bluuebunny/crossref_metadata_2025 huggingface dataset:
Security event data collection and analysis in large corporate networks
Authors:   Orenburg State University, Pobedy av., 13, Orenburg, Russia, 460018, Chernova Ekaterina , Polezhaev Petr ,   Orenburg State University, Pobedy av., 13, Orenburg, Russia, 460018, Shukhman Alexander ,   Orenburg State University, Pobedy av., 13, Orenburg, Russia, 460018, Ushakov Yury ,   Orenburg State University, Pobedy av., 13, Orenburg, Russia, 460018, Bolodurina Irina ,   Orenburg State University, Pobedy av., 13, Orenburg, Russia, 460018, Bakhareva Nadezhda ,   Povolzhskiy State University of Telecommunications and Informatics, L. Tolstoy str., 23, Samara, 443010
Published: December 2019

Every year computer networks become more complex, which directly affects the provision of a high level of information security. Different commercial services, critical systems, and information resources prevailing in such networks are profitable targets for terrorists, cyber-spies, and criminals. The consequences range from the theft of strategic, highly valued intellectual property and direct financial losses to significant damages to a brand and customer trust. Attackers have the advantage in complex computer networks – it is easier to hide their tracks. The detection and identification of security incidents are the most important and difficult tasks. It is required to detect security incidents as soon as possible, to analyze and respond to them correctly, so as not to complicate the work of the enterprise computer network. The difficulty is that different event sources offer different data formats or can duplicate events. In addition, some events do not indicate any problems on their own, but their sequence may indicate the presence of a security incident. All collection processes of security events must be performed in real-time, which means streaming data processing.
A multiuser web-interface for solution of systems of nonlinear equations
Authors:   Samara National Research University, Moskovskoe Shosse 34А, Samara, Russia, 443086, Danilenko Aleksandra , Zhdanov Ivan ,   University of Stuttgart, Keplerstraße 7, Stuttgart, Germany, 70174
Published: December 2019

In this article, the idea of creating web-applications is considered by the example of developing a multiuser web-interface for the automated search for roots of non-linear equations in the Django package. The automated system is implemented in the Python programming language. It is proposed to create a web application based on a client-server technology, where the client part implements the user interface, forms queries to the server and processes the responses from it. The server part receives the request from the client, performs necessary calculations, then forms a web page and sends it to the client online. The developed application is designed for nonlinear equations systems solution. The system has the ability to save solutions on the server and the PC, and to visualize the step-by-step solution and plotting. The system efficiency was tested on real data.
Hybridization of fuzzy time series and fuzzy ontologies in the diagnosis of complex technical systems
Authors:   Ulyanovsk State Technical University, Severny Venetz street, 32, Ulyanovsk, Russia, 432027, Yarushkina Nadezhda , Moshkin Vadim ,   Ulyanovsk State Technical University, Severny Venetz street, 32, Ulyanovsk, Russia, 432027, Andreev Ilya ,   Ulyanovsk State Technical University, Severny Venetz street, 32, Ulyanovsk, Russia, 432027, Ishmuratova Gelya ,   Ulyanovsk State Technical University, Severny Venetz street, 32, Ulyanovsk, Russia, 432027
Published: December 2019

The article provides a formal description of fuzzy ontologies and features of the representation of elements of fuzzy axioms in FuzzyOWL notation. An ontological model for assessing the state of helicopter units has been developed. According to the proposed approach, the summarizing of the state of a complex technical system is carried out by means of an inference based on a fuzzy ontology. As part of this work, experiments were conducted to search for anomalous situations and search for possible faulty helicopter units using the developed approach to the integration of fuzzy time series and fuzzy ontology. The proposed approach of hybridization of fuzzy time series and fuzzy ontologies made it possible to reliably recognize anomalous situations with a certain degree of truth, and to find possible faulty aggregates corresponding to each anomalous situation.
Adaptive algorithm of conforming image matching
Authors:   Samara National Research University, Moskovskoe Shosse 34А, Samara, Russia, 443086, Fursov Vladimir ,   Image Processing Systems Institute of RAS - Branch of the FSRC "Crystallography and Photonics" RAS, Molodogvardejskaya street 151, Samara, Russia, 443001, Goshin Yegor ,   Samara National Research University, Moskovskoe Shosse 34А, Samara, Russia, 443086,   Image Processing Systems Institute of RAS - Branch of the FSRC "Crystallography and Photonics" RAS, Molodogvardejskaya street 151, Samara, Russia, 443001, Pugachev Kirill ,   Samara National Research University, Moskovskoe Shosse 34А, Samara, Russia, 443086
Published: November 2019

This paper presents an adaptive algorithm of conforming image matching based on the principle of conformity. The algorithm consists of several main stages. At the first stage, we find the corresponding points using a minimum value of conformity as the measure of points’ similarity. We define a conformity function as the sum of all possible combinations of squared differences of pixel intensity values on the fragments that are matched. Then, we perform an adaptive procedure of errors correction considering an intensity gradient distribution. An important feature of the algorithm is the finding of error points using a criterion of maximum value of samples’ conformity for every fragment of the disparity map. The results of experiments on the "Teddy" test images are shown.
Comparison of the characteristics of the genetic algorithm and the method of coordinates search for optimization of temperature modes indoor areas
Authors:   Kalashnikov Izhevsk State Technical University, Studencheskaya, 7, Izhevsk, Russia, 426069, Shuravin Alexander , Vologdin Sergey ,   Kalashnikov Izhevsk State Technical University, Studencheskaya, 7, Izhevsk, Russia, 426069
Published: December 2019

