Noise Filtering Algorithm Using Gaussian Mixture Models for High-Resolution Mass Spectra of Natural Organic Matter.

High-resolution mass spectra of natural organic matter (NOM) contain a large number of noise signals. These signals interfere with the correct molecular composition estimation during nontargeted analysis because formula-assignment programs find empirical formulas for such peaks as well. Previously proposed noise filtering methods that utilize the profile of the intensity distribution of mass spectrum peaks rely on a histogram to calculate the intensity threshold value. However, the histogram profile can vary depending on the user settings. In addition, these algorithms are not automated, so they are handled manually. To overcome the mentioned drawbacks, we propose a new algorithm for noise filtering in mass spectra. This filter is based on Gaussian Mixture Models (GMMs), a machine learning method to find the intensity threshold value. The algorithm is completely data-driven and eliminates the need to work with a histogram. It has no customizable parameters and automatically determines the noise level for each individual mass spectrum. The algorithm performance was tested on mass spectra of natural organic matter obtained by averaging a different number of microscans (transients), and the results were compared with other noise filters proposed in the literature. Finally, the effect of this noise filtering approach on the fraction of peaks with assigned formulas was investigated. It was shown that there is always an increase in the identification rate, but the magnitude of the effect changes with the number of microscans averaged. The increase can be as high as 15%.

Albumin Retains Its Transport Function after Interaction with Cerium Dioxide Nanoparticles.

The interaction of inorganic nanomaterials with biological fluids containing proteins can lead not only to the formation of a protein corona and thereby to a change in the biological activity of nanoparticles but also to a significant effect on the structural and functional properties of the biomolecules themselves. This work studied the interaction of nanoscale CeO2, the most versatile nanozyme, with human serum albumin (HSA). Fourier transform infrared spectroscopy, MALDI-TOF mass spectrometry, UV-vis spectroscopy, and fluorescence spectroscopy confirmed the formation of HSA-CeO2 nanoparticle conjugates. Changes in protein conformation, which depend on the concentration of both citrate-stabilized CeO2 nanoparticles and pristine CeO2 nanoparticles, did not affect albumin drug-binding sites and, accordingly, did not impair the HSA transport function. The results obtained shed light on the biological consequences of the CeO2 nanoparticles' entrance into the body, which should be taken into account when engineering nanobiomaterials to increase their efficiency and reduce the side effects.

The Thermophysical and Physicochemical Properties of the Aqueous Dispersion of Graphene Oxide Dual-Beam Thermal Lens Spectrometry.

Modern heat-conducting materials require special attention to analyze their thermophysical properties. Compared to classical methods, thermal lens spectrometry (TLS) has advantages due to its high sensitivity to physical and chemical composition. To avoid a systematic error in the analysis of complex systems, it is necessary to realize the limits of the applicability of the method. This study considers the features of thermal-diffusivity measurements by TLS in the stationary state for dispersed systems with absorbances up to 0.05. The limits of applicability of the method in analyzing heterogeneous systems are shown, and a mathematical apparatus is proposed for indicating a systematic error in finding thermal diffusivity that does not exceed 1%. Graphene oxide (GO), which has attractive physicochemical properties, was used as the object of analysis. GO belongs to 2D objects, the study of which requires highly sensitive methods and special attention when discussing the results. The thermophysical properties of aqueous dispersions of graphene oxide in a wide range of concentrations (up to 2 g/L) and lateral sizes (up to 4 µm) were studied by TLS. It has been found that with increasing nanophase concentration, the thermal diffusivity of graphene oxide dispersions passes through a minimum, which can be used in solving thermal insulation problems. It has been established that prolonged laser irradiation of the dispersion leads to a change in thermal diffusivity, which indicates the photochemical reduction of graphene oxide.

Green and Sustainable Ultrasound-Assisted Anodic Electrochemical Preparation of Graphene Oxide Dispersions and Their Antioxidant Properties.

