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Search results for: COMPARISON OF PHYLOGENETIC TREES, MATCHING METRICS, PHYLOGENETIC TREE DISTANCE
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On a matching distance between rooted phylogenetic trees
PublicationThe 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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Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages
PublicationThe 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 Arbitrary Unrooted Phylogenetic Trees Using Generalized Matching Split Distance
PublicationIn 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
PublicationAbility 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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Matching Split Distance for Unrooted Binary Phylogenetic Trees
PublicationRekonstrukcja 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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Matching Split Distance for Unrooted Binary Phylogenetic Trees
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Comparing phylogenetic trees using a minimum weight perfect matching
PublicationA 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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Analyzing sets of phylogenetic trees using metrics
PublicationThe 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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Visual TreeCmp : Comprehensive Comparison of Phylogenetic Trees on the Web
Publication1. 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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Analyzing sets of phylogenetic trees obtained from bayesian MCMC process using topology metrics
PublicationThe 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
PublicationThis 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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Polynomial triset metric for unrooted phylogenetic trees
Publicationthe 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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Critical Case Stochastic Phylogenetic Tree Model via the Laplace Transform
PublicationBirth–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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Properties of the triset metric for phylogenetic trees
Publicationthe 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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High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease
PublicationBACKGROUND: 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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Antibiotic resistance, virulence, and phylogenetic analysis of Escherichia coli strains isolated from free-living birds in human habitats
PublicationWild 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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Phylogenetic Placement and Taxonomy of the Genus Hederorkis (Orchidaceae)
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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
PublicationThe 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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Palicella, a new genus of lichenized fungi and its phylogenetic position withinLecanoraceae
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Lower bound on the distance k-domination number of a tree
PublicationW artykule przedstawiono dolne ograniczenie na liczbę k-dominowania w drzewach oraz scharakteryzowano wszystkie grafy ekstremalne.
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Morphologic, Phylogenetic and Chemical Characterization of a Brackish Colonial Picocyanobacterium (Coelosphaeriaceae) with Bioactive Properties
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Comparison of Absorbed and Intercepted Fractions of PAR for Individual Trees Based on Radiative Transfer Model Simulations
PublicationThe fraction of absorbed photosynthetically active radiation (fAPAR) is a key parameter for estimating the gross primary production (GPP) of trees. For continuous, dense forest canopies, fAPAR, is often equated with the intercepted fraction, fIPAR. This assumption is not valid for individual trees in urban environments or parkland settings where the canopy is sparse and there are well-defined tree crown boundaries. Here, the distinction...
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Narratives on cutting down trees on private land. A comparison of urban and rural municipalities in Poland using the Q-deliberation method
PublicationIncreased development in rural and urban areas leads to a decrease in tree cover and reduces the ecosystem services that trees provide. Municipal authorities must consider managing trees on private land to ensure that residents have access to trees and green spaces. In doing so, they must frequently confront conflicting stakeholder views, which are driven by diverse public and private interests and impacted by the type of landscape...
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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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TreeCmp: Comparison of Trees in Polynomial Time
PublicationMetryki filogenetyczne umożliwiają ocenę jakości wyników analizy filogenetycznej oraz wiarygodności algorytmów przeprowadzających taką analizę. Aplikacja TreeCmp oferuje efektywne, wielomianowe implementacje ośmiu takich metryk (dla drzew nieukorzenionych i zawierających korzeń) zdefiniowanych dla dowolnych filogenez (nie koniecznie binarnych). Program ten jako pierwszy umożliwia wyznaczanie nowych metryk, definiowanych w oparciu...
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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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Modelling of residential sales price with kriging using different distance metrics in different correlation functions
PublicationThe modelling and estimation of sales prices based on economical conditions are important for housing sector especially in developing countries. Analysts are focused on the subject to analyze price movements and estimate the future trend of the sales prices for housing sector. In this study, we tried to generate a robust and efficient model related to the subject. Firstly, we investigated economic variables affecting housing sales...
