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Search results for: MULTIPLE SEQUENCE ALIGNMENT
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Improvement of time difference of arrival measurements resolution by using fractional delay filters in a direct sequence-code division multiple access radionavigation system
PublicationThis study presents a method of improving time measurements resolution in a direct sequence-code division multiple access receiver by using a fine code tracking loop based on fractional delay filtering of a despreading sequence. It briefly describes the structure of a generic digital code tracking loop and the proposed modification which allows to measure time difference of arrival values with the subsample resolution, together...
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Expression of a GDSL esterase from Pseudomonas sp. S9 in Pichiapastoris
PublicationCold active lipolytic enzymes are promising to replace the conventional enzymes processes of biotechnological industries. One of the most important feature of the cold-active lipases and esterases is that they offer economic benefits through energy saving. In general, they exhibit high activity at low temperatures and low thermostability at moderate temperatures. Lipolytic enzyme EstS9 was isolated from Pseudomonas sp. S9. A multiple...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Experiments on Preserving Pieces of Information in a Given Order in Holographic Reduced Representations and the Continuous Geometric Algebra Model
PublicationGeometric Analogues of Holographic Reduced Representations (GAc, which is the continuous version of the previously developed discrete GA model) employ role-filler binding based on geometric products.Atomic objects are real-valued vectors in n-dimensional Euclidean space and complex statements belong to a hierarchy of multivectors. The property of GAc and HRR studied here is the ability to store pieces of information in a given...
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Study of the Performance of DSSS UAC System Depending on the System Bandwidth and the Spreading Sequence
PublicationA signal transmitted in an Underwater Acoustic Communication (UAC) system operating in a shallow-water channel suffers from strong time dispersion due to multipath propagation. This causes the Inter-Symbol Interference (ISI) observed in the received signal, which significantly limits the communication system’s reliability and transmission rate. In such propagation conditions, the Direct-Sequence Spread Spectrum (DSSS) method is...
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Numerically efficient algorithm for compact microwave device optimization with flexible sensitivity updating scheme
PublicationAn efficient trust-region algorithm with flexible sensitivity updating management scheme for electromagnetic (EM)-driven design optimization of compact microwave components is proposed. During the optimization process, updating of selected columns of the circuit response Jacobian is performed using a rank-one Broyden formula (BF) replacing finite differentiation (FD). The FD update is omitted for directions sufficiently well aligned...
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Path Loss Modelling for Location Service Applications
PublicationThe aim of this paper is the path loss modeling for the radiolocation services in radiocommunication networks, particularly in cellular networks. The main results of the measurements obtained in the physical layer of the UMTS are introduced. A new method for the utilization of the multipath propagation phenomenon to improve the estimation of the distance between the mobile station (MS) and the base station (BS) is outlined. This...
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Radio Link Measurement Methodology for Location Service Applications
PublicationThe aim of this paper is the methodology of measurements executed in a radio link for the realization of radiolocation services in radiocommunication networks, particularly in cellular networks. The main results of the measurements obtained in the physical layer of the universal mobile telecommunications system (UMTS) are introduced. A new method for the utilization of the multipath propagation phenomenon to improve the estimation...
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Multi-task Video Enhancement for Dental Interventions
PublicationA microcamera firmly attached to a dental handpiece allows dentists to continuously monitor the progress of conservative dental procedures. Video enhancement in video-assisted dental interventions alleviates low-light, noise, blur, and camera handshakes that collectively degrade visual comfort. To this end, we introduce a novel deep network for multi-task video enhancement that enables macro-visualization of dental scenes. In particular,...
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Terminal charging scheduling of battery electric buses based on vehicle routing problem
PublicationElectric buses are considered to be a viable solution for reducing emission in dense urban areas. However, the greater charging time is a huge challenge for operators. In this paper, charging scheduling method was elaborated based on vehicle routing problem using mixed-integer linear programming model. The main novelty of the paper is the combination of modelling aspect, namely flexible turn sequence and heterogeneous shared charging...
