procedure (i) for classifying road crossings based on their impact on walkability and, subsequently, (ii) for prioritising street improvements, in urban-rural fringe areas. In the peripheral urban-rural fringes, pedestrian mobility is usually less developed and people generally depend more on cars for their everyday chores. Partly this is inevitable given the structural features and supply of services and activities in such areas, but part is due to a frequent neglect of pedestrian mobility in planning and urban design. Measures to improve this state of affairs can include the design of more pedestrian-friendly environments offering to potential users a greater level of security, comfort and convenience when walking to their designated destinations. Our evaluation procedure combines a walkability assessment methodology with the ELECTRE TRI rating procedure, in order to assist planners and decision makers in designing physical streets to enhance the continuity, safety and quality of pedestrian paths. Improving the walking accessibility in the fringe areas of towns is a way to reduce the physical and perceptual distance which separates these contexts from the rest of the city, thus leading to a progressive integration of urban functions

Vertigo and dizziness in children: An update

Background: Vertigo and dizziness are relatively infrequent in paediatric patients, but specific data on the prevalence of these disorders are limited and influenced by various factors, including the age of the examined population. These conditions often have a significant impact on patients’ and parents’ quality of life. The aim of this paper is to investigate the prevalence of different aetiologies of vertigo in the paediatric population through a systematic review. Methods: According to PRISMA guidelines, a systematic review of the literature was performed. Medline and Embase were searched from January 2011 through to 10 September 2021. The search yielded 1094 manuscripts, which were reduced to 7 upon the application of inclusion criteria. Results: A total of 2470 paediatric patients were evaluated by the selected papers. Vestibular Migraine was the most frequently diagnosed condition, occurring alone or in association with other diseases. Overall, audio-vestibular disorders represented the second cause of vertigo, and the prevalence appears to increase according to age growth. Over the years, even though we assisted in the amelioration of diagnostic rates, partially related to an improvement in diagnostic tools, the aetiology of vertigo remains still unclear in a variable percentage of patients. Conclusion: Vertigo in children, despite being an uncommon symptom, requires a multidisciplinary approach, often involving Paediatricians, Neurologists and Otorhinolaryngologists. A comprehensive evaluation of children suffering from vertigo is crucial for establishing a successful therapy and reducing parental worries

Multi-Analytical Techniques to Define the Mineralogical and Petrophysical Characteristics and Provenance of Siliceous Lithic Findings: The Case Study of La Calvera Rock Shelter (Cantabria, Spain)

This archaeometric study aims at characterizing the archaeological finds belonging to the lithic industry from La Calvera rock shelter (Camaleño, Cantabria) and at hypothesizing the possible provenance of each material. The site, located in the mountainous area of Picos de Europa National Park (more than 1000 m a.s.l.) close to the megalithic complex of Peña Oviedo, is characterized by the presence of hearths and charcoal remains, ancient pottery, and a rich lithic assemblage composed of siliceous rocks dating back to >8000 BP and linked to the first Holocene occupations of the Cantabrian Mountains. For the study of the rock shelter’s lithic assemblage, a multi-analytical approach was used: SEM-EDS and XRD analyses were performed to define the microtextural characteristics of samples and to identify the amorphous/crystalline phases; physical and mechanical tests were conducted to define the petrophysical properties (density, porosity, imbibition and saturation indexes, mechanical strength) of the samples. Preliminary data of chemical compositions, obtained by portable XRF, are also presented. The results show that the different siliceous materials (quartzite, cherts, hyaline quartz) can be distinguished through the basic analytical techniques used here. In addition, most of the archaeological samples have mineralogical and petrographic features similar to the natural samples coming from nearby outcrops, corroborating the hypothesis of a local material supply. The presence of local sources of useful raw materials could have favoured the site’s occupation. Finally, the diverse compositional and textural feature of the analysed materials result in different mechanical properties (porosity, density, hardness, workability), so they likely had different uses and technical functions

Defluoridation of water through the transformation of octacalcium phosphate into fluorapatite