The article substantiates the relevance of optimization algorithms research for solving various applied problems and for the science of artificial intelligence. The need to solve problems of optimizing the thermal-hydraulic modes of buildings (as part of the project "Smart City") is explained. The paper presents a mathematical formulation of the problem of optimizing the temperature mode of rooms using adjustable devices. Existing work provides two methods for solving the posed problem. They are the coordinates search method and the genetic algorithm. The article contains the description of the above mentioned algorithms (including the mathematical apparatus used). The results of the computational experiment (for the considered optimization methods) are presented. These experimental results show that the genetic algorithm provides better optimization results than the coordinates search method, but it has a large computational cost. The hypothesis was confirmed that in order to increase the efficiency of solving the considered class of problems it is necessary to combine the genetic algorithm and the coordinates search method.
Increasing signal/acoustic interference ratio in telecommunications audio exchange by adaptive filtering methods
Authors:   Murom Institute (branch) ", Kropotov Yuriy ,   Vladimir State University named after Alexander and Nicholay Stoletovs",   , Orlovskaya street, 23, Murom, Russia, 602264, Belov Aleksey ,   Murom Institute (branch) "Vladimir State University named after Alexander and Nicholay Stoletovs", Orlovskaya street, 23, Murom, Russia, 602264, Proskuryakov Aleksander ,   Murom Institute (branch) "Vladimir State University named after Alexander and Nicholay Stoletovs", Orlovskaya street, 23, Murom, Russia, 602264
Published: December 2019

The paper deals with the issues of increasing signal/noise ratio in telecommunication audio exchange systems. The study of characteristics of speech signals and acoustic noises, such as mathematical expectation, dispersion, relative intensity of acoustic speech signals and various types of acoustic noises and interference is carried out. It is shown that in the design of telecommunications systems, in particular loudspeaker systems operating under the influence of external acoustic noise of high intensity, it is necessary to solve the problem of developing algorithms to effectively suppress the above mentioned interference to ensure the necessary signal/noise ratio in communication systems. A mathematical model of the autocorrelation function of the speech signal by using the Lagrange interpolation polynomial of order 10, considered the creation of adaptive algorithms to suppress acoustic noise by linear filtering methods. Thus suppression of acoustic noises and hindrances is possible at the expense of operated change of area of a cutting in the interval from 0 Hz to 300-1000 Hz, depending on a hindrance conditions.
The syllable intelligibility in the system of information transmission by speech signals depending on the intensity of acoustic noise
Authors:   Murom Institute (branch) «Vladimir State University named after Alexander and Nicholay Stoletovs», Orlovskaya street, 23, Murom, Vladimir Region, Russia, 602264, Kropotov Yuriy , Belov Aleksey ,   Murom Institute (branch) «Vladimir State University named after Alexander and Nicholay Stoletovs», Orlovskaya street, 23, Murom, Vladimir Region, Russia, 602264, Kolpakov Aleksandr ,   Murom Institute (branch) «Vladimir State University named after Alexander and Nicholay Stoletovs», Orlovskaya street, 23, Murom, Vladimir Region, Russia, 602264, Proskuryakov Aleksander ,   Murom Institute (branch) «Vladimir State University named after Alexander and Nicholay Stoletovs», Orlovskaya street, 23, Murom, Vladimir Region, Russia, 602264
Published: December 2019

The paper investigates the effect of the signal-to-noise ratio on syllable intelligibility under the intense influence of external acoustic interference when exchanging voice messages in telecommunication systems of public address systems. The article discusses the effect on the syllable intelligibility of the signal / external acoustic noise ratio, examines the effect of the integral articulation index, the dependence of the perception coefficient of formants on the relative level of formant intensity, the dependence of the formant parameter on the geometric mean frequency of the i-th spectrum of the speech signal. In accordance with the results of studies of the integral articulation index depending on the signal-to-noise ratio, a function of syllable intelligibility depending on the signal-to-noise ratio was obtained, using which it is possible to determine the maximum value of the output signal-to-noise ratio in the audio exchange telecommunications system to obtain a given syllable intelligibility. At the same time, experimentally determined the value of the signal-to-noise ratio in the telecommunications system of audio exchange to obtain a syllable intelligibility of at least 93% for ensure full perception of the transmitted speech information.
Analysis of the structure of the relationship between the descriptions of objects of classes and evaluation of their compactness
Authors:   Ulyanovsk Technical University. Institute of Aviation Technologies and Management, Sozidateley avenue, 13A, Ulyanovsk, Russia, 432072, Zguralskaya Ekaterina
Published: December 2019

