Lodz University of Technology

Mayerhoefer M.E., Materka A., Langs G., Häggström I., Szczypiński P., Gibbs P., Cook G.

Radiomics is a rapidly evolving field of research concerned with the extraction of quantitative metrics-the so-called radiomic features-within medical images. Radiomic features capture tissue and lesion characteristics such as heterogeneity and shape and may, alone or in combination with demographic, histologic, genomic, or proteomic data, be used for clinical problem solving. The goal of this continuing education article is to provide an introduction to the field, covering the basic radiomics workflow: feature calculation and selection, dimensionality reduction, and data processing. Potential clinical applications in nuclear medicine that include PET radiomics-based prediction of treatment response and survival will be discussed. Current limitations of radiomics, such as sensitivity to acquisition parameter variations, and common pitfalls will also be covered.

Markowiak-Kopeć P., Śliżewska K.

The relationship between diet and the diversity and function of the intestinal microbiome and its importance for human health is currently the subject of many studies. The type and proportion of microorganisms found in the intestines can determine the energy balance of the host. Intestinal microorganisms perform many important functions, one of which is participation in metabolic processes, e.g., in the production of short-chain fatty acids—SCFAs (also called volatile fatty acids). These acids represent the main carbon flow from the diet to the host microbiome. Maintaining intestinal balance is necessary to maintain the host’s normal health and prevent many diseases. The results of many studies confirm the beneficial effect of probiotic microorganisms on the balance of the intestinal microbiome and produced metabolites, including SCFAs. The aim of this review is to summarize what is known on the effects of probiotics on the production of short-chain fatty acids by gut microbes. In addition, the mechanism of formation and properties of these metabolites is discussed and verified test results confirming the effectiveness of probiotics in human nutrition by modulating SCFAs production by intestinal microbiome is presented.

Decking W., Abeghyan S., Abramian P., Abramsky A., Aguirre A., Albrecht C., Alou P., Altarelli M., Altmann P., Amyan K., Anashin V., Apostolov E., Appel K., Auguste D., Ayvazyan V., et. al.

The European XFEL is a hard X-ray free-electron laser (FEL) based on a high-electron-energy superconducting linear accelerator. The superconducting technology allows for the acceleration of many electron bunches within one radio-frequency pulse of the accelerating voltage and, in turn, for the generation of a large number of hard X-ray pulses. We report on the performance of the European XFEL accelerator with up to 5,000 electron bunches per second and demonstrating a full energy of 17.5 GeV. Feedback mechanisms enable stabilization of the electron beam delivery at the FEL undulator in space and time. The measured FEL gain curve at 9.3 keV is in good agreement with predictions for saturated FEL radiation. Hard X-ray lasing was achieved between 7 keV and 14 keV with pulse energies of up to 2.0 mJ. Using the high repetition rate, an FEL beam with 6 W average power was created. The first operation of the European X-ray free-electron laser facility accelerator based on superconducting technology is reported. The maximum electron energy is 17.5 GeV. A laser average power of 6 W is achieved at a photon energy of 9.3 keV.

Twarda-Clapa A., Olczak A., Białkowska A.M., Koziołkiewicz M.

Advanced glycation end-products (AGEs) constitute a non-homogenous, chemically diverse group of compounds formed either exogeneously or endogeneously on the course of various pathways in the human body. In general, they are formed non-enzymatically by condensation between carbonyl groups of reducing sugars and free amine groups of nucleic acids, proteins, or lipids, followed by further rearrangements yielding stable, irreversible end-products. In the last decades, AGEs have aroused the interest of the scientific community due to the increasing evidence of their involvement in many pathophysiological processes and diseases, such as diabetes, cancer, cardiovascular, neurodegenerative diseases, and even infection with the SARS-CoV-2 virus. They are recognized by several cellular receptors and trigger many signaling pathways related to inflammation and oxidative stress. Despite many experimental research outcomes published recently, the complexity of their engagement in human physiology and pathophysiological states requires further elucidation. This review focuses on the receptors of AGEs, especially on the structural aspects of receptor–ligand interaction, and the diseases in which AGEs are involved. It also aims to present AGE classification in subgroups and to describe the basic processes leading to both exogeneous and endogeneous AGE formation.

Ashfaq A., Clochard M., Coqueret X., Dispenza C., Driscoll M.S., Ulański P., Al-Sheikhly M.

