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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublicationGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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Lighting requirements for pedestrian crossings - positive contrast
PublicationFor many years now in Poland there has been a large number of road accidents at pedestrian crossings during night periods [5, 11]. One of the technical solutions that can improve this condition is the use of proper lighting for pedestrian crossings. The designated pedestrian crossing should be visible in different weather conditions and at different times of the day. In case of night vision restrictions use artificial lighting...
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Set of Experience and Decisional DNA: Experience-Based Knowledge Structures
PublicationThis chapter presents a description of Set of Experience Knowledge Structure (SOEKS) and Decisional DNA (DDNA), argumentation for a knowledge representation, composition, configuration and metrics. SOEKS is a combination of filtered and amalgamated information obtained from formal decision events. It facilitates effective explicit representation of decisional experience taken from different technologies. SOEKS comprises variables,...
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Potential and Use of the Googlenet Ann for the Purposes of Inland Water Ships Classification
PublicationThis article presents an analysis of the possibilities of using the pre-degraded GoogLeNet artificial neural network to classify inland vessels. Inland water authorities monitor the intensity of the vessels via CCTV. Such classification seems to be an improvement in their statutory tasks. The automatic classification of the inland vessels from video recording is a one of the main objectives of the Automatic Ship Recognition and...
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Segmentation-Based BI-RADS ensemble classification of breast tumours in ultrasound images
PublicationBackground: The development of computer-aided diagnosis systems in breast cancer imaging is exponential. Since 2016, 81 papers have described the automated segmentation of breast lesions in ultrasound images using arti- ficial intelligence. However, only two papers have dealt with complex BI-RADS classifications. Purpose: This study addresses the automatic classification of breast lesions into binary classes (benign vs. ma- lignant)...
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Deterministic rendezvous of asynchronous bounded-memory agents in polygonal terrains
PublicationTwo mobile agents, modeled as points starting at differentlocations of an unknown terrain, have to meet. The terrain is a polygon with polygonal holes. We consider two versions of this rendezvous problem: exact RV, when the points representing the agents have to coincide at some time, and epsilon-RV, when these points have to get at distance less than epsilon in the terrain. In any terrain, each agent chooses its trajectory, but...
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2-bondage in graphs
PublicationA 2-dominating set of a graph G=(V,E) is a set D of vertices of G such that every vertex of V(G)D has at least two neighbors in D. The 2-domination number of a graph G, denoted by gamma_2(G), is the minimum cardinality of a 2-dominating set of G. The 2-bondage number of G, denoted by b_2(G), is the minimum cardinality among all sets of edges E' subseteq E such that gamma_2(G-E') > gamma_2(G). If for every E' subseteq E we have...
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Improving css-KNN Classification Performance by Shifts in Training Data
PublicationThis paper presents a new approach to improve the performance of a css-k-NN classifier for categorization of text documents. The css-k-NN classifier (i.e., a threshold-based variation of a standard k-NN classifier we proposed in [1]) is a lazy-learning instance-based classifier. It does not have parameters associated with features and/or classes of objects, that would be optimized during off-line learning. In this paper we propose...
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On Computational Aspects of Greedy Partitioning of Graphs
PublicationIn this paper we consider a problem of graph P-coloring consisting in partitioning the vertex set of a graph such that each of the resulting sets induces a graph in a given additive, hereditary class of graphs P. We focus on partitions generated by the greedy algorithm. In particular, we show that given a graph G and an integer k deciding if the greedy algorithm outputs a P-coloring with a least k colors is NP-complete for an infinite...
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Analysis of MArkers of Exposure to Constituents of Environmental Tobacco Smoke (ETS)
PublicationTobacco smoke is a complex mixture of more than 4000 chemical compounds, many of which are harmful to human health. These compounds belong to various chemical classes, including amides, imides, lactams, carboxylic acids, aldehydes, ketones, alcohols, phenols, amines, hydrocarbons, ethers, and inorganic compounds. There are three types of tobacco smoke streams: the mainstream, the sidestream, and environmental tobacco smoke (ETS)....
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Food Classification from Images Using a Neural Network Based Approach with NVIDIA Volta and Pascal GPUs
PublicationIn the paper we investigate the problem of food classification from images, for the Food-101 dataset extended with 31 additional food classes from Polish cuisine. We adopted transfer learning and firstly measured training times for models such as MobileNet, MobileNetV2, ResNet50, ResNet50V2, ResNet101, ResNet101V2, InceptionV3, InceptionResNetV2, Xception, NasNetMobile and DenseNet, for systems with NVIDIA Tesla V100 (Volta) and...