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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
PublicationWe 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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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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COMPARISON OF SELECTED MORPHOLOGICAL AND RHEOLOGICAL PARAMETERS OF BLOOD IN A GROUP OF OLDER LONG DISTANCE RUNNERS AND UNTRAINED MEN
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Intra-operative biopsy in chronic sinusitis detects pathogenic Escherichia coli that carry fimG/H, fyuA and agn43 genes coding biofilm formation
PublicationThe aim of this study was to investigate whether or not surgical biopsy of sinus tissue in chronic sinusitis, not responsive to treatment, would detect E. coli. We intended to evaluate E. coli virulence genes, therefore dispute the causal role of such an unusual microorganism in chronic sinusitis, as well as consider effective pathogen-targeted therapy. Patients with E. coli isolated by intra-operative puncture biopsy were included...
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Stereo vision with Equal Baseline Multiple Camera Set (EBMCS) for obtaining depth maps of plants
PublicationThis paper presents a method of improving the estimation of distances between an autonomous harvesting robot and plants with ripe fruits by using the vision system based on five cameras. The system is called Equal Baseline Multiple Camera Set (EBMCS). EBMCS has some features of a camera matrix and a camera array. EBMCS is regarded as a set of stereo cameras for estimating distances by obtaining disparity maps and depth maps. This...
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Psychological and physical components in forming preferences on urban greenery management – The case of trees
PublicationPublic opinion is increasingly important in managing urban greenery. In this regard, this study demonstrates the importance of sociological (environmental worldviews), psychological (place attachment, perceived benefits of trees), and physical factors (type of building people live in, and urban greenery) in forming residents’ opinions on whether the municipality or landowners should decide about tree removal on private land. Logistic...
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Accessibility to urban green spaces: A critical review of WHO recommendations in the light of tree-covered areas assessment
PublicationEasy accessibility of Urban Green Spaces (UGSs) is essential to the quality of life in urban areas. The World Health Organization (WHO) recommendations focus on spatial access to UGSs, define as accessible those larger than 0.5 ha situated up to 300 m of residential areas, and disregard the social significance of smaller green spaces. This paper assesses the extent to which the WHO recommendations permit the identification of locations...
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On extremal sizes of locally k-tree graphs
PublicationA graph G is a locally k-tree graph if for any vertex v the subgraph induced by the neighbours of v is a k-tree, k>=0, where 0-tree is an edgeless graph, 1-tree is a tree. We characterize the minimum-size locally k-trees with n vertices. The minimum-size connected locally k-trees are simply (k + 1)-trees. For k >= 1, we construct locally k-trees which are maximal with respect to the spanning subgraph relation. Consequently, the...
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Average Size of a Suffix Tree for Markov Sources
PublicationWe study a suffix tree built from a sequence generated by a Markovian source. Such sources are more realistic probabilistic models for text generation, data compression, molecular applications, and so forth. We prove that the average size of such a suffix tree is asymptotically equivalent to the average size of a trie built over n independentsequences from the same Markovian source. This equivalenceis only known for memoryless...
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Improving methods to calculate the loss of ecosystem services provided by urban trees using LiDAR and aerial orthophotos
PublicationIn this paper we propose a methodology for combining remotely sensed data with field measurements to assess selected tree parameters (diameter at breast height (DBH) and tree species) required by the i-Tree Eco model to estimate ecosystem services (ES) provided by urban trees. We determined values of ES provided by trees in 2017 in Racibórz (a city in South Poland) and estimated the loss of ES from January 1, 2017 to March 5, 2017,...
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Use of Bi-Temporal ALS Point Clouds for Tree Removal Detection on Private Property in Racibórz, Poland
PublicationTrees growing on private property have become an essential part of urban green policies. In many places, restrictions are imposed on tree removal on private property. However, monitoring compliance of these regulations appears difficult due to a lack of reference data and public administration capacity. We assessed the impact of the temporary suspension of mandatory permits on tree removal, which was in force in 2017 in Poland,...