Ionizing radiation has become the most effective way to modify natural and synthetic polymers through crosslinking, degradation, and graft polymerization. This review will include an in-depth analysis of radiation chemistry mechanisms and the kinetics of the radiation-induced C-centered free radical, anion, and cation polymerization, and grafting. It also presents sections on radiation modifications of synthetic and natural polymers. For decades, low linear energy transfer (LLET) ionizing radiation, such as gamma rays, X-rays, and up to 10 MeV electron beams, has been the primary tool to produce many products through polymerization reactions. Photons and electrons interaction with polymers display various mechanisms. While the interactions of gamma ray and X-ray photons are mainly through the photoelectric effect, Compton scattering, and pair-production, the interactions of the high-energy electrons take place through coulombic interactions. Despite the type of radiation used on materials, photons or high energy electrons, in both cases ions and electrons are produced. The interactions between electrons and monomers takes place within less than a nanosecond. Depending on the dose rate (dose is defined as the absorbed radiation energy per unit mass), the kinetic chain length of the propagation can be controlled, hence allowing for some control over the degree of polymerization. When polymers are submitted to high-energy radiation in the bulk, contrasting behaviors are observed with a dominant effect of cross-linking or chain scission, depending on the chemical nature and physical characteristics of the material. Polymers in solution are subject to indirect effects resulting from the radiolysis of the medium. Likewise, for radiation-induced polymerization, depending on the dose rate, the free radicals generated on polymer chains can undergo various reactions, such as inter/intramolecular combination or inter/intramolecular disproportionation, b-scission. These reactions lead to structural or functional polymer modifications. In the presence of oxygen, playing on irradiation dose-rates, one can favor crosslinking reactions or promotes degradations through oxidations. The competition between the crosslinking reactions of C-centered free radicals and their reactions with oxygen is described through fundamental mechanism formalisms. The fundamentals of polymerization reactions are herein presented to meet industrial needs for various polymer materials produced or degraded by irradiation. Notably, the medical and industrial applications of polymers are endless and thus it is vital to investigate the effects of sterilization dose and dose rate on various polymers and copolymers with different molecular structures and morphologies. The presence or absence of various functional groups, degree of crystallinity, irradiation temperature, etc. all greatly affect the radiation chemistry of the irradiated polymers. Over the past decade, grafting new chemical functionalities on solid polymers by radiation-induced polymerization (also called RIG for Radiation-Induced Grafting) has been widely exploited to develop innovative materials in coherence with actual societal expectations. These novel materials respond not only to health emergencies but also to carbon-free energy needs (e.g., hydrogen fuel cells, piezoelectricity, etc.) and environmental concerns with the development of numerous specific adsorbents of chemical hazards and pollutants. The modification of polymers through RIG is durable as it covalently bonds the functional monomers. As radiation penetration depths can be varied, this technique can be used to modify polymer surface or bulk. The many parameters influencing RIG that control the yield of the grafting process are discussed in this review. These include monomer reactivity, irradiation dose, solvent, presence of inhibitor of homopolymerization, grafting temperature, etc. Today, the general knowledge of RIG can be applied to any solid polymer and may predict, to some extent, the grafting location. A special focus is on how ionizing radiation sources (ion and electron beams, UVs) may be chosen or mixed to combine both solid polymer nanostructuration and RIG. LLET ionizing radiation has also been extensively used to synthesize hydrogel and nanogel for drug delivery systems and other advanced applications. In particular, nanogels can either be produced by radiation-induced polymerization and simultaneous crosslinking of hydrophilic monomers in “nanocompartments”, i.e., within the aqueous phase of inverse micelles, or by intramolecular crosslinking of suitable water-soluble polymers. The radiolytically produced oxidizing species from water, •OH radicals, can easily abstract H-atoms from the backbone of the dissolved polymers (or can add to the unsaturated bonds) leading to the formation of C-centered radicals. These C-centered free radicals can undergo two main competitive reactions; intramolecular and intermolecular crosslinking. When produced by electron beam irradiation, higher temperatures, dose rates within the pulse, and pulse repetition rates favour intramolecular crosslinking over intermolecular crosslinking, thus enabling a better control of particle size and size distribution. For other water-soluble biopolymers such as polysaccharides, proteins, DNA and RNA, the abstraction of H atoms or the addition to the unsaturation by •OH can lead to the direct scission of the backbone, double, or single strand breaks of these polymers.

Kemona A., Piotrowska M.

Growing water and land pollution, the possibility of exhaustion of raw materials and resistance of plastics to physical and chemical factors results in increasing importance of synthetic polymers waste recycling, recovery and environmentally friendly ways of disposal. Polyurethanes (PU) are a family of versatile synthetic polymers with highly diverse applications. They are class of polymers derived from the condensation of polyisocyanates and polyalcohols. This paper reports the latest developments in the field of polyurethane disposal, recycling and recovery. Various methods tested and applied in recent years have proven that the processing of PU waste can be economically and ecologically beneficial. At the moment mechanical recycling and glycolysis are the most important ones. Polyurethanes’ biological degradation is highly promising for both post-consumer and postproduction waste. It can also be applied in bioremediation of water and soil contaminated with polyurethanes. Another possibility for biological methods is the synthesis of PU materials sensitive to biological degradation. In conclusion, a high diversity of polyurethane waste types and derivation results in demand for a wide range of methods of processing. Furthermore, already existing ones appear to be enough to state that the elimination of not reprocessed polyurethane waste in the future is possible.