A fast method for preparing aqueous graphene oxide (GO) dispersions by electrochemical oxidation of a graphite anode without preliminary intercalation with oxidizing agents is proposed. Ultrasonic probing was used in the modulation mode of ultrasonic waves (work/rest) for more efficient graphite oxidation-exfoliation. It is shown that the 4/2 s mode of ultrasonic modulation is the most effective due to the probe material's low corrosion while maintaining the optimum synthesis temperature not exceeding 30-35 °C and achieving the best characteristics of the resulting product. Three cases of anodic oxidation of graphite to obtain graphene oxide were considered: (1) a combined cathode-anode compartment, (2) a split cathode-anode salt-bridged compartment, and (3) separated anode compartment with a 3.5 kDa dialysis membrane. It was determined that the approach to synthesis with a divided cathode-anode compartment makes it possible to obtain GO sheets with fewer defects compared to chemical methods or methods with a combined cathode-anode compartment and makes it possible to control the oxidation degree of the material (C:O ratio) by varying the current density. The prepared samples showed good stability for more than six months. The spectral and morphological characteristics were studied. Using chemiluminometry in the luminol/Co(II)/H2O2 system, the antioxidant properties concerning three key reactive oxygen species (H2O2, superoxide anion radical, and hydroxyl radical) were demonstrated. It was also shown that the prepared GO dispersions do not induce lipid and phospholipid peroxidation.

Composition of the Cytochrome c Complex with Cardiolipin by Thermal Lens Spectrometry.

Thermal lens spectrometry along with spectrophotometric titration were used to assess the composition of the complex of oxidized cytochrome c (ferricytochrome c) with 1,1',2,2'-tetraoleyl cardiolipin, which plays a key role in the initiation of apoptosis. Spectrophotometric titration was carried out for micromolar concentrations at which the complex is mainly insoluble, to assess the residual concentration in the solution and to estimate the solubility of the complex. Thermal lens spectrometry was used as a method of molecular absorption spectroscopy, which has two advantages over conventional optical transmission spectroscopy: the higher sensitivity of absorbance measurements and the possibility of studying the light absorption by chromophores and heat transfer in complex systems, such as living cells or tissues. Thermal lens measurements were carried out at nanomolar concentrations, where the complex is mainly in solution, i.e., under the conditions of its direct measurements. From the thermal lens measurements, the ratios of cytochrome c and cardiolipin in the complex were 50 at pH 7.4; 30 at pH 6.8; and 10 at pH 5.5, which fit well to the spectrophotometric data. The molecular solubility of the complex at pH 6.8-7.4 was estimated as 30 µmol/L.

Thermal Diffusivity of Aqueous Dispersions of Silicon Oxide Nanoparticles by Dual-Beam Thermal Lens Spectrometry.

The growing interest in heat-conducting nanofluids requires highly sensitive methods for analyzing the thermal properties. Thermal lens spectrometry (TLS), despite its advantages over classical methods, does not have a general approach for measuring and interpreting results for dispersed systems. In this paper, for nanofluids of silicon oxide in water in a wide range of concentrations and sizes, the selection of measurement parameters for transient and steady-state thermal lensing is justified, and the interpretation of the results of thermal diffusivity measurements is substantiated. The features of the measurements of thermal diffusivity by TLS under stationary states for dispersed systems are considered. Using this approach, it is possible to detect and distinguish thermal effects with high accuracy. For dispersions of silicon oxide, with increasing concentrations, the thermal diffusivity passes through a minimum threshold. Silicon oxide dispersions can be used both as coolants or as heat-removing liquids by selecting the particle size and concentration.

Accuracy of Measurements of Thermophysical Parameters by Dual-Beam Thermal-Lens Spectrometry.

