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Discrimination of hospital isolates of Acinetobacter baumannii using repeated sequences and whole genome alignment differential analysis
PublikacjaAn optimized method for bacterial strain differentiation, based on combination of Repeated Sequences and Whole Genome Alignment Differential Analysis (RS&WGADA), is presented in this report. In this analysis, 51 Acinetobacter baumannii multidrug-resistance strains from one hospital environment and patients from 14 hospital wards were classified on the basis of polymorphisms of repeated sequences located in CRISPR region, variation...
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A novel method of Mycobacterium tuberculosis complex strain differentiation using polymorphic GC-rich gene sequences.
PublikacjaTuberculosis is one of the leading infectious diseases. In this work, a new genotyping method of Mycobacterium tuberculosis (Mtb) complex strain is presented. 27 Mtb genomes were analyzed for the presence of length polymorphism within polymorphic GC-rich gene sequences. Four genes, Rv3345c, Rv3507, Rv0747 and Rv3511, showing variation in length depending on the Mtb strain were selected for designing primer sequences flanking variable...
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Spectroscopic studies on physicochemical properties of selected unsymmetrical bisacridine derivatives and NMR analysis of their interactions with the model sequence Pu22 aided by molecular dynamics
PublikacjaIn recent years, new promising acridine derivatives have appeared, belonging to the unsymmetrical bisacridines (UAs) family with high anticancer activity. Both their physicochemical properties and their mechanism of action at the molecular level have not been thoroughly analyzed so far. Four derivatives were selected for the study, termed as: C-2028, C-2041, C-2045 and C-2053. The first aim of this work was to determine the protonation...
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Influence of amino acid sequence on the interaction of short peptides containing 3-[2-(9-anthryl)benzoxazol-5-yl]-alanine with β-cyclodextrin
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Novel Highly Thermostable Endolysin from Thermus scotoductus MAT2119 Bacteriophage Ph2119 with Amino Acid Sequence Similarity to Eukaryotic Peptidoglycan Recognition Proteins
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Allelic length of a CA dinucleotide repeat in theegfr gene correlates with the frequency of amplifications of this sequence—first results of an inter-ethnic breast cancer study
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Improvement of time difference of arrival measurements resolution by using fractional delay filters in a direct sequence-code division multiple access radionavigation system
PublikacjaThis study presents a method of improving time measurements resolution in a direct sequence-code division multiple access receiver by using a fine code tracking loop based on fractional delay filtering of a despreading sequence. It briefly describes the structure of a generic digital code tracking loop and the proposed modification which allows to measure time difference of arrival values with the subsample resolution, together...
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TspGWI, a thermophilic class-IIS restriction endonuclease from Thermus sp.,recognizes novel asymmetric sequence 5´-ACGGA(N11/9)-3
PublikacjaA novel prototype class-IIS restriction endonuclease, TspGWI, was isolated from the thermophilic bacterium Thermus sp. GW. The recognition sequence and cleavage positions have been established: TspGWI recognizes the non-palindromic 5-bp sequence 5′-ACGGA-3′ and cleaves the DNA 11 and 9 nt downstream in the top and bottom strand, respectively. In addition, an accompanying endonuclease, TspGWII, an isoschizomer of Pst I, was found...
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An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublikacjaAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
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The motion influence on respiration rate estimation from low-resolution thermal sequences during attention focusing tasks
PublikacjaGlobal aging has led to a growing expectancy for creating home-based platforms for indoor monitoring of elderly people. A motivation is to provide a non-intrusive technique, which does not require special activities of a patient but allows for remote monitoring of elderly people while assisting them with their daily activities. The goal of our study was to evaluate motion performed by a person focused on a specific task and check...
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Detection of specific UL49 sequences of Marek's disease virus CVI988/Rispens strain using loop-mediated isothermal amplification
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PCR-Based Genotyping of Mycobacterium tuberculosis with New GC-Rich Repeated Sequences and IS6110 Inverted Repeats Used as Primers.
