Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy.

All coronaviruses are characterized by spike glycoproteins whose S1 subunits contain the receptor binding domain (RBD). The RBD anchors the virus to the host cellular membrane to regulate the virus transmissibility and infectious process. Although the protein/receptor interaction mainly depends on the spike's conformation, particularly on its S1 unit, their secondary structures are poorly known. In this paper, the S1 conformation was investigated for MERS-CoV, SARS-CoV, and SARS-CoV-2 at serological pH by measuring their Amide I infrared absorption bands. The SARS-CoV-2 S1 secondary structure revealed a strong difference compared to those of MERS-CoV and SARS-CoV, with a significant presence of extended ß-sheets. Furthermore, the conformation of the SARS-CoV-2 S1 showed a significant change by moving from serological pH to mild acidic and alkaline pH conditions. Both results suggest the capability of infrared spectroscopy to follow the secondary structure adaptation of the SARS-CoV-2 S1 to different environments.

Terahertz continuous wave spectroscopy: a portable advanced method for atmospheric gas sensing.

Motivated by the increasing demand to monitor the air-quality, our study proved the feasibility of a new compact and portable experimental approach based on Terahertz (THz) continuous wave high resolution spectroscopy, to detect the presence of the air's contaminants as greenhouse gases (GHG) and volatile organic compounds (VOCs). In this specific work, we first characterized, determining their molar absorption coefficient in the spectral region (0.06-1.2) THz, the pure optical response of the vapor of five VOCs: methanol, ethanol, isopropanol, 1-butanol and 2-butanol. In particular, 1-butanol and 2-butanol are characterized for the first time in literature at THz frequencies. Then we studied the optical response of their mixtures achieved with ambient air and ethanol. The results show that it is possible for a differentiation of single components by describing their spectral absorption in terms of the linear combination of pure compounds absorption. This proof of concept for this apparatus study and set-up paves the way to the use of THz Continuous wave high resolution spectroscopy for the environmental tracking of air pollutants.

High Sensitivity Monitoring of VOCs in Air through FTIR Spectroscopy Using a Multipass Gas Cell Setup.

Human exposure to Volatile Organic Compounds (VOCs) and their presence in indoor and working environments is recognized as a serious health risk, causing impairments of varying severities. Different detecting systems able to monitor VOCs are available in the market; however, they have significant limitations for both sensitivity and chemical discrimination capability. During the last years we studied systematically the use of Fourier Transform Infrared (FTIR) spectroscopy as an alternative, powerful tool for quantifying VOCs in air. We calibrated the method for a set of compounds (styrene, acetone, ethanol and isopropanol) by using both laboratory and portable infrared spectrometers. The aim was to develop a new, and highly sensitive sensor system for VOCs monitoring. In this paper, we improved the setup performance, testing the feasibility of using a multipass cell with the aim of extending the sensitivity of our system down to the part per million (ppm) level. Considering that multipass cells are now also available for portable instruments, this study opens the road for the design of new high-resolution devices for environmental monitoring.

Characterization and assessment of the potential toxicity/pathogenicity of fibrous glaucophane.

In California, the metamorphic blueschist occurrences within the Franciscan Complex are commonly composed of glaucophane, which can be found with a fibrous habit. Fibrous glaucophane's potential toxicity/pathogenicity has never been determined and it has not been considered by the International Agency for Research on Cancer (IARC) as a potential carcinogen to date. Notwithstanding, outcrops hosting fibrous glaucophane are being excavated today in California for building/construction purposes (see for example the Calaveras Dam Replacement Project - CDRP). Dust generated by these excavation activities may expose workforces and the general population to this potential natural hazard. In this work, the potential toxicity/pathogenicity of fibrous glaucophane has been determined using the fibre potential toxicity index (FPTI). This model has been applied to a representative glaucophane-rich sample collected at San Anselmo, Marin County (CA, USA), characterized using a suite of experimental techniques to determine morphometric, crystal-chemical parameters, surface reactivity, biodurability and related parameters. With respect to the asbestos minerals, the FPTI of fibrous glaucophane is remarkably higher than that of chrysotile, and comparable to that of tremolite, thus supporting the application of the precautionary approach when excavating fibrous glaucophane-rich blueschist rocks. Because fibrous glaucophane can be considered a potential health hazard, just like amphibole asbestos, it should be taken into consideration in the standard procedures for the identification and assessment of minerals fibres in soil and air samples.

Beryllium natural background concentration and mobility: a reappraisal examining the case of high Be-bearing pyroclastic rocks.

