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Catalog Publications
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublicationWe 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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Analysis of server-side and client-side Web-GIS data processing methods on the example of JTS and JSTS using open data from OSM and geoportal
PublicationThe last decade has seen a rapid evolution of processing, analysis and visualization of freely available geographic data using Open Source Web-GIS. In the beginning, Web-based Geographic Information Systems employed a thick-client approach which required installation of platform-specific browser plugins. Later on, research focus shifted to platform-independent thin client solutions in which data processing and analysis was performed...
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Computational Methods for Liver Vessel Segmentation in Medical Imaging: A Review
PublicationThe segmentation of liver blood vessels is of major importance as it is essential for formulating diagnoses, planning and delivering treatments, as well as evaluating the results of clinical procedures. Different imaging techniques are available for application in clinical practice, so the segmentation methods should take into account the characteristics of the imaging technique. Based on the literature, this review paper presents...
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MAPPING SOUTH BALTIC NEAR-SHORE BATHYMETRY USING SENTINEL-2 OBSERVATIONS
PublicationOne of the most promising new applications of remote observation satellite systems (RO) is the near-shore bathymetry estimation based on spaceborn multispectral imageries. In recent years, many experiments aiming to estimate bathymetry in optically shallow water with the use of remote optical observations have been presented. In this paper, optimal models of satellite derived bathymetry (SDB) for relatively turbid waters of the...
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Numerical model for thin liquid film with evaporation and condensation on solid surfaces in systems with conjugated heat transfer
PublicationCondensation and evaporation processes from wetted surfaces are of utmost importance in many technological or industrial applications. In many devices such as home-appliances and air conditioning systems just to name a few, condensation and evaporation processes greatly impact their performance and energy efficiency; The physics of these processes is quite complex, involving conjugate heat transfer among solid–liquid film-gaseous...
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Spatiotemporal dynamics of the active perirheic zone in a natural wetland floodplain
PublicationAbstract The ecologically and biogeochemically significant perirheic zone is a part of the floodplain where waters originating from both the river and adjacent floodplain are present. In this study, we investigate the spatiotemporal dynamics of the active perirheic zone, i.e. river and floodplain waters and their transient mixing extent. This is achieved by using the Hydraulic Mixing-Cell method, a complement to a fully integrated...
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublicationCritical 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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Web-based GIS as a tool for supporting marine research
PublicationZbieranie danych morskich podczas badań hydroakustycznych jest złożonym zadaniem, na które składają się nie tylko pomiary, ale także analiza, weryfikacja i interpretacja informacji uzyskanych przez różne czujniki. Automatyczna integracja, wizualizacja i przetwarzanie zgromadzonych danych pozwala na bardziej precyzyjne rozpoznanie badanych zjawisk. W pracy przedstawiono dedykowany sieciowy system syntezy i rozpowszechniania danych...
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Wetlands in flux: looking for the drivers in a central European case
PublicationPlanet Earth is undergoing significant changes which are driven by natural and anthropogenic factors. However, it is difficult to identify the drivers and their effect on the environment and ecosystems because there are many interdependencies. In this study we present a multi-parameter approach to assess the effect of changes in human-induced and natural drivers on a wetland ecosystem. The study area is one of the most prominent...
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Current trends in consumption of multimedia content using online streaming platforms: A user-centric survey
PublicationIn its early days, consumption of multimedia content was only possible at a stationary terminal device. The music player was located at home, and had to have a physical drive. Over the last decade, there has been an enormous increase in the number of online streaming platforms. These services enable users to consume rich multimedia content on various devices. Thanks to the widespread and availability of portable devices, any person...
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Processing of LiDAR and Multibeam Sonar Point Cloud Data for 3D Surface and Object Shape Reconstruction
PublicationUnorganised point cloud dataset, as a transitional data model in several applications, usually contains a considerable amount of undesirable irregularities, such as strong variability of local point density, missing data, overlapping points and noise caused by scattering characteristics of the environment. For these reasons, further processing of such data, e.g. for construction of higher order geometric models of the topography...
