Gdańsk University of Technology

In 2008 we published the fi rst set of guidelines for standardiz- ing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the fi eld. Our knowledge base and relevant new tech- nologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in differ- ent organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between meas urements that monitor the num- bers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the com- plete process including the amoun t and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accu mulation must be differentiated from stimuli that increas e autophagic activity, de fi ned as increased autophagy induction coupled with in creased delivery to, and degra- dation within, lysosomes (in most higher eukaryotes and some pro- tists such as Dictyostelium ) or the vacuole (in plants and fungi). In otherwords,itisespeciallyimportantthatinvestigatorsnewtothe fi eld understand that the appearance of more autophagosomes does not necessarily equate with mo re autophagy. In fact, in many cases, autophagosomes accumu late because of a block in traf fi cking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may re fl ect a reductionindegradativeactivity .Itisworthemphasizingherethat lysosomal digestion is a stage of au tophagy and evaluating its com- petence is a crucial part of the evaluation of autophagic fl ux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appro- priate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no indi- vidual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy- related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a speci fi c marker for an autophagic process. In these guidelines, we con- sider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the fi eld

Developing a mechanistic understanding of the impact of food structure and composition on human health has increasingly involved simulating digestion in the upper gastrointestinal tract. These simulations have used a wide range of different conditions that often have very little physiological relevance, and this impedes the meaningful comparison of results. The standardized protocol presented here is based on an international consensus developed by the COST INFOGEST network. The method is designed to be used with standard laboratory equipment and requires limited experience to encourage a wide range of researchers to adopt it. It is a static digestion method that uses constant ratios of meal to digestive fluids and a constant pH for each step of digestion. This makes the method simple to use but not suitable for simulating digestion kinetics. Using this method, food samples are subjected to sequential oral, gastric and intestinal digestion while parameters such as electrolytes, enzymes, bile, dilution, pH and time of digestion are based on available physiological data. This amended and improved digestion method (INFOGEST 2.0) avoids challenges associated with the original method, such as the inclusion of the oral phase and the use of gastric lipase. The method can be used to assess the endpoints resulting from digestion of foods by analyzing the digestion products (e.g., peptides/amino acids, fatty acids, simple sugars) and evaluating the release of micronutrients from the food matrix. The whole protocol can be completed in ~7 d, including ~5 d required for the determination of enzyme activities.

Green analytical chemistry focuses on making analytical procedures more environmentally benign and safer to humans. The amounts and toxicity of reagents, generated waste, energy requirements, the number of procedural steps, miniaturization, and automation are just a few of the multitude of criteria considered when assessing an analytical methodology's greenness. The use of greenness assessment criteria requires dedicated tools. We propose the Analytical GREEnness calculator, a comprehensive, flexible, and straightforward assessment approach that provides an easily interpretable and informative result. The assessment criteria are taken from the 12 principles of green analytical chemistry (SIGNIFICANCE) and are transformed into a unified 0-1 scale. The final score is calculated based on the SIGNIFICANCE principles. The result is a pictogram indicating the final score, performance of the analytical procedure in each criterion, and weights assigned by the user. Freely available software makes the assessment procedure straightforward. It is open-source and downloadable from https://mostwiedzy.pl/AGREE.

The dictum that ``information is physical'' indicates that we should understand how features of quantum physics, in particular, the phenomenon of quantum coherence, can be understood to be, and quantified as, a resource for the processing of information. This Colloquium discusses how to characterize, quantify, and manipulate quantum coherence, in application areas ranging from many-body and solid state physics to biological and nanoscale systems.

