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Wyniki wyszukiwania dla: PHYLOGENETIC ANALYSIS
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Phylogenetic analysis of mysterious burials revealed in the former penal labor camp Treblinka I
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Phylogenetic and geographic analysis of fowl adenovirus field strains isolated from poultry in Poland
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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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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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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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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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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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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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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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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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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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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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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
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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t-SNE Highlights Phylogenetic and Temporal Patterns of SARS-CoV-2 Spike and Nucleocapsid Protein Evolution
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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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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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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 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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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 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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Analysis of a gene expression model
PublikacjaWe study a mathematical model of gene transcription and protein synthesis with negative feedback. We consider a system of equations taking into account the number of active binding sites, the way in which dimers bind to DNA and time delay in translation process. For a simplified model that consist of three ordinary differential equations with time delay we derive conditions for stability of the positive steady state and for the...
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Multibody models for gait analysis
PublikacjaThe aim of this study was to create multibody biomechanical models to analyze a normal gait of the human. Proposed models can be used to identify joint moments of the lower limbs during normal gait in the single and double support phases. Applying Newton-Euler formulation, following planar models were developed: 1) a mathematical 6DOF model describing a gait in the sagittal plane of the body for single support phase and double...
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Differential analysis of impedance data
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The amplitude analysis of impedance spectra
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Analysis of human behavioral patterns
PublikacjaWidespread usage of Internet and mobile devices entailed growing requirements concerning security which in turn brought about development of biometric methods. However, a specially designed biometric system may infer more about users than just verifying their identity. Proper analysis of users’ characteristics may also tell much about their skills, preferences, feelings. This chapter presents biometric methods applied in several...
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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.
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THE COMPARATIVE ANALYSIS OF ECOLOGICAL LUBRICANTS
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The analysis of stationary electrochemical noise.
PublikacjaSzum elektrochemiczny jest techniką cieszącą się rosnącym zainteresowaniem. Jedną z podstawowych charakterystyk przebiegów otrzymywanych za pomocą omawianej metody jest widmowa gęstość mocy. Prawidłowa estymacja powyższej wielkości wiąże się z koniecznością zachowania wymogu stacjonarności szumu elektrochemicznego. W niniejszej pracy autorzy proponują zastosowanie rozkładu Wignera-Villego do oceny stopnia niestacjonarności przebiegów...
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On aspects of tensile structures analysis.
PublikacjaW pracy dokonano omówienia podstawowych aspektów analizy konstrukcji napiętych. Przedstawiono krótki rys historyczny tego typu konstrukcji, zwracając uwagę m.in. na konstrukcje membranowe, cięgnowe, pneumatyczne.
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Analysis of transformer inrush currents
PublikacjaW artykule przedstawiono model i wyniki obliczeń prądu i strumienia magnetycznego w układzie zawierającym transformator trójfazowy i wyłącznik. Opracowano obwodowy model łącznika z łukiem elektrycznym. Model łuku zbudowano w oparciu o jego statyczną i dynamiczną charakterystykę prądowo-napięciową. Przeprowadzone symulacje wykazały, że wartość maksymalna prądu włączania transformatora zależy zarówno od chwili włączenia napięcia...
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Trace analysis - challenges and problems
PublikacjaW pracy przedstawiono podstawowe problemy związane z oznaczaniem składników śladowych i ultraśladowych w próbkach o złożonym składzie matrycy. W oparciu o dane literaturowe omówiono sposoby zapobiegania błędom jakimi mogą być obarczone wyniki oznaczeń końcowych.
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Atmospheric precipitation sampling for analysis
PublikacjaW pracy dokonano przeglądu różnych próbników stosowanych do pobierania próbek opadów atmosferycznych (wody deszczowe, mgła, wody spływne). Zaprezentowano urządzenia o różnym stopniu automatyzacji, od najprostszych konstrukcji do urządzeń kosztownych i wysoce zautomatyzowanych. W wielu publikacjach pomijane są informacje o stosowanej metodyce pobierania próbek oraz o położeniu stanowiska obserwacyjnego. Informacje te są jednak niezbędne,...
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An annotated timeline of sensitivity analysis
PublikacjaThe last half a century has seen spectacular progresses in computing and modelling in a variety of fields, applications, and methodologies. Over the same period, a cross-disciplinary field known as sensitivity analysis has been making its first steps, evolving from the design of experiments for laboratory or field studies, also called ‘in-vivo’, to the so-called experiments ‘in-silico’. Some disciplines were quick to realize the...