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Wyniki wyszukiwania dla: PHYLOGENETIC SIGNAL
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An automatic system for identification of random telegraph signal (RTS) noise in noise signals
PublikacjaIn the paper the automatic and universal system for identification of Random Telegraph Signal (RTS) noise as a non-Gaussian component of the inherent noise signal of semiconductor devices is presented. The system for data acquisition and processing is described. Histograms of the instantaneous values of the noise signals are calculated as the basis for analysis of the noise signal to determine the number of local maxima of histograms...
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Application of Complementary Signals in Built-In Self Testers for Mixed-Signal Embedded Electronic Systems
PublikacjaThis paper concerns the implementation of shape-designed complementary signals (CSs), matched to the frequency characteristic of the circuit under test, in built-in self testers (BISTs), dedicated to mixed-signal embedded electronic systems for testing their analog sections. The essence of the proposed method and solution of CS BIST is low-cost realization on the base of hardware and software resources of microcontrollers used...
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Analyzing sets of phylogenetic trees obtained from bayesian MCMC process using topology metrics
PublikacjaThe reconstruction of evolutionary trees is one of the primary objectives in phylogenetics. Such a tree represents historical evolutionary relationship between different species or organisms. Tree comparisons are used for multiple purposes, from unveiling the history of species to deciphering evolutionary associations amongorganisms and geographical areas.In the paper, we describe a general method for comparing hylogenetic trees....
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Construction of phylogenetic trees with topological constraints
PublikacjaThis paper proposes a method of reconstruction of phylogenetic trees based on heuristic search with topological constraints. Using topological constraints it is possible to reduce the set of solutions as well as to enforce that the result is consistent with a given hypothesis about the evolution process within some group of species. Along with this work a number of algorithms used for phylogenetic analysis were implemented. Those...
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Properties of the triset metric for phylogenetic trees
Publikacjathe following paper presents a new polynomial time metric for unrootedphylogenetic trees (based on weighted bipartite graphs and the method ofdetermining a minimum perfect matching) and its properties. also many its properties are presented.
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Phylogenetic Placement and Taxonomy of the Genus Hederorkis (Orchidaceae)
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Polynomial triset metric for unrooted phylogenetic trees
Publikacjathe following paper presents a polynomial triset metric for unrooted phylogenetic trees (based on weighted bipartite graphs and the method of determining a minimum edge cover) and its basic characteristics. also a list of further directions of research and examples of the wider use of this metric is presented.
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Analyzing sets of phylogenetic trees using metrics
PublikacjaThe reconstruction of evolutionary trees is one of the primary objectives in phylogenetics. Such a tree represents historical evolutionary relationships between different species or organisms. Tree comparisons are used for multiple purposes, from unveiling the history of species to deciphering evolutionary associations among organisms and geographical areas. In this paper, we describe a general method for comparing phylogenetictrees...
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On a matching distance between rooted phylogenetic trees
PublikacjaThe Robinson–Foulds (RF) distance is the most popular method of evaluating the dissimilarity between phylogenetic trees. In this paper, we define and explore in detail properties of the Matching Cluster (MC) distance, which can be regarded as a refinement of the RF metric for rooted trees. Similarly to RF, MC operates on clusters of compared trees, but the distance evaluation is more complex. Using the graph theoretic approach...
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
PublikacjaRekonstrukcja drzew ewolucji jest jednym z głównych celów w bioinformatyce. Drzewa filogenetyczne reprezentuje historię ewolucji i związki pokrewieństwa między różnymi gatunkami. W pracy proponujemy nową ogólną metodę określania odległości między nieukorzenionymi drzewami filogenetycznymi, szczególnie użyteczną dla dużych zbiorów gatunków. Następnie podajemy szczegółowe własności jednej metryki określonej przy użyciu tej metody...
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Visual TreeCmp : Comprehensive Comparison of Phylogenetic Trees on the Web
Publikacja1. We present Visual TreeCmp—a package of applications for comparing phylogenetic tree sets. 2. Visual TreeCmp includes a graphical web interface allowing the visualization of compared trees and command line application extended by comparison methods recently proposed in the literature. 3. The phylogenetic tree similarity analysis in Visual TreeCmp can be performed using eighteen metrics, of which 11 are dedicated to rooted trees...
