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Wyniki wyszukiwania dla: phylogenetic analysis
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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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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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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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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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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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Phylogenetic Placement and Taxonomy of the Genus Hederorkis (Orchidaceae)
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Antibiotic resistance, virulence, and phylogenetic analysis of Escherichia coli strains isolated from free-living birds in human habitats
PublikacjaWild birds can be colonized by bacteria, which are often resistant to antibiotics and have various virulence profiles. The aim of this study was to analyze antibiotic resistance mechanisms and virulence profiles in relation to the phylogenetic group of E. coli strains that were isolated from the GI tract of wildfowl. Out of 241 faecal samples, presence of E. coli resistant to a cephalosporin (ESBL/AmpC) was estimated for 33 isolates...
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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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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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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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Palicella, a new genus of lichenized fungi and its phylogenetic position withinLecanoraceae
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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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Morphologic, Phylogenetic and Chemical Characterization of a Brackish Colonial Picocyanobacterium (Coelosphaeriaceae) with Bioactive Properties
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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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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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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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How can analysts use multicriteria decision analysis?
PublikacjaProper decision making in multifacitated situation is very challenging task. It is especially difficult if there are many alternatives and criteria that are often contradictory. Analytical chemistry and related sciences involve many situations where decisions on complex problems are made. The support tools may be the use of MCDA (Multi-criteria Decision Analysis) algorithms. They formalize the decision process, make it transparent...
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Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia
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Phylogenetic placement of Lepraria cryptovouauxii sp. nov. (Lecanorales, Lecanoromycetes, Ascomycota) with notes on other Lepraria species from South America
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Phylogenetic placement of Leptosphaeria polylepidis, a pathogen of Andean endemic Polylepis tarapacana, and its newly discovered mycoparasite Sajamaea mycophila gen. et sp. nov.
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The Role of Analysis Patterns in Systems Analysis
PublikacjaWzorce analizy są techniką, która ma wspomagać analizę systemów.W referacie zaprezentowano analizę cech charakterystycznych wzorców analizy oraz przegląd zagadnień związanych z zastosowaniem ich w procesie wytwarzania oprogramowania. Następnie przedstawiono metodę analizy systemów z zastosowaniem wzorców analizy oraz studium przypadku analizy z wykorzystaniem wzorców analizy dla systemu wspomagającego małą przychodnię lekarską.
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Analysis
PublikacjaNew food products and diverse formulations containing the regulated steviol glycoside(s) as well as Stevia extracts or Stevia leaves have been brought on the global market. The upcoming multitude of such food products, but also their falsification and adulteration, does have impact on food analysis. Robust high-throughput methods that cope with different food matrices are required for food control to ensure food safety. The analysis...
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CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
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Phylogenetic relationship and antimicrobial resistance in Escherichia coli isolated from the Reda River and the Oliwski Stream, Northern Poland = Lekooporność i przynależność filogenetyczna szczepów Escherichia Coli izolowanych z rzeki Redy i Potoku Oliwskiego
PublikacjaThe high abundance of fecal bacteria in surface water is usually related to poor agricultural practice, pollution caused by domesticated and wild animals as well as with septic tank failures. Identification of fecal contamination sources seems to be crucial in order to effectively estimate the inherent risk. In this study, the phylogenetic relationship of 30 isolates of E. coli, originated from surface water, was estimated by employing...
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Analysis of drinking water
PublikacjaOpisano źródła organicznych i nieorganicznych zanieczyszczeń wody do picia w tym: lotnych związków chlorowcoorganicznych, pestycydów, wielopierścieniowych węglowodorów aromatycznych, polichlorowanych bifenyli, fenoli, kwasów chlorooctowych, aldehydów, ketonów itp. a także metody ich oznaczania. Przedstawiono schemat technik izolacji i oznaczania końcowego oraz schemat metod wykorzystujących analizę fazy nadpowierzchniowej. Opisano...
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Analysis of drinking water
PublikacjaOpisano źródła organicznych i nieorganicznych zanieczyszczeń wody do picia w tym: lotnych związków chlorowcoorganicznych, pestycydów, wielopierścieniowych węglowodorów aromatycznych, polichlorowanych bifenyli, fenoli, kwasów chlorooctowych, aldehydów, ketonów itp. a także metody ich oznaczania. Przedstawiono schemat technik izolacji i oznaczania końcowego oraz schemat metod wykorzystujących analizę fazy nadpowierzchniowej. Opisano...
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On FEM analysis of Cosserat-type stiffened shells. Static and stability linear analysis
PublikacjaThe present research investigates the theory and numerical analysis of shells stiffened with beams in the framework based on the geometrically exact theories of shells and beams. Shell’s and beam’s kinematics are described by the Cosserat surface and the Cosserat rod respectively, which are consistent including deformation and strain measures. A FEM approximation of the virtual work principle leads to the conforming shell and beam...
