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Search results for: CASP, COVID, EMA, MODEL ACCURACY, PROTEIN STRUCTURE PREDICTION, SARS-COV-2
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Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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Editorial: Knowledge management and ontologies. Part 2
PublicationPrzedstawiono najnowsze kierunki badań w zakresie obszaru zarządzania wiedzą i ontologicznej reprezentacji wiedzy.
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Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70
PublicationThe J-domain protein Zuotin is a multi-domain eukaryotic Hsp70 co-chaperone. Though it is primarily ribosome-associated, positioned at the exit of the 60S subunit tunnel where it promotes folding of nascent polypeptide chains, Zuotin also has off-ribosome functions. Domains of Zuotin needed for 60S association and interaction with Hsp70 are conserved in eukaryotes. However, whether the 4-helix bundle (4HB) domain is conserved remains...
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Development of a Formability Prediction Model for Aluminium Sandwich Panels with Polymer Core
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Experimental analysis of the behaviour of different types of joints in the steel structure model subjected to earthquake loading
PublicationThe present paper reports the results of the experimental study performed to investigate the behaviour of two different types of joints (destroyed and welded ones) in the model of the steel structure under seismic excitations. The structure was subjected to three earthquakes, namely Kobe, Loma Prieta and Northridge, using the shaking table investigation. The results obtained from the study...
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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
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Construction and purification of his6-Thermus thermophilus MutS protein.
PublicationGen mutS z termofilnej bakterii Thermus thermophilus zamplifikowano przy użyciu PCR, sklonowano i przeprowadzono jego ekspresję w E. coli. Rekombinantowe białko MutS zawierające oligohistydynową domenę na N-końcu oczyszczono w jednoetapowej procedurze przy wykorzystaniu chromatografii powinowactwaNi(2+). Zdolność do rozpoznania niekomplementarności białka his(6)-MutS potwierdzono w eksperymentach ochrony DNA przed trawieniem...
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Reactions of tBu2P-PLi-P(tBu)2 with [(Et3P)2MCl2] (M = Ni, Pd, Pt). Synthesis and properties of [(1,2-h-tBu2P=P-P(tBu)2)M(PEt3)Cl] (M=Ni, Pd)
PublicationtBu2P-PLi-P(tBu)2*2THF reaguje z [(Et3P)2MCl2] (M = Ni, Pd) dając odpowiednio [(1,2-h-tBu2P=P-P(tBu)2)Ni(PEt3)Cl] i [(1,2-h-tBu2P=P-P(tBu)2)Pd(PEt3)Cl]. Związek tBu2P-PLi-P(tBu)2 utlenia się i ligand tBu2P-P-P(tBu)2 przyjmuje w produktach strukturę bocznie związanego kationu z krótkim wiązaniem P-P. Reakcja ze związkami platyny nie dała oczekiwanych produktów.
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Synthesis and structure determination of 2,3-diaryl-9,9-dioxo-1H-9-thia-1,4,4a,7,10-pentaazaphenanthrene-2-ols
Publication3-Amino-1,1-dioxopyrido[4,3-e]-1,4,2-dithiazine has been synthesized and applied to the synthesis of 3-amino-2-(4-thioxo-1,4-dihydropyridin-3-ylsulfonyl)guanidine. The reaction of the aminoguanidine with the appropriate 1,2-diarylethane-1,2-diones afforded 2,3-diaryl-9,9-dioxo-1H-9-thia-1,4,4a,7,10-pentaazaphenanthrene-2-ol derivatives. The structure of these compounds, which represent a novel heterocyclic ring system, was confirmed...
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Stability of delay induced oscillations in gene expression of Hes1 protein model
PublicationW pracy prezentowana jest matematyczna analiza modelu ekspresji genu białka Hes1. Rozważamy układ równań z dwoma opóźnieniami - w produkcji białka Hes1 oraz jego mRNA. Dowodzimy istnienia i jednoznaczności oraz nieujemności rozwiązań. Pokazujemy istnienie dokładnie jednego dodatniego stanu stacjonarnego. Wykazujemy, że stabilność stanu stacjonarnego zależy od sumy opóźnień. Podajemy warunek dostateczny na wystąpienie bifurkacji...
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Computer-Aided Diagnosis of COVID-19 from Chest X-ray Images Using Hybrid-Features and Random Forest Classifier
PublicationIn recent years, a lot of attention has been paid to using radiology imaging to automatically find COVID-19. (1) Background: There are now a number of computer-aided diagnostic schemes that help radiologists and doctors perform diagnostic COVID-19 tests quickly, accurately, and consistently. (2) Methods: Using chest X-ray images, this study proposed a cutting-edge scheme for the automatic recognition of COVID-19 and pneumonia....