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DS-CDMA receiver in Software Defined Radio technology. Admission to the implementation of a RAKE receiver
PublicationProgrammable radio is one of the latest trends in the construction of multi-standard receivers. The technology, called Software Defined Radio (SDR), is also an ideal test platform that allows to try out different algorithms of signal receiving. This particular feature led to choose this platform to implement a DS-CDMA receiver (Direct Sequence Code Division Multiple Access). The use of SDR allows for a gradual upgrade of data processing...
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Image Classification Based on Video Segments
PublicationIn the dissertation a new method for improving the quality of classifications of images in video streams has been proposed and analyzed. In multiple fields concerning such a classification, the proposed algorithms focus on the analysis of single frames. This class of algorithms has been named OFA (One Frame Analyzed).In the dissertation, small segments of the video are considered and each image is analyzed in the context of its...
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Structural features responsible for control of the eukaryotic GlcN-6-P synthase activity
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. As UDP-GlcNAc, the final product of the hexosamine path, constitutes one of the essential substrates for assembly of bacterial and fungal cell walls, the enzyme is an interesting target for antimicrobial therapy.The structure of E. coli enzyme, known since 2001, forms a dimer of two identical...
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Automatic labeling of traffic sound recordings using autoencoder-derived features
PublicationAn approach to detection of events occurring in road traffic using autoencoders is presented. Extensions of existing algorithms of acoustic road events detection employing Mel Frequency Cepstral Coefficients combined with classifiers based on k nearest neighbors, Support Vector Machines, and random forests are used. In our research, the acoustic signal gathered from the microphone placed near the road is split into frames and converted...
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A Method for Underwater Wireless Data Transmission in a Hydroacoustic Channel under NLOS Conditions
PublicationWireless data transmission in the hydroacoustic channel under non-line-of-sight (NLOS) propagation conditions, for example, during a wreck penetration, is difficult to implement reliably. This is mostly due to the multipath propagation, which causes a reduction in the quality of data reception. Therefore, in this work an attempt has been made to develop a reliable method of wireless underwater communication test it under the NLOS...
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A New Double Digestion Ligation Mediated Suppression PCR Method for Simultaneous Bacteria DNA-Typing and Confirmation of Species: An Acinetobacter sp. Model
PublicationWe have designed a new ddLMS PCR (double digestion Ligation Mediated Suppression PCR) method based on restriction site polymorphism upstream from the specific target sequence for the simultaneous identification and differentiation of bacterial strains. The ddLMS PCR combines a simple PCR used for species or genus identification and the LM PCR strategy for strain differentiation. The bacterial identification is confirmed in the...
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Endoscopic Video Classification with the Consideration of Temporal Patterns
PublicationThe article describes a novel approach to automatic recognition and classification of diseases in endoscopic videos. Current directions of research in this field are discussed. Most presented methods focus on processing single frames and do not take into consideration the temporal relationship between continuous classifications. Existing approaches that consider the temporal structure of an incoming frame sequence are focused on...
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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Conservation and diversity of MutS proteins
PublicationThe homologues of MutS, mismatch repair protein, exist in all prokaryotes, with the exception of Actinobacteria, Mollicutes and part of the Archaea. Multiple alignments of 316 MutS amino acid sequences from 169 species revealed conserved residues and sequence motifs distinguishing MutS homologues. All MutS homologues show high conservation within the ATPase domain. MutS1, the homologue responsible for DNA mismatch recognition,...
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3D Object Shape Reconstruction from Underwater Multibeam Data and Over Ground Lidar Scanning
PublicationThe technologies of sonar and laser scanning are an efficient and widely used source of spatial information with regards to underwater and over ground environment respectively. The measurement data are usually available in the form of groups of separate points located irregularly in three-dimensional space, known as point clouds. This data model has known disadvantages, therefore in many applications a different form of representation,...
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Human verbal memory encoding is hierarchically distributed in a continuous processing stream
PublicationProcessing of memory is supported by coordinated activity in a network of sensory, association, and motor brain regions. It remains a major challenge to determine where memory is encoded for later retrieval. Here we used direct intracranial brain recordings from epilepsy patients performing free recall tasks to determine the temporal pattern and anatomical distribution of verbal memory encoding across the entire human cortex. High...
