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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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MERPSYS: An environment for simulation of parallel application execution on large scale HPC systems
PublicationIn this paper we present a new environment called MERPSYS that allows simulation of parallel application execution time on cluster-based systems. The environment offers a modeling application using the Java language extended with methods representing message passing type communication routines. It also offers a graphical interface for building a system model that incorporates various hardware components such as CPUs, GPUs, interconnects...
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublicationG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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A method for counting people attending large public events
PublicationThe algorithm for people counting in crowded scenes, based on the idea of virtual gate which uses optical flow method is presented. The concept and practical application of the developed algorithm under real conditions is depicted. The aim of the work is to estimate the number of people passing through entrances of a large sport hall. The most challenging problem was the unpredicted behavior of people while entering the building....
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Behavior Analysis and Dynamic Crowd Management in Video Surveillance System
PublicationA concept and practical implementation of a crowd management system which acquires input data by the set of monitoring cameras is presented. Two leading threads are considered. First concerns the crowd behavior analysis. Second thread focuses on detection of a hold-ups in the doorway. The optical flow combined with soft computing methods (neural network) is employed to evaluate the type of crowd behavior, and fuzzy logic aids detection...
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A FPTAS for minimizing total completion time in a single machine time-dependent scheduling problem
PublicationIn this paper a single machine time-dependent scheduling problem with total completion time criterion is considered. There are given n jobs J1,…,Jn and the processing time pi of the ith job is given by pi=a+bisi, where si is the starting time of the ith job (i=1,…,n),bi is its deterioration rate and a is the common base processing time. If all jobs have deterioration rates different and not smaller than a certain constant u>0,...
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Tryton Supercomputer Capabilities for Analysis of Massive Data Streams
PublicationThe recently deployed supercomputer Tryton, located in the Academic Computer Center of Gdansk University of Technology, provides great means for massive parallel processing. Moreover, the status of the Center as one of the main network nodes in the PIONIER network enables the fast and reliable transfer of data produced by miscellaneous devices scattered in the area of the whole country. The typical examples of such data are streams...
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Genetic Programming with Negative Selection for Volunteer Computing System Optimization
PublicationVolunteer computing systems like BOINC or Comcute are strongly supported by a great number of volunteers who contribute resources of their computers via the Web. So, the high efficiency of such grid system is required, and that is why we have formulated a multi-criterion optimization problem for a volunteer grid system design. In that dilemma, both the cost of the host system and workload of a bottleneck host are minimized. On...
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Performance/energy aware optimization of parallel applications on GPUs under power capping
PublicationIn the paper we present an approach and results from application of the modern power capping mechanism available for NVIDIA GPUs to the bench- marks such as NAS Parallel Benchmarks BT, SP and LU as well as cublasgemm- benchmark which are widely used for assessment of high performance computing systems’ performance. Specifically, depending on the benchmarks, various power cap configurations are best for desired trade-off of performance...
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Modeling energy consumption of parallel applications
PublicationThe paper presents modeling and simulation of energy consumption of two types of parallel applications: geometric Single Program Multiple Data (SPMD) and divide-and-conquer (DAC). Simulation is performed in a new MERPSYS environment. Model of an application uses the Java language with extension representing message exchange between processes working in parallel. Simulation is performed by running threads representing distinct process...
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Massive surveillance data processing with supercomputing cluster
PublicationIn recent years, increasingly complex algorithms for automated analysis of surveillance data are being developed. The rapid growth in the number of monitoring installations and higher expectations of the quality parameters of the captured data result in an enormous computational cost of analyzing the massive volume of data. In this paper a new model of online processing of surveillance data streams is proposed, which assumes the...
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Performance and Power-Aware Modeling of MPI Applications for Cluster Computing
PublicationThe paper presents modeling of performance and power consumption when running parallel applications on modern cluster-based systems. The model includes basic so-called blocks representing either computations or communication. The latter includes both point-to-point and collective communication. Real measurements were performed using MPI applications and routines run on three different clusters with both Infiniband and Gigabit Ethernet...