The study is conducted to assess the compactness of descriptions of objects of classes on the numerical axis and in the multidimensional attribute space. The computation of compactness is possible only in the defined boundaries of areas of the attribute space. In the one-dimensional case, the boundaries are calculated by the frequency of occurrence of the values of features of objects of classes in the interval. In the multidimensional case, a subset of the boundary objects of the classes is used for a given metric. A comparative analysis is given of the values of the compactness measure by latent attributes on the numerical axis and by the sets of initial features from which they are synthesized.
Using Models of Parallel Specialized Processors to Solve the Problem of Signal Separation
Authors:   Samara State Transport University, Svobody street, 2B, Samara, Russia, 443066, Zasov Valery
Published: December 2019

This paper considers models of highly efficient specialized processors used for parallel data processing as part of solving the problem of extracting individual signals from an additive mixture of several signals. The proposed models of recursive, nonrecursive, and regularization-based parallel specialized processors provide versatility in solving the problem of signal separation with various algorithms. An advantage of regularization-based processors is that they make the solution stable under conditions where the parameters of objects exhibit expected uncertainty when the inverse problem of signal separation is ill-posed. This paper presents the results we obtained from an asymptotic analysis of the computational complexity involved. The results identify the time it takes to solve problems by using specialized processors. The paper also identifies the conditions for the efficient use of specialized processors.
Orbital angular momentum acoustic modes demultiplexing by machine learning methods
Authors:   Volgograd State University, Universitetskiy prt., 100, Volgograd, Russia, 400062, Stankevich Dmitry
Published: December 2019

Orbital angular momentum (OAM) multiplexing is a promising method for MIMO multiplexing strategy. OAM multiplexing has previously been demonstrated for underwater acoustic communication, where data transmission was carried out within a single acoustic beam. Inner-product method is most often used for OAM demultiplexing, but it is sensitive to changes of signal parameters. For example, parameters changes can be associated with wave propagation through heterogeneous medium. I propose and demonstrate an approach using of machine learning methods to increase demultiplexing accuracy to 96% for non-stationary signals. In article presents experimental and numerical investigation results of proposed method.
The implementation of ”Kuznyechik” encryption algorithm using NVIDIA CUDA technology
Authors:   Samara National Research University, Moskovskoe Shosse 34А, Samara, Russia, 443086, Borisov Alexey , Myasnikov Evgeniy ,   Samara National Research University, Moskovskoe Shosse 34А, Samara, Russia, 443086
Published: December 2019

In this paper, we discuss various options for implementing the ”Kuznyechik” block encryption algorithm using the NVIDIA CUDA technology. We use lookup tables as a basis for the implementation. In experiments, we study the influence of the size of the block of threads and the location of lookup tables on the encryption speed. We show that the best results are obtained when the lookup tables are stored in the global memory. The peak encryption speed reaches 30.83 Gbps on the NVIDIA GeForce GTX 1070 graphics processor .
The electrocardiogram signal morphology analysis based on convolutional neural network
Authors:   Kalashnikov Izhevsk State Technical University, Studencheskaya 7, Izhevsk, Russia, 426069, Zavoyskih Mikhail , Korobeynikov Alexander ,   Kalashnikov Izhevsk State Technical University, Studencheskaya 7, Izhevsk, Russia, 426069,   IzhTeleMed Ltd., Lenina, 110, Izhevsk, Russia, 426009, Menlitdinov Aleksey ,   IzhTeleMed Ltd., Lenina, 110, Izhevsk, Russia, 426009, Lyuminarskiy Vladislav ,   Kalashnikov Izhevsk State Technical University, Studencheskaya 7, Izhevsk, Russia, 426069, Kuzelin Yurij ,   Republican Clinical Diagnostic Center, Lenina 87B, Izhevsk, Russia, 426009
Published: November 2019

The analysis of electrocardiogram signal morphology based on convolutional neural network is considered. Input data is obtained by splitting the signal into cardiac cycles. The calculation the average cycle is performed to exclude the artefacts. The Haar wavelet transform of the average cycle is performed. The images of size 200x6 are input data for the recognition system: 200 – number of counts constituting the cycle; 6 – number of Haar transform time scales. This work is a reconsideration of the previous work of the authors. The training samples base of marked cardiac cycle segments is the same (1500 cycles): the average cycle and the segment’s start and end indexes. In the previous work, the original composite system consisting of several modules was used as a recognition system. In current work it is proposed to use the convolutional neural network with the special structure: 4 convolutional layers, 2 dense layers, and 200 outputs for every of 3 segment. The recognition system based on neural network showed results slightly superior to the previous system. The percent of acceptable localization of the segments is the following: P – 82.2%, QRS – 88.7%, and T – 85.4%. The proposed system effectively solves the problem using the standard modules of modern artificial neural networks.
Game-theoretic model of wide social groups’ behavior with stimulation of volunteering activities
Authors:   Samara National Research University, Moskovskoe Shosse, 34, Samara, Russia, 443086, Geraskin Mikhail
Published: November 2019

The problem of developing tools for the stimulation system of socially optimal actions (volunteering) is considered. Based on the study of the population’s differentiation according to the propensity to an altruism, the game-theoretic model of the social group’s behavior is formed, accounting for the incentives for volunteering. In the cases of the linear decreasing incentive function and the linear cost functions of agents, the Cournot-Nash equilibrium mechanism in the corresponding game is proved. An existence of the equilibrium actions and an impact of incentives on the volunteers’ time distribution are confirmed by the simulation of the volunteers’ behavior in Russia.
Analysis of the credit turnover in the "Retailer-BankInsurer" system with variations in market factors
Authors:   Samara National Research University, Moskovskoye shosse, 34A, Samara, Russia, 443086, Geraskin Mikhail , Kuznetsova Olga ,   Samara National Research University, Moskovskoye shosse, 34A, Samara, Russia, 443086
Published: November 2019