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Anomalous Behavior of Hyaluronan Crosslinking Due to the Presence of Excess Phospholipids in the Articular Cartilage System of Osteoarthritis
PublicationLubrication of articular cartilage is a complex multiscale phenomenon in synovial joint organ systems. In these systems, synovial fluid properties result from synergistic interactions between a variety of molecular constituent. Two molecular classes in particular are of importance in understanding lubrication mechanisms: hyaluronic acid and phospholipids. The purpose of this study is to evaluate interactions between hyaluronic acid...
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Extended investigation of performance-energy trade-offs under power capping in HPC environments
Publication—In the paper we present investigation of performance-energy trade-offs under power capping using modern processors. The results are presented for systems targeted at both server and client markets and were collected from Intel Xeon E5 and Intel Xeon Phi server processors as well as from desktop and mobile Intel Core i7 processors. The results, when using power capping, show that we can find various interesting combinations of...
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Double bondage in graphs
PublicationA vertex of a graph is said to dominate itself and all of its neighbors. A double dominating set of a graph G=(V,E) is a set D of vertices of G such that every vertex of G is dominated by at least two vertices of D. The double domination number of a graph G, denoted by gamma_d(G), is the minimum cardinality of a double dominating set of G. The double bondage number of G, denoted by b_d(G), is the minimum cardinality among all sets...
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On the size of identifying codes in triangle-free graphs
PublicationIn an undirected graph G, a subset C⊆V(G) such that C is a dominating set of G, and each vertex in V(G) is dominated by a distinct subset of vertices from C, is called an identifying code of G. The concept of identifying codes was introduced by Karpovsky, Chakrabarty and Levitin in 1998. For a given identifiable graph G, let gammaID(G) be the minimum cardinality of an identifying code in G. In this paper, we show that for any connected...
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Analysis of the impact of AOP on source code quality: Paradox of aspect-oriented separation of concerns
PublicationAlmost four decades ago, Parnas advocated modularity for the sake of changeability, independent development, and comprehensibility. The recipe for modularization is to define a clean interface, hide an implementation detail, keep low coupling and high cohesion. Although modules have taken many forms over the years from functions and procedures to classes, no form has been capable of expressing so-called crosscutting concerns in...
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In search of the new: American volunteers’ opinions about their participation in the Teaching English in Poland (TEIP) Program
PublicationThe Teaching English in Poland (TEIP) program relies on summer camps during which native English speakers, American volunteers, teach Polish children and adolescents using the language immersion method – during everyday activities, sports and art classes, and similar occasions. A vital aspect of the evaluation of the program is researching its impact on the young people; however, the opinions of the volunteers regarding their...
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Determining pesticide contamination in honey by LC-ESI-MS/MS - Comparison of pesticide recoveries of two liquid-liquid extraction based approaches
PublicationHoney, a valuable food product, may be contaminated by xenobiotics during its production and/or harvest. The determination of trace levels of contaminants in a complex matrix like honey still presents a challenge to analytical chemists. The aim of this work was to assess and compare the extraction efficiencies of 30 pesticide residues (acaricides, insecticides, herbicides, fungicides), belonging to over 15 different chemical classes....
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Lipidomics of Staphylococcus aureus – a new insight into the antibiotic resistant phenotype
PublicationStaphylococcus aureus is an aggressive pathogen responsible for a variety of diseases, in cluding life-threatening sepsis. Many strains of these bacteria are resistant to multiple classes of antibiotics, which is a substantial clinical problem in the treatment of S. aureus infections. We developed a comprehensive untargeted lipidomic workflow, including sample preparation, liquid chromatography-quadrupole-time-of-flight mass spectrometry...
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Separability Assessment of Selected Types of Vehicle-Associated Noise
PublicationMusic Information Retrieval (MIR) area as well as development of speech and environmental information recognition techniques brought various tools in-tended for recognizing low-level features of acoustic signals based on a set of calculated parameters. In this study, the MIRtoolbox MATLAB tool, designed for music parameter extraction, is used to obtain a vector of parameters to check whether they are suitable for separation of...
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Assessment of Lipophilicity Indices Derived from Retention Behavior of Antioxidant Compounds in RP-HPLC
PublicationReverse phase high pressure liquid chromatography was employed in order to evaluate the lipophilicity of antioxidant compounds from different classes, such as phenolic acids, flavanones, flavanols, flavones, anthocyanins, stilbenes, xantonoids, and proanthocyanidins. The retention time of each compound was measured using five different HPLC columns: RP18 (LiChroCART, Purosphere RP-18e), C8 (Zorbax, Eclipse XDBC8), C16-Amide (Discovery...
