Wyniki wyszukiwania dla: MONOTONE SEQUENCES
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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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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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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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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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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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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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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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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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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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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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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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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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Searching by heterogeneous agents
PublikacjaIn this work we introduce and study a pursuit-evasion game in which the search is performed by heterogeneous entities. We incorporate heterogeneity into the classical edge search problem by considering edge-labeled graphs: once a search strategy initially assigns labels to the searchers, each searcher can be only present on an edge of its own label. We prove that this problem is not monotone even for trees and we give instances...
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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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Dorota Wojtowicz-Jankowska dr hab. inż. arch.
OsobyStarszy wykładowca na Wydziale Architektury Politechniki Gdańskiej. W latach 1996 – 2014 pracowała w Katedrze Użyteczności Publicznej, a obecnie jest zatrudniona w Katedrze Projektowania Środowiskowego. W roku 2006 uzyskała tytuł doktora. Od roku 2011 jest członkiem POIA RP. W latach 2014 – 2017 była członkiem Rady Wydziału. W pracy badawczej zajmuje się problematyką związaną z przestrzeniami ekspozycyjnymi. W obszarze jej zainteresowań...
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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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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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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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Systems of boundary value problems of advanced differential equations
PublikacjaThis paper considers the existence of extremal solutions to systems of advanced differential equations with corresponding nonlinear boundary conditions. The monotone iterative method is applied to obtain the existence results. An example is provided for illustration.
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Quasi-solutions for generalized second order differential equations with deviating arguments
PublikacjaThis paper deal with boundary value problems for generalized second order differential equations with deviating arguments. Existence of quasi-solutions and solutions are proved by monotone iterative method. Examples with numerical results are added.
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International Conference on Logic Programming and Non-monotonic Reasoning
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Boundary problems for fractional differential equations
PublikacjaIn this paper, the existence of solutions of fractional differential equations with nonlinear boundary conditions is investigated. The monotone iterative method combined with lower and upper solutions is applied. Fractional differential inequalities are also discussed. Two examples are added to illustrate the results.
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Fractional equations of Volterra type involving a Riemann Liouville derivative
PublikacjaIn this paper, we discuss the existence of solutions of fractional equations of Volterra type with the Riemann Liouville derivative. Existence results are obtained by using a Banach fixed point theorem with weighted norms and by a monotone iterative method too. An example illustrates the results.
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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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Database of the convergence analysis results of the nonstandard approximation of the generalized Burgers–Huxley equation for the solution bounded within [0,1].
Dane BadawczeThe presented dataset is a result of the convergence analysis of the Mickens-type, nonlinear, finite-difference discretization of a generalized Burgers–Huxley partial differential equation.
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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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Searching by Heterogeneous Agents
PublikacjaIn this work we introduce and study a pursuit-evasion game in which the search is performed by heterogeneous entities. We incorporate heterogeneity into the classical edge search problem by considering edge-labeled graphs. In such setting a searcher, once a search strategy initially decides on the label of the searcher, can be present on an edge only if the label of the searcher and the label of the edge are the same. We prove...
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Zero-visibility cops and robber and the pathwidth of a graph
PublikacjaWe examine the zero-visibility cops and robber graph searching model, which differs from the classical cops and robber game in one way: the robber is invisible. We show that this model is not monotonic. We show that the zero-visibility copnumber of a graph is bounded above by its pathwidth and cannot be bounded below by any nontrivial function of the pathwidth. As well, we define a monotonic version of this game and show that the...
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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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Zero-Visibility Cops and Robber Game on a Graph
PublikacjaWe examine the zero-visibility cops and robber graph searching model, which differs from the classical cops & robber game in one way: the robber is invisible. We show that this model is not monotonic. We also provide bounds on both the zero-visibility copnumber and monotonic zero-visibility copnumber in terms of the pathwidth.
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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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The Linear Array 2x1 of Slot Monopoles for 6-8.5 GHZ UWB Standard
PublikacjaThe results of numerical simulations and measurements of 2x1 linear array of slot monopoles are presented in the paper. At the begining a single slot monopole was designed. Next the 2x1 linear array of these monopoles was numerically tested for various configurations of the feeding network. The single monopole and the array were fabricated and the results of the measurements of the reflection coefficients and the radiationpatterns...