These days deep learning is the fastest-growing field in the field of Machine Learning (ML) and Deep Neural Networks (DNN). Among many of DNN structures, the Convolutional Neural Networks (CNN) are currently the main tool used for the image analysis and classification purposes. Although great achievements and perspectives, deep neural networks and accompanying learning algorithms have some relevant challenges to tackle. In this paper, we have focused on the most frequently mentioned problem in the field of machine learning, that is the lack of sufficient amount of the training data or uneven class balance within the datasets. One of the ways of dealing with this problem is so called data augmentation. In the paper we have compared and analyzed multiple methods of data augmentation in the task of image classification, starting from classical image transformations like rotating, cropping, zooming, histogram based methods and finishing at Style Transfer and Generative Adversarial Networks, along with the representative examples. Next, we presented our own method of data augmentation based on image style transfer. The method allows to generate the new images of high perceptual quality that combine the content of a base image with the appearance of another ones. The newly created images can be used to pre-train the given neural network in order to improve the training process efficiency. Proposed method is validated on the three medical case studies: skin melanomas diagnosis, histopathological images and breast magnetic resonance imaging (MRI) scans analysis, utilizing the image classification in order to provide a diagnose. In such kind of problems the data deficiency is one of the most relevant issues. Finally, we discuss the advantages and disadvantages of the methods being analyzed.

In this work, blue applicability grade index (BAGI) is proposed as a new metric tool for evaluating the practicality of an analytical method.

Titanium dioxide represents an effective photocatalyst for water and air purification and for self-cleaning surfaces. Additionally, it can be used as antibacterial agent because of strong oxidation activity and superhydrophilicity. TiO2 shows relatively high reactivity and chemical stability under ultraviolet light (λ < 387nm), whose energy exceeds the band gap of 3.3 eV in the anatase crystalline phase. The development of photocatalysts exhibiting high reactivity under visible light (λ > 400 nm) should allow the main part of the solar spectrum, even under poor illumination of interior lighting, to be used. Visible light-activated TiO2 could be prepared by metal-ion implantation, reducing of TiO2, nonmetal doping or sensitizing of TiO2 with dyes. This paper reviews preparation methods of doped-TiO2 with metallic and nonmetallic species, including various types of dopants and doping methods currently available. The mechanism of heterogeneous photocatalysis in the presence of TiO2 is also discussed. Keywords: Doped-TiO2, metal-doping, monmetal-doping, TiO2 preparation methods, heterogeneous photocatalysis

Researchers and brand managers have limited understanding of the effects social media communication has on how consumers perceive brands. We investigated 504 Facebook users in order to observe the impact of firm-created and user-generated (UG) social media communication on brand equity (BE), brand attitude (BA) and purchase intention (PI) by using a standardized online survey throughout Poland. To test the conceptual model, we analyzed 60 brands across three different industries: non-alcoholic beverages, clothing and mobile network operators. When analyzing the data, we applied the structural equation modeling technique to both investigate the interplay of firm-created and user-generated social media communication and examine industry-specific differences. The results of the empirical studies showed that user-generated social media communication had a positive influence on both brand equity and brand attitude, whereas firm-created social media communication affected only brand attitude. Both brand equity and brand attitude were shown to have a positive influence on purchase intention. In addition, we assessed measurement invariance using a multi-group structural modeling equation. The findings revealed that the proposed measurement model was invariant across the researched industries. However, structural path differences were detected across the models.

It is not easy to find appropriate tools for the evaluation of the “green” nature of analytical methodologies which involve the use of compounds, materials, or chemicals manufactured prior to the analytical step.

Chitin is a polysaccharide composed from N-acetyl-D-glucosamine units. It is the second most abundant biopolymer on Earth and found mainly in invertebrates, insects, marine diatoms, algae, fungi, and yeasts. Recent investigations confirm the suitability of chitin and its derivatives in chemistry, biotechnology, medicine, veterinary, dentistry, agriculture, food processing, environmental protection, and textile production. The development of technologies based on the utilization of chitin derivatives is caused by their polyelectrolite properties, the presence of reactive functional groups, gel-forming ability, high adsorption capacity, biodegradability and bacteriostatic, and fungistatic and antitumour influence. Resources of chitin for industrial processing are crustacean shells and fungal mycelia. Fungi contain also chitosan, the product of N-deacetylation of chitin. Traditionally, chitin is isolated from crustacean shells by demineralization with diluted acid and deproteinization in a hot base solution. Furthermore, chitin is converted to chitosan by deacetylation in concentrated NaOH solution. It causes changes in molecular weight and a degree of deacetylation of the product and degradation of nutritionally valuable proteins. Thus, enzymatic procedures for deproteinization of the shells or mold mycelia and for chitin deacetylation were investigated. These studies show that chitin is resistant to enzymatic deacetylation. However, chitin deacetylated partially by chemical treatment can be processed further by deacetylase. Efficiency of enzymatic deproteinization depends on the source of crustacean offal and the process conditions. Mild enzymatic treatment removes about 90% of the protein and carotenoids from shrimp-processing waste, and the carotenoprotein produced is useful for feed supplementation. In contrast, deproteinization of shrimp shells by Alcalase led to the isolation of chitin containing about 4.5% of protein impurities and recovery of protein hydrolysate.