Thermal-lens spectrometry is a sensitive technique for determination of physicochemical properties and thermophysical parameters of various materials including heterogeneous systems and nanoparticles. In this paper, we consider the issues of the correctness (trueness) of measurements of the characteristic time of the thermal-lens effect and, thus, of the thermal diffusivity determined by dual-beam mode-mismatching thermal lensing. As sources of systematic errors, major factors-radiation sources, sample-cell and detector parameters, and general measurement parameters-are considered using several configurations of the thermal-lens setups, and their contributions are quantified or estimated. Furthermore, with aqueous ferroin and Sudan I in ethanol as inert colorants, the effects of the intermolecular distance of the absorbing substance on the correctness of finding the thermophysical parameters are considered. The recommendations for checking the operation of the thermal-lens setup to ensure the maximum accuracy are given. The results obtained help reducing the impact of each investigated factor on the value of systematic error and correctly measure the thermophysical parameters using thermal-lens spectrometry.

Effects of Aqueous Dispersions of C60, C70, and Gd@C82 Fullerenes on DNA Oxidative Damage/Repair and Apoptosis in Human Embryonic Lung Fibroblasts.

Fullerenes and metallofullerenes play an active role in homeostasis of reactive oxygen species and may cause oxidative damage to cells. As pristine fullerenes are a basis for derivatization, studying oxidative DNA damage/repair and apoptosis is important in terms of genotoxicity and cytotoxicity for their biomedical application. Aqueous dispersions of C60, C70, and Gd@C82 (5 nM and 1.5 µM) were cultured with human fetal lung fibroblasts for 1, 3, 24, and 72 h. Oxidative DNA damage/repair was assessed through concentration of 8-oxodG, double-strand breaks, and activation of BRCA1. Activity of apoptosis was assessed through the BCL2/BAX ratio. All three fullerenes caused oxidative modification of DNA at the early stages; C60 caused the most long-term damage, Gd@C82 caused the most short-term damage, and C70 caused "wave-like" dynamics. The dynamics of DNA repair correlated with the dynamics of oxidative damage, but Gd@C82 caused more prolonged activation of the repair system than C60 or C70. The oxidative toxicity of Gd@C82, is minor and the oxidative toxicity of C60 is mild and short-term, in contrast to C70. In relation to the studied effects, the fullerenes can be arranged in a safety row of Gd@C82 > C60 > C70.

Salivary Antioxidant Capacity and Magnesium in Generalized Anxiety Disorder.

Generalized anxiety disorder (GAD) is a prevalent disorder. The search for biomarkers may contribute to new knowledge about molecular pathogenesis and treatment. Since oxidative stress and micronutrient imbalance play a key role in the development of mental disorders, we aimed to study salivary antioxidant capacity and magnesium in patients with GAD in an anxiety model of solving problems with increasing complexity. The study subgroup consisted of 15 patients with GAD, and 17 healthy volunteers of the same age made up the control subgroup. Participants took a test with six levels of difficulty, which included false feedback. In this test, the participants were asked to remember the colors of balloons and react when the color changed. The reaction time, the number of correct answers, as well as biochemical parameters such as the antioxidant capacity of saliva and salivary magnesium, were assessed. There was no difference in the results of the quest between the subgroups; however, anxious participants spent more time at the moment of experimental frustration due to incorrect feedback and additional negative psycho-emotional load. Antioxidant capacity did not differ between the subgroups both before and after the experimental session. Average antioxidant capacity also did not change significantly at the endpoint of the experiment. However, the endpoint antioxidant capacity correlated negatively with the reaction time in anxious patients in the second block (where the false feedback as a frustrating factor appeared). Magnesium was initially significantly higher in the group of anxious participants and decreased at the experiment endpoint; in healthy patients, there were no changes in salivary magnesium at the endpoint. In conclusion, the compensatory potential of oxidative metabolism and magnesium in patients with GAD was spent with additional psycho-emotional stress, in contrast to healthy individuals, but it was sufficient to avoid exhaustion during experimental frustrating exposure.