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First-order differential equations with nonlocal boundary conditions
PublikacjaWe study a first-order boundary value problem subject to some boundary conditions given by Riemann-Stieltjes integrals. Using a monotone iterative method, we formulate sufficient conditions which guarantee the existence of extremal or quasi-solutions in the corresponding region bounded by upper and lower solutions of our problems. The case when a unique solution exists is also investigated. Some examples are given to illustrate...
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Fractional Problems with Right-Handed Riemann-Liouville Fractional Derivatives
PublikacjaIn this paper, we investigate the existence of solutions for advanced fractional differential equations containing the right-handed Riemann-Liouville fractional derivative both with nonlinear boundary conditions and also with initial conditions given at the end point T of interval [0,T ]. We use both the method of successive approximations, the Banach fixed point theorem and the monotone iterative technique, as well. Linear problems...
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Systematic approach to binary classification of images in video streams using shifting time windows
Publikacjain the paper, after pointing out of realistic recordings and classifications of their frames, we propose a new shifting time window approach for improving binary classifications. We consider image classification in tewo steps. in the first one the well known binary classification algorithms are used for each image separately. In the second step the results of the previous step mare analysed in relatively short sequences of consecutive...
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The effect of preliminary creep-strain on material behavior under LCF tension/compression and pure torsion regimes
PublikacjaThis paper presents the results of experimental tests of monotonic tension and torsion, creep-rupture and preliminary creep at 200C and 300C, as well as low-cycle fatigue of 2024 T3511 aluminum alloy. The fatigue process was conducted at room temperature for uniaxial tension/compression and torsion. The as-received material and pre-deformed material were also investigated during creep at elevated temperature. Basic monotonic,...
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Fractional problems with advanced arguments
PublikacjaThis paper concerns boundary fractional differential problems with advanced arguments. We investigate the existence of initial value problems when the initial point is given at the end point of an interval. Nonhomogeneous linear fractional differential equations are also studied. The existence of solutions for fractional differential equations with advanced arguments and with boundary value problems has been investigated by using...
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Evidence of mutations conferring resistance to clarithromycin in wastewater and activated sludge
PublikacjaThe occurrence of clarithromycin in wastewater samples and of the activated sludge bacteria possibly resistant to this pharmaceutical was the object of the study. Samples of wastewater or activated sludge were taken from a municipal wastewater treatment plant in summer and winter and characterised regarding their clarithromycin concentrations and the presence of nucleic acid fragments (Cla-sequences) known to be responsible for...
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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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On-line Search in Two-Dimensional Environment
PublikacjaWe consider the following on-line pursuit-evasion problem. A team of mobile agents called searchers starts at an arbitrary node of an unknown network. Their goal is to execute a search strategy that guarantees capturing a fast and invisible intruder regardless of its movements using as few searchers as possible. We require that the strategy is connected and monotone, that is, at each point of the execution the part of the graph...
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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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MutS3: a MutS homologue of unknown biological function
PublikacjaThe homologues of MutS proteins are widespread among both Prokaryotes and Eukaryotes. MutS designated as MutS1 is a part of MMR (mismatch repair) system which is responsible for removal of mispaired bases and small insertion/deletion loops in DNA. Initially, the only MutS homologues known were those engaged in mismatch repair and these were later designated as MutS1. Subsequently, the MutS2 homologue was distinguished. MutS2 does...
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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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Structure and the space vector modulation for a medium-voltage power-electronic-transformer based on two seven-level cascade H-bridge inverters
PublikacjaThis study presents the structure and the space vector pulse-width modulation (SVPWM) for power electronic transformer (PET) based on two seven-level cascade H-bridge (CHB) inverters. The DC links of CHB inverters are coupled with nine dual-active bridge (DAB) converters with medium-frequency transformers. The DC-link voltages are equalised with two methods – through the control of DAB voltages...
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Determination of long-chain aldehydes using a novel quartz crystal microbalance sensor based on a biomimetic peptide
PublikacjaThere is an increasingly popular trend aimed at improvement of fundamental metrological parameters of sensors via implementation of materials mimicking biological olfactory systems. This study presents investigation on usefulness of the peptide mimicking HarmOBP7 region as a receptor element of the piezoelectric sensor for selective analysis of long-chain aldehydes. Identification of odorant binding proteins creates new possibilities...
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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...