The article considers the possible states of the "Retailer-Bank-Insurer" system. The Pareto-efficient agents’ strategies, which maximize the total profit of the system, are described. The agents’ models parameters influence on the change in the state of the system is analyzed. Additionally, the influence of the complementarity effect on the change in the retailer’s optimal sales volume is investigated. The values of the agents’ parameters, which cause the transition of the system from one state to another are determined.
Performance comparison of machine learning methods in the bus arrival time prediction problem
Authors:   Samara National Research University, Moskovskoye shosse, 34, Samara, Russia, 443086, Agafonov Anton , Yumaganov Alexander ,   Samara National Research University, Moskovskoye shosse, 34, Samara, Russia, 443086
Published: November 2019

The problem of predicting the movement of public transport is one of the most popular problems in the field of transport planning due to its practical significance. Various parametric and non-parametric models are used to solve this problem. In this paper, heterogeneous information affecting the prediction value is used to predict the arrival time of public transport, and a comparison of the main machine learning algorithms for the public transport arrival time forecasting is given: neural networks, support vector regression. An experimental analysis of the algorithms was carried out on real traffic information about bus routes in Samara, Russia.
The detection of conflicts in the requirements specification based on an ontological model and a production rule system
Authors:   Novosibirsk State Technical University, Karla Marksa ave., 20, Novosibirsk, Russia, 630073, Murtazina Marina , Avdeenko Tatiana ,   Novosibirsk State Technical University, Karla Marksa ave., 20, Novosibirsk, Russia, 630073
Published: November 2019

The paper presents an approach to organizing the detection of conflicts between requirements based on an ontological model and a system of production rules. Requirements in the form of plain text are converted to instances of OWL ontologies for analysis. There are three basic elements “subject”, “action” and “object” in the requirements. These elements become classes of the ontology. The object properties between instances of the same classes are defined in the ontology. In the system of rules it is determined that one of four types of relations can be established between a pair of the requirements: isConflict, isDuplicate, isInterconnect, isNotInterconnect. We develop the software product in the Python language for building and applying production rules system for classes and property objects of the ontology. Protégé 5.2 is used to work with the ontology. Also Python library PySwip and development environment SWI-Prolog 7.6.4 are used in the work. The paper also considers the issues of extracting requirements ontology instances from the automated processing results of textual requirements. The UDPipe with Russian language model is used for text processing.
Application of convolution neural networks in eye fundus image analysis
Authors:   Samara National Research University, Moskovskoe Shosse 34А, Samara, Russia, 443086, Ilyasova Natalya ,   Image Processing Systems Institute of RAS - Branch of the FSRC "Crystallography and Photonics" RAS, Molodogvardejskaya street 151, Samara, Russia, 443001, Shirokanev Aleksandr ,   Samara National Research University, Moskovskoe Shosse 34А, Samara, Russia, 443086,   Image Processing Systems Institute of RAS - Branch of the FSRC "Crystallography and Photonics" RAS, Molodogvardejskaya street 151, Samara, Russia, 443001, Klimov Ilya ,   Samara National Research University, Moskovskoe Shosse 34А, Samara, Russia, 443086
Published: November 2019

In this work, we proposed a new approach to analyzing eye fundus images that relies upon the use of a convolutional neural network (CNN). The CNN architecture was constructed, followed by network learning on a balanced dataset composed of four classes of images, composed of thick and thin blood vessels, healthy areas, and exudate areas. The learning was conducted on 12x12 images because an experimental study showed them to be optimal for the purpose. The test error was no higher than 4% for all sizes of the samples. Segmentation of eye fundus images was performed using the CNN. Considering that exudates are a primary target of laser coagulation surgery, the segmentation error was calculated on the exudate class, amounting to 5%. In the course of this research, the HSL color system was found to be most informative, using which the segmentation error was reduced to 3%.
Description and formation of the database perimeter for systematisation and storage of multi-structured data
Authors:   Samara National Research University, Moskovskoe Shosse, 34А, Samara, Russia, 443086, Nechitaylo Alexandr , Vasilchuk Olga ,   Volga Region State University of Service, Gagarin st., 4, Togliatti, Russia, 445677, Gnutova Anna ,   Samara National Research University, Moskovskoe Shosse, 34А, Samara, Russia, 443086
Published: November 2019

For storage of big data, as a rule, relational databases are used. For multilateral research and analysis of the processes occurring in large economic systems, financiers, economists and other technical specialists use graphs with actual names of enterprises, cities, regions, etc. to move from the physical names of the studied regions to the corresponding parameters of relational databases.
Neural network model in digital prediction of geometric parameters for relative position of the aircraft engine parts
Authors:   Samara National Research University, Moskovskoe Shosse, 34А, Samara, Russia, 443086, Bolotov Michael , Pechenin Vadim ,   Samara National Research University, Moskovskoe Shosse, 34А, Samara, Russia, 443086, Ruzanov Nikolay ,   Samara National Research University, Moskovskoe Shosse, 34А, Samara, Russia, 443086, Balyakin Dmitrij ,   Samara National Research University, Moskovskoe Shosse, 34А, Samara, Russia, 443086
Published: November 2019

