Dataset of human platelets SERS spectra from individuals with acute coronary syndrome.

This article contains Raman experimental data, obtained by means of Centaur U («NanoScanTechnology¼, Russia) Raman spectrometer, which was used for early structure changes and biomarkers identification in individuals with cardiovascular pathology in vitro. The data include analyzed Raman spectra of human platelets taken from individuals with acute coronary syndrome.

Dataset on vibrational spectra of amber and amber-like resins.

The article presents experimental data on vibrational spectroscopy of worldwide amber and amber-like resins. IR spectra were obtained using SHIMADZU IRPrestige-2 (Japan). Raman spectra were obtained using a Virsa Raman analyzer (UK). The data includes analyzed IR and Raman spectra of amber and amber-like resins, obtained to identify markers that determine spectral characteristics of natural resin and its deposits.

Raman spectra simulation of antiplatelet drug-platelet interaction using DFT.

The paper reflects the results of molecular docking and mathematical DFT simulation for antiplatelet drugs and the target platelet receptor/ferment interaction in the limited area. The results of Raman spectra simulation are implemented and obtained from the interaction of the clopidogrel metabolite of the P2Y12 receptor. The interaction of aspirin with the COX-1 enzyme was also investigated. As a result, theoretical Raman spectra of the drug-receptor area were obtained. The theoretical data were compared with the experimental SERS results. The characteristic bands corresponding to metabolite/ferment and antiplatelet drug vibrations were clarified. The prospects of obtaining results for pathologies based on platelet conformations during cardiovascular diseases have been demonstrated.

Accessing Properties of Molecular Compounds Involved in Cellular Metabolic Processes with Electron Paramagnetic Resonance, Raman Spectroscopy, and Differential Scanning Calorimetry.

In this work, we review some physical methods of macroscopic experiments, which have been recently argued to be promising for the acquisition of valuable characteristics of biomolecular structures and interactions. The methods we focused on are electron paramagnetic resonance spectroscopy, Raman spectroscopy, and differential scanning calorimetry. They were chosen since it can be shown that they are able to provide a mutually complementary picture of the composition of cellular envelopes (with special attention paid to mycobacteria), transitions between their molecular patterning, and the response to biologically active substances (reactive oxygen species and their antagonists-antioxidants-as considered in our case study).

Synthesis Methods and Optical Sensing Applications of Plasmonic Metal Nanoparticles Made from Rhodium, Platinum, Gold, or Silver.

The purpose of this paper is to provide an in-depth review of plasmonic metal nanoparticles made from rhodium, platinum, gold, or silver. We describe fundamental concepts, synthesis methods, and optical sensing applications of these nanoparticles. Plasmonic metal nanoparticles have received a lot of interest due to various applications, such as optical sensors, single-molecule detection, single-cell detection, pathogen detection, environmental contaminant monitoring, cancer diagnostics, biomedicine, and food and health safety monitoring. They provide a promising platform for highly sensitive detection of various analytes. Due to strongly localized optical fields in the hot-spot region near metal nanoparticles, they have the potential for plasmon-enhanced optical sensing applications, including metal-enhanced fluorescence (MEF), surface-enhanced Raman scattering (SERS), and biomedical imaging. We explain the plasmonic enhancement through electromagnetic theory and confirm it with finite-difference time-domain numerical simulations. Moreover, we examine how the localized surface plasmon resonance effects of gold and silver nanoparticles have been utilized for the detection and biosensing of various analytes. Specifically, we discuss the syntheses and applications of rhodium and platinum nanoparticles for the UV plasmonics such as UV-MEF and UV-SERS. Finally, we provide an overview of chemical, physical, and green methods for synthesizing these nanoparticles. We hope that this paper will promote further interest in the optical sensing applications of plasmonic metal nanoparticles in the UV and visible ranges.

FDTD Simulations for Rhodium and Platinum Nanoparticles for UV Plasmonics.

