Machine Learning Meets Cancer.

The role of machine learning (a part of artificial intelligence-AI) in the diagnosis and treatment of various types of oncology is steadily increasing. It is expected that the use of AI in oncology will speed up both diagnostic and treatment planning processes. This review describes recent applications of machine learning in oncology, including medical image analysis, treatment planning, patient survival prognosis, and the synthesis of drugs at the point of care. The fast and reliable analysis of medical images is of great importance in the case of fast-flowing forms of cancer. The introduction of ML for the analysis of constantly growing volumes of big data makes it possible to improve the quality of prescribed treatment and patient care. Thus, ML is expected to become an essential technology for medical specialists. The ML model has already improved prognostic prediction for patients compared to traditional staging algorithms. The direct synthesis of the necessary medical substances (small molecule mixtures) at the point of care could also seriously benefit from the application of ML. We further review the main trends in the use of artificial intelligence-based technologies in modern oncology. This review demonstrates the future prospects of using ML tools to make progress in cancer research, as well as in other areas of medicine. Despite growing interest in the use of modern computer technologies in medical practice, a number of unresolved ethical and legal problems remain. In this review, we also discuss the most relevant issues among them.

Hydrogenation of ethylene over palladium: evolution of the catalyst structure by operando synchrotron-based techniques.

Palladium-based catalysts are exploited on an industrial scale for the selective hydrogenation of hydrocarbons. The formation of palladium carbide and hydride phases under reaction conditions changes the catalytic properties of the material, which points to the importance of operando characterization for determining the relation between the relative fractions of the two phases and the catalyst performance. We present a combined time-resolved characterization by X-ray absorption spectroscopy (in both near-edge and extended regions) and X-ray diffraction of a working palladium-based catalyst during the hydrogenation of ethylene in a wide range of partial pressures of ethylene and hydrogen. Synergistic coupling of multiple techniques allowed us to follow the structural evolution of the palladium lattice as well as the transitions between the metallic, hydride and carbide phases of palladium. The nanometric dimensions of the particles resulted in the considerable contribution of both surface and bulk carbides to the X-ray absorption spectra. During the reaction, palladium carbide is formed, which does not lead to a loss of activity. Unusual contraction of the unit cell parameter of the palladium lattice in the spent catalyst was observed upon increasing hydrogen partial pressure.

Nanomaterials for Deep Tumor Treatment.

According to statistics, cancer is the second leading cause of death in the world. Thus, it is important to solve this medical and social problem by developing new effective methods for cancer treatment. An alternative to more well-known approaches, such as radiotherapy and chemotherapy, is photodynamic therapy (PDT), which is limited to the shallow tissue penetration (< 1 cm) of visible light. Since the PDT process can be initiated in deep tissues by X-ray irradiation (X-ray induced PDT, or XPDT), it has a great potential to treat tumors in internal organs. The article discusses the principles of therapies. The main focus is on various nanoparticles used with or without photosensitizers, which allow the conversion of X-ray irradiation into UV-visible light. Much attention is given to the synthesis of nanoparticles and analysis of their characteristics, such as size and spectral features. The results of in vitro and in vivo experiments are also discussed.

Novel Copper-Containing Cytotoxic Agents Based on 2-Thioxoimidazolones.

A series of 73 ligands and 73 of their Cu+2 and Cu+1 copper complexes with different geometries, oxidation states of the metal, and redox activities were synthesized and characterized. The aim of the study was to establish the structure-activity relationship within a series of analogues with different substituents at the N(3) position, which govern the redox potentials of the Cu+2/Cu+1 redox couples, ROS generation ability, and intracellular accumulation. Possible cytotoxicity mechanisms, such as DNA damage, DNA intercalation, telomerase inhibition, and apoptosis induction, have been investigated. ROS formation in MCF-7 cells and three-dimensional (3D) spheroids was proven using the Pt-nanoelectrode. Drug accumulation and ROS formation at 40-60 µm spheroid depths were found to be the key factors for the drug efficacy in the 3D tumor model, governed by the Cu+2/Cu+1 redox potential. A nontoxic in vivo single-dose evaluation for two binuclear mixed-valence Cu+1/Cu+2 redox-active coordination compounds, 72k and 61k, was conducted.

Dehydrogenation of Ethylene on Supported Palladium Nanoparticles: A Double View from Metal and Hydrocarbon Sides.

