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MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences
Publikacja—Machine Learning (ML) methods have been used with varying degrees of success on protein prediction tasks, with two inherent limitations. First, prediction performance often depends upon the features extracted from the proteins. Second, experimental data may be insufficient to construct reliable ML models. Here we introduce MP3vec, a transferable representation for protein sequences that is designed to be used specifically for sequence-to-sequence...
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Thermal sequences database of the skin flaps in breast reconstruction and burns
PublikacjaThis paper presents a database of Active Dynamic Thermography (ADT) thermal sequences gathered throughout 6 year study on ADT application in skin flap blood perfusion monitoring and burn wounds diagnosis. For skin flap monitoring the database comprises of data collected during three different breast reconstruction procedures. The patients were monitored pre, intra and post surgically within 90 days period. The sequences were used...
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Thermal sequences database of the skin flaps in breast reconstruction and burns
PublikacjaThis paper presents a database of Active Dynamic Thermography (ADT) thermal sequences gathered throughout 6 year study on ADT application in skin flap blood perfusion monitoring and burn wounds diagnosis. For skin flap monitoring the database comprises of data collected during three different breast reconstruction procedures. The patients were monitored pre, intra and post surgically within 90 days period. The sequences were used...
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Text-mining Similarity Approximation Operators for Opinion Mining in BI tools
PublikacjaThe concept of the Text-mining Similarity Approximation Operators for Opinion Mining as extensions to Natural Language Interface Database is defined. The new operators: “keywords of” dimension; subsetting operator “about C is q”; aggregation operator “by similar C” are proposed. These operators are based on the Latent Semantic Analysis and Social Network Analysis
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Fiber Optic Pulse Sequencers/Desequencers
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Temporal sequence of the human RBCs' vesiculation observed in nano-scale with application of AFM and complementary techniques
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SacNI, an isoschizomer of BanII isolated from streptomyces achromogenes recognizes the 5′-GRGCY/C sequence
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Light-dependent and light-independent protochlorophyllide oxidoreductases share similar sequence motifs -in silico studies
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Strain sequence effect on fatigue life and fracture surface topography of 7075-T651 aluminium alloy
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublikacjaMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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A Fast Method of Separation of the Noisy Background from the Head-Cross Section in the Sequence of MRI Scans
PublikacjaThe paper presents a new method of removing the noisy background from the sequence of magnetic resonance imaging (MRl) scans. The sequence of scans is required in order to monitor a passage of a contrast agent through the brain tissue. The scans contain the noisy head-cross data and also the noisy background data. The latter has to be removed and excluded from a further analysis. It is achieved by applying some basic morphological...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublikacjaTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
PublikacjaThe structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA...
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Strain sequence effect on fatigue life and fracture surface topography of 7075-T651 aluminium alloy
PublikacjaThe paper studies the effect of strain-loading sequence on fatigue lifetime and fracture surface topographies in 7075-T651 aluminum alloy specimens. Fatigue tests were performed in two ways: (i) constant-amplitude loading and (ii) two series of variable amplitude loading with non-zero mean strain values. The topography of the fatigue fractures was measured over their entire surfaces with the help of an optical confocal measurement...
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Simulation of Direct-Sequence Spread Spectrum Data Transmission System for Reliable Underwater Acoustic Communications
PublikacjaUnderwater acoustic communication (UAC) system designers tend to transmit as much information as possible, per unit of time, at as low as possible error rate. It is a particularly difficult task in a shallow underwater channel in which the signal suffers from strong time dispersion due to multipath propagation and refraction phenomena. The direct-sequence spread spectrum technique (DSSS) applied successfully in the latest standards...
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Analysis of the parameters of respiration patterns extracted from thermal image sequences
PublikacjaRemote estimation of vital signs is an important and active area of research. The goal of this work was to analyze the feasibility of estimating respiration parameters from video sequences of faces recorded using a mobile thermal camera. Different estimators were analyzed and experimentally verified. It was demonstrated that the respiration rate, periodicity of respiration, and presence and length of apnea periods could be reliably...
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Active Learning on Ensemble Machine-Learning Model to Retrofit Buildings Under Seismic Mainshock-Aftershock Sequence
PublikacjaThis research presents an efficient computational method for retrofitting of buildings by employing an active learning-based ensemble machine learning (AL-Ensemble ML) approach developed in OpenSees, Python and MATLAB. The results of the study shows that the AL-Ensemble ML model provides the most accurate estimations of interstory drift (ID) and residual interstory drift (RID) for steel structures using a dataset of 2-, to 9-story...