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Time-Domain Description of Point-Source Acoustic Wavefields as a Useful Approach in Ultrasonic Techniques
PublicationIn traditional acoustics, field problems are usually treated in the frequency domain, broadband fields being reduced to superposition of harmonic spectrum components. However, this approach is inherently acausal and it is known that in case of arbitrary signals, the distribution-based, time-domain description can be more effective. The present paper is an attempt to expand the time-domain linear systems formalism onto space problems...
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Time-domain description of point-source acoustic wavefields as a useful approach in ultrasonic techniques
PublicationIn traditional acoustics, field problems are usually treated in the frequency domain, broadband fields being reduced to superposition of harmonic spectrum components. However, this approach is inherently acausal and it is known that in case of arbitrary signals, the distribution-based, time-domain description can be more effective. The present paper is an attempt to expand the time-domain linear systems formalism onto space problems...
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INTER-LAYER SHARING OF BACKUP PATH CAPACITIES PROVIDING FAST SERVICE RECOVERY IN IP-MPLS/WDM NETWORKS
PublicationIn this paper, we investigate the issue of providing the transmission continuity in IP-MPLS/WDM networks in the presence of failures of nodes/links. Special focus is put on assuring fast restoration of flows affected after a failure in a scenario assuming sharing the backup path capacities in order to decrease the overall bandwidth consumption. In particular, we propose a new approach to inter-layer sharing of link capacity reserved...
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Identification of synergistic and antagonistic actions of environmental pollutants: Bisphenols A, S and F in the presence of DEP, DBP, BADGE and BADGE·2HCl in three component mixtures
PublicationEcosystems are facing increased pressure due to the emission of many classes of emerging contaminants. However, very little is known about the interactions of these pollutants, such as bisphenols (BPs), plasticizers or pharmaceuticals. By employing bioluminescent bacteria (Microtox assay), we were able to define interactions between selected emerging pollutants (namely BPA, BPS, BPF, BADGE, BADGE·2HCl, DEP, DBP) in ternary mixtures, at...
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Automatic labeling of traffic sound recordings using autoencoder-derived features
PublicationAn approach to detection of events occurring in road traffic using autoencoders is presented. Extensions of existing algorithms of acoustic road events detection employing Mel Frequency Cepstral Coefficients combined with classifiers based on k nearest neighbors, Support Vector Machines, and random forests are used. In our research, the acoustic signal gathered from the microphone placed near the road is split into frames and converted...
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Theory versus experiment for vacuum Rabi oscillations in lossy cavities. II. Direct test of uniqueness of vacuum
PublicationThe paper continues the analysis of vacuum Rabi oscillations we started in part I [Phys. Rev. A 79, 033836 (2009)]. Here we concentrate on experimental consequences for cavity QED of two different classes of representations of harmonic-oscillator Lie algebras. The zero-temperature master equation, derived in part I for irreducible representations of the algebra, is reformulated in a reducible representation that models electromagnetic...
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Non-isolating bondage in graphs
PublicationA dominating set of a graph $G = (V,E)$ is a set $D$ of vertices of $G$ such that every vertex of $V(G) \setminus D$ has a neighbor in $D$. The domination number of a graph $G$, denoted by $\gamma(G)$, is the minimum cardinality of a dominating set of $G$. The non-isolating bondage number of $G$, denoted by $b'(G)$, is the minimum cardinality among all sets of edges $E' \subseteq E$ such that $\delta(G-E') \ge 1$ and $\gamma(G-E')...
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Non-isolating 2-bondage in graphs
PublicationA 2-dominating set of a graph G=(V,E) is a set D of vertices of G such that every vertex of V(G)D has at least two neighbors in D. The 2-domination number of a graph G, denoted by gamma_2(G), is the minimum cardinality of a 2-dominating set of G. The non-isolating 2-bondage number of G, denoted by b_2'(G), is the minimum cardinality among all sets of edges E' subseteq E such that delta(G-E') >= 1 and gamma_2(G-E') > gamma_2(G)....
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Edge coloring of graphs of signed class 1 and 2
PublicationRecently, Behr (2020) introduced a notion of the chromatic index of signed graphs and proved that for every signed graph (G, σ) it holds that ∆(G) ≤ χ′(G,σ) ≤ ∆(G) + 1, where ∆(G) is the maximum degree of G and χ′ denotes its chromatic index. In general, the chromatic index of (G, σ) depends on both the underlying graph G and the signature σ. In the paper we study graphs G for which χ′(G, σ) does not depend on σ. To this aim we...
