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Search results for: computer phylogenetics
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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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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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Phylogenetic Placement and Taxonomy of the Genus Hederorkis (Orchidaceae)
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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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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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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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Matching Split Distance for Unrooted Binary Phylogenetic Trees
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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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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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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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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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Computer synchronization of power generators
PublicationAktualną staje się kwestia opracowania odpowiednich algorytmów pomiarów i obliczeń, według których będzie możliwe prowadzenie procesu automatycznej synchronizacji bezpośrednio z wykorzystaniem komputera. W artykule przedstawiono komputerową metodę realizacji warunku fazowego podczas synchronizacji oraz podano wyniki jej badań symulacyjnych oraz badań na obiektach rzeczywistych.
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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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Industrial computer networks and functional safety
PublicationW rozdziale monografii przedstawiono wybrane aspekty bezpieczeństwa funkcjonalnego na przykładzie przemysłowych sieci komputerowych stosowanych w obiektach infrastruktury krytycznej. Pierwszą cześć rozdziału poświęcono omówieniu klasycznych rozwiązań w zakresie sieci komputerowych. Drugą część rozdziału stanowi analiza przypadku typowej przemysłowej sieci komputerowej z uwzględnieniem aspektów bezpieczeństwa funkcjonalnego.
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Computer-aided Measurements of Turbine Blades
PublicationPrzedstawiono skomputeryzowane pomiary profili łopatek turbinowych po szlifowaniu. W pracy wykorzystano program komputerowy, który może być zastosowany bezpośrednio przez operatora obrabiarki, opracowany na bazie Microsoft Excel.
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Gesture-based computer control system
PublicationIn the paper a system for controlling computer applications by hand gestures is presented. First, selected methods used for gesture recognition are described. The system hardware and a way of controlling a computer by gestures are described. The architecture of the software along with hand gesture recognition methods and algorithms used are presented. Examples of basic and complex gestures recognized by the system are given.
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Erosion of privacy in computer vision systems
PublicationW pracy przedstawiono problemy, które mogą wystąpić, gdy technologia komputerowego wzroku zostanie zaimplementowana w urządzeniach wykorzystywanych w codziennym życiu. Przeprowadzono także dyskusję socjologicznych konsekwencji stosowania biometrii, automatycznego śledzenia ruchu i interpretacji obrazu. Omówiono też problemy wynikające z połączenia komputerowego wzroku z możliwościami oferowanymi przez Internet.
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Computer modeling and testing of structural metamaterials
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Computer aided funcional safety assessment
PublicationReferat porusza wybrane zagadnienia związane z oceną bezpieczeństwa funkcjonalnego w nawiązaniu do normy międzynarodowej IEC 61508. Podkreśla się znaczenie modelowania probabilistycznego systemów elektrycznych, elektronicznych i programowalnych elektronicznych (E/E/PE). Opisuje się wyznaczanie poziomu nienaruszalności bezpieczeństwa (SIL). W następnym kroku analizy weryfikuje się poziom SIL w procesie modelowania probabilistycznego...
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Computer application for railway track realignment
PublicationThe topic of this article is the issue of railway track realignment. For this purpose, a computer software application was created that supports computations and generates a report needed for regulation of the trajectory of the railway. This program gives the ability to import data from measurement of the railway trajectory and then perform the calculation of the mathematical realignment. The result of this calculation is the basis...
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Software Agents for Computer Network Security
PublicationThe chapter presents applications of multi-agent technology for design and implementation of agent-based systems intended to cooperatively solve several critical tasks in the area of computer network security. These systems are Agent-based Generator of Computer Attacks (AGCA), Multi-agent Intrusion Detection and Protection System (MIDPS), Agent-based Environment for Simulation of DDoS Attacks and Defense (AESAD) and Mobile Agent...
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Cost assessment of computer security activities
PublicationComprehensive cost-benefit analysis plays a crucial role in the decision-making process when it comes to investments in information security solutions. The cost of breaches needs to be analysed in the context of spending on protection measures. However, no methods exist that facilitate the quick and rough prediction of true expenditures on security protection systems. Rafal Leszczyna of Gdansk University of Technology presents...