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Modified SPWM Technique with Zero-Sequence Voltage Injection for a Five-Phase, Three-Level NPC Inverter
PublikacjaThis article presents a modified sinusoidal pulse-width modulation (SPWM) scheme for a five-phase, three-level neutral-point-clamped inverter. The modulation scheme deploys a modified min–max function to inject the zero-sequence components into the reference modulating signals; hence enabling the effective utilization of the DC-link voltage. Balanced split-input DC-link voltages were achieved through further incorporation of adjustable...
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Draft genome sequence of antimicrobial producing Paenibacillus alvei strain MP1 reveals putative novel antimicrobials
PublikacjaA Paenibacillus strain isolated in previous research exhibited antimicrobial activity against relevant human pathogens including Staphylococcus aureus and Listeria monocytogenes. In this study, the genome of the aforementioned strain, designated as MP1, was shotgun sequenced. The draft genome of strain MP1 was subject to multiple genomic analyses to taxonomically characterize it and identify the genes potentially responsible for...
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PCR amplification with primers based on IS2404 and GC-rich repeated sequence reveals polymorphism in Mycobacterium ulcerans
PublikacjaOpracowano prostą w wykonaniu metodę genotypowania szczepów bakterii z gatunku Mycobacterium ulcerans. Polimorfizm genetyczny 32 badanych izolatów Mycobacterium ulcerans odzwierciedla ich geograficzne pochodzenie z rejonów Afryki Centralnej, Ameryki Południowej i Łacińskiej, Azji Południowo-Wschodniej, Malezji oraz Australii.
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DATA MINING IN CONSTRUCTION RESEARCH
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Schema mining in XML documents.
PublikacjaW artykule przedstawiono algorytm COBWEB S+T służący do wywodzenia schematów z kolekcji dokumentów XML. Algorytm wykorzystuje model danych semistrukturalnych oraz alorytm COBWEB służący do grupowania koncepcyjnego. W artykule zaprezentowano również wyniki testów działania algorytmu.
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Application of Maximum-Length Sequences to impulse response measurement of hydroacoustic communications systems
PublikacjaThere is a growing interest in digital transmission of telemetry data on ultrasonic waves. The dependence of signal attenuation on squared frequency, specific to the hy-droacoustic systems, induces problems that do not exist in monochromatic, narrowband radio communications systems. For adapting the transmission parameters to current propagation conditions, a precise knowledge of instantaneous changes of channel performances is...
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Comparative studies of the Acinetobacter genus and the species identification method based on the recA sequences
PublikacjaZaproponowano metodę genotypowania bakterii rodzaju Acinetobacter, opartą o analizę sekwencji genów recA, amplifikację fragmentów genu recA i analizę profili fragmentów restrykcyjnych po cięciu produktów reakcji PCR enzymami restrykcyjnymi (recA PCR/RFLP). Profile RFLP otrzymane za pomocą enzymu Tsp509I są użyteczne w identyfikacji poszczególnych gatunków bakterii rodzaju Acinetobacter. Na podstawie analizy otrzymanych sekwencji...
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Minimization of the number of periodic points for smooth self-maps of simply-connected manifolds with periodic sequence of Lefschetz numbers
PublikacjaLet f be a smooth self-map of m-dimensional, m ≥ 4, smooth closed connected and simply-connected manifold, r a fixed natural number. For the class of maps with periodic sequence of Lefschetz numbers of iterations the authors introduced in [Graff G., Kaczkowska A., Reducing the number of periodic points in smooth homotopy class of self-maps of simply-connected manifolds with periodic sequence of Lefschetz numbers, Ann. Polon. Math....
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Peptide splicing in a double‐sequence analogue of trypsin inhibitor SFTI‐1 substituted in the P1 positions by peptoid monomers
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Cloning, expression in Komagataella phaffii, and biochemical characterization of recombinant sequence variants of Pseudomonas sp. S9 GDSL-esterase
PublikacjaTwo recombinant Komagataella phaffii (formerly Pichia pastoris) yeast strains for production of two sequential variants of EstS9 esterase from psychrotolerant bacterium Pseudomonas sp. S9, i.e. αEstS9N (a two-domain enzyme consisting of a catalytic domain and an autotransporter domain) and αEstS9Δ (a single-domain esterase) were constructed. However, only one of recombinant K. phaffii strains, namely Komagataella phaffii X-33/pPICZαestS9Δ,...
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Sequence variants of p21 gene of the MRL/MpJ mouse: a possible association with the deficit of p21 protein and regenerative phenotype.