PublikacjaW pracy przedstawiono nową metodę genotypowania Mycobacterium tuberculosis. Zastosowanie oligonukleotydu Mtb1 5'-CCG-GCG-GGG-CCG-GCG-G lub Mtb2 5'-CGG-CGG-CAA-CGG-CGG-C wraz z oligonukleotydami specyficznymi do terminalnych sekwencji elementu insercyjnego IS6110 pozwala na różnicowanie szczepów Mycobacterium tuberculosis w metodzie PCR. Opracowana metoda może być wykorzystana w badaniach epidemiologicznych gruźlicy.
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Chromatic cost coloring of weighted bipartite graphs
PublikacjaGiven a graph G and a sequence of color costs C, the Cost Coloring optimization problem consists in finding a coloring of G with the smallest total cost with respect to C. We present an analysis of this problem with respect to weighted bipartite graphs. We specify for which finite sequences of color costs the problem is NP-hard and we present an exact polynomial algorithm for the other finite sequences. These results are then extended...
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Detection of Helicobacter rodentium-like DNA in the liver tissue of patients with chronic liver diseases by polymerase chain reaction–denaturing gradient gel electrophoresis and DNA sequence analysis
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A strong preference for the TA/TA dinucleotide step discovered for an acridine-based, potent antitumor dsDNA intercalator, C-1305: NMR-driven structural and sequence-specificity studies
PublikacjaTriazoloacridinone C-1305, a potent antitumor agent recommended for Phase I clinical trials, exhibits high activity towards a wide range of experimental colon carcinomas, in many cases associated with complete tumor regression. C-1305 is a well-established dsDNA intercalator, yet no information on its mode of binding into DNA is available to date. Herein, we present the NMR-driven and MD-refined reconstruction of the 3D structures...
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Wybrane metody lokalizacji twarzy na obrazie statycznym i ruchomym=Selected methods of face localization on still images and in video sequences
PublikacjaW pracy zaprezentowano wybrane metody lokalizacji, wykorzystujące różne podejścia i rodzaje informacji: algorytm działający w oparciu o analizę barwy i kształtu, metodę map krawędzi oraz elastyczne wzorce służące do precyzyjnej lokalizacji cech. Oprócz tego przedstawiono dwie metody śledzenia twarzy na obrazie ruchomym.
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A new Toxoplasma gondii chimeric antigen containing fragments of SAG2, GRA1, and ROP1 proteins—impact of immunodominant sequences size on its diagnostic usefulness
PublikacjaThis study presents the first evaluation of new Toxoplasma gondii recombinant chimeric antigens containing three immunodominant regions of SAG2, GRA1, and one of two ROP1 fragments differing in length for the serodiagnosis of human toxoplasmosis. The recombinant chimeric antigens SAG2-GRA1-ROP1L (with large fragment of ROP1, 85-396 amino acid residues) and SAG2-GRA1-ROP1S (with a small fragment of ROP1, 85-250 amino acid residues)...
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Characterization of a cryptic plasmid pSFKW33 from Shewanella sp. 33b
PublikacjaA cryptic plasmid pSFKW33 from psychrotrophic bacterium Shewanella sp. 33B, an isolate from the Gulf of Gdansk (the Baltic Sea), was sequenced and characterized. It is an 8021 bpcircular molecule with 38% GC content, which shows a distinctive nucleotide sequence without homology to other known plasmids. The nucleotide sequence analysis predicts eight open reading frames. The deduced amino acid sequence of ORF-1 shared significant...
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On the Origin of Protein Superfamilies and Superfolds
PublikacjaDistributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to...
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Germline DNA Retention in Murine and Human Rearranged T Cell Receptor Gene Coding Joints: Alternative Recombination Signal Sequences and V(D)J Recombinase Errors
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Curlicues generated by circle homeomorphisms
PublikacjaWe investigate the curves in the complex plane which are generated by sequences of real numbers being the lifts of the points on the orbit of an orientation preserving circle homeomorphism. Geometrical properties of these curves such as boundedness, superficiality, local discrete radius of curvature are linked with dynamical properties of the circle homeomorphism which generates them: rotation number and its continued fraction...