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Integration, Processing and Dissemination of LiDAR Data in a 3D Web-GIS
PublicationThe rapid increase in applications of Light Detection and Ranging (LiDAR) scanners, followed by the development of various methods that are dedicated for survey data processing, visualization, and dissemination constituted the need of new open standards for storage and online distribution of collected three-dimensional data. However, over a decade of research in the area has resulted in a number of incompatible solutions that offer...
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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A Parallax Shift Effect Correction Based on Cloud Height for Geostationary Satellites and Radar Observations
PublicationThe effect of cloud parallax shift occurs in satellite imaging, particularly for high angles of satellite observations. This study demonstrates new methods of parallax effect correction for clouds observed by geostationary satellites. The analytical method that could be found in literature, namely the Vicente et al./Koenig method, is presented at the beginning. It approximates a cloud position using an ellipsoid with semi-axes...
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Survey of Methodologies, Approaches, and Challenges in Parallel Programming Using High-Performance Computing Systems
PublicationThis paper provides a review of contemporary methodologies and APIs for parallel programming, with representative technologies selected in terms of target system type (shared memory, distributed, and hybrid), communication patterns (one-sided and two-sided), and programming abstraction level. We analyze representatives in terms of many aspects including programming model, languages, supported platforms, license, optimization goals,...
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Evaluation of RTKLIB's Positioning Accuracy Using low-cost GNSS Receiver and ASG-EUPOS
PublicationThe paper focuses on a comparison of different positioning methods provided by free and open source software (FOSS) package called RTKLIB. The RTKLIB supports real‐time and post‐processed positioning. The most important modes of operation tested by the authors are Kinematic, Static, Fixed and Precise Point Positioning (PPP). The data for evaluation were obtained from low‐cost Global Navigation Satellite System (GNSS) receiver....
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G2DC-PL+: a gridded 2 km daily climate dataset for the union of the Polish territory and the Vistula and Odra basins
PublicationG2DC-PL+, a gridded 2 km daily climate dataset for the union of the Polish territory and the Vistula and Odra basins, is an update and extension of the CHASE-PL Forcing Data – Gridded Daily Precipitation and Temperature Dataset – 5 km (CPLFD-GDPT5). The latter was the first publicly available, high-resolution climate forcing dataset in Poland, used for a range of purposes including hydrological modelling and bias correction of...
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Innovative Web-Based Geographic Information System for Municipal Areas and Coastal Zone Security and Threat Monitoring Using EO Satellite Data
PublicationThe paper presents a novel design of a Web-based Safe City & Coastal Zone GIS (SCCZ-GIS). The system integrates data acquired from different remote sensing and geospatial data sources for the purpose monitoring the security of the coastal zone, its inhabitants and Critical Infrastructure. The system utilises several innovative technologies and solutions, and is capable of direct co-operation with different remote sensing data sources...
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Improving the Accuracy of Automatic Reconstruction of 3D Complex Buildings Models from Airborne Lidar Point Clouds
PublicationDue to high requirements of variety of 3D spatial data applications with respect to data amount and quality, automatized, effcient and reliable data acquisition and preprocessing methods are needed. The use of photogrammetry techniques—as well as the light detection and ranging (LiDAR) automatic scanners—are among attractive solutions. However, measurement data are in the form of unorganized point clouds, usually requiring transformation...
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Three-dimensional geographically weighted inverse regression (3GWR) model for satellite derived bathymetry using Sentinel-2 observations
PublicationCurrent trends of development of satellite derived bathymetry (SDB) models rely on applying calibration techniques including analytical approaches, neuro-fuzzy systems, regression optimization and others. In most of the cases, the SDB models are calibrated and verified for test sites, that provide favourable conditions for the remote derivation of bathymetry such as high water clarity, homogenous bottom type, low amount of sediment...