The consumption of water with fluoride concentration higher than 1.5 mg/L (WHO recommended limit) is recognized to cause serious diseases, and fluoride removal from natural contaminated waters is a health priority for more than 260 million people worldwide. The octacalcium phosphate (OCP), a mineralogical precursor of bioapatite, is here tested as a fluoride remover. A new two-step method for the synthesis of OCP is proposed: 1) synthesis of brushite from calcium carbonate and phosphoric acid; 2) subsequent hydrolysis of brushite. Fluoride removal experiments are performed in batch-mode using different initial concentrations of fluoride (from 40 to 140 mg/L) and reaction times. Most of fluoride is removed within the first 2 h of all experiments, and the drinkable limit of 1.5 mg/L is reached within a minimum of 3 h for an initial fluoride concentration of 40 mg/L. The experimental fluoride removal capacity of OCP is 25.7 mg/g, and 4 g of OCP can effectively treat 1 L of water with fluoride concentration up to 50 times higher than the drinking limit of 1.5 mg/L. XRD and chemical characterization of the solid phases, before and after the removal experiments, indicate that OCP transforms into fluorapatite (FAP) uptaking fluoride from solution

From mining wastes to mineral sources - investigating the REE-bearing occurrences in the Arburèse District (SW Sardinia)

In recent years, the search for possible sources of REE minerals in Europe involved numerous old mine areas with high volumes of mining wastes that may offer significant amounts of Critical Raw Materials (CRMs). In some cases, strong evidence of CRMs anomalous concentrations arises from environmental characterization of wastes, so that an interesting problem is that of finding their sources, i.e., the original CRMs - rich mineral phases in the residual ore. An excellent example is provided by the Arburèse district of SW Sardinia, for about 150 years a major Pb-Zn source in Italy, now an area under study for remediation of its severe environmental problems, including >10 Mt of waste deposits. The district exploited a large system (>10 km) of low-temperature polymetallic veins hosted in Lower Paleozoic siliciclastic rocks belonging to the Variscan Nappe zone, arranged in two main geometrical trends relative to the late Variscan Arbus pluton: “peripheral” and “intersecting”. Recent investigations in the Montevecchio mine area discovered high Zn (up to 2.65 wt.%) and Pb (1.23 wt.%) grades in stratified tailing materials belonging to the Sanna old processing plant. Remarkably, ICP-MS analyses on the same materials revealed total REE+ Y contents attaining about 600 ppm. XRD studies confirmed a tailing composition essentially made of gangue minerals (quartz, siderite and micas) with goethite, baryte and traces of Zn carbonates and Pb sulfates. Chondrite-normalized REE patterns are coherent with the hydrothermal character of the source: however, both the REE mineralogical host(s) in tailings and in the Montevecchio ore are still undetermined. In the search of REE-bearing phases in the ores, some relevant insights are provided by studies on the southern branch of the Arburèse system, where the veins of “peripheral” system are hosted in late Ordovician-Silurian sedimentary sequences. In this part of the district the polymetallic veins assume the character of five-elements (Ni-Co-As-Bi-Ag) veins, with a rich Ni-Co-Fe arsenide – quartz association (1) overprinted by a Zn-Pb-Cu sulfide – siderite – quartz association (2), very similar to that dominating in Montevecchio. Investigations in the Pira Inferida mine sector highlighted the presence of LREE fluorocarbonates (synchysite-Ce and bastnaesite-Ce) and phosphates (monazite) associated with rutile and apatite. LREE minerals have been detected by SEM-EDS as tiny crystals in the quartz-sericitic gangue of the Montevecchio-type (2) mineral association. The same minerals are found in millimetric aggregates in the oxide zone of the veins, sporadically reported by mineral collectors in other mine sites of the same system. Overall, these occurrences, similar to those found in other low-temperature vein systems of Sardinia (e.g., Silius vein system), appear reliable mineral REE sources for Montevecchio mine wastes; they may be therefore used as proxies for REE exploration and assessment in the district