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Executing Multiple Simulations in the MERPSYS Environment
PublicationThe chapter investigates the steps necessary to perform a simulation instance in the MERPSYS environment and discusses potential limitations in case when vast numbers of simulations are required. An extended architecture is proposed which includes a JMS-based simulation queue and multiple distributed simulators, overcoming the potential bottlenecks. The chapter introduces also methods for preparing suites of multiple simulations...
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublicationWe present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...
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Increasing the Efficiency of Ontology Alignment by Tracking Changes in Ontology Evolution
PublicationIn this paper we present a development of our ontology alignment framework based on varying semantics of attributes. Emphasising the analysis of explicitly given descriptions of how attributes change meanings they entail while being included within different concepts have been proved useful. Moreover, we claim that it is consistent with the intuitive way how people see the real world and how they find similarities and correspondences...
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The Boltzmann sequence-structure channel
PublicationWe rigorously study a channel that maps binary sequences to self-avoiding walks in the two-dimensional grid, inspired by a model of protein statistics. This channel, which we also call the Boltzmann sequence-structure channel, is characterized by a Boltzmann/Gibbs distribution with a free parameter corresponding to temperature. In our previous work, we verified experimentally that the channel capacity has a phase transition for...
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Role of bead sequence in underwater welding
PublicationThis paper presents examinations of the role of the bead sequence in underwater welding. Two specimens of wet welded layers made by covered electrodes with the use of normalized S355G10+N steel were welded by a reasonable bead sequence. For each specimen, metallographic macro- and micro-scopic tests were done. Then, Vickers HV10 hardness measurements were conducted for each pad weld in the welded layer. The results show that welding...
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Designing of Track Axis Alignment with the Use of Satellite Measurements and Particle Swarm Optimization
PublicationDesigning of the track’s alignment is a key issue from the point of view of maintaining of proper geometries. The paper presents a design method for sections of railway line located in the horizontal arch. The method is adapted to the technique of mobile satellite measurements. The general principles of this measurement method have been described in the article. A project's solution has been presented using mathematical notation...
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Phase Transition in a Sequence-Structure Channel
PublicationWe study an interesting channel which maps binary sequences to self-avoiding walks in the two-dimensional grid, inspired by a model of protein folding from statistical physics. The channel is characterized by a Boltzmann/Gibbs distribution with a free parameter corresponding to temperature. We estimate the conditional entropy between the input sequence and the output fold, giving an upper bound which exhibits an unusual phase transition...
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Multiple-Input Multiple-Output Technique for Underwater Acoustic Communication System
PublicationThe performance of an underwater acoustic communication (UAC) system is limited due to tough propagation conditions in the UAC channel. Multiple-Input Multiple-Output (MIMO) technique can improve the reliability of the data transmission system, increase its speed, increase its range, and reduce the energy consumption. The paper presents an implementation method of MIMO technique in the form of coding the Space-Time Block Code and...
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On the regularity of the displacement sequence of an orientation preserving circle homeomorphism
PublicationWe investigate the regularity properties of the displacemnet sequence of an orientation preserving circle homeomorphism. is rational, then ηn(z) is asymptotically periodic with semi-period q. This
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The process of identification of the track's geometrical layout and the alignment project based on the of satellite measurements
PublicationIn the paper a methodology of restoring of railway track’s geometrical shape in a horizontal plane on the base of conducted mobile satellite surveying was presented. The authors proposed a calculating algorithm for designing the track sections placed in horizontal arcs. In the algorithm an analytical methodology with mathematical formulas is applied. The procedure has an universal character, i.e. provides the possibility of varying...
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Application of Maximum Lenght Sequence in Silent Sonar
PublicationSilent sonars are designed to reduce the distance over which their sounding pulses can be detected by intercept sonars. In order to meet this objective, we can use periodical sounding signals that have low power, a very long duration and wide spectrum. If used in the silent sonar's receiver, matched filtration ensures very good detection of motionless or slow moving targets. However, it is more difficult to detect echo signals...