PublikacjaThe MRL/MpJ mouse is known for its enhanced regeneration abilities that manifested themselves by scarless ear-hole wound closure. The deficit of p21 found in the MRL is associated with the regenerative capacity as the p21 gene knockout in a mouse strain unrelated to the MRL mouse results in an ear-hole closure effect, similar to that observed in the MRL mouse. Cdkn1a gene encodes p21 protein, a cyclin-dependent kinase inhibitor,...
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A New Direct-Sequence Spread Spectrum Signal Detection Method for Underwater Acoustic Communications in Shallow-Water Channel
PublikacjaDirect-Sequence Spread Spectrum (DSSS) is one of the modulation and coding techniques used in Underwater Acoustic Communication (UAC) systems for reliable data transmision even at low signal levels. However, in a shallow water channel, there is a strong multipath propagation which causes a phase fluctuation of the received signal, affecting the performance of the spread-spectrum system. The article presents a differential method...
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Assessment of Wide-Sense Stationarity of an Underwater Acoustic Channel Based on a Pseudo-Random Binary Sequence Probe Signal
PublikacjaThe performances of Underwater Acoustic Communication (UAC) systems are strongly related to the specific propagation conditions of the underwater channel. Designing the physical layer of a reliable data transmission system requires a knowledge of channel characteristics in terms of the specific parameters of the stochastic model. The Wide-Sense Stationary Uncorrelated Scattering (WSSUS) assumption simplifies the stochastic description...
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Differences in sequences between HBV-relaxed circular DNA and covalently closed circular DNA
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Approximative sequences and almost homoclinic solutions for a class of second order perturbed Hamiltonian systems
PublikacjaIn this work we will consider a class of second order perturbed Hamiltonian systems with a superquadratic growth condition on a time periodic potential and a small aperiodic forcing term. To get an almost homoclinic solution we approximate the original system by time periodic ones with larger and larger time periods. These approximative systems admit periodic solutions, and an almost homoclinic solution for the original system...
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Reversible data hiding in encrypted DICOM images using sorted binary sequences of pixels
PublikacjaIn this paper, a novel reversible data hiding method for encrypted DICOM images is proposed. The method utilizes binary decomposition of the input data paired with a sorting process of the obtained binary sequences to ensure efficient data embedding in each predefined data block for specific most significant bit (MSB) planes while exploiting the properties of run-length encoding. The proposed scheme is lossless, and based on the...
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Ensemble Classifier for Mining Data Streams
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Data Mining Applications and Methods in Medicine
PublikacjaIn this paper we describe the research area of data mining and its applications in medicine. The origins of data mining and its crucial features are shortly presented. We discuss the specificity of medicine as an application area for computer systems. Characteristic features of the medical data are investigated. Common problems in the area are also presented as well as the strengths and capabilities of the data mining methods....
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Mining relations between wikipedia categories
PublikacjaOpisano metody indukcji powiązań pomiędzy kategoriami organizującymi zbiór dokumentów. Przedstawiono wyniki zastosowania proponowanego podejścia dla poprawy systemu kategorii Wikipedii.
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Agile Commerce in the light of Text Mining
PublikacjaThe survey conducted for this study reveals that more than 84% of respondents have never encountered the term “agile commerce” and do not understand its meaning. At the same time, they are active participants of this strategy. Using digital channels as customers more often than ever before, they have already been included in the agile philosophy. Based on the above, the purpose of the study is to analyse major text sets containing...
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Multimedia data mining for e-Commerce.
PublikacjaPrzedstawiono studium porównawcze metod eksploracji danych dla e-Commerce.Skupiono się na studium przypadku aplikacji medycznych - wyszukiwania przypadków podobnych.
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Release systems based on self-assembling RADA16-I hydrogels with a signal sequence which improves wound healing processes
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Performance of the Direct Sequence Spread Spectrum Underwater Acoustic Communication System with Differential Detection in Strong Multipath Propagation Conditions
PublikacjaThe underwater acoustic communication (UAC) operating in very shallow-water should ensure reliable transmission in conditions of strong multipath propagation, significantly disturbing the received signal. One of the techniques to achieve this goal is the direct sequence spread spectrum (DSSS) technique, which consists in binary phase shift keying (BPSK) according to a pseudo-random spreading sequence. This paper describes the DSSS...