Beryllium is widely distributed in soils at low levels, but it can also occur naturally in higher concentrations in a variety of materials exploited for many industrial applications. Beryllium is also one of the most toxic natural elements and is known to be a human carcinogen. A concise account of the literature data on baseline concentrations of Be in soils illustrates the possibility of worldwide presence of areas with a high natural background concentration of Be (up to 300 mg/kg), the crustal abundance of which is generally estimated to be in the range 2-6 mg/kg. Nevertheless, the number of available data is rather limited in comparison with those about other toxic elements such as Pb, Cd and Cr. This has probably caused the choice of low values of concentration level as the reference for the definition of soil contamination: these values are not always realistic and are not applicable to large areas. As a case study, we report and analyse a diffuse, unusually high (up to 80 mg/kg, average approximately 20 mg/kg), natural occurrence of beryllium in loose and poorly consolidated pyroclastic layers related to the Pleistocene activity of the Vico volcano. Additionally, the analysis of Be leachability has been carried out, providing evidence of a not negligible mobility in contrast with the scarce data presented in the literature that usually indicate beryllium as an element with low mobility in oxidising surface environmental conditions. This research marks the beginning of a possible reappraisal of beryllium geochemical behaviour and background levels, providing more realistic reference values for risk assessment and land management.

Deep learning for asbestos counting.

The PCM (phase contrast microscopy) method for asbestos counting needs special sample treatments, hence it is time consuming and rather expensive. As an alternative, we implemented a deep learning procedure on images directly acquired from the untreated airborne samples using standard Mixed Cellulose Ester (MCE) filters. Several samples with a mix of chrysotile and crocidolite with different concentration loads have been prepared. Using a 20x objective lens coupled with a backlight illumination system a number of 140 images were collected from these samples, which along with additional 13 highly fibre loaded artificial images constituted the database. About 7500 fibres were manually recognised and annotated following the National Institute for Occupational Safety and Health (NIOSH) fibre counting Method 7400 as input for the training and validation of the model. The best trained model provides a total precision of 0.84 with F1-Score of 0.77 at a confidence of 0.64. A further post-detection refinement to ignore detected fibres < 5 µm in length improves the final precision. This method can be considered as a reliable and competent alternative to conventional PCM.

A new approach to deposit homogeneous samples of asbestos fibres for toxicological tests in vitro.

In this paper we describe the results obtained with a novel method to prepare depositions of asbestos fibres for toxicological tests in vitro. The technique is based on a micro-dispenser, working as an inkjet printer, able to deposit micro-sized droplets from a suspension of fibres in a liquid medium; we used here a highly evaporating liquid (ethanol) to reduce the experimental time, however other solvents could be used. Both the amount and spatial distribution of fibres on the substrate can be controlled by adjusting the parameters of the micro-dispenser such as deposition area, deposition time, uniformity and volume of the deposited liquid. Statistical analysis of images obtained by optical and scanning electron microscopy shows that this technique produces an extremely homogeneous distribution of fibers. Specifically, the number of deposited single fibres is maximized (up to 20 times), a feature that is essential when performing viability tests where agglomerated or untangled fibrous particles need to be avoided.

Real-time quantitative detection of styrene in atmosphere in presence of other volatile-organic compounds using a portable device.

Exposure to styrene is a major safety concern in the fibreglass processing industry. This compound is classified by the International Agency for Research on Cancer as a possible human carcinogen. Several types of analytical equipment exist for detecting volatile organic compounds (VOCs) in the atmosphere; however, most of them operate ex-situ or do not provide easy discrimination between different molecules. This work introduces an improved and portable method based on FTIR spectroscopy to analyse toxic gaseous substances in working sites down to a concentration of less than 4 ppm. Styrene and a combination of VOCs typically associated with it in industrial processes, such as acetone, ethanol, xylene and isopropanol, have been used to calibrate and test the methodology. The results demonstrate that the technique offers the possibility to discriminate between different gaseous compounds in the atmosphere with a high degree of confidence and obtain very accurate quantitative information on their concentration, down to the ppm level, even when different VOCs are present in a mixture.

Occurrence and characterization of tremolite asbestos from the Mid Atlantic Ridge.

Tremolite is one of the most common amphibole species and, in the fibrous form (i.e., characterized by crystals/particles consisting of fibres with length > 5 µm, width < 3 µm and aspect ratio > 3), one of the six asbestos minerals. Until now the attention of crystallographers has focused only on samples from continental environment. Here we report the first chemical and structural data of a tremolite asbestos found along the Mid Atlantic Ridge (MAR) at the eastern intersection of the Romanche Transform Fault (Equatorial MAR). Tremolite is associated with chlorite and lizardite and was formed through the green shale facies lower than zeolite in a predominantly fluid system. MAR tremolite asbestos shows very slight deviations from the ideal crystal structure of tremolite. Differences in cation site partitioning were found with respect to tremolite asbestos from ophiolitic complexes, attributed to the different chemical-physical conditions during the mineral formation. In particular, oceanic tremolite asbestos is enriched in Al and Na, forming a trend clearly distinct from the continental tremolites.

Raman spectroscopy and laser-induced degradation of groutellite and ramsdellite, two cathode materials of technological interest.