The quality of aircraft and rocket engines depends primarily on the geometric accuracy of assembly units and parts. Mathematical models implemented in the form of computer models are used to predict quality indicators (in particular, assembly parameters). Direct modeling of the conjugation process using numerical conjugation and finite-element models of assemblies requires significant computational resources and is often accompanied by problems convergence of solutions. In order to solve the above problems, it is possible to use neural network models describing the main regularities of the pairing process based on the accumulated results. The work presents a neural network model for predicting assembly parameters of the parts based on the use of actual surfaces of the parts obtained as a result of mathematical modeling. Assembly on conical surfaces is considered. A convolutional neural network was used to predict assembly parameters.
Optimization of urban freight transportation based on evolutionary modelling
Authors:   Samara National Research University, Moskovskoe Shosse 34А, Samara, Russia, 443086, Gladchenko Elizaveta , Saprykin Oleg ,   Samara National Research University, Moskovskoe Shosse 34А, Samara, Russia, 443086, Tikhonov Aleksey ,   Samara National Research University, Moskovskoe Shosse 34А, Samara, Russia, 443086
Published: November 2019

Logistics problems require special attention, because every year they become more complicated and multivariable. On the one hand, a supply chain management includes incessant monitoring of such issues as requests elaboration, paths determination, routing of shipments, multimodal choice, set up of transhipments, fleet choice and maintenance, warehousing, packaging and others. On the other hand, dozens of people are involved in the logistics process. All these moments complicate the decision-making that is why data driven decisions are required nowadays. As well as shipment problems are NP-hard, the heuristic methods should be applied to resolve them. In this article we propose a genetic algorithm to solve the complex problem that consists of the Travelling Salesman Problem combined with the Knapsack Problem. We have developed an urban freight transportation model which is focused on the minimization of the underway time as well as on the maximization of the truck’s loading. A significant contribution in our method is the census of traffic frequency by using traffic zoning. The developed approach has been implemented using the Python programming language in the Zeppelin environment. The first version of the system has been approved in the city of Samara (Russia) with test demand dataset.
Inter-alpha-inhibitor, hyaluronan and inflammation.
Authors: Fries Erik , Kaczmarczyk Aneta
Published: December 2019

Inter-alpha-inhibitor is an abundant plasma protein whose physiological function is only now beginning to be revealed. It consists of three polypeptides: two heavy chains and one light chain called bikunin. Bikunin, which has antiproteolytic activity, carries a chondroitin sulphate chain to which the heavy chains are covalently linked. The heavy chains can be transferred from inter-alpha-inhibitor to hyaluronan molecules and become covalently linked. This reaction seems to be mediated by TSG-6, a protein secreted by various cells upon stimulation by inflammatory cytokines. Inter-alpha-inhibitor has been shown to be required for the stabilization of the cumulus cell-oocyte complex during the expansion that occurs prior to ovulation. Hyaluronan-linked heavy chains in the extracellular matrix of this cellular complex have recently been shown to be tightly bound to TSG-6. Since TSG-6 binds to hyaluronan, its complex with heavy chains could stabilize the extracellular matrix by cross-linking hyaluronan molecules. Heavy chains linked to hyaluronan molecules have also been found in inflamed tissues. The physiological role of these complexes is not known but there are indications that they might protect hyaluronan against fragmentation by reactive oxygen species. TSG-6 also binds to bikunin thereby enhancing its antiplasmin activity. Taken together, these results suggest that inter-alpha-inhibitor is an anti-inflammatory agent which is activated by TSG-6.
Kinetics and specificity of guinea pig liver aldehyde oxidase and bovine milk xanthine oxidase towards substituted benzaldehydes.
Authors: Panoutsopoulos Georgios I , Beedham Christine
Published: December 2019

Molybdenum-containing enzymes, aldehyde oxidase and xanthine oxidase, are important in the oxidation of N-heterocyclic xenobiotics. However, the role of these enzymes in the oxidation of drug-derived aldehydes has not been established. The present investigation describes the interaction of eleven structurally related benzaldehydes with guinea pig liver aldehyde oxidase and bovine milk xanthine oxidase, since they have similar substrate specificity to human molybdenum hydroxylases. The compounds under test included mono-hydroxy and mono-methoxy benzaldehydes as well as 3,4-dihydroxy-, 3-hydroxy-4-methoxy-, 4-hydroxy-3-methoxy-, and 3,4-dimethoxy-benzaldehydes. In addition, various amines and catechols were tested with the molybdenum hydroxylases as inhibitors of benzaldehyde oxidation. The kinetic constants have shown that hydroxy-, and methoxy-benzaldehydes are excellent substrates for aldehyde oxidase (Km values 5x10(-6) M to 1x10(-5) M) with lower affinities for xanthine oxidase (Km values around 10(-4) M). Therefore, aldehyde oxidase activity may be a significant factor in the oxidation of the aromatic aldehydes generated from amines and alkyl benzenes during drug metabolism. Compounds with a 3-methoxy group showed relatively high Vmax values with aldehyde oxidase, whereas the presence of a 3-hydroxy group resulted in minimal Vmax values or no reaction. In addition, amines acted as weak inhibitors, whereas catechols had a more pronounced inhibitory effect on the aldehyde oxidase activity. It is therefore possible that aldehyde oxidase may be critical in the oxidation of the analogous phenylacetaldehydes derived from dopamine and noradrenaline.
Single-stranded DNA-binding proteins (SSBs) -- sources and applications in molecular biology.
Authors: Kur Józef , Olszewski Marcin , Długołecka Anna , Filipkowski Paweł
Published: November 2019

Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombination, and repair in bacteria, archaea and eukarya. The SSBs share a common core ssDNA-binding domain with a conserved OB (oligonucleotide/oligosaccharide binding) fold. This ssDNA-binding domain was presumably present in the common ancestor to all three major branches of life. In recent years, there has been an increasing interest in SSBs because they are useful for molecular biology methods and for analytical purposes. In this review, we concentrate on recent advances in the discovery of new sources of SSBs as well as certain aspects of their applications in analytical sciences.
MutS as a tool for mutation detection.
Authors: Stanisławska-Sachadyn Anna , Sachadyn Paweł
Published: November 2019

MutS, a DNA mismatch-binding protein, seems to be a promising tool for mutation detection. We present three MutS based approaches to the detection of point mutations: DNA retardation, protection of mismatched DNA against exonuclease digestion, and chimeric MutS proteins. DNA retardation in polyacrylamide gels stained with SYBR-Gold allows mutation detection using 1-3 microg of Thermus thermophilus his6-MutS protein and 50-200 ng of a PCR product. The method enables the search for a broad range of mutations: from single up to several nucleotide, as mutations over three nucleotides could be detected in electrophoresis without MutS, due to the mobility shift caused by large insertion/deletion loops in heteroduplex DNA. The binding of DNA mismatches by MutS protects the complexed DNA against exonuclease digestion. The direct addition of the fluorescent dye, SYBR-Gold, allows mutation detection in a single-tube assay. The limited efficiency of T4 DNA polymerase as an exonuclease hampers the application of the method in practice. The assay required 300-400 ng of PCR products in the range of 200-700 bp and 1-3 microg of MutS. MutS binding to mismatched DNA immobilised on a solid phase can be observed thanks to the activity of a reporter domain linked to MutS. We obtained chimeric bifunctional proteins consisting of T. thermophilus MutS and reporter domains, like beta-galactosidase or GFP. Very low detection limits for beta-galactosidase could theoretically enable mutation detection not only by the examination of PCR products, but even of genomic DNA.
Animal cloning by nuclear transfer: state-of-the-art and future perspectives.
Authors: Dinnyes Andras , Szmolenszky Agnes
Published: November 2019

Model organisms are essential to study the genetic basis of human diseases. Transgenic mammalian models, especially genetic knock-out mice have catalysed the progress in this area. To continue the advancement, further sophisticated and refined models are crucially needed to study the genetic basis and manifestations of numerous human diseases. Coinciding with the start of the new era of post-genomic research, new tools for establishment of transgenesis, such as nuclear transfer and gene targeting in somatic cells, have become available, offering a unique opportunity for the generation of transgenic animal models. The new technology provides important tools for comparative functional genomics to promote the interpretation and increase the practical value of the data generated in numerous mouse models. This paper discusses the state-of-the-art of the nuclear replacement technology and presents future perspectives.
Helper-dependent adenoviral vectors in experimental gene therapy.
Authors: Józkowicz Alicja , Dulak Józef
Published: November 2019

In the majority of potential applications gene therapy will require an effective transfer of a transgene in vivo resulting in high-level and long-term transgene expression, all in the absence of significant toxicity or inflammatory responses. The most efficient vehicles for delivery of foreign genes to the target tissues are modified adenoviruses. Adenoviral vectors of the first generation, despite the high infection efficacy, have an essential drawback: they induce strong immune response, which leads to short term expression of the transgene, and limits their usefulness in clinical trials. In contrast, helper-dependent adenoviral vectors (HdAd) lacking all viral coding sequences display only minimal immunogenicity and negligible side-effects, allowing for long-term transgene expression. Thus, HdAd vehicles have become the carrier of choice for adenoviral vector-mediated experimental gene therapy, effectively used in animal models for delivery of transgenes into the liver, skeletal muscle, myocardium or brain. Strong and long-lasting expression of therapeutic genes has allowed for successful treatment of dyslipidemias, muscular dystrophy, obesity, hemophilia, and diabetes. Additionally, the large cloning capacity of HdAd, up to 37 kb, facilitates the use of physiologically regulated, endogenous promoters, instead of artificial viral promoter sequences. This enables also generation of the single vectors expressing multiple genes, which can be potentially useful for treatment of polygenic diseases. In this review we characterize the basic features of HdAd vectors and describe some of their experimental and potential clinical applications.
Use of cell therapy as a means of targeting chemotherapy to inoperable pancreatic cancer.
Authors: Günzburg Walter H , Salmons Brian
Published: November 2019