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Firing map for periodically and almost-periodically driven integrate-and-fire models: a dynamical systems approach
PublikacjaWe consider the Leaky Integrate-and-Fire and Perfect Integrator models of neuron’s dynamics with the input function being periodic and almost-periodic (in the sense of Stepanov). In particular we analyze properties and dynamics of the so-called firing map, which iterations give timings of consecutive spikes of a neuron. In case of a periodic input function we provide a detailed description of the sequence of interspike-intervals,...
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Conserved motifs of MutL proteins
PublikacjatThe MutL protein is best known for its function in DNA mismatch repair (MMR). However, there isevidence to suggest that MutL is not only the linker connecting the functions of MutS and MutH in MMR,but that it also participates in other repair systems, such as Very Short Patch (VSP), Base Excision (BER)and Nucleotide Excision Repair (NER). This study set out to identify the most highly conserved aminoacid sequence motifs in MutL...
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Impact of Shifting Time-Window Post-Processing on the Quality of Face Detection Algorithms
PublikacjaWe consider binary classification algorithms, which operate on single frames from video sequences. Such a class of algorithms is named OFA (One Frame Analyzed). Two such algorithms for facial detection are compared in terms of their susceptibility to the FSA (Frame Sequence Analysis) method. It introduces a shifting time-window improvement, which includes the temporal context of frames in a post-processing step that improves the...
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SiMiSnoRNA: Collection of siRNA, miRNA, and snoRNA database for RNA Interference
PublikacjaObjective:The discovery of sequence specific gene silencing which occurs due to the presence of double-stranded RNAs has considerable impact on biology, revealing an unknown level of regulation of gene expression. This process is known as RNA interference (RNAi) or RNA silencing in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecule. Two types of small RNA molecules - small...
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Photoinduced electron transfer in 5-bromouracil labeled DNA. A contrathermodynamic mechanism revisited by electron transfer theories
PublikacjaThe understanding of the 5-bromouracil (BrU) based photosensitization mechanism of DNA damage is of large interest due to the potential applications in photodynamic therapy. Photoinduced electron transfer (ET) in BrU labeled duplexes comprising the 50 -GBrU or 50 -ABrU sequence showed that a much lower reactivity was found for the 50 -GBrU pattern. Since the ionization potential of G is lower than that of A, this sequence selectivity...
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A new division of bacterial UvrA homologues
PublikacjaThe UvrA protein is a DNA-binding and damage-recognition enzyme which participates in the prokaryotic type nucleotide excision repair (NER) pathway. It has recently been noted that some bacterial genomes comprise additional uvrA genes which encode five distinct types of UvrA homologue. We investigated the sequences of over 2400 bacterial genomes and found 130 examples of bacteria containing uvrA 2 genes. The sequence analyses conducted...
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A cryptic ribosome binding site, false signals in reporter systems and avoidance of protein translation chaos
PublikacjaThe expression of reporter gene may be induced by activation of cryptic signalling sequences, as we found while constructing the mutS-lacZ fusion gene. We cloned the Escherichia coli lacZ gene encoding beta-galactosidase into a plasmid vector carrying the Thermus thermophilus mutS gene. The clones expected to produce beta-galactosidase as the C-terminal fusion were selected for the complementation of beta-galactosidase activity...
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EASY ACCESS TOOL FOR SMALL INTERFERING RNA (siRNA) DATA
PublikacjaFor many decades it was an accepted dogma of molecular genetics that the expression of genes is a “one-way-road” leading only in one direction from DNA to RNA to proteins. Recent discoveries in modern molecular genetics have challenged this dogma showing that specific RNA molecules play a central role in controlling the activity of genes by changing the structure of DNA sequences, targeting other RNAs for degradation or blocking...
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Functionalized Peptide Fibrils as a Scaffold for Active Substances in Wound Healing
PublikacjaTechnological developments in the field of biologically active peptide applications in medicine have increased the need for new methods for peptide delivery. The disadvantage of peptides as drugs is their low biological stability. Recently, great attention has been paid to self-assembling peptides that can form fibrils. Such a formulation makes bioactive peptides more resistant to enzymatic degradation and druggable. Peptide fibrils...