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Average Structure, Local Structure, Photoluminescence, and NLO Properties of Scheelite Type NaCe(WO4)2
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Chitosan-protein scaffolds loaded with lysostaphin as potential antistaphylococcal wound dressing materials.
PublicationAIMS: The development of technology for preparing chitosan-protein scaffolds loaded with lysostaphin, which potentially could be used as dressing for wound treatment and soft tissue infections caused by Staphylococcus aureus. METHODS AND RESULTS: The unique technology of chitosan solubilization using gaseous CO(2) instead of organic or inorganic acids was used for the incorporation of lysostaphin, the enzyme that exhibits bactericidal...
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2D Mathematical Model of the Commutator Sliding Contact of an Electrical Machine
PublicationW artykule przedstawiono model matematyczny 2D komutatorowego zestyku ślizgowego z wieloma stopniami swobody. W modelu uwzględniono zmienne wymuszenia działające na szczotkę. Wymuszenia te są wynikiem falistości wirującego komutatora. Szczotka została zamodelowana jako system wielu mas, elementów sprężystych i tłumików rozłożonych w kierunku stycznym i promieniowym. Zamodelowano wszystkie oddziaływania lepkosprężyste pomiędzy komutatorem...
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Angiotensin receptor blockers and cancer – Relationship dismissed by VALUE data while waiting for EMA and FDA reports
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Optical method supported by machine learning for dynamics of C‐reactive protein concentrations changes detection in biological matrix samples
PublicationIn this article we present the novel spectroscopy method supported with machine learning for real-time detection of infectious agents in wastewater. In the case of infectious diseases, wastewater monitoring can be used to detect the presence of inflammation biomarkers, such as the proposed C-reactive protein, for monitoring inflammatory conditions and mass screening during epidemics for early detection in communities of concern,...
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Dichlorido-1Cl,3Cl-hexakis[1,1,2,2,3,3(n5)-methylcyclopentadienyl]di-μ2-oxido-1:2κ2O:O;2:3κ2O:O-trihafnium(IV)
PublicationTytułowy związek jest trójrdzeniową cząsteczką. Dwie jednostki (MeCp)2HfCl połączone są z (MeCp)2Hf przez mostki tlenowe. Mostki Hf-O-Hf są prawie liniowe. Geometria trzech atomów Hf jest tetraedryczna.
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INVESTIGATION INTO INTERFEROMETRIC SONAR SYSTEM ACCURACY
PublicationThe results of the accuracy measurements of phase differencing bathymetric sonar (PDBS) system in shallow waters are presented in the article. The measurement results were compared with the theoretical calculations for sonar system accuracy and international standards for hydrographic surveys. The proposed formulas enable to assess a priori sonar system performance using system quality factor (SQF), which takes into account influence...
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General Active-RC filter model for computer-aided design
PublicationW pracy przedstawiono ogólną topologię filtru aktywnego RC czasu ciągłego. Proponowany model umożliwia zunifikowaną analizę wszystkich możliwych realizacji układowych filtrów aktywnych RC jako szczególnych przypadków danej struktury ogólnej. Poprawność modelu teoretycznego została zweryfikowana poprzez symulacje w programie SPICE.
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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The importance of trust and altruistic social orientation for COVID-19 distress
PublicationBackground: The COVID-19 pandemic, the biggest global health crisis in decades, has been a difficult experience for nations all over the world. In the present study we wanted to assess to what extent a positive attitude towards others, expressed in altruistic social orientation and a high level of trust, would be linked to lower levels of COVID-19 distress in infected and non-infected individuals. Participants and procedure:...
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Oriented Gaussian beams for high-accuracy computation with accuracy control of X-ray propagation through a multi-lens system
PublicationA highly accurate method for calculating X-ray propagation is developed. Within this approach, the propagating wave is represented as a superposition of oriented Gaussian beams. The direction of wave propagation in each Gaussian beam agrees with the local direction of propagation of the X-ray wavefront. When calculating the propagation of X-ray waves through lenses, the thin lens approximation is applied. In this approximation,...
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Neuroeconomy and Neuromarketing: The Study of the Consumer Behaviour in the COVID-19 Context
PublicationTo address the study of consumer behavior in the post-COVID-19 era, the present Research Topic brings together a set of papers that attempt to study how different factors triggered by the pandemic have achieved a significant effect on consumers' behavioral intentions. These papers examine different subtopics related to food, health products, collaborative economy and, of course, neuroscience. Globally, the objectives of this special...