Although approved for the treatment of pancreatic cancer, the chemotherapeutic agent ifosfamide is not an effective therapy for this type of tumour. Ifosfamide must be activated by cytochrome P450 (P450) enzymes in the liver, initially to a short lived intermediate and then to toxic metabolites that are subsequently distributed by the circulatory system. Particularly for pancreatic cancer, this liver-mediated conversion results in relatively high systemic toxicities and poor therapeutic concentrations at the liver-distant site of the tumour. Activation of ifosfamide at the site of the tumour may allow lower doses to be used, while increasing the therapeutic index due to the resultant active concentrations generated locally. A cell-based therapy has been conceived where encapsulated, 293-derived cells genetically modified to overexpress a cytochrome P450 enzyme, are implanted near solid tumours. The cells are encapsulated in polymers of cellulose sulphate in order to provide a means of immunoprotection in vivo as well as to physically constrain them to the vicinity of the tumour. A major advantage of this strategy is that it allows one standard cell line to be applied to all patients and this approach can be extended to the treatment of other tumour types. After proof of principle studies in animal models, a phase I/II clinical trial was initiated in patients with stage III/IV nonresectable pancreatic cancer. Encapsulated cells were angiographically placed into the tumour vasculature of 14 patients and followed by systemic low dose ifosfamide treatment. Angiographic delivery of encapsulated cells proved feasible in all but one patient, and was well tolerated with no capsule or ifosfamide treatment-related adverse events. Four of the treated patients showed tumour regressions after capsule delivery and ifosfamide treatment in computer-tomography scans. The other 10 patients showed no further tumour growth (i.e. stable disease) during 20 weeks observation period. The median life expectancy of the patient collective was extended two fold as compared to age and status matched historical controls, with a 3-fold improvement in one year survival being attained. Evidence for a clinical benefit of the treatment was also obtained on the basis of standard parameters for quality of life. This approach has been evaluated by the European Medicines Evaluation Agency (EMEA) and orphan drug status has been granted. A pivotal clinical trial is now being planned with the help of the EMEA. Taken together, the data from this clinical trial suggest that encapsulated cytochrome P450-expressing cells combined with chemotherapy may be useful for the local treatment of a number of solid tumours and support the performance of further clinical studies of this new treatment.
Strategies for overcoming ABC-transporters-mediated multidrug resistance (MDR) of tumor cells.
Authors: Borowski Edward , Bontemps-Gracz Maria M , Piwkowska Agnieszka
Published: November 2019

The development of multidrug resistance (MDR) of tumors is a major cause of failure in antitumor chemotherapy. This type of cross-resistance is due to the expression of ABC transporter glycoproteins actively effluxing the drug from the cells against the concentration gradient at the expense of metabolic energy, thus preventing the accumulation in cells of therapeutic concentration of active agents. In this review strategies for overcoming this adverse phenomenon are discussed. They comprise the control of expression of MDR glycoprotein transporters and control of the functioning of the expressed transporter proteins. The latter approach is discussed in more detail, comprising the following general strategies: (i) development of compounds that are not substrates of efflux pump(s), (ii) use of agents that inactivate (inhibit) MDR proteins, (iii) design of cytostatics characterized by fast cellular uptake, surpassing their mediated efflux, (iv) use of compounds competing with the drug for the MDR protein-mediated efflux. Positive and negative aspects of these strategies are analysed, with special attention put on strategy based on the use of MDR modulators in combination therapy, allowing the restoration of cytotoxic activity of clinical cytostatics towards resistant tumor cells.
Definition of immunogenic carbohydrate epitopes.
Authors: Paschinger Katharina , Fabini Gustáv , Schuster David , Rendić Dubravko , Wilson Iain B H
Published: November 2019

Carbohydrates are known as sources of immunological cross-reactivity of allergenic significance. In celery and in cypress pollen, the major allergens Api g 5 and Cup a 1 are recognised by antisera raised against anti-horseradish peroxidase and by patients' IgE which apparently bind carbohydrate epitopes; mass spectrometric analysis of the tryptic peptides and of their N-glycans showed the presence of oligosaccharides carrying both xylose and core alpha1,3-fucose residues. Core alpha1,3-fucose residues are also a feature of invertebrates: genetic and biochemical studies on the fruitfly Drosophila melanogaster, the parasitic trematode Schistosoma mansoni and the nematode worm Caenorhabditis elegans indicate that these organisms possess core alpha1,3-fucosyltransferases. Various experiments have shown that fucosyltransferases from both fly and worm are responsible in vivo and in vitro for the synthesis of N-glycans which cross-react with anti-horseradish peroxidase; thus, we can consider these enzymes as useful tools in generating standard compounds for testing cross-reactive carbohydrate epitopes of allergenic interest.
New generation of peptide antibiotics.
Authors: Dubin Adam , Mak Paweł , Dubin Grzegorz , Rzychon Małgorzata , Stec-Niemczyk Justyna , Wladyka Benedykt , Maziarka Katarzyna , Chmiel Dorota
Published: November 2019