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Clothes Detection and Classification Using Convolutional Neural Networks
PublicationIn this paper we describe development of a computer vision system for accurate detection and classification of clothes for e-commerce images. We present a set of experiments on well established architectures of convolutional neural networks, including Residual networks, SqueezeNet and Single Shot MultiBox Detector (SSD). The clothes detection network was trained and tested on DeepFashion dataset, which contains box annotations...
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Robustness in Compressed Neural Networks for Object Detection
PublicationModel compression techniques allow to significantly reduce the computational cost associated with data processing by deep neural networks with only a minor decrease in average accuracy. Simultaneously, reducing the model size may have a large effect on noisy cases or objects belonging to less frequent classes. It is a crucial problem from the perspective of the models' safety, especially for object detection in the autonomous driving...
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Levels of creativity in architectural education
PublicationArchitectural design combines engineering science and art, thus stimulating creativity is a challenge in the didactic process. There are various levels of creativity that can be attained through architectural education. From idea to architecture (FITA) is a teaching method based on metaphorical and analogical reasoning that was developed, implemented and tested during architectural design classes in the Faculty of Architecture...
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Process Control and Investigation of Oxidation Kinetics of Postoxidative Effluents Using Gas Chromatography with Pulsed Flame Photometric Detection (GC-PFPD)
PublicationThis article presents the results of investigations on the use of headspace analysis and gas chromatography with pulsed flame photometric detection (HSA-GC-PFPD) to evaluate the effectiveness of oxidation of postoxidative effluents from the production of bitumens. Samples of effluents from the bitumen oxidation unit were used in the experiments. In addition, the kinetics of effluent oxidation was also investigated. The content...
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Review of the determination of modern used pesticides in water samples
PublicationThe increasingly widespread application of pesticides causes that larger amounts of them are entering the environment. Their presence in sources of drinking water, essential to life, is a particular danger. For these reasons it is important to monitor and analyse pesticide residues in the environment. The analysis of environmental samples for the presence of pesticides is very difficult. Firstly, the processes involved in sample...
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A Text as a Set of Research Data. A Number of Aspects of Data Acquisition and Creation of Datasets in Neo-Latin Studies
PublicationIn this paper, the authors, who specialise in part in neo-Latin studies and the his-tory of early modern education, share their experiences of collecting sources for Open Research Data sets under the Bridge of Data project. On the basis of inscription texts from St. Mary’s Church in Gdańsk, they created 29 Open Research Data sets. In turn, the text of the lectures of the Gdańsk scholar Michael Christoph Hanow, Praecepta de arte...
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Creating a Realible Music Discovery and Recomendation System
PublicationThe aim of this paper is to show problems related to creating a reliable music dis-covery system. The SYNAT database that contains audio files is used for the purpose of experiments. The files are divided into 22 classes corresponding to music genres with different cardinality. Of utmost importance for a reliable music recommendation system are the assignment of audio files to their appropriate gen-res and optimum parameterization...
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Problems of modelling toxic compounds emitted by a marine internal combustion engine for the evaluation of its structure parameters
PublicationThe paper presents the possibility of using an analytical study of the engine exhaust ignition to evaluate the technical condition of the selected components. Software tools available for the analysis of experimental data commonly use multiple regression model that allows the study of the effects and iterations between model input quantities and one output variable. The use of multi-equation models gives a lot of freedom in the...
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Antimicrobial resistance of fecal indicators in disinfected wastewater
PublicationThe main objective of the study was to assess the potential of three systems (UV irradiation, ozonation, and micro/ultrafiltration) operated in a pilot scale in removal of antimicrobial-resistant fecal bacteria from secondary effluent of the local wastewater treatment plant (700,000 population equivalent). The effectiveness of the processes was analysed using the removal ratio of fecal indicators (Escherichia coli and Enterococcus...
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Physical crosslinking of hyaluronic acid in the presence of phospholipids in an aqueous nano-environment
PublicationHyaluronic acid and phospholipids are two components in the synovial joint cavity that contribute to joint lubrication synergistically. Molecular dynamics simulations were performed and hydrogen bonds in hyaluronic acid were analyzed to identify specific sites that are responsible for its physical cross-linking. Two molecular masses of hyaluronic acid, 10 kDa and 160 kDa, were considered. We use molecular dynamics simulations and...
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Analysis of the relationship between the length of eye fixation and the parameters of advertisements visible from the road
PublicationIn Poland, many advertising signs addressed to motorists are located along the roadside. Advertisements do not serve any traffic related purpose and can distract drivers making them less reliable and as a consequence, reduce road safety. The existing regulations only apply to the carriageway. The research is conducted as part of the RID project. The objective of the RID project is to create a "Manual for positioning roadside advertising...