Dissolved fluoride removal by OCP, a precursor of apatite

The consumption of water with fluoride concentration higher than 1.5 mg/L (WHO recommended limit) is recognized to cause serious diseases. Fluoride removal from natural contaminated waters is a worldwide priority for more than 200 million people. The octacalcium phosphate (OCP), a mineralogical precursor of bio-apatite, is here tested as a fluoride remover. A new two-step method for the synthesis of OCP is proposed; it consists of 1) synthesis of brushite from calcium carbonate and phosphoric acid and, 2) subsequent hydrolysis of brushite. Fluoride removal experiments were performed in batch-mode using 200 mg of OCP in 50 ml solutions with different initial concentrations of fluoride (from 40 to 140 mg/L). Most of fluoride is removed within the first two hours, whereas the WHO limit of 1.5 mg/L is reached within a minimum of 3 hours for a starting Fconcentration of 40 mg/L, and in about 12 hours for a starting F-concentration of 80 mg/L. One gram of OCP can remove up to 26 mg of fluoride. The pH of the solution after the treatment is within the range of drinking water. XRD characterization of the solid phases, before and after the experiments, indicates that OCP transforms into fluorapatite via Fremoval from solution

Multidisciplinary study of biological parameters and fatigue evolution in quay crane operators

In intermodal terminals the handling of containers and the number of accidents still depends on a wide range of human errors due to fatigue despite the automation level reached nowadays. For this reason it is very important to increase knowledge about the factors affecting the propensity of operators to make errors, increasing the chance of accidents happening. The aim of this work is to propose a novel approach to assess fatigue and performance lev els in quay crane operators as a function of physiological parameters and of the many varying boundary conditions encountered in daily work. During their work, quay crane operators have to deal with variable environmental conditions, such as task type, wind speed and direction, lighting conditions that redu ce visibility that can require an exacting level of attention. In the trial eight operators have been examined in a session lastin g four hours. All actual conditions are reproduced through a fully imme rsive quay crane simulator. The operator completes the assigned task (the same for each one) and can see through four wide monito rs a high quality virtual reality view of the simulation. Most biological parameters are acquired using different devices including a Holter ECG monitor, electromyographic monitoring the four trunk muscles most involved in the test, eye tracker and seat - body pressure interface for both seat pan and backrest. Changes in physiological parameters have been monitored during the trial and interesting correlations with performance levels and boundary conditions ha ve been f ound for each operator, in accord ance with their age and skills. The present study can form the basis for further investigations aimed at developing a cost effective, reliable and robust system for monitoring increasing fat igue and for predicting the critical conditions that may result in an acciden

Coxiella burnetii Shedding in Milk and Molecular Typing of Strains Infecting Dairy Cows in Greece

Ruminants are considered the commonest animal reservoir for human infection of Coxiella burnetii, the Q fever causative agent. Considering the recently described importance of human Q fever in Greece, we aimed at providing the first comprehensive direct evidence of C. burnetii in dairy cows in Greece, including the genetic characterization of strains. The 462 examined dairy farms represented all geographical areas of Greece. One bulk tank milk sample was collected from every farm and tested for the presence of C. burnetii. Molecular genotyping of strains, performed directly on samples, revealed the existence of two separate clades characterized by single nucleotide polymorphism (SNP) genotypes of type 1 and type 2. The two clades were clearly distinguished in multiple locus variable-number tandem repeat analysis (MLVA) by two discriminative loci: MS30 and MS28. Whereas MLVA profiles of SNP-type 2 clade were closely related to strains described in other European cattle populations, the MLVA profile observed within the SNP type 1 clade highlighted a peculiar genetic signature for Greece, related to genotypes found in sheep and goats in Europe. The shedding of C. burnetii bearing this genotype might have yet undefined human epidemiological consequences. Surveillance of the genetic distribution of C. burnetii from different sources is needed to fully understand the epidemiology of Q fever in Greece