The article describes the results of finite-difference time-domain (FDTD) mathematical modeling of electromagnetic fields distortion near the surfaces of two transition metals: rhodium (Rh) and platinum (Pt) on glass (SiO2) substrates. Results were compared with calculated optical properties of classical SERS generating metals (Au and Ag). We have performed FDTD-based theoretical calculations for UV SERS-active nanoparticles (NPs) and structures based on hemispheres of Rh and Pt and planar surfaces, consisting of single NPs with varied gaps between them. The results have been compared with gold stars, silver spheres and hexagons. The prospects of the theoretical approach for single NPs and planar surfaces modeling to evaluate optimal field amplification and light scattering parameters have been shown. The presented approach could be applied as a basis for performing the methods of controlled synthesis for LPSR tunable colloidal and planar metal-based biocompatible optical sensors for UV and deep-UV plasmonics. The difference between UV-plasmonic NPs and plasmonics in a visible range has been evaluated.

Determination of Anthracene Derivatives in Baltic Amber Using SERS.

The article describes the results of Raman spectroscopy and SERS for the study of fluorescent components of Baltic amber via the extraction method. Using SERS, it was possible to confirm the presence of anthracene derivatives in amber: tetracene and benzanthracene. It has been shown that SERS methods are effective for the detection of aromatic compounds; they increase the registered Raman signal and make it possible to identify peaks characteristic of the compounds under study. By combining experimental methods with DFT simulations, anthracene derivatives were modeled and confirmed to be present in the structure of Baltic amber. A combination of the proposed methods can be used to distinguish between different types of amber and isolate the necessary amber components. The obtained results are promising for compiling spectral maps of ambers for their possible classification by their place of origin.

Application of vibrational spectroscopy and nuclear magnetic resonance methods for drugs pharmacokinetics research.

OBJECTIVES: The development of new methods for determining the concentration of drugs is an actual topic today. The article contains a detailed review on vibrational spectroscopy and nuclear magnetic resonance methods using for pharmacokinetic research. This study is devoted to the possibility of using vibrational spectroscopy and 1H nuclear magnetic resonance spectroscopy to determine the concentration of drugs and the use of these groups of techniques for therapeutic drug monitoring. CONTENT: The study was conducted by using scientific libraries (Scopus, Web of Science Core Collection, Medline, GoogleScholar, eLIBRARY, PubMed) and reference literature. A search was conducted for the period from 2011 to 2021 in Russian and English, by combinations of words: 1H nuclear magnetic resonance (1H NMR), vibrational spectroscopy, Surface-Enhanced Raman spectroscopy, drug concentration, therapeutic drug monitoring. These methods have a number of advantages and are devoid of some of the disadvantages of classical therapeutic drug monitoring (TDM) methods - high performance liquid chromatography and mass spectrometry. This review considers the possibility of using the methods of surface-enhanced Raman scattering (SERS) and 1H NMR-spectroscopy to assess the concentration of drugs in various biological media (blood, urine), as well as to study intracellular metabolism and the metabolism of ophthalmic drugs. 1Н NMR-spectroscopy can be chosen as a TDM method, since it allows analyzing the structure and identifying metabolites of various drugs. 1Н NMR-based metabolomics can provide information on the side effects of drugs, predict response to treatment, and provide key information on the mechanisms of action of known and new drug compounds. SUMMARY AND OUTLOOK: SERS and 1Н NMR-spectroscopy have great potential for further study and the possibility of introducing them into clinical practice, including for evaluating the efficacy and safety of drugs.

FDTD Simulations of Shell Scattering in Au@SiO2 Core-Shell Nanorods with SERS Activity for Sensory Purposes.

The article describes the results of Finite-Difference Time-Domain (FDTD) mathematical modeling of electromagnetic field parameters near the surfaces of core-shell gold-based nanorods in the Au@SiO2 system. Three excitation linewidths (λ = 532, 632.8, and 785 nm) were used for theoretical experiments. Electric field parameters for Au nanorods, Au@SiO2 nanorods, and hollow SiO2 shells have been calculated and evaluated. The correlations between electric field calculated parameters with nanorod morphology and shell size parameters have been clarified. The optical properties of nanoobjects have been simulated and discussed. The highest maximum calculated value of the electric field tension was E = 7.34 V/m. The enhancement coefficient was |E/E0|4 = 3.15 × 107 and was obtained on a rod with a SiO2 shell with dimensional parameters of height 70 nm, rod width 20 nm, and shell thickness 20 nm. As a result, a flexible simulation algorithm has been developed for the simulation of electric field parameters in each component of the Au@SiO2 system. The developed simulation algorithm will be applicable in the future for any other calculations of optical parameters in any similar component of the core-shell system.