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Genetic predisposition to inflammatory bowel disease
PublikacjaInflammatory bowel disease (IBD) is a chronic, incurable inflammatory disease of the digestive system. The two main disease entities included in the IBD are ulcerative colitis and Crohn's disease. According to epidemiological studies there are more and more new cases every year. In especially among the youngest patients with symptoms of malnutrition and growth inhibition to land up in hospitalwith cancer suspected. The purpose...
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Improving Traffic Light Recognition Methods using Shifting Time-Windows
PublikacjaWe propose a novel method of improving algorithms recognizing traffic lights in video sequences. Our focus is on algorithms for applications which notify the driver of a light in sight. Many existing methods process images in the recording separately. Our method bases on the observation that real-life videos depict underlying continuous processes. We named our method FSA (Frame Sequence Analyzed). It is applicable for any underlying...
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Improving methods for detecting people in video recordings using shifting time-windows
PublikacjaWe propose a novel method for improving algorithms which detect the presence of people in video sequences. Our focus is on algorithms for applications which require reporting and analyzing all scenes with detected people in long recordings. Therefore one of the target qualities of the classification result is its stability, understood as a low number of invalid scene boundaries. Many existing methods process images in the recording...
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Cloning, expression, and biochemical characterization of a coldactive GDSL-esterase of a Pseudomonas sp. S9 isolated from Spitsbergen island soil
PublikacjaAn estS9 gene, encoding an esterase of the psychrotolerant bacterium Pseudomonas sp. S9 was cloned and sequenced. The deduced sequence revealed a protein of 636 amino acid residues with a molecular mass of 69 kDa.Further amino acid sequence analysis revealed that the EstS9 enzyme contained a G-D-S-L motif centered at a catalytic serine, an N-terminal catalytic domain and a C-terminal autotransporter domain. Two recombinant E. coli...
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EM-Driven Multi-Objective Optimization of Antenna Structures in Multi-Dimensional Design Spaces
PublikacjaFeasible multi-objective optimization of antenna structures is presented. An initial set of Pareto optimal solutions is found using a multi-objective evolutionary algorithm (MOEA) working with a fast surrogate antenna model obtained by kriging interpolation of coarse-discretization EM simulation data. To make the surrogate construction computationally feasible in multi-dimensional design space, the space subset containing non-dominated...
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Optimal edge-coloring with edge rate constraints
PublikacjaWe consider the problem of covering the edges of a graph by a sequence of matchings subject to the constraint that each edge e appears in at least a given fraction r(e) of the matchings. Although it can be determined in polynomial time whether such a sequence of matchings exists or not [Grötschel et al., Combinatorica (1981), 169–197], we show that several questions about the length of the sequence are computationally intractable....
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DETERMINATION OF OBJECTIVES FOR URBAN FREIGHT POLICY
PublikacjaBackground: Decisions regarding strategic planning of urban freight transport very often are based on superficial assumptions inadequately reflecting the actual character of encountered challenges. The trend may be observed to adapt isolated solutions without supporting measures and verification of expected outcomes. Selected urban freight solutions have a significant potential to alleviate transport related problems, but they...
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A Generalized Version of the Lions-Type Lemma
PublikacjaIn this short paper, I recall the history of dealing with the lack of compactness of a sequence in the case of an unbounded domain and prove the vanishing Lions-type result for a sequence of Lebesgue-measurable functions. This lemma generalizes some results for a class of Orlicz–Sobolev spaces. What matters here is the behavior of the integral, not the space
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Sensorless Control of Polyphase Induction Machines
PublikacjaThe basics of transformations of polyphase systems into orthogonal systems are explained. Vector models of induction machines in orthogonal planes are analysed and multiscalar models for rotor flux and main flux together with stator current are presented. A speed observer based on an extended model of the induction machine for selected variables is applied in the control system for the induction machine. On the basis of the model...
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Equivalence of equicontinuity concepts for Markov operators derived from a Schur-like property for spaces of measures
PublikacjaVarious equicontinuity properties for families of Markov operators have been – and still are – used in the study of existence and uniqueness of invariant probability for these operators, and of asymptotic stability. We prove a general result on equivalence of equicontinuity concepts. It allows comparing results in the literature and switching from one view on equicontinuity to another, which is technically convenient in proofs....