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Comparing phylogenetic trees using a minimum weight perfect matching
PublikacjaA phylogenetic tree represents historical evolutionary relationshipbetween different species or organisms. There are various methods for reconstructing phylogenetic trees.Applying those techniques usually results in different treesfor the same input data. An important problem is to determinehow distant two trees reconstructed in such a wayare from each other. Comparing phylogenetic trees is alsouseful in mining phylogenetic information...
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Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages
PublikacjaThe ability to quantify a dissimilarity of different phylogenetic trees is required in various types of phylogenetic studies, for example, such metrics are used to assess the quality of phylogeny construction methods and to define optimization criteria in supertree building algorithms. In this article, starting from the already described concept of matching metrics, we define three new metrics for rooted phylogenetic trees. One...
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Palicella, a new genus of lichenized fungi and its phylogenetic position withinLecanoraceae
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Critical Case Stochastic Phylogenetic Tree Model via the Laplace Transform
PublikacjaBirth–and–death models are now a common mathematical tool to describe branching patterns observed in real–world phylogenetic trees. Liggett and Schinazi (2009) is one such example. The authors propose a simple birth–and–death model that is compatible with phylogenetic trees of both influenza and HIV, depending on the birth rate parameter. An interesting special case of this model is the critical case where the birth rate equals the...
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Morphologic, Phylogenetic and Chemical Characterization of a Brackish Colonial Picocyanobacterium (Coelosphaeriaceae) with Bioactive Properties
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Comparing Arbitrary Unrooted Phylogenetic Trees Using Generalized Matching Split Distance
PublikacjaIn the paper, we describe a method for comparing arbitrary, not necessary fully resolved, unrooted phylogenetic trees. Proposed method is based on finding a minimum weight matching in bipartite graphs and can be regarded as a generalization of well-known Robinson-Foulds distance. We present some properties and advantages of the new distance. We also investigate some properties of presented distance in a common biological problem...
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Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions
PublikacjaAbility to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in...
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Phylogenetic and geographic analysis of fowl adenovirus field strains isolated from poultry in Poland
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Phylogenetic analysis of mysterious burials revealed in the former penal labor camp Treblinka I
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Using a square-wave signal for fault diagnosis of analog parts of mixed-signal electronic embedded systems
PublikacjaArtykuł przedstawia nowe podejście do detekcji i lokalizacji pojedynczych katastroficznych i parametrycznych uszkodzeń części analogowych w mieszanych sygnałowo elektronicznych systemach wbudowanych. Podejście składa się z trzech etapów: tworzenia słownika uszkodzeń na podstawie krzywych identyfikacyjnych, etapu pomiarowego w którym układ badany pobudzany jest falą prostokątną generowaną przez mikrokontroler a odpowiedź jest próbkowana...
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A phylogenetic and morphological study of Polystachya sect. Superpositae (Orchidaceae) with description of a new species from Cameroon
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High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease
PublikacjaBACKGROUND: It is not clear which species of bacteria may be involved in inflammatory bowel disease (IBD). One way of determining which bacteria might be likely candidates is to use culture-independent methods to identify microorganisms that are present in diseased tissues but not in controls. AIMS: (1) To assess the diversity of microbial communities of biopsy tissue using culture-independent methods; (2) to culture the bacteria...
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Tools for signal analysis of gas sensors
PublikacjaStatystyki drugiego rzedu oraz jklasyczna analiza widmowa są zwykle stosowane do badania sygnałów losowych o rozkładzie gaussowskim. Są one jednak często nieodpowiednie w przypadku analizy niestacjonarnych sygnałów niegaussowskich. Pewne narzędzia do analizy takich sygnałów sa dostępne w bibliotekach środowiska MATLAB. Zostały one wykorzystane do do analizy fluktuacji sygnałów czujników gazów. W artykule przedstawiono system do...