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Effect of cyclodextrins on coupling of o-ethoxybenzenediazonium salt with pyrrole, imidazole and 2-methylimidazole
PublicationBadano wpływ B-cyklodekstryny na reakcje sprzęgania soli o-etoksybenzenodiazoniowych z pirolem, imidazolem i 2-metyloimidazolem. Porównano wydajności produktów sprzęgania wyizolowanych w poszczególnych reakcjach. W przypadku reakcji z pirolem i imidazolem prowadzonych z udziałem cyklodekstryny zaobserwowano spadek wydajności produktów sprzęgania, podczas gdy w reakcji z 2-metyloimidazolem obecność cyklodekstryny stymulowała powstawanie...
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Function and Frustration of Multi-Drug ABC Exporter Protein and Design of Model Proteins for Drug Delivery Using Protein Hydration Thermodynamics
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Application of reversed-phase thin layer chromatography and QSRR modelling for prediction of protein binding of selected β-blockers
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Silo music: Experimental investigations and a mechanical model
PublicationW artykule opisano zagadnienie zjawisk akustycznych oraz drgań występujących w silosach podczas przepływu materiałów granulowanych.
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Geometrically Nonlinear Analysis of Functionally Graded Shells Based on 2-D Cosserat Constitutive Model
PublicationIn this paper geometrically nonlinear analysis of functionally graded shells in 6-parameter shell theory is presented. It is assumed that the shell consists of two constituents: ceramic and metal. The mechanical properties are graded through the thickness and are described by power law distribution. Formulation based on 2-D Cosserat constitutive model is used to derive constitutive relation for functionally graded shells. Numerical...
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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublicationThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....
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Reliability model of two-shaft turbine combustion engine with heat regenerator
PublicationW artykule przedstawiono możliwość zastosowania teorii procesów semimarkowskich do opisu niezawodności turbinowego silnika spalinowego. Opracowano model niezawodnościowy w formie siedmiostanowego procesu semimarkowskiego, umożliwiający określenie prawdopodobieństw przebywania silnika w stanie zdatności oraz wyróżnionych stanach niezdatności.
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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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Modified Peptide Molecules As Potential Modulators of Shelterin Protein Functions; TRF1
PublicationIn this work, we present studies on relatively new and still not well-explored potential anticancer targets which are shelterin proteins, in particular the TRF1 protein can be blocked by in silico designed "peptidomimetic" molecules. TRF1 interacts directly with the TIN2 protein, and this protein-protein interaction is crucial for the proper functioning of telomere, which could be blocked by our novel modified peptide molecules....
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Anti-crisis activities and export performance in the Covid-19 pandemic: The case of Polish exporters
PublicationThe article aims to investigate the impact of anti-crisis activities undertaken by the Polish exporting firms on their export sales during the Covid-19 pandemic. We used a quantitative research design. We conducted the survey on the sample of 161 manufacturing Polish exporting firms between April 21 and June 25, 2021. To verify the assumed relationships, we used the probit regression model. The main novelty is a firm-level analysis...
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An Intelligent Approach to Short-Term Wind Power Prediction Using Deep Neural Networks
PublicationIn this paper, an intelligent approach to the Short-Term Wind Power Prediction (STWPP) problem is considered, with the use of various types of Deep Neural Networks (DNNs). The impact of the prediction time horizon length on accuracy, and the influence of temperature on prediction effectiveness have been analyzed. Three types of DNNs have been implemented and tested, including: CNN (Convolutional Neural Networks), GRU (Gated Recurrent...
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Assessment of the Accuracy of a Virtual Multi-Channel Temperature Measuring Instrument
PublicationThe multi-channel temperature measurement system developed works with NTC thermistors. The article presents the results of theoretical and empirical evaluation of accuracy obtained in measurement channels. The basis for the theoretical assessment is the mathematical model for each of the measurement channels and the characteristics of the system elements included in the circuits of the measurement channel. Two different methods were...
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Child-Robot Interaction Studies During COVID-19 Pandemic
PublicationThe coronavirus disease (COVID-19) pandemic affected our lives deeply, just like everyone else, the children also suffered from the restrictions due to COVID-19 affecting their education and social interactions with others, being restricted from play areas and schools for a long time. Although social robots provide a promising solution to support children in their education, healthcare, and social interaction with others, the precautions...