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Release systems based on self-assembling RADA16-I hydrogels with a signal sequence which improves wound healing processes
PublikacjaSelf-assembling peptides can be used for the regeneration of severely damaged skin. They can act as scaffolds for skin cells and as a reservoir of active compounds, to accelerate scarless wound healing. To overcome repeated administration of peptides which accelerate healing, we report development of three new peptide biomaterials based on the RADA16-I hydrogel functionalized with a sequence (AAPV) cleaved by human neutrophil elastase...
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B-GALACTOSIDASE ARTHROBACTER SP. 32cB - OBTAINING THE GENE SEQUENCE, CONSTRUCTION OF THE EXPRESSION SYSTEM, BIOSYNTHESIS AND BIOCHEMICAL CHARACTERIZATION OF THE ENZYME
PublikacjaINTRODUCTION: β-Galactosidase is an enzyme which catalyzes the hydrolysis of O glycosidic bond in β-galactosides. Another activity of β galactosidase is a transglycosylation activity. The main industrial use of this protein is the hydrolysis of lactose in milk in a cooling conditions. Synthesis of galactooligosaccharides, which are mostly used as a prebiotics added to some foods or available as dietary supplements, is only one...
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Inhibitory activity of double‐sequence analogues of trypsin inhibitor SFTI‐1 from sunflower seeds: an example of peptide splicing
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Identification of evolutionary conserved DNA sequence and corresponding S21 ribosomal protein region for diagnostic purposes of all Borrelia spirochetes
PublikacjaIt is still under investigation, whether all Borrelia sp. causing Lyme borreliosis and other diseases are already identified and properly classified as human pathogens. For this reason, it is of great importance to develop a diagnostic ELISA test that detects all Borrelia sp. The aim of this study was to identify conserved DNA and protein regions present in all currently known Borrelia sp. In experimental studies 31 available Borrelia...
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Improving Accuracy of Contactless Respiratory Rate Estimation by Enhancing Thermal Sequences with Deep Neural Networks
PublikacjaEstimation of vital signs using image processing techniques have already been proved to have a potential for supporting remote medical diagnostics and replacing traditional measurements that usually require special hardware and electrodes placed on a body. In this paper, we further extend studies on contactless Respiratory Rate (RR) estimation from extremely low resolution thermal imagery by enhancing acquired sequences using Deep...
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Lamp of adjustable spectrum for photographic usage
PublikacjaPhotography is a unique rapidly growing interdisciplinary field encompassing aspects of science, art and technology. Expectations of photographers are steadily increasing with the development of technology. One of the areas playing a crucial role in photography is lighting. Consequently, several types of light sources for photographic use have been developed. The ongoing research in this field concentrates on lamps with tunable...
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Analysis of the usage possibility of the electromagnetic curtain
PublikacjaIn the article the definition of IED has been presented as well as its classification and countering methods. The concept of AEGIS device for neutralization of RCIED has been presented. The usage possibility of AEGIS device in civilian environments has been analy sed
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Efficiency of new method of removing noisy background from the sequence of MRI scans depending on structure elements used to morphological processing
PublikacjaPrzedstawiono nową metodę usuwania zaszumionego tła z sekwencji skanów MRI. Każdy skan zawiera przekrój mózgu i tło, oba zaszumione. Tło należy wykluczyć z dalszej analizy. Eliminacji tła dokonano dzięki zastosowaniu opisanego algorytmu wykorzystującego podstawowe operacje morfologiczne: dylację, erozję, otwarcie i zamknięcie do uprzednio zbinaryzowanych zbiorów MRI. Zaprezentowano wyniki przetwarzania otrzymane dla różnych kształtów...
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Relation of the polymorphism of cyp51A sequence and the susceptibility of Aspergillus fumigatus isolates to triazoles determined by commercial gradient test (Etest) and by reference methods
PublikacjaThe aim of this study was to evaluate the accuracy of commercial gradient test (Etest) in the detection of triazole resistant Aspergillus fumigatus isolates using reference microdilution methods and the analysis of sequences of the cyp 51A gene. The study was performed on twenty clinical isolates which were identified as Aspergillus fumigatus based on the DNA sequences of the ITS1-2 fragment of ribosomal DNA and the β-tubulin gene,...
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Reducing the number of periodic points in the smooth homotopy class of a self-map of a simply-connected manifold with periodic sequence of Lefschetz numbers
PublikacjaLet f be a smooth self-map of an m-dimensional (m >3) closed connected and simply-connected manifold such that the sequence of the Lefschetz num- bers of its iterations is periodic. For a fixed natural r we wish to minimize, in the smooth homotopy class, the number of periodic points with periods less than or equal to r. The resulting number is given by a topological invariant J[f] which is defned in combinatorial terms and is...