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Modelling Wetland Growing Season Rainfall Interception Losses Based on Maximum Canopy Storage Measurements
PublicationThis study estimates rainfall interception losses from natural wetland ecosystems based on maximum canopy storage measurements. Rainfall interception losses play an important role in water balance, which is crucial in wetlands, and has not yet been thoroughly studied in relation to this type of ecosystem. Maximum canopy storage was measured using the weight method. Based on these measurements, daily values of interception losses...
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A novel method for archiving multibeam sonar data with emphasis on efficient record size reduction and storage
PublicationOver the past few years considerable advances in sonar technology, spatial positioning capabilities and computer processing power have lead to significant improvements in mapping, imaging and technologies of seafloor exploration. Recently, modern multibeam echosounder systems (MBES) capable of recording backscatter data for the whole water column, not just for the seabed, have become available thus providing data allowing for...
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Application of Web-GIS for Dissemination and 3D Visualization of Large-Volume LiDAR Data
PublicationThe increasing number of digital data sources, which allow for semi-automatic collection and storage of information regarding various aspects of life has recently granted a considerable rise in popularity to the term “Big data”. As far as geospatial data is concerned, one of the major sources of Big data are Light Detection And Ranging (LiDAR) scanners, which produce high resolution three-dimensional data on a local scale. The...
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Application of Web-GIS and Geovisual Analytics to Monitoring of Seabed Evolution in South Baltic Sea Coastal Areas
PublicationRegular surveys of coastal zone seabed deliver important information about geomorphologic processes such as silting of waterways. The recent introduction of the Sentinel series of sensors has allowed for the use of satellite sensing for shallow bathymetry morphology monitoring. In this context, this article presents a dedicated Geographic Information System for Baltic Sea shallow water depth monitoring on the basis of Sentinel-2...
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Mobile navigation system for visually impaired users in the urban environment
PublicationThis paper describes the prototype version of a mobile application supporting independent movement of theblind. Its objective is to improve the quality of life of visually impaired people, providing them with navigationalassistance in urban areas. The authors present the most important modules of the application. The module forprecise positioning using DGPS data from the ASG-EUPOS network as well as enhancements of positioning...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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The potential of Web-GIS and geovisual analytics in the context of marine cadastre
PublicationThe importance of the marine environment to human existence makes it imperative that information models represent the multidimensional nature of reality as closely as possible in order to facilitate good governance. Information regarding jurisdiction, as well as the effects of formal law and community interests on the marine environment (e.g. nature and spatial extents as well as rights, responsibilities, restrictions etc.) would...
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Feature Weighted Attention-Bidirectional Long Short Term Memory Model for Change Detection in Remote Sensing Images
PublicationIn remote sensing images, change detection (CD) is required in many applications, such as: resource management, urban expansion research, land management, and disaster assessment. Various deep learning-based methods were applied to satellite image analysis for change detection, yet many of them have limitations, including the overfitting problem. This research proposes the Feature Weighted Attention (FWA) in Bidirectional Long...
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Application of Shape From Shading Technique for Side Scan Sonar Images
PublicationSide scan sonar (SSS) is one of the most widely used imaging systems in the underwater environment. It is relatively cheap and easy to deploy in comparison with more powerful sensors like multibeam echosounder or synthetic aperture sonar. Although, the SSS does not provide directly the seafloor bathymetry measurements. Its outputs are usually in a form of grey level acoustic images of seafloor. However, the analysis of such images...
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DAB vs DAB+ Radio Broadcasting: a Subjective Comparative Study
PublicationIn the age of digital media, delivering high quality content to consumers is one of the most demanding tasks. There exist numerous broadcasting standards, with different pros and cons, and the DAB/DAB (Digital Audio Broadcasting) system is one of the most popular among them. From an engineer’s perspective, efficient resource management under limited bandwidth conditions has always been a challenge. In this paper a subjective quality...