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Comparative Study on Assisted Solvent Extraction Techniques for the Extraction of Biologically Active Compounds from Sideritis raeseri and Sideritis scardica
PublicationThe plants in the Sideritis genus are postulated to exhibit several important medicinal properties due to their unique chemical composition. To isolate the targeted phytochemical compounds, the selection of a suitable extraction method is of primary importance. In this work, a comparative study on the phytochemical profiles of various Sideritis raeseri and Sideritis scardica extracts has been carried out. An untargeted metabolomics...
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Antimicrobial resistance of Pseudomonas spp. isolated from wastewater and wastewater-impacted marine coastal zone
PublicationIn this study, species distribution and antimicrobial susceptibility of cultivated Pseudomonas spp. were studied in influent (INF), effluent (EFF), and marine outfall (MOut) of wastewater treatment plant (WWTP). The susceptibility was tested against 8 antimicrobial classes, active against Pseudomonas spp.: aminoglycosides, carbapenems, broad-spectrum cephalosporins from the 3rd and 4th generation, extended-spectrum penicillins,...
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Comparative Study of Taste Substance Sensing by Liquid Membrane Oscillator and Electrochemical Systems With All-Solid-State Electrodes
PublicationIn food industry, different types of sensors are used for characterizing and quantifying taste substances. Therefore, it is important to establish the principal advantages and disadvantages of these sensors for optimal application. In this paper, two possible systems are compared for sensing the four fundamental tastes: sour (citric acid), salty (sodium chloride), sweet (sucrose), and bitter (caffeine or quinine hydrochloride). One...
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The Many Faces of Enterococcus spp.—Commensal, Probiotic and Opportunistic Pathogen
PublicationEnterococcus spp. are Gram-positive, facultative, anaerobic cocci, which are found in the intestinal flora and, less frequently, in the vagina or mouth. Enterococcus faecalis and Enterococcus faecium are the most common species found in humans. As commensals, enterococci colonize the digestive system and participate in the modulation of the immune system in humans and animals. For many years reference enterococcal strains have...
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Enhancing Availability for Critical Services
PublicationTraditional approaches to provide classes of resilient service take the physical network availability as an input and then deploy redundancy and restoration techniques at various layers, often without full knowledge of mappings between layers. This makes it hard (and often inefficient) to ensure the high availability required by critical services which are typically a small fraction of the total traffic. Here, the innovative technique...
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Untargeted Lipidomics Analysis of the Cyanobacterium Synechocystis sp. PCC 6803: Lipid Composition Variation in Response to Alternative Cultivation Setups and to Gene Deletion
PublicationCyanobacteria play an important role in several ecological environments, and they are widely accepted to be the ancestors of chloroplasts in modern plants and green algae. Cyanobacteria have become attractive models for metabolic engineering, with the goal of exploring them as microbial cell factories. However, the study of cyanobacterial lipids’ composition and variation, and the assessment of the lipids’ functional and structural...
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Market Structure and Market Power in Selected Sectors of The Polish Economy Based on COICOP Classification
PublicationThis paper present new and simple measures of market structure and market power. Based on the classical models of market structures, where a given structure is determined by the number of enterprises, indexes of degree of monopoly have been estimated, representing an average number of entities per branch. Additionally, market power indexes have been determined as an average revenue per an enterprise in a given branch. This approach...
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A few steps more towards NPT bound entanglement
PublicationIn this paper, existence of bound entangled states with nonpositive partial transpose (NPT) is considered. As one knows, existence of such states would in particular imply nonadditivity of distillable entanglement. Moreover, it would rule out a simple mathematical description of the set of distillable states. The particular state, known to be 1-copy nondistillable and supposed to be bound entangled, is considered. The problem of...
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Analysis of antibiotic resistance in Escherichia coli isolated from the Reda River and the Oliwski Stream using basic statistical methods = Zastosowanie metod ststystycznych do analizy antybiotykoodporności bakterii wskaźnikowych pochodzących z rzeki Redy i Potoku Oliwskiego
PublicationIn this study distribution of antimicrobial resistance patterns among fecal indicator bacteria (Escherichia coli and Enterococcus spp.) was examined in two watercourses. The susceptibility analyses were carried out against the antimicrobial agents, important in treating human E. coli and enterococcal infection. Water samples were obtained from the Oliwski Stream and from the Reda River. On each watercourse the five representative...