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Multimodal Genetic Algorithm with Phase Analysis to Solve Complex Equations of Electromagnetic Analysis
PublikacjaIn this contribution, a new genetic-algorithm-based method of finding roots and poles of a complex function of a complex variable is presented. The algorithm employs the phase analysis of the function to explore the complex plane with the use of the genetic algorithm. Hence, the candidate regions of root and pole occurrences are selected and verified with the use of discrete Cauchy's argument principle. The algorithm is evaluated...
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Maritime transportation risk analysis: Review and analysis in light of some foundational issues
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Geometrically nonlinear analysis of shells - Benchmark problems for Autocad Robot Analysis Professional
PublikacjaThe aim of this work is to verify the suitability of commercial engineering software for geometrically nonlinear analysis of shells. This paper deals with the static, geometrically nonlinear analysis of shells made of an isotropic material. The Finite Element Method (FEM) is chosen to solve the problem. The results of the commercial software Autocad Robot Structural Analysis Professional (ARSAP) are compared with the litera-ture...
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Multimodal Particle Swarm Optimization with Phase Analysis to Solve Complex Equations of Electromagnetic Analysis
PublikacjaIn this paper, a new meta-heuristic method of finding roots and poles of a complex function of a complex variable is presented. The algorithm combines an efficient space exploration provided by the particle swarm optimization (PSO) and the classification of root and pole occurrences based on the phase analysis of the complex function. The method initially generates two uniformly distributed populations of particles on the complex...
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Using Principal Component Analysis and Canonical Discriminant Analysis for multibeam seafloor characterisation data
PublikacjaThe paper presents the seafloor characterisation based on multibeam sonar data. It relies on using the integrated model and description of three types of multibeam data obtained during seafloor sensing: 1) the grey-level sonar images (echograms) of seabed, 2) the 3D model of the seabed surface which consists of bathymetric data, 3) the set of time domain bottom echo envelopes received in the consecutive sonar beams. The classification...
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Differential analysis of impedance data
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The amplitude analysis of impedance spectra
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Damage identification by wavelet analysis
PublikacjaW pracy omówiono metodę identyfikacji rodzaju nieciagłości w 1 wymiarowych elementach konstrukcji wykorzystującą pomiar propagacji fali sprężystej i jej analizę metodą transformacji falkowej.
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Analysis of aircraft magnetic interference
PublikacjaThe magnetometric method is used among other things on mobile platforms (planes, helicopters) in military systems and in geological research. Optically-pumped and SQUID magnetometers are used in magnetic systems on airplanes. To be able to attain the sensitivity of modern magnetometers in flight, it is important that maneuver-related magnetic interference effects be minimized. The mathematical model of an aircraft as a source of...
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Modal analysis of a steel grandstand
PublikacjaAmong the issues related to the idea of sustainable society is the safety of civil engineering structures devoted to satisfy different needs of people. One of the types of structures devoted to satisfy recreational needs are grandstands, which are used during sport events or music concerts. It is obligatory to consider interaction between structure and crowd load especially when the crowd movement involves rhythmic jumping, dancing,...
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Polarization rotaror - analysis and design
PublikacjaW artykule przedstawiono metodę analizy wielosekcyjnego polaryzatora złożonego z periodycznych szyków obiektów cylindrycznych. W celu analizy badanej struktury zastosowano metodę pełnofalową opartą na metodzie dopasowania rodzajów.
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Sensitivity analysis of a composite footbridge
PublikacjaThis work include an example of sensitivity analysis for the design of a composite footbridge. A sandwich structure is used, consisting two high-strength skins separated by a core material. The analysis was conducted for two numerical models. The first one is a simple, single-span beam of a composite cross-section (laminate and foam), with different Young’s modulus for each material. Calculations were made by means of a MATLAB-based...
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Comparative Analysis of Exoskeletal Actuators
PublikacjaSince the beginning of the development of exoskeletons in the early 1960s there was a constant need for improving their actuators technology. Requirements for high power and torque for the lower body and very high precision for the hand motion, while maintaining the flexibility of biological muscles, are still not fully satisfied. The problem lies not just in the lack of appropriate actuator technology, but also in the inability...
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Spectral Analysis of Capital Markets
PublikacjaIn this paper the problem of cycles existence in capital markets is addressed. A spectral analysis algorithm, which reduces signal-to-noise ratio, is proposed to derive cycle periodograms for the yield function of DJIA, WIG~20, and NIKKEI 225 indices. Peaks of the the periodograms provide premises to postulate the existence of some possible cycles. The 3.5 year periodicity in all 3 indices, which can be related to Kitchin cycle...
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Data Analysis in Bridge of Data
PublikacjaThe chapter presents the data analysis aspects of the Bridge of Data project. The software framework used, Jupyter, and its configuration are presented. The solution’s architecture, including the TRYTON supercomputer as the underlying infrastructure, is described. The use case templates provided by the Stat-reducer application are presented, including data analysis related to spatial points’ cloud-, audio- and wind-related research.