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Effect of chemical structure on complexation efficiency of aromatic drugs with cyclodextrins: The example of dibenzazepine derivatives
PublicationIt is widely believed that the hydrophobic effect governs the binding of guest molecules to cyclodextrins (CDs). However, it is also known that high hydrophobicity of guest molecules does not always translate to the formation of stable inclusion complexes with CDs. Indeed, a plethora of other factors can play a role in the efficiency of guest–CD interactions, rendering structure-based prediction of the complexation efficiency with...
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Effective Collaboration of Entrepreneurial Teams—Implications for Entrepreneurial Education
PublicationIn the situation of a permanent change and increased competition, business ventures are more and more often undertaken not by individuals but by entrepreneurial teams. The main aim of this paper is to examine the team principles implemented by eective entrepreneurial teams and how they dier in nascent and established teams. We also focused on the relationship between the implementation of these rules by entrepreneurial team members...
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User Trust Levels and Their Impact on System Security and Usability
PublicationA multilateral trust between a user and a system is considered. First of all we concentrate on user trust levels associated with the context-oriented CoRBAC model. Consequently, there were computed user profiles on the basis of its implementation in the information processing system “My GUT”. Furthermore, analysis of these profiles and the impact of user trust levels on system security and usability have been discussed.
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Multi-level Virtualization and Its Impact on System Performance in Cloud Computing
PublicationThe results of benchmarking tests of multi-level virtualized environments are presented. There is analysed the performance impact of hardware virtualization, container-type isolation and programming level abstraction. The comparison is made on the basis of a proposed score metric that allows you to compare different aspects of performance. There is general performance (CPU and memory), networking, disk operations and application-like...
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Intercultural Challenges in Virtual Teams
Publication: Virtual teams are usually geographically dispersed and consist of members from different countries and cultures. They influences internal communication processes and can cause personal conflicts, misunderstandings or lack of trust. Intercultural diversity is also significant for goal setting and team effectiveness. The aim of this article is to check if virtual team members appreciate the cultural diversity or rather suffer from lack...
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Using a computational model to compare objective negotiations in real and virtual environments
PublicationZaprezentowano obliczeniowy model negocjacji uwzględniający warunki początkowe, przebieg negocjacji i wyniki negocjacji. Przedstawiono komputerowy system wspomagający rejestrację przebiegu negocjacji i ich wyników oraz analizę negocjacji zgodną z proponowanym modelem.
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On the independence number of some strong products of cycle-powers
PublicationIn the paper we give some theoretical and computational results on the third strong power of cycle-powers, for example, we have found the independence numbers alpha((C^2_10)^⊠3) = 30 and alpha((C^4 _14)^⊠3) = 14. A number of optimizations have been introduced to improve the running time of our exhaustive algorithm used to establish the independence number of the third strong power of cycle-powers. Moreover, our results establish...
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Mobile Offloading Framework: Solution for Optimizing Mobile Applications Using Cloud Computing
PublicationNumber of mobile devices and applications is growing rapidly in recent years. Capabilities and performance of these devices can be tremendously extended with the integration of cloud computing. However, multiple challenges regarding implementation of these type of mobile applications are known, like differences in architecture, optimization and operating system support. This paper summarizes issues with mobile cloud computing and...
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Interactive Information Search in Text Data Collections
PublicationThis article presents a new idea for retrieving in text repositories, as well as it describes general infrastructure of a system created to implement and test those ideas. The implemented system differs from today’s standard search engine by introducing process of interactive search with users and data clustering. We present the basic algorithms behind our system and measures we used for results evaluation. The achieved results...
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Multidimensional Approach to Quality Analysis of IPSec and HTTPS Applications
PublicationNiniejsza praca omawia aspekty bezpieczeństwa i wydajności aplikacji rozproszonych działających w środowisku sieci publiczno-prywatnych, stworzonych za pośrednictwem technologii IPSec i HTTPS. Jako przykłady implementacji pokazane są: jeden z największych polskojęzycznych portali motoryzacyjnych: www.auto.gda.pl oraz brama IPSec działająca w środowisku ATCA. Przedstawiona w referacie analiza pod kątem wydajności i bezpieczeństwa...