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Balanced Spider Monkey Optimization with Bi-LSTM for Sustainable Air Quality Prediction
PublicationA reliable air quality prediction model is required for pollution control, human health monitoring, and sustainability. The existing air quality prediction models lack efficiency due to overfitting in prediction model and local optima trap in feature selection. This study proposes the Balanced Spider Monkey Optimization (BSMO) technique for effective feature selection to overcome the local optima trap and overfitting problems....
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A novel method of local chirp-rate estimation of LFM chirp signals in the time-frequency domain
PublicationIn the paper, novel dynamic representations of a complex signal in the time-frequency domain are introduced. The proposed approach is based on using the gradient of the short-time Fourier transform complex phase. A channelized instantaneous complex frequency (CICF) and a complex local group delay (CLGD) are included in the presented signal representations. An application of the newly-introduced distributions is demonstrated by...
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Tool Wear Monitoring Using Improved Dragonfly Optimization Algorithm and Deep Belief Network
PublicationIn recent decades, tool wear monitoring has played a crucial role in the improvement of industrial production quality and efficiency. In the machining process, it is important to predict both tool cost and life, and to reduce the equipment downtime. The conventional methods need enormous quantities of human resources and expert skills to achieve precise tool wear information. To automatically identify the tool wear types, deep...
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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublicationWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
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Cultural Heritage in Spatial Planning
PublicationThe cultural heritage objects of each country should have a major impact on the development of space. Unfortunately, most often the investment needs prevail and only the most precious historical objects are protected. Thus often a monument is preserved, but its surroundings (which put it in context) are lost forever. This article addressed the issues of cultural heritage in relation to the spatial planning system in Poland. The...
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Flooding Extent Mapping for Synthetic Aperture Radar Time Series Using River Gauge Observations
PublicationThe flooding extent area in a river valley is related to river gauge observations such as discharge and water elevations. The higher the water elevations, or discharge, the larger the flooding area. Flooding extent maps are often derived from synthetic aperture radar (SAR) images using thresholding methods. The thresholding methods vary in complexity and number of required parameters. We proposed a simple thresholding method that...
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System architecture of an INSPIRE-compliant green cadastre system for the EU Member State of Poland
PublicationIn response to the need for a sustainable agricultural policy, which would support activities such as decision making in precise agriculture and mitigation of crop threats, a concept agricultural information system was developed for the area of Poland. This innovative concept, called Green Cadastre (GC), proposes to create a uniform system designed for use on a national scale by both state administration as well as local farmers....
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High-Resolution Discharge Forecasting for Snowmelt and Rainfall Mixed Events
PublicationDischarge events induced by mixture of snowmelt and rainfall are strongly nonlinear due to consequences of rain-on-snow phenomena and snowmelt dependence on energy balance. However, they received relatively little attention, especially in high-resolution discharge forecasting. In this study, we use Random Forests models for 24 h discharge forecasting in 1 h resolution in a 105.9 km 2 urbanized catchment in NE Poland: Biala River....
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Characterizing surface and air temperature in the Baltic Sea coastal area using remote sensing techniques and GIS
PublicationEstimation of surface temperature using multispectral imagery retrieved from satellite sensors constitutes several problems in terms of accuracy, accessibility, quality and evaluation. In order to obtain accurate results, currently utilized methods rely on removing atmospheric fluctuations in separate spectral windows, applying atmospheric corrections or utilizing additional information related to atmosphere or surface characteristics...
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Performance of Passive and Active Balancing Systems of Lithium Batteries in Onerous Mine Environment
PublicationTo use lithium-iron-phosphate battery packs in the supply systems of any electric mining equipment and/or machines, the required conditions of work safety must be met. This applies in particular to coal mines endangered by fire and/or explosion. To meet the spark-safety conditions, the cells (together with the battery management system—BMS) must be isolated from the influence of the environment, and therefore placed in special...