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Music signal equalization in a changing environment
PublikacjaThe paper presents the concept of an automatic system for music signal correction, considering room frequency response and music genre being played. The proposed algorithm, based on the room frequency response, compensates acoustic conditions surrounding the sound source. Additionally, the compensation process considers the signal content by recognizing music genre. As part of the described research, a series of subjective tests...
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t-SNE Highlights Phylogenetic and Temporal Patterns of SARS-CoV-2 Spike and Nucleocapsid Protein Evolution
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t-SNE Highlights Phylogenetic and Temporal Patterns of SARS-CoV-2 Spike and Nucleocapsid Protein Evolution
PublikacjaWe propose applying t-distributed stochastic neighbor embedding to protein sequences of SARS-CoV-2 to construct, visualize and study the evolutionary space of the coronavirus. The basic idea is to explore the COVID-19 evolution space by using modern manifold learning techniques applied to evolutionary distances between variants. Evolutionary distances have been calculated based on the structures of the nucleocapsid and spike proteins.
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Analysis of Positioning Error and Its Impact on High Frequency Performance Parameters of Differential Signal Coupler of Differential Signal Coupler
PublikacjaThis paper presents the analysis of the effect of differential signal coupler positioning accuracy on its high frequency performance parameters for contact-less high speed chip-to-chip data transmission on PCB application. Our considerations are continuation of the previous works on differential signal coupler concept, design methodology and analysis for high speed data transmission monitoring presented in [1, 2]. The theoretical...
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Reconstruction of input signal of sensor with frequency output
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Digital structures for high-speed signal processing
PublikacjaThe work covers several issues of realization of digital structures for pipelined processing of real and complex signals with the use of binary arithmetic and residue arithmetic. Basic rules of performing operations in residue arithmetic are presented along with selected residue number systems for processing of complex signals and computation of convolution. Subsequently, methods of conversion of numbers from weighted systems to...
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The Use of Wavelet Analysis to Denoising of Electrocardiography Signal
PublikacjaThe electrocardiography examination, due to its accessibility and simplicity, has an important role in diagnostics of the heart ailments. It enables quick detection of various heart defects, undetectable by other kinds of diagnostic tools, so it is very popular. Nevertheless, the measured signal is exposed to a different disturbances. Among them, the electromagnetic interferences, drift of reference electrode and high frequency...
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Optimal ECG lead for deriving respiratory signal
PublikacjaEDR is an interesting measuring technique that allows an indirect assessment of respiratory activity. This is an alternative solution to direct methods that are based on the measurement of air flow, which require a specialized sensor or even a system. However, due to inter-personal anatomical differences, the optimal ECG lead (placement of the electrodes) ensuring the best EDR signal quality is not fixed. An influence of ECG lead...
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A random signal generation method for microcontrollers with DACs
PublikacjaA new method of noise generation based on software implementation of a 7-bit LFSR based on a common polynomial PRBS7 using microcontrollers equipped with internal ADCs and DACs and a microcontroller noise generator structure are proposed in the paper. Two software applications implementing the method: written in ANSI C and based on the LUT technique and written in AVR Assembler are also proposed. In the method the ADC results are...
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Respiratory signal of bathing person - preliminary study
PublikacjaThe scope of this paper is analysis of applicability of modern biomedical acquisition system installed in bathtub towards reception of respiratory signals of bathing person. An analysis of the possibility of such measurement is shown as well as preliminary results.
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SIMPLY AND LOW COAST ELECTROMYOGRAPHY SIGNAL AMPLIFIER
PublikacjaRecently, there has been a noticeable increase in interest in solu tions utilizing electrical signals accompanying muscle activity. Electromyography (EMG) is a technique for recording, analysis and evaluating the electrical activity produced by striated muscle. Its great popularity is due, among other, to the ability to measure with non-invasive electrodes (calle d as sEMG surface electromyography)....
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A Study on Audio Signal Processed by "Instant Mastering"
PublikacjaAn increasing amount of music produced in home- and project-studios results in development and growth of "automatic mastering services". The presented investigation explores changes introduced to audio signal by various online mastering platforms. A music set consisting of 10 songs produced in small facilities was processed by eight on-line automatic mastering services. Additionally, some laboratory-constructed signals were tested....
