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Wyniki wyszukiwania dla: GEOINFORMATICS
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Geoinformation technologies in the identification of meandering section of the river
PublikacjaPublikacja traktuje o wykorzystaniu naziemnego skaningu laserowego dla potrzeb analiz przestrzennych w zakresie meandrowania rzeki.
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GeoSPAR Project. Validation and selection methods of geoinformation analysis using GIS for ranking and forecasting of terrorist threats and criminal events
PublikacjaThe paper presents the description of work activities which have already been done within the first two stages – WorkPackage 1 and WorkPackage 2 - of the GeoSPAR Project. In such a context the general conceptual design of the GIS system and associate web service was presented and analysed. In addition, the operational and technical requirements for the GeoSPAR system have been specified and discussed; with special emphasis on system...
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Comparison of mass spectrometry data and bioinformatics predictions to assess the bona fide localization of proteins identified in cell wall proteomics studies
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A NEW MASTER'S DEGREE PROGRAM IN GEODESY
PublikacjaFaculty of Civil and Environmental Engineering (WILiS) at Gdansk University of Technology (GUT) offers studies in the fields of Geodesy and Cartography. The bachelor program (7 semesters) was started ten years ago in 2009. It provides the student with the basic skills and knowledge in the fields of surveying, geodesy and more generally geomatics and cartography. It is strongly related to expertise knowledge of civil building (geodetic...
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Operational Enhancement of Numerical Weather Prediction with Data from Real-time Satellite Images
PublikacjaNumerical weather prediction (NWP) is a rapidly expanding field of science, which is related to meteorology, remote sensing and computer science. Authors present methods of enhancing WRF EMS (Weather Research and Forecast Environmental Modeling System) weather prediction system using data from satellites equipped with AMSU sensor (Advanced Microwave Sounding Unit). The data is acquired with Department of Geoinformatics’ ground...
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Wearable system supporting navigation of the blind
PublikacjaImproving blind people comfort of life is a problem ofgreat importance. Fortunately, new technolgies provide us withadditional methods to improve everyday life of the blind and visuallyimpaired. The paper presents experimental system made byresearchers from Department of Geoinformatics of Gdansk Universityof Technology, which is capable of finding the route from theindicated source to chosen destination, using dedicated digital...
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Molywood: streamlining the design and rendering of molecular movies
PublikacjaMotivation High-quality dynamic visuals are needed at all levels of science communication, from the conference hall to the classroom. As scientific journals embrace new article formats, many key concepts – particularly in structural biology – are also more easily conveyed as videos than still frames. Notwithstanding, the design and rendering of a complex molecular movie remain an arduous task. Here, we introduce Molywood, a robust...
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Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms
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BatchI: Batch effect Identification in high-throughput screening data using a dynamic programming algorithm
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AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective
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AQUA-DUCT: a ligands tracking tool
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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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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
PublikacjaThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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Potential and Use of the Googlenet Ann for the Purposes of Inland Water Ships Classification
PublikacjaThis article presents an analysis of the possibilities of using the pre-degraded GoogLeNet artificial neural network to classify inland vessels. Inland water authorities monitor the intensity of the vessels via CCTV. Such classification seems to be an improvement in their statutory tasks. The automatic classification of the inland vessels from video recording is a one of the main objectives of the Automatic Ship Recognition and...
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Identification of evolutionary conserved DNA sequence and corresponding S21 ribosomal protein region for diagnostic purposes of all Borrelia spirochetes
PublikacjaIt is still under investigation, whether all Borrelia sp. causing Lyme borreliosis and other diseases are already identified and properly classified as human pathogens. For this reason, it is of great importance to develop a diagnostic ELISA test that detects all Borrelia sp. The aim of this study was to identify conserved DNA and protein regions present in all currently known Borrelia sp. In experimental studies 31 available Borrelia...
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New Method for Determination of Adjustment Corrections for Crane Rail Axes
PublikacjaElectronic tacheometers are currently a standard instrument used in geodetic work, including also geodetic engineering measurements. One of the many applications of tacheometers in engineering geodesy are 3D control measurements of crane rail axes. This paper proposes a new method of computing adjustment corrections for crane rail axes based on 3D polar measurements performed with an electronic tacheometer. The intermediary method...
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A concept of using static gps masurements for determination of vertical and horizontal land deformations in the main and old city of Gdańsk
PublikacjaArtykuł opisuje koncepcję wykorzystania statycznych pomiarów GPS (stacje GPS) przy analizie przemieszczeń gruntu na terenie Głównego i Starego Miasta w Gdańsku.
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Use laser to measure girder deflection
PublikacjaThe paper presents a new, simple way to measure deflection of selected intens using the device dkkz-2010, which user a laser light source.
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Survey for newly built sport facilities
PublikacjaThe article presents selected surveying and construction problem on two newly built sports facilities in Gdańsk. The papers contains selected results of surveying.
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Displacements of chimney in the light of computer calculations and surveying
PublikacjaThe article presents the numerical analysis of reinforced concrete chimney displacements, which was carried out geodetic measurements.