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Impact of the anion and chalcogen on the crystal structure and properties of 4,6-dimethyl-2-pyrimido(thio)nium halides
PublicationBy the reaction of urea or thiourea, acetylacetone and hydrogen halide (HF, HBr or HI), we have obtained seven new 4,6-dimethyl-2-pyrimido(thio)nium salts, which were characterized by single-crystal X-ray diffraction, namely, 4,6-dimethyl-2-oxo-2,3-dihydropyrimidin-1-ium bifluoride, C₆H₉N₂O⁺·HF₂⁻ or (dmpH)F₂H, 4,6-dimethyl-2-oxo-2,3-dihydropyrimidin-1-ium bromide, C₆H₉N₂O⁺·Br⁻ or (dmpH)Br, 4,6-dimethyl-2-oxo-2,3-dihydropyrimidin-1-ium...
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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublicationThe stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called “structurally different...
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Akaike's final prediction error criterion revisited
PublicationWhen local identification of a nonstationary ARX system is carried out, two important decisions must be taken. First, one should decide upon the number of estimated parameters, i.e., on the model order. Second, one should choose the appropriate estimation bandwidth, related to the (effective) number of input-output data samples that will be used for identification/ tracking purposes. Failure to make the right decisions results...
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Modelling and Analysis of the Positioning Accuracy in the Loading Systems of Mobile Cranes
PublicationIn this work, the authors analyse the influence of the order and range of sequential movements of a crane's working members on the accuracy of the final cargo positioning. The analysis was conducted on the basis of a specially developed method in which the authors proposed the introduction of a geometrical indicator of positioning the load in the intermediate positions (after completing each movement sequence) and in the target...
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Tree-based homogeneous ensemble model with feature selection for diabetic retinopathy prediction
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Machine learning-based prediction of preplaced aggregate concrete characteristics
PublicationPreplaced-Aggregate Concrete (PAC) is a type of preplaced concrete where coarse aggregate is placed in the mold and a Portland cement-sand grout with admixtures is injected to fill the voids. Due to the complex nature of PAC, many studies were conducted to determine the effects of admixtures and the compressive and tensile strengths of PAC. Considering that a prediction tool is needed to estimate the compressive and tensile...
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Machine learning-based prediction of preplaced aggregate concrete characteristics
PublicationPreplaced-Aggregate Concrete (PAC) is a type of preplaced concrete where coarse aggregate is placed in the mold and a Portland cement-sand grout with admixtures is injected to fill the voids. Due to the complex nature of PAC, many studies were conducted to determine the effects of admixtures and the compressive and tensile strengths of PAC. Considering that a prediction tool is needed to estimate the compressive and tensile strengths...
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublicationIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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Numerical Estimation of Hull Hydrodynamic Derivatives in Ship Maneuvering Prediction
PublicationPrediction of the maneuvering characteristics of the ship at the design stage can be done by means of model tests, computational simulations or a combination of both. The model tests can be realized as direct simulation of the standard maneuvers with the free running model, which gives the most accurate results, but is also the least affordable as it requires very large tank or natural lake, as well as complex equipment of the...
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(7Z,7'Z)-7,7'-(1,2,4-trithiolane-3,5-diylidene)bis[2-methylquinolin-8(7H)-one] chloroform disolvate
PublicationTytułowy związek, C22H14N2O2S3*2CHCl3 został otrzymany jako produkt reakcji pomiędzy kwasem 8-hydroksy-2-metylochinolinokarboditionowym a trifluorooctanem magnezu (lub manganu). Procesy utlenienia oraz eliminacji siarki spowodowały kondensację dwóch cząsteczek kwasu z wytworzeniem pięcioczłonowego aromatycznego pierścienia heterocyklicznego S3C2 (tritiolanu). Cząsteczka wykazuje symetrię C2. Związek ko-krystalizuje z dwoma cząsteczkami...
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Industry-level analysis of COVID-19’s impact in emerging markets – evidence from Pakistan
PublicationPurpose – The main purpose of this study is to evaluate COVID-19’s impact on the emerging stock markets. Design/methodology/approach – To evaluate the influence of COVID-19, this study uses a novel method of event study methodology to measure the impact of COVID-19 on emerging stock markets. The research’s sample includes a total of 79 firms from 26 industries that are included in the KSE-100 Index from the Pakistan Stock Exchange....
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Accuracy and Availability of EGNOS - Results of Observations
PublicationAccording to SBAS concept the user should receive timely the correct information about the system integrity and corrections to the pseudoranges measurements, which leads to better accuracyof coordinates. In theory the whole system is permanently monitored by RIMS stations, so it is impossible to deliver the faulty information to the user. The quality of the system is guaranteed inside the border of the system coverage however in...