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Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia
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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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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
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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Interakcja człowiek-komputer
PublicationKsiążka omawia najważniejsze zagadnienia kształtowania interakcji człowiek-komputer, występujące podczas projektowania produktu informatycznego. Tematyka książki obejmuje metody stosowane kolejno podczas określania wymagań, projektowania, testowania i oceny rozwiązań interfejsu użytkownika. Przyjęty sposób prezentacji materiału ma na celu również podkreślenie, że wysoka jakość użytkowa produktu informatycznego nie wynika wyłącznie...
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Wygnij swój komputer.
PublicationW artykule przedstawiono wspolczesne trendy w rozwoju interfejsów uzytkownika wybranych rozwiazan infomatycznych.
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Komputer w labiryncie
PublicationProgramiści piszą programy, które potrafią robić wiele różnych rzeczy: odtwarzać filmy, prognozować pogodę, pomagać w nauce języków obcych czy matematyki. Ale czy wiesz, że można zaprogramować komputer tak, aby tworzył labirynty? W dodatku takie, które zawierają tajne informacje!
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A computer system for the complete design of ship propellers
PublicationPraca zawiera opis metody obliczeniowej pozwalającej na zaprojektowanie okrętowej śruby napędowej dla również obliczeniowo wyznaczonego niejednorodnego pola prędkości za kadłubem statku o znanej geometrii i parametrach ruchu. Metoda pozwala na właściwe ujęcie efektu skali i konsekwencji obecności płetwy sterowej za projektowaną śrubą.
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Computer modeling of the solution conformation of cyclic enkephalins
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Computer Aided Design of Wood Pellet Machines
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Complex human computer interface for las patient
PublicationW pracy zaprezentowano system umożliwiający komunikację osobie sparaliżowanej z komputerem przy pomocy wzroku.
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Computer based system for strabismus and amblyopia therapy
PublicationW publikacji opisano system komputerowy do badania i treningu zeza i amblyopii.W przypadku zeza i amblyopii lub tak zwanego syndromu leniwego oka terapia polega na zasłanianiu oka dominującego przez kilka godzin dziennie lub rozmywanie obrazu w tym oku poprzez zastasowanie kropli do oczu lub silnych soczewek w okularach. Taki sposób terapii powoduje zaburzenie widzenia obuocznego. Proponowane rozwiązanie zachowuje widzenie obuoczne....
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Generalized access control in hierarchical computer network
PublicationThe paper presents the design of the security layer for a distributed system located in the multizone hierarchical computer network. Depending on the zone from which a client’s request comes to the system and the type of the request, it will be either authorized or rejected. There is one common layer for the access to all the business services and interactions between them. Unlike the commonly used RBAC model, this system enforces...
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Utilization of fuzzy rules in computer character animation
PublicationThe chapter presents a method for automatic enhancement of computer character animation utilizing fuzzy inference. First the user designs a prototype version of animation, with keyframes only for important poses, roughly describing the action. Then animation is enriched with new motion phases calculated by the fuzzy inference system using descriptors given by the user. Various degrees of motion fluency and naturalness are possible...
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Computer analysis of multiple-choice examination documents
PublicationOpisany system AATE wyposażony jest w edytor testów, za pomocą którego egzaminator przygotowuje test egzaminacyjny. Utworzony test ze swoimi parametrami jest pamiętany w bazie danych i następnie może być wydrukowany. Po przeprowadzeniu egzaminu wypełnione formularze za pomocą skanera z podajnikiem wprowadza się do komputera. W komputerze system analizuje formularze i odczytane odpowiedzi porównuje się z wzorcami przechowywanymi...
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Personal adaptive tuning of mobile computer audio
PublicationAn integrated methodology for enhancing audio quality in mobile computers is presented. The key features are adaptation of the characteristics of the acoustic track to the changing conditions and to the user's individual preferences. Original signal processing algorithms are introduced, which concern: linearization of frequency response, dialogue intelligibility enhancement and dynamics processing tuned up to the user's preferences....
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Computer Support of Analysis of Optical Spectra Measurements
PublicationThe verification of measurement errors has a big impact on the assessment of the accuracy of conducted measurements and obtained results. In many cases, computer simulation results are compared with measurement results in order to evaluate measurement errors. The purpose of our research was to check the accuracy of measurements made with a Fabry–Perot interferometer working in the transmission mode. In the measurement setup, a...