Infrared Spectroscopy in Aqueous Solutions: Capabilities and Challenges.

Fourier-transform infrared (FTIR) spectroscopy provides rapid, reliable, quantitative, and qualitative analysis of samples in different aggregation states, i.e., gases, thin films, solids, liquids, etc. However, when analyzing aqueous solutions, particular issues associated with the rather pronounced IR absorption characteristics of water appear to interfere with the solute determination. In this review, Fourier-transform infrared spectroscopic techniques and their analytical capabilities for analyzing aqueous solutions are reviewed, and highlight examples are discussed.

High-Throughput Preparation of Uncontaminated Graphene-Oxide Aqueous Dispersions with Antioxidant Properties by Semi-Automated Diffusion Dialysis.

A semi-automated diffusion-dialysis purification procedure is proposed for the preparation of uncontaminated graphene oxide (GO) aqueous dispersions. The purification process is integrated with analytical-signal processing to control the purification degree online by several channels: oxidation-reduction potential, conductivity, and absorbance. This approach reduces the amounts of reagents for chemical treatment during dialysis. The total transition metal (Mn and Ti) content was reduced to a sub-ppb level (assessed by slurry nebulization in inductively coupled plasma optical atomic emission spectroscopy). Purified aqueous GO samples possess good stability for about a year with a zeta-potential of ca. -40 mV and a lateral size of ca. sub-µm. Purified GO samples showed increased antioxidant properties (up to five times compared to initial samples according to chemiluminometry by superoxide-radical (O2-) generated in situ from xanthine and xanthine oxidase with the lucigenin probe) and significantly decreased peroxidase-like activity (assessed by the H2O2-L-012 system).

FTIR Photoacoustic and ATR Spectroscopies of Soils with Aggregate Size Fractionation by Dry Sieving.

Granulometric fractionation as a source of additional information on organic-matter and inorganic matrix components of soils using FTIR-photoacoustic spectroscopy (FTIR-PAS) supported by attenuated-total reflection FTIR spectroscopy (ATR-FTIR) for a wide range of aggregate fractions (10-5000 µm) was used to compare the sensitivity, reproducibility, information contents, and representativity of fractionated samples. For chernozem and sod-podzolic soils and different agricultural-use chernozem samples, differences in the composition were found, manifested in normalized spectra of microaggregate fractions, with the range of 10-100 µm bearing the complete information. Most changes are observed in the soil organic matter range (1900-1340 cm-1), although these changes are slight, and in the soil-matrix region (550-300 cm-1). The latter region increases the intensity of bands corresponding to amorphous silica and clay minerals in fine fractions, while the intensity of bands attributed to quartz lattice vibrations decreases. FTIR-PAS spectra do not differ considerably at high interferometer modulation frequencies as the signal-penetration depth is comparable with particle sizes. The soil fractions below 20 µm result in the maximum sensitivity, reproducibility, and signal-to-noise ratio, showing no changes from coarser fractions by the information content and, thus, providing representative samples for analysis. The fractionation shows more differences in the sod-podzolic and chernozem soil fractions than the whole soil spectra. FTIR-PAS provides better sensitivity and reproducibility in the 4000-2000 cm-1 region and ATR-FTIR in the 2000-100 cm-1 region.

Thermal Conductivity of Detonation Nanodiamond Hydrogels and Hydrosols by Direct Heat Flux Measurements.