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Comparison of selected electroencephalographic signal classification methods
PublikacjaA variety of methods exists for electroencephalographic (EEG) signals classification. In this paper, we briefly review selected methods developed for such a purpose. First, a short description of the EEG signal characteristics is shown. Then, a comparison between the selected EEG signal classification methods, based on the overview of research studies on this topic, is presented. Examples of methods included in the study are: Artificial...
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General analysis of braodband signal spatial filtration.
PublikacjaPrzedstawiono ogólną metodę wyznaczania charakterystyk kierunkowych filtrów przestrzennych dla hydroakustycznych sygnałów przestrzennych. Omówiono wpływ szerokości widma odbieranych sygnałów na szerokość wiązki i poziom listków bocznych. Pokazano skutki oszczędnych metod filtracji przestrzennej stosowanych przy odbiorze sygnałów wąskopasmowych, gdy odbierane są sygnały szerokopasmowe.
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Log signals simulation.
PublikacjaSymulatory logów (urządzeń mierzących prędkość w nawigacji morskiej), które używane są do testowania oraz szkolenia operatorów radarów i systemów antykolizyjnych, powinny posiadać również wyjście impulsowe, które w logu rzeczywistym pochodzi z licznika przebytej drogi, w postaci zadanej liczby impulsów na milę morską. Urządzenie takie to przetwornik cyfrowo-częstotliwościowy w formie programowanego cyfrowo dzielnika częstotliwości....
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Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia
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Investigations of speech signal parameters with regard to articulation influences
PublikacjaW pracy zostało podjęte zagadnienie parametryzacji sygnału mowy w kontekście ekstrakcji cech biometrycznych. Analizowane parametry to parametry cepstralne (cepstrum liniowe i mel-cepstrum, czyli MFCC), parametry liniowej predykcji (LPC) oraz momenty widmowe i parametr F0. Zastosowano analize w krótkich stałych segmentach sygnału z zastosowaniem dużego zakładkowania, tzw. ''implicite segmentation''. Umożliwiło to zaobserwowanie...
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Gait Recognition: A Challenging Task for MEMS Signal Identification
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A Distributed System of Signal Acquisition for Induction Motors Diagnostic
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Determination of electrode impedance by means of exponential chirp signal
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System of speech signal processing and visualisation for linguistic purposes
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Medley filters - simple tools for efficient signal smoothing
PublikacjaMedley filters are defined as convex combinations of elementary smoothing filters (averaging, median) with different smoothing bandwidths. It is shown that when adaptive weights of such a mixture are evaluated using the recently proposed Bayesian rules, one obtains a tool which often outperforms the state-of-the-art wavelet-based smoothing algorithms. Additionally, unlike wavelet-based procedures, medley filters can easily cope...
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A study on signal processing methods applied to hearing aids
PublikacjaThis paper presents a short survey on current technology available in hearing aids with a focus on digital signal processing techniques used. First, factors influencing the hearing aid effectiveness are introduced. Then, examples of the present DSP methods and strategies are provided. Also, a description of current limitations of hearing aids and future trends of development are shown. Finally, the notion of computational auditory...
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Sleep Apnea Detection by Means of Analyzing Electrocardiographic Signal
PublikacjaObstructive sleep apnea (OSA) is a condition of cyclic, periodic ob-struction (stenosis) of the upper respiratory tract. OSA could be associated with serious cardiovascular problems, such as hypertension, arrhythmias, hearth failure or peripheral vascular disease. Understanding the way of connection between OSA and cardiovascular diseases is important to choose proper treatment strategy. In this paper, we present a method for integrated...
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Efficient signal processing in spectroscopic optical coherence tomography
PublikacjaSpectroscopic optical coherence tomography (SOCT) is an extension of a standard OCT technique, which allows to obtain depth-resolved, spectroscopic information on the examined sample. It can be used as a source of additional contrast in OCT images e.g. by encoding certain features of the light spectrum into the hue of the image pixels. However, SOCT require computation of time-frequency distributions of each OCT A-scan, what is...