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Partial dominated schedules and minimizing the total completion time of deteriorating jobs
PublicationA problem of scheduling deteriorating jobs on a single processor is considered. The processing time of a job is given by a function pi=ai+bisi, where si is the starting time of the job, ai>=0, bi>=0, for i=1,...,n. Jobs are non-preemptive and independent and there are neither ready times nor deadlines. The goal is to minimize the total weighted completion time. We show how to employ the concept of non-dominated schedules to construct...
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Categorization of Cloud Workload Types with Clustering
PublicationThe paper presents a new classification schema of IaaS cloud workloads types, based on the functional characteristics. We show the results of an experiment of automatic categorization performed with different benchmarks that represent particular workload types. Monitoring of resource utilization allowed us to construct workload models that can be processed with machine learning algorithms. The direct connection between the functional...
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DESIGN OF THE DUAL CONSTELLATION GPS/GALILEO MOBILE DEVICE FOR IMPROVING NAVIGATION OF THE VISUALLY IMPAIRED IN AN URBAN AREA
PublicationIt is well known by users of Personal Navigation Device (PND) and other GPS-based devices that positioning suffers from (local) significant decreases of accuracy in partially obscured environments like urbanized areas, where buildings (especially high buildings), trees or terrain block large portions of the sky. In such areas, GPS receiver performance is usually deteriorated by the reduced number of currently available satellite...
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Early stage of critical clusters growth in phenomenological and Molecular Dynamic simulation models
PublicationW artykule opisano wzrost klastrów krytycznych w ramach klasycznego podejścia fenomenologicznego oraz dynamiczno-molekularnego (MD). Została wyprowadzona nowa formuła opisujaca liczbę klastrów krytycznych. Sformułowano równania opisujace wczesne etapy wzrostu kropli o rozmiarach krytycznych. Opisano wyniki symulacji dynamiczno-molekularnych powstawania klastrów w jednorodnej parze przesyconej oraz podano czasowe zmiany rozkładu...
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Effect of heat treatment on the diffusion intermixing and structure of the Cu thin film on Si (111) substrate: a molecular dynamics simulation study
PublicationThis work is devoted to the study of the diffusion process at the interface between copper films with a thickness of 2, 3, 4, 7 and 10 atomic monolayers and silicon substrate by molecular dynamics simulation method. For this purpose, the variation of the concentration of copper and silicon along the perpendicular direction to the interface was investigated. An analysis of the density profile along this direction made it possible...
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Selection of Relevant Features for Text Classification with K-NN
PublicationIn this paper, we describe five features selection techniques used for a text classification. An information gain, independent significance feature test, chi-squared test, odds ratio test, and frequency filtering have been compared according to the text benchmarks based on Wikipedia. For each method we present the results of classification quality obtained on the test datasets using K-NN based approach. A main advantage of evaluated...
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Static and dynamic approach of social roles identification using PISNA and subgraphs matching
PublicationIdentyfikacja ról w sieci społecznej jest jednym z podstawowych zagadnień analiza takich sieci. W artykule przedstawiamy nowe podejście do tego zagadnienia. Pokazujemy w jaki sposób można dokonać identyfikacji ról poprzez tworzenie specjalnych struktur grafowych tzw. grafów wzorcowych. Przy definiowaniu tychże grafów wspieramy się metodą PISNA. Proponujemy statyczne i dynamiczne podejście do identyfikacji ról. Pokazujemy, w jaki...
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Practical Evaluation of Internet Systems' Security Mechanisms
PublicationA proposed Internet systems security layer with context-oriented security mechanisms reduces the risk associated with possible vulnerabilities. A metric of the system trust level is proposed, and then evaluated according to a university Internet system.
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Primary role identification in dynamic social networks
PublicationIdentyfikacja ról w sieci społecznej jest jednym z podstawowych zagadnień analizy takich sieci. W artykule przedstawiamy nowe podejście do tego zagadnienia. Pokazujemy w jaki sposób można dokonać identyfikacji ról poprzez wykorzystanie zaproponowanego modelu zachowań aktorów. Model taki tworzą podgrafy wzorcowe oraz diagramy stanów okreslające sekwencje aktywności w zachowaniu aktorów. Na bazie wyznaczonych modeli zachowań oraz...