Manganese oxides are important geomaterials, used in a large number of applications. For instance, as pigments in art works or in the treatment and removal of heavy metals from drinking water. Particularly, ramsdellite [Mn4+O2] and groutellite [(Mn0.5 4+,Mn0.5 3+)O1.5(OH)0.5], because of their 2 × 1 frameworks that enable proton diffusion, are very important cathode materials. Manganese oxides commonly occur as crypto-crystalline and very fine mixtures of different Mn-phases, iron oxides, silicates and carbonates. Thus, proper characterization can be a difficult task using XRPD. The lack of Raman data on groutellite and the little and conflicting data on ramsdellite do not allow their proper identification by Raman spectroscopy. In this work we characterize natural mixtures of ramsdellite and groutellite by combining SEM-EDS, XRPD, FT-IR and Raman spectroscopy, to provide reference Raman spectra. Our data show that they have a typical and unmistakable spectra, allowing clear recognition. Moreover, we have investigated their laser-induced degradation. Our data show that groutellite transforms into ramsdellite, by the loss of H+ and the oxidation of Mn3+ to Mn4+, already at a very low laser power. Further increasing the laser power the formation of hausmannite [Mn2+Mn2 3+O4] occurs via the reduction of Mn cations. Our data can be used to study the discharge mechanism in cathodic battery materials, by monitoring the Mn reduction from ramsdellite to groutellite, and finally to groutite [α-Mn3+OOH]. Moreover, Raman mapping allows the study of their distribution in all the investigated samples and, indirectly, those of H+ and Mn3+, which plays a key-role in electrochemical activity of these compounds.

Mineralogy and textures of riebeckitic asbestos (crocidolite): The role of single versus agglomerated fibres in toxicological experiments.

Asbestos may cause adverse effects, but relationship between mineralogy and texture of fibres versus toxicity is still lacking. Toxicological studies can be interpreted and compared only if quantitative features of fibres are determined. Here, riebeckitic ("crocidolite") amphibole fibres were analysed by XRPD, FTIR, SEM-EDS and EMP-WDS; only crystals with stochiometry A□BNa2C(Fe2+2.5Mg0.5)CFe3+2TSi8O22W(OH)2 are present in the starting material used for the experiments. Fibres deposited from solutions of 0.1, 1, 10, 25, 50, 75 and 100mg/L were counted by image analysis using SEM images. At 0.1 and 1mg/L the fibres are well separated, whereas between 1 and 10mg/L they start to agglomerate. In-vitro tests performed on fibres deposited at the same mg/L concentrations show that the toxic potential follows a curvilinear increasing trend with a decreasing rate. Since the range of sizes of single fibres and their mineralogy are constant, this decreasing rate can be only attributed to the increasing amount of agglomerated fibres. Hence, single versus agglomerated fibre population is a factor that cannot be neglected in defining the final adverse effects of asbestos. The analytical protocol proposed here is valuable for any aero-dispersed dust, in polluted environments, as well as in the interpretation of experimental studies.

Calcium tartrate esahydrate, CaC4H4O6·6H2O: a structural and spectroscopic study.

The crystal structure of calcium tartrate esahydrate, CaC4H4O6·6H2O, has been solved by the charge-flipping method from single-crystal X-ray diffraction data and refined to R = 0.021, based on 1700 unique observed diffractions. Salient crystallographic data are: a = 7.7390 (1), b = 12.8030 (2), c = 5.8290 (1) Å, Z = 2, and space group P21212. During the refinement step it was possible to locate all H atoms by difference Fourier synthesis. The tartrate molecule has a (-)-gauche conformation and is coordinated to two calcium ions to form infinite chains along the a axis which alternate Ca polyhedra with tartrate molecules. The chains are interlinked by a three-dimensional network of hydrogen bonds from four water molecules surrounding the Ca ion, reinforced by hydrogen bonds from one interstitial water molecule. Micro-Raman and FT-IR spectroscopic data are provided.

Graphitic Patterns on CVD Diamond Plate as Microheating/Thermometer Devices.

A simple compact temperature sensor and microheater in a wide temperature range has been developed, realizing a laser-patterned resistive structure on the surface of a synthetic polycrystalline diamond plate. Imaging and spectroscopy techniques used to investigate morphology, structure, and composition of the pattern showed that it incorporates different nondiamond carbon phases. Transport experiments revealed the semiconducting behavior of this microresistor. Thermal power measurements versus temperature are presented. A possible application of this device that may easily match compact experimental layouts avoiding both thermal anchoring offset and mechanical stress between sample and sensor is discussed. The patterned structure undergoes testing as a microthermometer, providing fast response and excellent stability versus time. It exhibits a good sensitivity that coupled to an easy calibration procedure minimizes errors and guarantees high accuracy. Plot of temperature versus input power of the resistive patterned line used as microheater shows a linear behavior in an extended temperature range.