The increasing antibiotic resistance of pathogenic bacteria calls for the development of alternative antimicrobial strategies. Possible approaches include the development of novel, broad-spectrum antibiotics as well as specific targeting of individual bacterial virulence factors. It is impossible to decide currently which strategy will prove more successful in the future since they both promise different advantages, but also introduce diverse problems. Considering both approaches, our laboratory's research focuses on the evaluation of hemocidins, broad-spectrum antibacterial peptides derived from hemoglobin and myoglobin, and staphostatins, specific inhibitors of staphopains -- Staphylococcus aureus secreted proteases that are virulence factors regarded as possible targets for therapy. The article summarizes recent advances in both fields of study and presents perspectives for further development and possible applications.
The chaperone-usher pathway of bacterial adhesin biogenesis -- from molecular mechanism to strategies of anti-bacterial prevention and modern vaccine design.
Authors: Piatek Rafał , Zalewska Beata , Bury Katarzyna , Kur Józef
Published: November 2019

The chaperone-usher system determines the biogenesis of surface-exposed adhesive structures responsible for virulence of many Gram-negative bacteria. Investigations of the last 20 years have resolved the mechanism of this pathway on a structural level for different species of pathogenic bacteria. The purpose of this review is to present the molecular mechanisms of the biogenesis of adhesive structures assembled via the chaperone-usher pathway. The obtained mechanistic data allow one to propose potential strategies of anti-bacterial action. Additionally, the specific properties of the polymeric adhesive structures (pili and fimbriae) of the chaperone-usher system allow their use as effective and safe recombinant vaccines carrying foreign epitopes in thousands of copies on bacterial cell surface.
Glucosamine-6-phosphate synthase, a novel target for antifungal agents. Molecular modelling studies in drug design.
Authors: Wojciechowski Marek , Milewski Sławomir , Mazerski Jan , Borowski Edward
Published: November 2019

Fungal infections are a growing problem in contemporary medicine, yet only a few antifungal agents are used in clinical practice. In our laboratory we proposed the enzyme L-glutamine: D-fructose-6-phosphate amidotransferase (EC 2.6.1.16) as a new target for antifungals. The structure of this enzyme consists of two domains, N-terminal and C-terminal ones, catalysing glutamine hydrolysis and sugar-phosphate isomerisation, respectively. In our laboratory a series of potent selective inhibitors of GlcN-6-P synthase have been designed and synthesised. One group of these compounds, including the most studied N3-(4-methoxyfumaroyl)-l-2,3-diaminopropanoic acid (FMDP), behave like glutamine analogs acting as active-site-directed inactivators, blocking the N-terminal, glutamine-binding domain of the enzyme. The second group of GlcN-6-P synthase inhibitors mimic the transition state of the reaction taking place in the C-terminal sugar isomerising domain. Surprisingly, in spite of the fact that glutamine is the source of nitrogen for a number of enzymes it turned out that the glutamine analogue FMDP and its derivatives are selective against GlcN-6-P synthase and they do not block other enzymes, even belonging to the same family of glutamine amidotransferases. Our molecular modelling studies of this phenomenon revealed that even within the family of related enzymes substantial differences may exist in the geometry of the active site. In the case of the glutamine amidotransferase family the glutamine binding site of GlcN-6-P synthase fits a different region of the glutamine conformational space than other amidotransferases. Detailed analysis of the interaction pattern for the best known, so far, inhibitor of the sugar isomerising domain, namely 2-amino-2-deoxy-D-glucitol-6-phosphate (ADGP), allowed us to suggest changes in the structure of the inhibitor that should improve the interaction pattern. The novel ligand was designed and synthesised. Biological experiments confirmed our predictions. The new compound named ADMP is a much better inhibitor of glucosamine-6-phosphate synthase than ADGP.
Molecular modelling of membrane activity of amphotericin B, a polyene macrolide antifungal antibiotic.
Authors: Baginski Maciej , Sternal Kamil , Czub Jacek , Borowski Edward
Published: November 2019

Amphotericin B (AmB) is a well known polyene macrolide antibiotic used to treat systemic fungal infections. Despite its toxicity AmB is still regarded as a life-saving drug. The lack of adequate knowledge of the AmB mechanism of action is a serious obstacle to efficient development of new less toxic derivatives. Complementary to various experimental approaches, computational chemistry methods were used to study AmB mechanism of action. A programme lasting for a decade, that was run by our group covered studies of: i) molecular properties of AmB and its membrane targets, ii) structure and properties of AmB membrane channels, and iii) interaction of AmB with the membrane.
Bio-markers: traceability in food safety issues.
Authors: Raspor Peter
Published: November 2019

Research and practice are focusing on development, validation and harmonization of technologies and methodologies to ensure complete traceability process throughout the food chain. The main goals are: scale-up, implementation and validation of methods in whole food chains, assurance of authenticity, validity of labelling and application of HACCP (hazard analysis and critical control point) to the entire food chain. The current review is to sum the scientific and technological basis for ensuring complete traceability. Tracing and tracking (traceability) of foods are complex processes due to the (bio)markers, technical solutions and different circumstances in different technologies which produces various foods (processed, semi-processed, or raw). Since the food is produced for human or animal consumption we need suitable markers to be stable and traceable all along the production chain. Specific biomarkers can have a function in technology and in nutrition. Such approach would make this development faster and more comprehensive and would make possible that food effect could be monitored with same set of biomarkers in consumer. This would help to develop and implement food safety standards that would be based on real physiological function of particular food component.