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Testing for conformance of parallel programming pattern languages
PublicationThis paper reports on the project being run by TUG and IMAG, aimed at reducing the volume of tests required to exercise parallel programming language compilers and libraries. The idea is to use the ISO STEP standard scheme for conformance testing of software products. A detailed example illustrating the ongoing work is presented.
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The Structure of Entrepreneurial Team Members’ Competencies: Between Effectuation and Causation
PublicationA conscious shaping of entrepreneurial competence is a relevant element of entrepreneurial education. In order to recognize which of the competencies regarded as entrepreneurial are characteristic of members of entrepreneurial teams, which is crucial for the work of those teams, it is necessary to identify the structure of those competencies. This quantitative study was conducted with the use of a survey method and involved 111...
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The congruence of mental models in entrepreneurial teams – implications for performance and satisfaction in teams operating in an emerging economy
PublicationPurpose – The paper aims to explore the relationship between the congruence of mental models held by the members of entrepreneurial teams operating in an emerging economy (Poland) and entrepreneurial outcomes (performance and satisfaction). Design/methodology/approach – The data obtained from 18 nascent and 20 established entrepreneurial teams was analysed to answer hypotheses. The research was quantitative and was conducted using...
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Systematic approach to binary classification of images in video streams using shifting time windows
Publicationin the paper, after pointing out of realistic recordings and classifications of their frames, we propose a new shifting time window approach for improving binary classifications. We consider image classification in tewo steps. in the first one the well known binary classification algorithms are used for each image separately. In the second step the results of the previous step mare analysed in relatively short sequences of consecutive...
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Parallelization of Selected Algorithms on Multi-core CPUs, a Cluster and in a Hybrid CPU+Xeon Phi Environment
PublicationIn the paper we present parallel implementations as well as execution times and speed-ups of three different algorithms run in various environments such as on a workstation with multi-core CPUs and a cluster. The parallel codes, implementing the master-slave model in C+MPI, differ in computation to communication ratios. The considered problems include: a genetic algorithm with various ratios of master processing time to communication...
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Short-range order structure and free volume distribution in liquid bismuth: X-ray diffraction and computer simulations studies
PublicationThe structure of liquid bismuth was studied by X-ray diffraction and computer simulation methods. The contraction of the atomic structure within the first coordination sphere in the temperature interval of 575- 1225 K is reported. The temperature dependencies of the coordination numbers and of the free volume are analysed. On the basis of the temperature dependencies of the free volume, the temperature dependencies of viscosity...
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Deformation degree estimators for several basic structural units in numerically simulated materials
PublicationW pracy wprowadzono i zdefiniowano kilka estymatorów stopnia deformacji dla serii bazowych jednostek strukturalnych typu CA_n (C-kation, A-anion) występujących w strukturach symulowanych numerycznie. Do wyznaczenia rozkładu wartości estymatoróww funkcji stopnia deformacji kształtu zadanego wielościanu zastosowano symulacje Monte Carlo. Otrzymane rozkłady są danymi referencyjnymi, które są bardzo użyteczne przy jakościowej analizie...
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E-mail user roles identification using OWL-based ontology approach
PublicationSieci społeczne jako struktury ukazujące społeczne powiązania pomiędzy osobami lub całymi organizacjami poddawane są często analizie w celu rozpoznania ról, jakie pełnią poszczególni aktorzy w danej sieci. Taka klasyfikacja ról odgrywanych przez aktorów może dostarczać wielu cennych informacji o danej sieci, gdyż daje nam całościowy obraz danej sieci pozwalając na zrozumienie, w jaki sposób sieć jest zorganizowana, i w jaki sposób...
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Application of virtual gate for counting people participating in large public events
PublicationThe concept and practical application of the developed algorithm forpeople counting in crowded scene is presented. The aim of the work is to estimatethe number of people passing towards entrances of a large sport hall. Thedetails of implemented the Virtual Gate algorithm are presented. The video signalfrom the camera installed in the building constituted the input for the algorithm.The most challenging problem was the unpredicted...