The methodology and results of thermal conductivity measurements by the heat-flow technique for the detonation nanodiamond suspension gels, sols, and powders of several brands in the range of nanoparticle concentrations of 2-100% w/w are discussed. The conditions of assessing the thermal conductivity of the fluids and gels (a FOX 50 heat-flow meter) with the reproducibility (relative standard deviation) of 1% are proposed. The maximum increase of 13% was recorded for the nanodiamond gels (140 mg mL-1 or 4% v/v) of the RDDM brand, at 0.687 ± 0.005 W m-1 K-1. The thermal conductivity of the nanodiamond powders is estimated as 0.26 ± 0.03 and 0.35 ± 0.04 W m-1 K-1 for the RUDDM and RDDM brands, respectively. The thermal conductivity for the aqueous pastes containing 26% v/v RUDDM is 0.85 ± 0.04 W m-1 K-1. The dignities, shortcomings, and limitations of this approach are discussed and compared with the determining of the thermal conductivity with photothermal-lens spectrometry.

Effects of Aqueous Dispersions of C60, C70 and Gd@C82 Fullerenes on Genes Involved in Oxidative Stress and Anti-Inflammatory Pathways.

BACKGROUND: Fullerenes and metallofullerenes can be considered promising nanopharmaceuticals themselves and as a basis for chemical modification. As reactive oxygen species homeostasis plays a vital role in cells, the study of their effect on genes involved in oxidative stress and anti-inflammatory responses are of particular importance. METHODS: Human fetal lung fibroblasts were incubated with aqueous dispersions of C60, C70, and Gd@C82 in concentrations of 5 nM and 1.5 µM for 1, 3, 24, and 72 h. Cell viability, intracellular ROS, NOX4, NFκB, PRAR-γ, NRF2, heme oxygenase 1, and NAD(P)H quinone dehydrogenase 1 expression have been studied. RESULTS & CONCLUSION: The aqueous dispersions of C60, C70, and Gd@C82 fullerenes are active participants in reactive oxygen species (ROS) homeostasis. Low and high concentrations of aqueous fullerene dispersions (AFD) have similar effects. C70 was the most inert substance, C60 was the most active substance. All AFDs have both "prooxidant" and "antioxidant" effects but with a different balance. Gd@C82 was a substance with more pronounced antioxidant and anti-inflammatory properties, while C70 had more pronounced "prooxidant" properties.

Antioxidant Potential of Aqueous Dispersions of Fullerenes C60, C70, and Gd@C82.

The antioxidant potential (capacity and activity) of aqueous fullerene dispersions (AFD) of non-functionalized C60, C70, and Gd@C82 endofullerene (in micromolar concentration range) was estimated based on chemiluminescence measurements of the model of luminol and generation of organic radicals by 2,2'-azobis(2-amidinopropane) dihydrochloride (ABAP). The antioxidant capacity was estimated by the TRAP method, from the concentration of half-suppression, and from the suppression area in the initial period. All three approaches agree and show that the antioxidant capacity of AFDs increased in the order Gd@C82 < C70 < C60. Mathematical modeling of the long-term kinetics data was used for antioxidant activity estimation. The effect of C60 and C70 is found to be quenching of the excited product of luminol with ABAP-generated radical and not an actual antioxidant effect; quenching constants differ insignificantly. Apart from quenching with a similar constant, the AFD of Gd@C82 exhibits actual antioxidant action. The antioxidant activity in Gd@C82 is 300-fold higher than quenching constants.

Green and rapid preparation of long-term stable aqueous dispersions of fullerenes and endohedral fullerenes: The pros and cons of an ultrasonic probe.

A green, scalable, and sustainable approach to prepare aqueous fullerene dispersions (AFD) C60, C70, endohedral metallofullerene Gd@C82, and their derivatives C60Cl6, C70Cl10, and supramolecular and ester-like derivatives, 10 fullerene species total, is proposed. For the first time, an immersed ultrasonic probe was used to preparing dispersions for pristine fullerenes without addends. Both ultrasound-assisted solvent-exchange and direct sonication techniques for AFD preparation using an immersed probe were tested. The average time for AFD preparation decreases 10-15 times compared to an ultrasound-bath-assisted technique, while final fullerene concentrations in AFDs remained at tens of ppm (up to 80 ppm). The aqueous dispersions showed long-term stability, a negatively charged surface with a zeta potential up to -32 mV with an average nanocluster diameter of no more than 180 nm. The total anionic and cationic compositions of samples were found by inductively coupled plasma atomic emission spectroscopy and chromatographic techniques. The highlights and challenges of using an ultrasound probe for AFD production are discussed.