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Inception and Propagation of Electrical Trees in the Presence of Space Charge in HVAC Extruded Cables
PublicationThis paper presents the space charge impact on the inception and propagation of electrical trees in cross-linked polyethylene (XLPE) insulation via simulations and experimentation. A 3D finite element analysis (FEA)-based modeling is proposed to simulate electrical trees via a needle embedded on the XLPE insulation. The proposed FEA model demonstrates the influence of the space charge magnitude and polarity on the initiation of...
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Incremental construction of Minimal Tree Automata [online]
PublicationWe describe an algorithm that allows the incremental addition or removal of unranked ordered trees to minimal frontier-to-root deterministic tree automaton (DTA). The algorithm takes a tree t and a minimal DTA A as input; it outputs a minimal DTA A' which accepts the language L(A) accepted by A incremented (or decremented) with the tree t. The algorithm can be used to efficiently maintain dictionaries which store large collections...
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Why are trees still such a major hazard to drivers in Poland?
PublicationRoadside trees are one of Poland's most serious road safety issues. Since 2009 more than 2800 people have been killed as a result of tree collisions; this represents about 15% of all of Poland's accident fatalities between 2009 and 2013. In some of the country's regions striking a tree caused more than 30% of all road accident fatalities. With no proper regulations, guidelines or examples of good practice, roadside environments...
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Characterization of d-xylose reductase, XyrB, from Aspergillus niger
PublicationD-xylose reductase is a member of the aldo-keto reductase family, and is involved in D-xylose and L-arabinose conversion through the Pentose Catabolic Pathway (PCP) in fungi. In this study, we biochemically characterized a newly identified second D-xylose reductase (XyrB) from Aspergillus niger. This NADPH-dependent reductase is able to efficiently convert D-xylose and L-arabinose, and it has the highest affinity for these sugars...
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Metabolic activity of tree saps of different origin towards cultured human cells in the light of grade correspondence analysis and multiple regression modeling
PublicationTree saps are nourishing biological media commonly used for beverage and syrup production. Although the nutritional aspect of tree saps is widely acknowledged, the exact relationship between the sap composition, origin, and effect on the metabolic rate of human cells is still elusive. Thus, we collected saps from seven different tree species and conducted composition-activity analysis. Saps from trees of Betulaceae, but not from...
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Trees having many minimal dominating sets
PublicationWe provide an algorithm for listing all minimal dominating sets of a tree of order n in time O(1.4656^n). This leads to that every tree has at most 1.4656^n minimal dominating sets. We also give an infinite family of trees of odd and even order for which the number of minimal dominating sets exceeds 1.4167^n, thus exceeding 2^{n/2}. This establishes a lower bound on the running time of an algorithm for listing all minimal dominating...
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The complexity of zero-visibility cops and robber
PublicationWe consider the zero-visibility cops & robber game restricted to trees. We produce a characterisation of trees of copnumber k and We consider the computational complexity of the zero-visibility Cops and Robber game. We present a heavily modified version of an already-existing algorithm that computes the zero-visibility copnumber of a tree in linear time and we show that the corresponding decision problem is NP-complete on a nontrivial...
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Effect of the Road Environment on Road Safety in Poland
PublicationRun-off-road accidents tend to be very severe because when a vehicle leaves the road, it will often crash into a solid obstacle (tree, pole, supports, front wall of a culvert, barrier). A statistical analysis of the data shows that Poland's main roadside hazard is trees and the severity of vehicles striking a tree in a run-off-road crash. The risks are particularly high in north-west Poland with many of the roads lined up with...
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Collaborative Exploration of Trees by Energy-Constrained Mobile Robots
PublicationWe study the problem of exploration of a tree by mobile agents (robots) that have limited energy. The energy constraint bounds the number of edges that can be traversed by a single agent. We use a team of agents to collectively explore the tree and the objective is to minimize the size of this team. The agents start at a single node, the designated root of the tree and the height of the tree is assumed to be less than the energy...