In this work, we present our discovery and characterization of a new kagome prototype structure, ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$. We also present the discovery of the isostructural compounds ${\mathrm{RbV}}_{3}{\mathrm{Sb}}_{5}$ and ${\mathrm{CsV}}_{3}{\mathrm{Sb}}_{5}$. All materials exhibit a structurally perfect two-dimensional kagome net of vanadium. Density-functional theory calculations indicate that the materials are metallic, with the Fermi level in close proximity to several Dirac points. Powder and single-crystal syntheses are presented, with postsynthetic treatments shown to deintercalate potassium from single crystals of ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$. Considering the proximity to Dirac points, deintercalation provides a convenient means to tune the Fermi level. Magnetization measurements indicate that ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$ exhibits behavior consistent with a the Curie-Weiss model at high temperatures, although the effective moment is low $(0.22{\ensuremath{\mu}}_{\text{B}}$ per vanadium ion). An anomaly is observed in both magnetization and heat capacity measurements at 80 K, below which the moment is largely quenched. Elastic neutron scattering measurements find no obvious evidence of long-range or short-range magnetic ordering below 80 K. The possibility of an orbital-ordering event is considered. Single-crystal resistivity measurements show the effect of deintercalation on the electron transport and allow estimation of the Kadowaki-Woods ratio in ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$. We find that $A/{\ensuremath{\gamma}}^{2}\ensuremath{\sim}61\phantom{\rule{4pt}{0ex}}\ensuremath{\mu}\mathrm{Ohm}$ cm ${\mathrm{mol}}_{\text{FU}}^{2}\phantom{\rule{4pt}{0ex}}{\mathrm{K}}^{2}\phantom{\rule{4pt}{0ex}}{\mathrm{J}}^{\ensuremath{-}2}$, suggesting that correlated electron transport may be possible. ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$ and its cogeners ${\mathrm{RbV}}_{3}{\mathrm{Sb}}_{5}$ and ${\mathrm{CsV}}_{3}{\mathrm{Sb}}_{5}$ represent a new family of kagome metals, and our results demonstrate that they deserve further study as potential model systems.

During the last five years, several methods have been proposed for handling nonlinear constraints using evolutionary algorithms (EAs) for numerical optimization problems. Recent survey papers classify these methods into four categories: preservation of feasibility, penalty functions, searching for feasibility, and other hybrids. In this paper we investigate a new approach for solving constrained numerical optimization problems which incorporates a homomorphous mapping between n-dimensional cube and a feasible search space. This approach constitutes an example of the fifth decoder-based category of constraint handling techniques. We demonstrate the power of this new approach on several test cases and discuss its further potential.

Nitrogen-doped titania photocatalysts were prepared from titanium tetraisopropoxide or titanium tetrachloride and thiourea. The yellow powders obtained after calcination at 400−600 °C photocatalyze the mineralization of 4-chlorophenol by visible light (λ ≥ 455 nm). Different from previously published data these materials do not contain sulfur but instead nitrogen as the doping component inducing visible light photocatalysis. The measured band gap narrowing of 40−80 meV and the anodic shift of the quasi Fermi potential of 40−90 mV are in agreement with recent results on nitrogen-doped titania.