Controlling water transport between micelles and aqueous microdroplets during sample enrichment.

Droplet microfluidics technologies have advanced rapidly, but enrichment in droplets has still been difficult. To deterministically control the droplet enrichment, the water transport from an aqueous microdroplet in organic continuous phase containing span 80 micelles was investigated. Organic phase containing Span-80-micelles contacted a NaCl aqueous solution to control hydration degree of the micelles, prior to being used in the microfluidic device. Then, the organic phase was continuously applied to the microdroplets trappled in microwells. Here, water was transported from the microdroplet to the organic phase micelles. This spontaneous emulsification process induced the droplet shrinkage and stopped when the microdroplet reached a certain diameter. The micelle hydration degree correlated well with the final water activity of droplets. The enrichment factor can be determined by the initial microdroplet salt concentration and by the micelle hydration degree. As a proof-of-concept experiment, enrichment of fluorescent nanoparticles and dye was demonstrated, and fluorescent resonance energy transfer was observed as expected. Another demonstration of bound-free separation was performed utilizing the avidin-biotin system. This technique has the potential to be a powerful pretreatment method for bioassays in droplet microfluidics.

Detonation Nanodiamonds: A Comparison Study by Photoacoustic, Diffuse Reflectance, and Attenuated Total Reflection FTIR Spectroscopies.

The qualitative analysis of nanodiamonds by FTIR spectrometry as photoacoustic (FTIR-PAS), diffuse-reflectance (DRIFT), and attenuated total reflection (ATR) modalities was evaluated for rapid and nondestructive analysis and comparison of nanodiamonds. The reproducibility and signal-gathering depth of spectra was compared. The assignment of characteristic bands showed that only six groups of bands were present in spectra of all the modalities with appropriate sensitivity: 1760 (C=O stretch, isolated carboxyl groups); 1640-1632 (H-O-H bend, liquid water); 1400-1370 (non-carboxyl C-O-H in-plane bend and CH2 deformation); 1103 (non-carboxyl C-O stretch); 1060 (in-plane C-H bend, non-aromatic hydrocarbons and carbohydrates); 940 cm-1 (out-of-plane carboxyl C-O-H bend). DRIFT provides the maximum number of bands and is capable of measuring hydrogen-bonded bands and CHx groups. ATR provides the good sensitivity for water and C-H/C-C bands in the range 2000-400 cm-1. FTIR-PAS reveals less bands than DRIFT but more intense bands than ATR-FTIR and shows the maximum sensitivity for absorption bands that do not appear in ATR-IR spectra and are expedient for supporting either DRIFT or FTIR-PAS along with depth-profiling. Thus, all three modalities are required for the full characterization of nanodiamonds surface functional groups.

FTIR photoacoustic spectroscopy for identification and assessment of soil components: Chernozems and their size fractions.

FTIR photoacoustic spectroscopy was used to approach inorganic matrix components and organic-matter constituents of chernozem size fractions (1-5000 µm, by dry sieving) with a different history of use (from intact steppe to permanent bare fallow, a continuous long-term field experiment). The conditions of FTIR photoacoustic measurements in continuous-scan modes were compared with attenuated total reflection measurements, the advantages of photoacoustic measurements resulting from a higher intensity of the incident radiation and signal-generating volume were discussed. Overtone peaks of quartz as a soil matrix component at 2000-1700 cm-1 were selected as a possible internal-standard (guide) bands for the comparison of photoacoustic spectra. For different land-use samples, differences in the composition were found, which are differently manifested in normalized spectra of size fractions, with millimeter-size, 20-100 µm, and silt fraction bearing the maximum information.