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Genetic Programming for Interaction Efficient Supporting in Volunteer Computing Systems
PublicationVolunteer computing systems provide a middleware for interaction between project owners and great number volunteers. In this chapter, a genetic programming paradigm has been proposed to a multi-objective scheduler design for efficient using some resources of volunteer computers via the web. In a studied problem, genetic scheduler can optimize both a workload of a bottleneck computer and cost of system. Genetic programming has been...
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Extended generalized blockmodeling for compound communities and external actors
PublicationWiększość sieci społecznych charakteryzuje się swoją wewnętrzną, unikatową strukturą. W artykule poddano analizie sieci społeczne złożone z wielu mniejszych grup społecznościowych, które określamy mianem złożonych sieci społecznych. Dla tego typu sieci zaproponowano rozszerzenie metody ogólnego modelowania blokowego biorąc pod uwagę specyficzną strukturę złożonych sieci społecznych oraz ich relacje z zewnętrznymi aktorami. W oparciu...
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Extended generalized blockmodeling for compound communities and external actors
PublicationNiektóre sieci społeczne wykazują się specyficzną strukturą wewnętrzną. W artykule rozpatrujemy społeczności, które składają się z mniejszych wspólnot. Takie społeczności nazywamy społecznościami złożonymi. Dla takich struktur zastosowalismy metodę ogólnego modelowania blokowego proponując odpowiednie rozrzerzenia dla tej metody. Wzięliśmy pod uwagę specyfikę złożonych struktur społecznych oraz ich relacje z aktorami zewnętrznymi...
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Clustering Context Items into User Trust Levels
PublicationAn innovative trust-based security model for Internet systems is proposed. The TCoRBAC model operates on user profiles built on the history of user with system interaction in conjunction with multi-dimensional context information. There is proposed a method of transforming the high number of possible context value variants into several user trust levels. The transformation implements Hierarchical Agglomerative Clustering strategy....
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Mobile devices and computing cloud resources allocation for interactive applications
PublicationUsing mobile devices such as smartphones or iPads for various interactive applications is currently very common. In the case of complex applications, e.g. chess games, the capabilities of these devices are insufficient to run the application in real time. One of the solutions is to use cloud computing. However, there is an optimization problem of mobile device and cloud resources allocation. An iterative heuristic algorithm for...
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Conformance testing of parallel languages
PublicationPrzedstawiono propozycję formalizacji opisu procesu generacji, wykonania ioceny testów zgodności dla języków i bibliotek programowania równoległego, wzakresie zgodności funkcjonalnej i wydajnościowej. Przykłady ilustrujące proponowany formalizm wykorzystują platformę programowania Athapascan.
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Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublicationF1-ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated...
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Task Allocation and Scalability Evaluation for Real-Time Multimedia Processing in a Cluster Envirinment
PublicationAn allocation algorithm for stream processing tasks is proposed (Modified best Fit Descendent, MBFD). A comparison with another solution (BFD) is provided. Tests of the algorithms in an HPC environment are descrobed and the results are presented. A proper scalability metric is proposed and used for the evaluation of the allocation algorithm.
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Using EO satellite data in Safe City and Coastal Zone web-GIS
PublicationThe paper presents a novel design of a web-based Safe City & Coastal Zone GIS (SCCZ-GIS) which integrates data acquired from different remote sensing and geospatial data sources for monitoring the security of the coastal zone, its inhabitants and Critical Infrastructure. The system utilizes several innovative technologies and directly co-operates with different remote sensing data sources and services, like a satellite ground station...
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Detection of the Oocyte Orientation for the ICSI Method Automation
PublicationAutomation or even computer assistance of the popular infertility treatment method: ICSI (Intracytoplasmic Sperm Injection) would speed up the whole process and improve the control of the results. This paper introduces a preliminary research for automatic spermatozoon injection into the oocyte cytoplasm. Here, the method for detection a correct orientation of the polar body of the oocyte is presented. Proposed method uses deep...