This study investigated – for the first time – the simultaneous degradation of benzene, toluene, ethylbenzene and o-xylene (BTEX) by persulfate (PS) and peroxymonosulfate (PMS) activated by asphaltenes (Asph) under ultrasound (US) irradiation. Advantageous properties such as high thermal stability, low production cost and extensive availability make asphaltenes as an appealing carbonaceous material for heterogeneous catalysis. The application of asphaltenes in PS/US increased the degradation of BTEXs from 31%, 34%, 35%, 32%–78%, 94%, 98% and 98%, while the removal of these compounds in PMS/US system was improved from 26%, 27%, 24%, 20%–76%, 91%, 97%, 97%, respectively. PS and PMS activation followed a typical sulfate-radical based advanced oxidation processes. In terms of activation of PS and PMS, the particles of asphaltenes intensified formation of reactive radicals by creating additional centers of cavitational events. Moreover, owing to π–π stacking interaction between asphaltenes and sp2-hybridized systems of BTEX, the contaminants undergo adsorption on the surface of asphaltenes and subsequent oxidation by formed radicals. The radical route of BTEX degradation in both PS/US/Asph and PMS/US/Asph systems was mainly contributed by sulfate (SO4•−) and hydroxyl radicals (HO•) and coexisting superoxide radical anions (O2•−) played a minor role.

The use of cavitation in advanced oxidation processes (AOPs) to treat acidic effluents and process water has become a promising trend in the area of environmental protection. The pH value of effluents – often acidified using an inorganic acid, is one of the key parameters of optimization process. However, in the majority of cases the effect of kind of inorganic acid on the effectiveness of degradation is not studied. The present study describes the results of investigations on the use of hydrodynamic cavitation (HC) for the treatment of a model effluent containing 20 organic compounds, representing various groups of industrial pollutants. The effluent was acidified using three different mineral acids. It was demonstrated that the kind of acid used strongly affects the effectiveness of radical processes of oxidation of organic contaminants as well as formation of harmful secondary pollutants. One of important examples is a risk of formation of p-nitrotolune. Sulfuric acid was the only chemical used for acidification which caused effective treatment with lack of formation of monitored type of secondary pollutants. The best treatment effectiveness – during a 6-hour cavitation process - in most cases much above 80% along with 90% TOC removal was obtained in the case of sulfuric acid. Nitric acid provided lower effectiveness (above 60% for most of the compounds). The worst performance are reported for hydrochloric acid – below 50% of degradation for most of the compounds.

Double-strand breaks (DSBs) are the most deleterious DNA lesions, which, if left unrepaired, may have severe consequences for cell survival, as they lead to chromosome aberrations, genomic instability, or cell death. Various physical, chemical, and biological factors are involved in DSB induction. Cells respond to DNA damage by activating the so-called DNA damage response (DDR), a complex molecular mechanism developed to detect and repair DNA damage. The formation of DSBs triggers activation of many factors, including phosphorylation of the histone variant H2AX, producing gammaH2AX. Phosphorylation of H2AX plays a key role in DDR and is required for the assembly of DNA repair proteins at the sites containing damaged chromatin as well as for activation of checkpoints proteins which arrest the cell cycle progression. In general, analysis of gammaH2AX expression can be used to detect the genotoxic effect of different toxic substances. When applied to clinical samples from cancer patients, evaluation of gammaH2AX levels may allow not only to monitor the efficiency of anticancer treatment but also to predict of tumor cell sensitivity to DNA damaging anticancer agents and toxicity of anticancer treatment toward normal cells.

Lignocellulosic biomass is an abundant and renewable resource that potentially contains large amounts of energy. It is an interesting alternative for fossil fuels, allowing the production of biofuels and other organic compounds. In this paper, a review devoted to the processing of lignocellulosic materials as substrates for fermentation processes is presented. The review focuses on physical, chemical, physicochemical, enzymatic, and microbiologic methods of biomass pretreatment. In addition to the evaluation of the mentioned methods, the aim of the paper is to understand the possibilities of the biomass pretreatment and their influence on the efficiency of biofuels and organic compounds production. The effects of different pretreatment methods on the lignocellulosic biomass structure are described along with a discussion of the benefits and drawbacks of each method, including the potential generation of inhibitory compounds for enzymatic hydrolysis, the effect on cellulose digestibility, the generation of compounds that are toxic for the environment, and energy and economic demand. The results of the investigations imply that only the stepwise pretreatment procedure may ensure effective fermentation of the lignocellulosic biomass. Pretreatment step is still a challenge for obtaining cost-effective and competitive technology for large-scale conversion of lignocellulosic biomass into fermentable sugars with low inhibitory concentration.