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Energy Management for PV Powered Hybrid Storage System in Electric Vehicles Using Artificial Neural Network and Aquila Optimizer Algorithm
PublicationIn an electric vehicle (EV), using more than one energy source often provides a safe ride without concerns about range. EVs are powered by photovoltaic (PV), battery, and ultracapacitor (UC) systems. The overall results of this arrangement are an increase in travel distance; a reduction in battery size; improved reaction, especially under overload; and an extension of battery life. Improved results allow the energy to be used efficiently,...
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GIS for remote sensing, analysis and visualisation of marine pollution and other marine ecosystem components
PublicationW artykule przedstawiono koncepcję oraz prototyp morskiego systemu GIS do zdalnego monitorowania w czasie rzeczywistym zanieczyszczeń środowiska morskiego. System pozwala na gromadzenie i integrowanie danych z różnego rodzaju sensorów, takich jak echosondy jednowiązkowe, sonary boczne i echosondy wielowiązkowe.
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On the Consumption of Multimedia Content Using Mobile Devices: a Year to Year User Case Study
PublicationIn the early days, consumption of multimedia content related with audio signals was only possible in a stationary manner. The music player was located at home, with a necessary physical drive. An alternative way for an individual was to attend a live performance at a concert hall or host a private concert at home. To sum up, audio-visual effects were only reserved for a narrow group of recipients. Today, thanks to portable players,...
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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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Efficient FPGA Implementation of an RFIR Filter Using the APC–OMS Technique with WTM for High-Throughput Signal Processing
PublicationNowadays, Finite Impulse Response (FIR) filters are used to change the attributes of a signal in the time or frequency domain. Among FIR filters, a reconfigurable filter has the advantage of changing the coefficient in real-time, while performing the operation. In this paper, the Anti-Symmetric Product Coding (APC) and Odd Multiple Storage (OMS) modules are utilized to implement the reconfigurable FIR filter (RFIR–APC–OMS). Herein,...
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A Cost-Effective Method for Reconstructing City-Building 3D Models from Sparse Lidar Point Clouds
PublicationThe recent popularization of airborne lidar scanners has provided a steady source of point cloud datasets containing the altitudes of bare earth surface and vegetation features as well as man-made structures. In contrast to terrestrial lidar, which produces dense point clouds of small areas, airborne laser sensors usually deliver sparse datasets that cover large municipalities. The latter are very useful in constructing digital...
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Operational algae bloom detection in the Baltic Sea using GIS and AVHRR data
PublicationDuring the blooming season, algal colonies can, in extreme cases, cover up to 200 000 square kilometres of the Baltic Sea water surface. Because the position and shape of the blooms may significantly change in very short time due to the influence of wind and waves, regular monitoring of the blooms' development is necessary. Currently, the desired monitoring frequency may only be achieved by means of remote sensing. The article...
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Recent Developments in Data-Assisted Modeling of Flexible Proteins
PublicationMany proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this...
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Measurement of Seafloor Acoustic Backscatter Angular Dependence at 150 kHz Using a Multibeam Echosounder
PublicationAcoustic seafloor measurements with multibeam echosounders (MBESs) are currently often used for submarine habitat mapping, but the MBESs are usually not acoustically calibrated for backscattering strength (BBS) and cannot be used to infer absolute seafloor angular dependence. We present a study outlining the calibration and showing absolute backscattering strength values measured at a frequency of 150 kHz at around 10–20 m water...
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Quality Evaluation of Voice Transmission Using BPL Communication System in MV Mine Cable Network
PublicationThis article presents results of a quality evaluation study, considering voice transmission in a 6 kV medium voltage cable network using the BPL (Broadband over Power Line) communication system. The tests are carried out under real mining conditions for the selected power cable without voltage, earthed at both sides. Such a method of monitoring work conditions is of great importance, especially during a disaster. Power cables are...