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Frequent Sequence Mining in Web Log Data
PublicationThe amount of information available even on a single web server can be huge. On the other hand, the amount of visitors (users) can often reach a number of at least six digits. Users vary in gender, age and education, and in consequence their information needs are different. Moreover, they subconsciously expect to get more adequate content after visiting the first few pages. The scope of this kind of problem relates to the domain...
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Distribution of the displacement sequence of an orientation preserving circle homeomorphism
PublicationIn some applications not only the knowledge of the behaviour of trajectories of a map is important, but also their displacements. We describe in detail the distribution of elements of the displacement sequence along a trajectory of an orientation preserving circle homeomorphism ϕ with irrational rotation number ϱ(ϕ). The values of displacement are dense in a set which depends on the map γ (semi-)conjugating ϕ with the rotation...
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A method to determine the tightening sequence for standing rigging of a mast
PublicationThe article proposes an alternative method to determine the sequence of generation of pre-tension forces in standing rigging of a mast. The proposed approach has been verified on both a virtual simulation experiment and laboratory tests. In this method, the desired tension values are obtained using the influence matrix which allows to calculate the effect of tension change in an individual rope on the tension distribution in the...
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Lexicon Based Algorithm for Domain Ontology Merging and Alignment
PublicationMore and more systems contain some kind of knowledge describing their field of operation. Such knowledge in many cases is stored as an ontology. A need arises for ability to quickly match those ontologies to enable interoperability of such systems. The paper presents a lexicon based algorithm for merging and aligning of OWL ontologies. The proposed similarity levels are being presented and the proposed algorithm is being described....
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Route vertical alignment design in the process of its regulation
PublicationW monografii przedstawiona została metoda opracowania projektu niwelety toru kolejowego na podstawie pomierzonych nierówności pionowych oraz praktyczny przykład jej zastosowania w procesie utrzymaniu dróg szynowych, a w szczególności w projektowaniu robót związanych z regulacją osi toru. Wykonany w ten sposób profil istniejącej linii kolejowej jest podstawą do obliczenia wartości podnoszeń toru. Wartości te nanosi się w terenie...
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Route vertical alignment design in the process of its regulation
PublicationRegulacja toru kolejowego ma za zadanie dostosowanie niewłaściwego lub też zdeformowanego położenia osi toru do położenia odpowiadającego parametrom technicznym wymaganym dla danej linii kolejowej. Projekt regulacji wykonywany jest na podstawie pomiaru geodezyjnego wysokości toków szynowych metodą punktów stałych, tzn. w oparciu o umieszczone na słupach wskaźniki regulacji osi toru, których wysokość jest znana. Wykonany w ten sposób...
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MutS3: a MutS homologue of unknown biological function
PublicationThe homologues of MutS proteins are widespread among both Prokaryotes and Eukaryotes. MutS designated as MutS1 is a part of MMR (mismatch repair) system which is responsible for removal of mispaired bases and small insertion/deletion loops in DNA. Initially, the only MutS homologues known were those engaged in mismatch repair and these were later designated as MutS1. Subsequently, the MutS2 homologue was distinguished. MutS2 does...
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Stanowisko do diagnostyki i regulacji wyzwalaczy przekaźników w obwodach lokomotyw elektrycznych
PublicationFast circuit breaker and protective relays play an important role of protecting locomotive’s electrical circuits from damage caused by short circuit or overload. Undisturbed operation and proper circuit protection depends on the technical condition and fine calibration of the over-current trips. Therefore the relays should be subject to periodic inspection and adjustment due to locomotive maintenance schedule. A test stand for...
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The accuracy of pulse rate estimation from the sequence of face images
PublicationThe goal of this paper is to analyze the accuracy of pulse rate estimation from the sequence of face images. Simulated and real signals were used to evaluate two pulse rate estimators; one for frequency domain and the second one for time domain using the autocorrelation function. The results show that the mean difference between the reference measurements and estimated pulse rate values are about 2bpm. In the analysis of short...