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Graph classes generated by Mycielskians
PublikacjaIn this paper we use the classical notion of weak Mycielskian M'(G) of a graph G and the following sequence: M'_{0}(G) =G, M'_{1}(G)=M'(G), and M'_{n}(G)=M'(M'_{n−1}(G)), to show that if G is a complete graph oforder p, then the above sequence is a generator of the class of p-colorable graphs. Similarly, using Mycielskian M(G) we show that analogously defined sequence is a generator of the class consisting of graphs for which the...
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Restricted open shop scheduling
PublikacjaIn the real applications the open shop scheduling models often require some additional constraints and adequate models. We concern the restrictions in the open shop scheduling related to an instance of the problem and to a feasible solution. Precisely, we require that each jobs consists of the bounded number of operations and each machine has a bounded load (i.e., the total number of operations executed on this machine in a schedule)....
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Deep Instance Segmentation of Laboratory Animals in Thermal Images
PublikacjaIn this paper we focus on the role of deep instance segmentation of laboratory rodents in thermal images. Thermal imaging is very suitable to observe the behaviour of laboratory animals, especially in low light conditions. It is an non-intrusive method allowing to monitor the activity of animals and potentially observe some physiological changes expressed in dynamic thermal patterns. The analysis of the recorded sequence of thermal...
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Moments of Hermite-Gaussian functionals
PublikacjaMoments of finite products of Hermite-Gaussian functionals are expressed by covariances of Gaussian sequence.
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Identification and molecular modeling of a novel lipase from an Antarctic soil metagenomic library.
PublikacjaIn this work, we present the construction of a metagenomic library in Escherichia coli using pUC19 vector and environmental DNA directly isolated from Antarctic topsoil and screened for lipolytic enzymes. The screening on agar supplemented with olive oil and rhodamine B revealed one clone with lipolytic activity (Lip1) out of 11,000 E. coli clones. This clone harbored a plasmid, pLip1, which has an insert of 4722 bp that has been...
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Analysis of Interspike-Intervals for the General Class of Integrate-and-Fire Models with Periodic Drive
PublikacjaWe study one-dimensional integrate-and-fire models of the general type x˙=F (t, x) and analyze properties of the firing map which iterations recover consecutive spike timings. We impose very week constraints for the regularity of the function F (t, x), e.g. often it suffices to assume that F is continuous. If additionally F is periodic in t, using mathematical study of the displacement sequence of an orientation preserving circle...
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Conservation and diversity of MutS proteins
PublikacjaThe homologues of MutS, mismatch repair protein, exist in all prokaryotes, with the exception of Actinobacteria, Mollicutes and part of the Archaea. Multiple alignments of 316 MutS amino acid sequences from 169 species revealed conserved residues and sequence motifs distinguishing MutS homologues. All MutS homologues show high conservation within the ATPase domain. MutS1, the homologue responsible for DNA mismatch recognition,...
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Assessment of diversity and composition of bacterial community in Sludge Treatment Reed Bed systems
PublikacjaDue to their low emission of odours and lack of the need to apply additional chemical agents, sludge treatment reed beds (STRBs) constitute an economically feasible and eco-friendly approach to sewage sludge management. Correctly designed and operated STRBs ensure effective reduction of the dry matter content coupled with the mineralisation of organic compounds. Successful operation of STRBs relies on complex interactions between...
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DETERMINING THE TIME CONSTANT USING TWO METHODS AND DEFINING THE THERMOCOUPLE RESPONSE TO SINE EXCITATION OF GAS TEMPERATURE
PublikacjaThis paper describes the two methods of determining the time constant of type K thermocouple, for two construction solutions: the exposed weld and the mantle fillet weld. This is an important parameter indicating the response time of the thermocouple on the recorded signal. The first method consists of determining the value of τ in the way of numerical simulation of heat exchange between the thermocouple and the current of gas...
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Asymptotic Expansion Method with Respect to Small Parameter for Ternary Diffusion Models
PublikacjaTernary diffusion models lead to strongly coupled systems of PDEs. We choose the smallest diffusion coefficient as a small parameter in a power series expansion whose components fulfill relatively simple equations. Although this series is divergent, one can use its finite sums to derive feasible numerical approximations, e.g. finite difference methods (FDMs).