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Route vertical alignment design in the process of its regulation
PublikacjaRegulacja 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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Determination of rectification corrections for semi gantry crane rail axes in the local 3D coordinate system
PublikacjaElectronic tacheometers are currently the standard instruments used in geodetic work, including also geodetic engineering measurements. The main advantage connected with this equipment is among others high accuracy of the measurement and thus high accuracy of the final determinations represented for example by the points’ coordinates. One of many applications of the tacheometers is the measurement of crane rail axes. This measurement...
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Satellite Laser Ranging technique as a tool for the determination of the Schwarzschild, de Sitter and Lense-Thirring effects
PublikacjaSatellite Laser Ranging (SLR) is a modern technique used in various research areas and applications related to geodesy and geodynamics. It is commonly used for tasks such as establishing the International Terrestrial Reference Frame (ITRF), monitoring Earth Orientation Parameters (EOP), determining the geocenter, measuring fundamental physical constants, calibrating microwave tracking techniques, conducting time transfer experiments,...
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The geodetic monitoring of the engineering structure – a practical solution of the problem in 3D space
PublikacjaThe study raises the issues concerning the automatic system designed for the monitoring of movement of controlled points, located on the roof covering of the Forest Opera in Sopot. It presents the calculation algorithm proposed by authors. It takes into account the specific design and location of the test object. High forest stand makes it difficult to use distant reference points. Hence the reference points used to study the stability...
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Ranking metrics in gene set enrichment analysis: do they matter?
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Adaptive filtering of microarray gene expression data based on Gaussian mixture decomposition
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BALCONY: an R package for MSA and functional compartments of protein variability analysis
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TreeCmp: Comparison of Trees in Polynomial Time
PublikacjaMetryki 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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Framework for extracting rails and setting-out railway line axis based on UAV photogrammetric measurements
PublikacjaTechnical diagnostics enables assessing the current technical condition of a railway line and adjacent infrastructure, and forecasting its changes over a specific time horizon. One of its elements is the periodic monitoring of rail position and their geometry. This article presents a new framework for the setting-out of a railway track axis. The process presented in the manuscript is based on the specific filtration and extraction...
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Assessment Of the Relevance of Best Practices in The Development of Medical R&D Projects Based on Machine Learning
PublikacjaMachine learning has emerged as a fundamental tool for numerous endeavors within health informatics, bioinformatics, and medicine. However, novices among biomedical researchers and IT developers frequently lack the requisite experience to effectively execute a machine learning project, thereby increasing the likelihood of adopting erroneous practices that may result in common pitfalls or overly optimistic predictions. The paper...
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In silico epitope prediction of Borrelia burgdorferi sensu lato antigens for the detection of specific antibodies
PublikacjaDespite many years of research, serodiagnosis of Lyme disease still faces many obstacles. Difficulties arise mainly due to the low degree of amino acid sequence conservation of the most immunogenic antigens among B. burgdorferi s.l. genospecies, as well as differences in protein production depending on the environment in which the spirochete is located. Mapping B-cell epitopes located on antigens allows for a better understanding...
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Point cloud in archaeological and historical survey
PublikacjaIn the last decade the potential of using the point clouds in archaeological research has been noted. Therefore, a number of guidelines concerning aspects of data acquisition (resolution and format) were developed. They also included the way of searching the imaged area to identify archaeological and historical cultural heritage sites. The purpose of this research was to analyze the point cloud for selected woodland survey. Forest...
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In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates
PublikacjaBacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active...
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublikacjaThe molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except...
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublikacjaWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
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Common functionally important motions of the nucleotide‐binding domain of H sp70
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Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublikacjaCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublikacjaWe 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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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublikacjaIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Novel staphylococci nucH taxonomical marker used in identification of human-associated Staphylococcus succinus subsp. casei
PublikacjaThe aim of our study was to assess the sequencing of unique nucH gene fragment based on performed bioinformatics analysis as a novel diagnostic method for the identification of difficult to identify staphylococcal human pathogenic strains. Initially, PCR-RFLP-rrn analysis specific to the spacers between 16SrDNA and 23SrDNA followed by HhaI restriction analysis was performed. Further, sequencing of nucH and 16S rDNA genes fragments...
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Inhibiting Activity of HIV-1: Protease, Reverse Transcriptase and Integrase All Together by Novel Compounds Using Computational Approaches
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Inhibiting activity of HIV-1: protease, reverse transcriptase and integrase all together by novel compounds using computational approaches (flexible and rigid docking)
PublikacjaAcquired immunodeficiency syndrome (AIDS), caused by human immunodeficiency virus type 1 (HIV-1) infection, is one of the most challenging diseases in recent decades. Nevertheless the shortcomings of chemical drugs such as toxicity, lack of curative effects, the search for more potent anti-HIV agents have been focused in our study. In current study, novel scaffold was designed having a benzyl and imidazole in it which are very...
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New Approaches for Escherichia coli Genotyping
PublikacjaEasy-to-perform, fast, and inexpensive methods of differentiation of Escherichia coli strains beyond the species level are highly required. Herein two new, original tools for genotyping of E. coli isolates are proposed. The first of the developed method, a PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) test uses a highly variable fliC gene, encoding the H antigen as a molecular target. The designing...
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
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