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Circular polarization diversity implementation for correlation reduction in wideband low-cost multiple-input-multiple-output antenna
PublicationIn this paper, a multiple-input-multiple-output (MIMO) antenna featuring circular polarization diversity, and designed on a common coplanar ground is presented. The proposed antenna design utilizes a coplanar waveguide (CPW) feeding technique with three parallel coplanar ground planes, and two feedlines in-between. For circular polarization (CP), quasi-loops are created by etching slots on the outermost ground planes. With this...
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Primary role identification in e-mail networks using pattern subgraphs and sequence diagrams
PublicationSocial networks often forms very complex structures that additionally change over time. Description of actors' roles in such structures requires to take into account this dynamics reflecting behavioral characteristics of the actors. A role can be defined as a sequence of different types of activities. Various types of activities are modeled by pattern subgraphs, whereas sequences of these activities are modeled by sequence diagrams....
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Multiple Group Membership and Collective Action Intention
PublicationDatasets from two studies conducted in Poland on the relation between identity fusion, group identification, multiple group membership, perceived injustice, and collective action intention. The presented studies, in the context of protests against attempts to restrict abortion law, were conducted to examine the link between belonging to multiple groups, group efficacy & identification, perceived injustice and collective...
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Butyrylcholinesterase signal sequence self-aggregates and enhances amyloid fibril formation in vitro
PublicationAlzheimer’s disease (AD) pathogenesis has been attributed to extracellular aggregates of amyloid β (Aβ) plaques and neurofibrillary tangles in the human brain. It has been reported that butyrylcholinesterase (BChE) also accumulates in the brain Aβ plaques in AD. We have previously found that the BChE substitution in 5′UTR caused an in-frame N-terminal extension of 41 amino acids of the BChE signal peptide. The resultant variant...
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A Fast Method of Separation of the Noisy Background from the Head-Cross Section in the Sequence of MRI Scans
PublicationThe paper presents a new method of removing the noisy background from the sequence of magnetic resonance imaging (MRl) scans. The sequence of scans is required in order to monitor a passage of a contrast agent through the brain tissue. The scans contain the noisy head-cross data and also the noisy background data. The latter has to be removed and excluded from a further analysis. It is achieved by applying some basic morphological...
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Zastosowanie algorytmu MSA (Multiple Similar Areas) do wyznaczania map głębi w wielowidokowych systemach widzenia komputerowego
PublicationArtykuł podejmuje temat pozyskiwania map głębi (ang. depth map) na podstawie zdjęć z wielu kamer w wyniku widzenia stereoskopowego. Mapa głębi zawierająca odległości od obiektów będących w zasięgu widzenia kamer pozyskana może zostać na podstawie zdjęć z co najmniej dwóch kamer pełniących funkcję kamery stereoskopowej. W mapach głębi pozyskanych w ten sposób występują jednak błędy. Artykuł dotyczy metod redukcji błędów dzięki zwiększeniu...
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Alignment of the CMS silicon tracker during commissioning with cosmic rays
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Discrimination of hospital isolates of Acinetobacter baumannii using repeated sequences and whole genome alignment differential analysis
PublicationAn optimized method for bacterial strain differentiation, based on combination of Repeated Sequences and Whole Genome Alignment Differential Analysis (RS&WGADA), is presented in this report. In this analysis, 51 Acinetobacter baumannii multidrug-resistance strains from one hospital environment and patients from 14 hospital wards were classified on the basis of polymorphisms of repeated sequences located in CRISPR region, variation...
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Distributed Evacuation in Graphs with Multiple Exits
PublicationWe consider the problem of efficient evacuation using multiple exits. We formulate this problem as a discrete problem on graphs where mobile agents located in distinct nodes of a given graph must quickly reach one of multiple possible exit nodes, while avoiding congestion and bottlenecks. Each node of the graph has the capacity of holding at most one agent at each time step. Thus, the agents must choose their movements strategy...