The concept of green chemistry is widely recognized in chemical laboratories. To properly measure an environmental impact of chemical processes, dedicated assessment tools are required. This paper summarizes the current state of knowledge in the field of development of green chemistry and green analytical chemistry metrics. The diverse methods used for evaluation of the greenness of organic synthesis, such as eco-footprint, E-Factor, EATOS, and Eco-Scale are described. Both the well-established and recently developed green analytical chemistry metrics, including NEMI labeling and analytical Eco-scale, are presented. Additionally, this paper focuses on the possibility of the use of multivariate statistics in evaluation of environmental impact of analytical procedures. All the above metrics are compared and discussed in terms of their advantages and disadvantages. The current needs and future perspectives in green chemistry metrics are also discussed.

Fifteen commercial titania (titanium(iv) oxide; TiO(2)) powders were modified with gold by photodeposition to prepare photocatalysts that work under irradiation with light in the visible range (vis). The gold-modified titania (Au/TiO(2)) powders were characterized by diffuse reflectance spectroscopy (DRS), field-emission scanning electron microscopy (FE-SEM), scanning transmission microscopy (STEM) and X-ray powder diffraction (XRD). It was shown that all tested powders could absorb visible light with an absorption maximum at localized surface plasmon resonance (LSPR) wavelengths (530-600 nm) and that the size and shape of gold nanoparticles determined the absorption ranges. The photocatalytic activity of Au/TiO(2) powders was examined both under ultraviolet and vis irradiation (mainly >450 nm) for acetic acid and 2-propanol photooxidation. It was found that the activity depended strongly on gold and titania properties, such as particle size and shape, surface area and crystalline form. Under vis irradiation, large rutile particles loaded with gold particles of a wide range of sizes showed the highest level of photocatalytic activity, possibly due to greater light absorption ability in a wide wavelength range resulting from transverse and longitudinal LSPR of rod-like gold particles. Action spectrum analyses showed that visible-light-induced oxidation of organic compounds by aerated gold-titania suspensions was initiated by excitation of LSPR absorption of gold. Although photocatalytic activity of nanosized gold particles under vis irradiation with a wavelength of ca. 430 nm and catalytic activity of gold-modified titania during dark reactions were also found, it was shown that the activities of Au/TiO(2) particles originated from activation of LSPR of gold by light of wavelength of 530-650 nm. Participation of molecular oxygen as an electron acceptor and titania as a conductor of electrons is suggested by comparing with results obtained under deaerated conditions and results obtained using a system containing gold-deposited silica instead of gold-titania, respectively. On the basis of these results, the mechanism of visible-light-induced oxidation of organic compounds on gold-titania is proposed.

Molecular-dynamics simulations were carried out for the SPC, SPCE, TIP4P, and TIP5P models of water at 298 K. From these results we determine the following quantities: the absolute entropy using the two-particle approximation, the mean lifetime of the hydrogen bond, the mean number of hydrogen bonds per molecule, and the mean energy of the hydrogen bond. From the entropy calculations we find that nearly all contributions to the total entropy originates from the orientation effects. Moreover, we determine the contributions to the total entropy which originate from the first, second, and higher solvation shells. It is interesting that the limits between solvation shells are clearly visible. The first solvation shell (0.22 < r < 0.36 nm) contributes approximately 43 J mol K to the total entropy; the second solvation shell (0.36 < r < 0.60 nm) contributes approximately 12 J mol K, while contributions from the third and other solvation shells are very small, approximately 2 J mol K in summary. This indicates that water molecules are strongly ordered up to 0.55-0.6 nm around the central water molecule, and beyond this limit the ordering diminishes. The results of calculations (entropy and hydrogen bonds) are compared with the experimental data for the choosing of the best water model. We find that the SPC and TIP4P models reproduce the best experimental values, and we recommend these models for computer simulations of the aqueous solution of biomolecules.