Microplastics in the first-year sea ice of the Novik Bay, Sea of Japan.

Sea ice is heavily contaminated with microplastics particles (MPs, <5 mm). First-year sea ice cores (38-41 cm thick) were taken in the beginning of spring in a narrow populated bay of the Sea of Japan. Two ice cores were examined (layer-by-layer, excluding surface) for MPs content: one using µ-FTIR for 25-300 µm (SMPs), and another one - with visual+Raman identification for 300-5000 µm particles (LMPs). The integral (25-5000 µm) bulk mean abundance of MPs was found to be 428 items/L of meltwater, with fibers making 19 % in SMPs size range and 59 % in LMPs. Integral mean mass of MPs was estimated in 34.6 mg/L, with 99.6 % contribution from fragments of LMPs. Comparison with simple fragmentation models confirms deficit of SMPs (especially of fibers in size range 150-300 µm), suggested to result from their leakage with brine. Multivariate statistical analysis indicates strong positive correlation of large fiber (>300 µm) counts and ice salinity.

Spectral homogeneity of human platelets investigated by SERS.

This paper describes a detailed study of the spectral homogeneity of human platelets using Surface-enhanced Raman spectroscopy (SERS). We used a combined approach based on multivariate methods as principal component analysis and pair correlation algorithms to investigate platelets spectral properties. The correlation coefficients for each sample have been calculated, and the average coefficient of determination has been estimated. The high degree of spectral homogeneity inside one probe and between them has been revealed. The prospects of obtained results usage for pathologies based on platelet conformations during cardiovascular diseases have been demonstrated.

Spectral and time-resolved photoluminescence of human platelets doped with platinum nanoparticles.

This paper describes a detailed study of spectral and time-resolved photoprocesses in human platelets and their complexes with platinum (Pt) nanoparticles (NPs). Fluorescence, quantum yield, and platelet amino acid lifetime changes in the presence and without femtosecond ablated platinum NPs have been studied. Fluorescence spectroscopy analysis of main fluorescent amino acids and their residues (tyrosine (Tyr), tryptophan (Trp), and phenylalanine (Phe)) belonging to the platelet membrane have been performed. The possibility of energy transfer between Pt NPs and the platelet membrane has been revealed. Förster Resonance Energy Transfer (FRET) model was used to perform the quantitative evaluation of energy transfer parameters. The prospects of Pt NPs usage deals with quenching-based sensing for pathology's based on platelet conformations as cardiovascular diseases have been demonstrated.

Numerical FDTD-based simulations and Raman experiments of femtosecond LIPSS.

The article describes the results of finite-difference time-domain (FDTD) mathematical modeling of electric field strength distribution near the gold laser-induced periodic surface structures (LIPSS). Both theoretical and experimental results have been described for two fabricated morphologies: round «hill-like¼ and grating structures. The structures were fabricated by using a femtosecond Yb-fiber laser with a wavelength of λ=1032 nm, pulse duration τ=280 fs, and repetition rate υ=25 kHz. Morphological properties of the surfaces have been investigated by means of scanning electron microscopy (SEM). The plasmonic activity was analyzed by means of the surface-enhanced Raman spectroscopy (SERS) technique. FDTD-calculated electric field values were converted into the electromagnetic field enhancement coefficient and the theoretical SERS intensity. The prospects of the theoretical approach for LIPSS to evaluate optimal field amplification and light scattering parameters has been shown. The presented approach could be applied as a basis for performing the methods of controlled synthesis for LIPPS.

FTDT simulations of local plasmonic fields for theranostic core-shell gold-based nanoparticles.