Adsorption of ethylene on palladium, a key step in various catalytic reactions, may result in a variety of surface-adsorbed species and formation of palladium carbides, especially under industrially relevant pressures and temperatures. Therefore, the application of both surface and bulk sensitive techniques under reaction conditions is important for a comprehensive understanding of ethylene interaction with Pd-catalyst. In this work, we apply in situ X-ray absorption spectroscopy, X-ray diffraction and infrared spectroscopy to follow the evolution of the bulk and surface structure of an industrial catalysts consisting of 2.6 nm supported palladium nanoparticles upon exposure to ethylene under atmospheric pressure at 50 °C. Experimental results were complemented by ab initio simulations of atomic structure, X-ray absorption spectra and vibrational spectra. The adsorbed ethylene was shown to dehydrogenate to C2H3, C2H2 and C2H species, and to finally decompose to palladium carbide. Thus, this study reveals the evolution pathway of ethylene on industrial Pd-catalyst under atmospheric pressure at moderate temperatures, and provides a conceptual framework for the experimental and theoretical investigation of palladium-based systems, in which both surface and bulk structures exhibit a dynamic nature under reaction conditions.

Operando X-ray absorption spectra and mass spectrometry data during hydrogenation of ethylene over palladium nanoparticles.

We report the series of Pd K-edge X-ray absorption spectra collected during hydrogenation of ethylene with variable ethylene/hydrogen ratio over carbon supported palladium nanoparticles. The data presented in this article includes normalized X-ray absorption spectra, k 2-weighted oscillatory χ(k) functions extracted from the extended X-ray absorption fine structure (EXAFS) and k 2-weighted Fourier-transformed EXAFS data, χ(R). Each spectrum is reported together with the hydrogen, ethylene and helium flow rates, adjusted during its collection. In addition, time evolution of the ratio of m/Z signals of 30 and 28 registered by online mass spectrometer is presented. The data analysis is reported in Bugaev et al., Catal. Today, 2019 [1].

Synthesis of Iron Oxide Nanoclusters by Thermal Decomposition.

Herein, we report a novel one-step solvothermal synthesis of magnetite nanoclusters (MNCs). In this report, we discuss the synthesis, structure, and properties of MNCs and contrast enhancement in T2-weighted MR images using magnetite nanoclusters. The effect of different organic acids, used as surfactants, on the size and shape of MNCs was investigated. The structure and properties of samples were determined by magnetic measurements, TGA, TEM, HRTEM, XRD, FTIR, and MRI. Magnetic measurements show that obtained MNCs have relatively high saturation magnetization values (65.1-81.5 emu/g) and dependence of the coercive force on the average size of MNCs was established. MNCs were transferred into an aqueous medium by Pluronic F-127, and T2-relaxivity values were determined. T2-Weighted MR phantom images clearly demonstrated that such magnetite nanoclusters can be used as contrast agents for MRI.

Physicochemical Properties of Magnetic Nanoparticles: Implications for Biomedical Applications In Vitro and In Vivo.

Magnetic and superparamagnetic iron oxide nanoparticles are emerging as promising candidates for various applications in biology and medicine, and especially in oncology. These applications, however, require that a specific set of physical, chemical, and biological properties be combined in a given sample of nanoparticles for them to act as intended. Some of these properties are fundamental: They strictly determine the nanoparticles' behavior both in vitro and in vivo. These properties are the charge, the solution stability and zeta potential, and the coating of the nanoparticles. A certain combination of these properties may satisfy a researcher in an in vitro study, but other properties should also be considered when in vivo applications are planned. For in vivo experiments, additional determinants of the quality of nanoparticles are their size, shape, modifications with targeting moieties, and degradation/excretion pathways. All these properties are in the focus of the present review.

Low toxic maghemite nanoparticles for theranostic applications.