Apostolopoulos V., Bojarska J., Chai T., Elnagdy S., Kaczmarek K., Matsoukas J., New R., Parang K., Lopez O.P., Parhiz H., Perera C.O., Pickholz M., Remko M., Saviano M., Skwarczynski M., et. al.

Peptides are fragments of proteins that carry out biological functions. They act as signaling entities via all domains of life and interfere with protein-protein interactions, which are indispensable in bio-processes. Short peptides include fundamental molecular information for a prelude to the symphony of life. They have aroused considerable interest due to their unique features and great promise in innovative bio-therapies. This work focusing on the current state-of-the-art short peptide-based therapeutical developments is the first global review written by researchers from all continents, as a celebration of 100 years of peptide therapeutics since the commencement of insulin therapy in the 1920s. Peptide “drugs” initially played only the role of hormone analogs to balance disorders. Nowadays, they achieve numerous biomedical tasks, can cross membranes, or reach intracellular targets. The role of peptides in bio-processes can hardly be mimicked by other chemical substances. The article is divided into independent sections, which are related to either the progress in short peptide-based theranostics or the problems posing challenge to bio-medicine. In particular, the SWOT analysis of short peptides, their relevance in therapies of diverse diseases, improvements in (bio)synthesis platforms, advanced nano-supramolecular technologies, aptamers, altered peptide ligands and in silico methodologies to overcome peptide limitations, modern smart bio-functional materials, vaccines, and drug/gene-targeted delivery systems are discussed.

Efenberger-Szmechtyk M., Nowak A., Czyzowska A.

Plant extracts contain large amounts of bioactive compounds, mainly polyphenols. Polyphenols inhibit the growth of microorganisms, especially bacteria. Their mechanism of action is still not fully understood but may be related to their chemical structure. They can cause morphological changes in microorganisms, damage bacterial cell walls and influence biofilm formation. Polyphenols also influence protein biosynthesis, change metabolic processes in bacteria cells and inhibit ATP and DNA synthesis (suppressing DNA gyrase). Due to the antioxidant and antibacterial activity of phenolic compounds, plant extracts offer an alternative to chemical preservatives used in the meat industry, especially nitrates (III). They can inhibit the growth of spoilage and pathogenic microflora, suppress oxidation of meat ingredients (lipids and proteins) and prevent discoloration. In this paper, we describe the factors that influence the content of polyphenols in plants and plant extracts. We present the antimicrobial activities of plant extracts and their mechanisms of action, and discuss the effects of plant extracts on the shelf-life of meat and meat products.

Noroozi F., Corneanu C.A., Kaminska D., Sapinski T., Escalera S., Anbarjafari G.

Automatic emotion recognition has become a trending research topic in the past decade. While works based on facial expressions or speech abound, recognizing affect from body gestures remains a less explored topic. We present a new comprehensive survey hoping to boost research in the field. We first introduce emotional body gestures as a component of what is commonly known as ”body language” and comment general aspects as gender differences and culture dependence. We then define a complete framework for automatic emotional body gesture recognition. We introduce person detection and comment static and dynamic body pose estimation methods both in RGB and 3D. We then comment the recent literature related to representation learning and emotion recognition from images of emotionally expressive gestures. We also discuss multi-modal approaches that combine speech or face with body gestures for improved emotion recognition. While pre-processing methodologies (e.g., human detection and pose estimation) are nowadays mature technologies fully developed for robust large scale analysis, we show that for emotion recognition the quantity of labelled data is scarce. There is no agreement on clearly defined output spaces and the representations are shallow and largely based on naive geometrical representations.

Białkowska K., Komorowski P., Bryszewska M., Miłowska K.

Cell cultures are very important for testing materials and drugs, and in the examination of cell biology and special cell mechanisms. The most popular models of cell culture are two-dimensional (2D) as monolayers, but this does not mimic the natural cell environment. Cells are mostly deprived of cell–cell and cell–extracellular matrix interactions. A much better in vitro model is three-dimensional (3D) culture. Because many cell lines have the ability to self-assemble, one 3D culturing method is to produce spheroids. There are several systems for culturing cells in spheroids, e.g., hanging drop, scaffolds and hydrogels, and these cultures have their applications in drug and nanoparticles testing, and disease modeling. In this paper we would like to present methods of preparation of spheroids in general and emphasize the most important applications.