The paper describes the results of finite-difference time-domain (FDTD) mathematical modeling of electromagnetic fields distortion near the surfaces of core-shell gold-based spherical gold nanoparticles (NPs). NPs were consistently functionalized by two shells of different thickness: a water shell, as a model substance for a drug, and an SiO2 shell, as a capsuling layer. The calculated field values were converted into the electromagnetic field enhancement coefficient and the surface-enhanced Raman scattering (SERS) intensity. Prospects of the theoretical approach for core-shell NPs modeling to evaluate optimal field amplification and light-scattering parameters have been shown. The presented approach could be applied as a basis for performing methods of controlled synthesis for colloidal core-shell theranostic NPs.

From macro to micro: dataset on plastic contamination along and across a sandy tide-less coast (the Curonian Spit, the Baltic Sea).

The contamination by macrolitter (>25 mm), mesolitter (5-25 mm), large microlitter (2-5 mm), large and small microplastics (L-MPs (2-5 mm) and S-MPs (0.5-2 mm), accordingly) in the surface beach sand at 6 locations along the 100-km-long marine coast of the Curonian Spit UNESCO National Park and the neighboring city beaches is quantified. In total, 55 samples obtained during 1-2 May 2018 are analyzed. Primary data is provided, along with exhaustive information on sampling dates and coordinates, sampling methods, extracting procedures, control measures, detection techniques, and µ-Raman spectroscopy verification. The number of items per m2 and items per kg dry weight (for MPs) is determined separately for fibres, films, and fragments. Distributions by size and plastic type are presented. Standard protocols, a modified NOAA method, and µ-Raman spectroscopy were applied to obtain the data, thus they can be used for comparative analyses.

Dataset of human platelets in healthy and individuals with cardiovascular pathology obtained by surface-enhanced Raman spectroscopy.

This data article contains Raman experimental data, obtained with Centaur U Raman spectrometer (Russia), which can be used for rapid and early structure changes and biomarkers identification in individuals with cardiovascular decease (CVD) pathology in vitro. The data include analyzed Surface-Enhanced Raman Scattering (SERS) spectra of human platelets taken from healthy individuals and individuals with cardiovascular pathology. Data can provide information about characteristic maxima of different cell components and its changes in platelets.

Dataset of single Mycobacterium tuberculosis bacteria cells with different antibiotic susceptibility obtained by Raman spectroscopy.

This data article contains Raman experimental data, obtained with Horiba Jobin-Yvon LabRam HR800 spectrometer (Japan), which can be used for rapid identification of Mycobacterium tuberculosis (MbT) bacteria (Beijing clade) in vitro. Data present analyzed Raman spectra of bacterial cells with various drug resistances obtained from pulmonary and extra pulmonary samples. Data can provide information about characteristic maxima of different structures in biological cell.

Ordinary differential equations and Boolean networks in application to modelling of 6-mercaptopurine metabolism.

We consider two approaches to modelling the cell metabolism of 6-mercaptopurine, one of the important chemotherapy drugs used for treating acute lymphocytic leukaemia: kinetic ordinary differential equations, and Boolean networks supplied with one controlling node, which takes continual values. We analyse their interplay with respect to taking into account ATP concentration as a key parameter of switching between different pathways. It is shown that the Boolean networks, which allow avoiding the complexity of general kinetic modelling, preserve the possibility of reproducing the principal switching mechanism.

The data obtained during the analysis of clinical blood samples for children acute lymphoblastic leukemia patients with severe side-effects.

The present work contains data obtained during the analysis of blood samples obtained from patients (number: 102, age: 0-2 years old) with confirmed acute lymphoblastic leukemia diagnosis. Among these total number, 48 patients who received a chemotherapy including 9 patients with side-effects were chosen. Final data include a table of protein masses (biomarkers of pathological processes at the chemotherapy) obtained by the MALDI-TOF spectroscopy from blood of 9 chosen patients (0-2 years old).

Dataset on metabolomics profile of acute leukemia blood obtained by the NMR methods.

This article contains NMR (nuclear magnetic resonance) experimental data, obtained by the NMR Varian 400 MHz spectrometer (USA) which can be used for the metabolites identification in human blood. Data include analyzed NMR spectra of plasma proteins extracted from human blood of 24 patients (0-5 years old) with the confirmed acute leukemia diagnosis. Data can provide information about metabolites and their concentration in blood.