BACKGROUND: Iron oxide nanoparticles have numerous and versatile biological properties, ranging from direct and immediate biochemical effects to prolonged influences on tissues. Most applications have strict requirements with respect to the chemical and physical properties of such agents. Therefore, developing rational design methods of synthesis of iron oxide nanoparticles remains of vital importance in nanobiomedicine. METHODS: Low toxic superparamagnetic iron oxide nanoparticles (SPIONs) for theranostic applications in oncology having spherical shape and maghemite structure were produced using the fast microwave synthesis technique and were fully characterized by several complementary methods (transmission electron microscopy [TEM], X-ray diffraction [XRD], dynamic light scattering [DLS], X-ray photoelectron spectroscopy [XPS], X-ray absorption near edge structure [XANES], Mossbauer spectroscopy, and HeLa cells toxicity testing). RESULTS: TEM showed that the majority of the obtained nanoparticles were almost spherical and did not exceed 20 nm in diameter. The averaged DLS hydrodynamic size was found to be ~33 nm, while that of nanocrystallites estimated by XRD was16 nm. Both XRD and XPS studies evidenced the maghemite (γ-Fe2O3) atomic and electronic structure of the synthesized nanoparticles. The XANES data analysis demonstrated the structure of the nanoparticles being similar to that of macroscopic maghemite. The Mossbauer spectroscopy revealed the γ-Fe2O3 phase of the nanoparticles and vibration magnetometry study showed that reactive oxygen species in HeLa cells are generated both in the cytoplasm and the nucleus. CONCLUSION: Quasispherical Fe3+ SPIONs having the maghemite structure with the average size of 16 nm obtained by using the fast microwave synthesis technique are expected to be of great value for theranostic applications in oncology and multimodal anticancer therapy.

Individual expression features of GPX2, NQO1 and SQSTM1 transcript variants induced by hydrogen peroxide treatment in HeLa cells

Abstract Pathway activity assessment-based approaches are becoming highly influential in various fields of biology and medicine. However, these approaches mostly rely on analysis of mRNA expression, and total mRNA from a given locus is measured in the majority of cases. Notably, a significant portion of protein-coding genes produces more than one transcript. This biological fact is responsible for significant noise when changes in total mRNA transcription of a single gene are analyzed. The NFE2L2/AP-1 pathway is an attractive target for biomedical applications. To date, there is a lack of data regarding the agreement in expression of even classical target genes of this pathway. In the present paper we analyzed whether transcript variants of GPX2, NQO1 and SQSTM1 were characterized by individual features of expression when HeLa cells were exposed to pro-oxidative stimulation with hydrogen peroxide. We found that all the transcripts (10 in total) appeared to be significantly individually regulated under the conditions tested. We conclude that individual transcripts, rather than total mRNA, are best markers of pathway activation. We also discuss here some biological roles of individual transcript regulation.

XAFS spectral analysis of the cadmium coordination geometry in cadmium thiolate clusters in metallothionein.

We report the combination of measurement and prediction of X-ray absorption fine structure (XAFS) data, where the term XAFS refers to the overall spectrum that encompasses both the X-ray Absorption Near Edge Structure (XANES) region as well as the Extended X-ray Absorption Fine Structure (EXAFS) region, to evaluate the cadmium thiolate cluster structures in the metalloprotein metallothionein. XAFS spectra were simulated using coordinates from molecular models of the protein calculated by molecular mechanics/molecular dynamics (MM3/MD), from NMR analyses, and from analysis of X-ray diffraction data. XAFS spectra were also simulated using the coordinates from X-ray crystallographic data for [Cd(SPh)4]2-, CdS, [Cd2(mu-SPh)2(SPh)4]2-, and [Cd4(mu-SPh)6(SPh)4]2-. The simulated XAFS data that were calculated using the FEFF8 program closely resemble the experimental data reported for [Cd(SPh)4]2-, CdS, [Cd2(mu-SPh)2(SPh)4]2-, [Cd4(mu-SPh)6(SPh)4]2-, rabbit liver metallothionein cadmium alpha-domain (Cd4-alpha MT), and cadmium rabbit liver betaalpha metallothionein (Cd7-betaalpha MT). MM3 force field parameters were modified to include cadmium-sulfur bonding and were initially set to values derived from published X-ray diffraction and EXAFS experimental data. The force field was further calibrated and adjusted through comparison between experimental spectra taken from the literature and simulated XAFS spectra calculated using the FEFF8 program in combination with atomic coordinates from MM3/MD energy minimization. MM3/MD techniques were used with the calibrated force field to predict the high-resolution structure of the metal clusters in rabbit liver Cd7-MT. Structures for Cd3S9 (beta) MT and Cd4S11 (alpha) MT domains from MM3/MD calculations and those previously reported for Cd7-MT on the basis of 1H and 113Cd NMR data were compared. Structural differences between the different models for these cadmium thiolate clusters were evident. Combining the measurement and simulation of XAFS data provides an excellent method of assessing, modeling, and predicting metal-binding sites in metalloproteins when X-ray absorption spectroscopy (XAS) data are available.