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Computer Aided Telediagnostics System for Stoma Patients
PublicationStoma surgery may concern patients with colorectal cancer and inflammatory bowel disease. More than half of patients diagnosed with colon cancer present at an advanced stage, and palliative treatment may involve stoma formation. This type of surgery may change the patient’s life strongly, therefore they should receive special medical care. The paper presents the assumptions, concept, and architecture of the Stoma-Alert diagnosis...
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Computer support of analysis optical spectra measurements
PublicationVerification of measurement errors has a big impact on assessment of accuracy of conducted measurements and obtained results. In many cases computer simulation results are compared with measurement results in order to evaluate measurement errors. The purpose of our research was to check the accuracy of measurements made with Fabry-Perot interferometer working in the transmission mode. In measurement setup, a 1310 nm superluminescent...
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Modelling and computer animation of geodetic field work
Publication3D modelling of objects is a way of obtaining information, while the visualization of geospatial data is becoming a production task in the scope of surveying. Visualization of geospatial data provides effective tools for analysis information about the land surface, land cover, its features, properties etc. Computer animations, both 2D images and 3D are becoming additional, expected and clear form for presentation results of geodetic...
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COMPUTER ANALYSIS OF HYDRAULIC CONDITIONS IN A SANITARY CHAMBER
PublicationThis paper presents analysis of hydraulic conditions of sewage flow down the slipway (ramp) in the collecting sanitary chamber connecting 3 collectors on the inlet: ⌀600, ⌀800 and ⌀1400 and one on the outlet ⌀1600 mm, with a maximum difference of elevation 5 m. The mathematical model has been made and hydraulic calculations were carried out in steady flow conditions. Then wastewater surface elevation, energy grade line elevation,...
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Modelling the malware propagation in mobile computer devices
PublicationNowadays malware is a major threat to the security of cyber activities. The rapid develop- ment of the Internet and the progressive implementation of the Internet of Things (IoT) increase the security needs of networks. This research presents a theoretical model of malware propagation for mobile computer devices. It is based on the susceptible-exposed- infected-recovered-susceptible (SEIRS) epidemic model. The scheme is based on...
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Displacements of chimney in the light of computer calculations and surveying
PublicationThe article presents the numerical analysis of reinforced concrete chimney displacements, which was carried out geodetic measurements.
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3D Computer Model of the Hip Joint Cartilage
PublicationThis paper presents 3D computer model of the hip joint cartilage in the ANSYS program. Model is made on the basis of anatomy and collected data on the material constants of bone and cartilage components. Analysis and comparison of biochemical model, viscoelastic and molecular mixed - aggregation serves to facilitate the creation of the next model of reality, which could be used in the design of joint prostheses. The correctness...
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COMPUTER-AIDED DESIGN OF ORGANOPHOSPHORUS INHIBITORS OF UREASE
PublicationBased on the structure of the most potential inhibitor diamidophosphate, various novel groups of inhibitors were developed by knowledge-based design approach with covalent carbon-phosphorus or carbon-phosphorus-carbon bond to improve hydrolytic stability to inhibit the microbial ureases. Designed compounds were evaluated with 10 (LigScore1, LigScore2, PLP1, PLP2, JAIN, PMF, PMF04, LUDI_1, LUDI_2 and LUDI_3) different scoring functions...
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New Applications of Multimodal Human-Computer Interfaces
PublicationMultimodal computer interfaces and examples of their applications to education software and for the disabled people are presented. The proposed interfaces include the interactive electronic whiteboard based on video image analysis, application for controlling computers with gestures and the audio interface for speech stretching for hearing impaired and stuttering people. Application of the eye-gaze tracking system to awareness...
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Brain-computer interaction based on EEG signal and gaze-tracking information = Analiza interackji mózg-komputer wykorzystująca sygnał EEg i informacje z systemu śledzenia punktu fiksacji wzroku
PublicationThe article presents an attempt to integrate EEG signal analysis with information about human visual activities, i.e. gaze fixation point. The results from gaze-tracking-based measurement were combined with the standard EEG analysis. A search for correlation between the brain activity and the region of the screen observed by the user was performed. The preliminary stage of the study consists in electrooculography (EOG) signal processing....