2021 - Repozytorium publikacji - Politechnika Gdańska

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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
- Emilia Lubecka
- Adam Liwo
2021 Pełny tekst JOURNAL OF COMPUTATIONAL CHEMISTRY
A method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances calculated from a set of 140 high-resolution non-homologous protein structures. The mean standard deviation over all types of proton pairs in the set was 0.44 Å after fitting. Validation against a set of 41 proteins with NMR-determined structures, which were not considered in parameterization, resulted in average standard deviation from average proton–proton distances of the NMR-determined structures of 0.25 Å, compared to 0.21 Å obtained with the PULCHRA all-atom-chain reconstruction algorithm and to the 0.12 Å standard deviation of the average-structure proton–proton distance of NMR-determined ensembles. The formulas provide analytical forces and can, therefore, be used in coarse-grained molecular dynamics.
Establishing the allosteric mechanism in CRISPR‐Cas9
- Łukasz Nierzwicki
- Pablo Ricardo Arantes
- Aakash Saha
- Giulia Palermo
2021 Pełny tekst Wiley Interdisciplinary Reviews-Computational Molecular Science
Allostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR‐Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three steps of the CRISPR‐Cas9 function: affecting DNA recognition, mediating the cleavage and interfering with the off‐target activity. An allosteric communication that activates concerted DNA cleavages was found to led through the L1/L2 loops, which connect the HNH and RuvC catalytic domains. The identification of these “allosteric transducers” inspired the development of novel variants of the Cas9 protein with improved specificity, opening a new avenue for controlling the CRISPR‐Cas9 activity. Discussed studies also highlight the critical role of the recognition lobe in the conformational activation of the catalytic HNH domain. Specifically, the REC3 region was found to modulate the dynamics of HNH by sensing the formation of the RNA:DNA hybrid. The role of REC3 was revealed to be particularly relevant in the presence of DNA mismatches. Indeed, interference of REC3 with the RNA:DNA hybrid containing mismatched pairs at specific positions resulted in locking HNH in an inactive “conformational checkpoint” conformation, thereby hampering off‐target cleavages. Overall, MD simulations established the fundamental mechanisms underlying the allosterism of CRISPR‐Cas9, aiding engineering strategies to develop new CRISPR‐Cas9 variants for improved genome editing.
Estimation of Average Speed of Road Vehicles by Sound Intensity Analysis
- Józef Kotus
- Grzegorz Szwoch
2021 Pełny tekst SENSORS
Constant monitoring of road traffic is important part of modern smart city systems. The proposed method estimates average speed of road vehicles in the observation period, using a passive acoustic vector sensor. Speed estimation based on sound intensity analysis is a novel approach to the described problem. Sound intensity in two orthogonal axes is measured with a sensor placed alongside the road. Position of the apparent sound source when a vehicle passes by the sensor is estimated by means of sound intensity analysis in three frequency bands: 1 kHz, 2 kHz and 4 kHz. The position signals calculated for each vehicle are averaged in the analysis time frames, and the average speed estimate is calculated using a linear regression. The proposed method was validated in two experiments, one with controlled vehicle speed and another with real, unrestricted traffic. The calculated speed estimates were compared with the reference lidar and radar sensors. Average estimation error from all experiment was 1.4% and the maximum error was 3.2%. The results confirm that the proposed method allow for estimation of time-averaged road traffic speed with accuracy sufficient for gathering traffic statistics, e.g., in a smart city monitoring station.
Estimation of structural stiffness with the use of Particle Swarm Optimization
- Michał Mazur
- Marek Galewski
- Krzysztof Kaliński
2021 Pełny tekst Latin American Journal of Solids and Structures
The paper presents the theoretical background and four applications examples of the new method for the estimation of support stiffness coefficients of complex structures modelled discretely (e.g. with the use of the Finite Element Model (FEM) method based on the modified Particle Swarm Optimization (PSO) algorithm. In real-life cases, exact values of the supports’ stiffness coefficients may change for various reasons (e.g. order of fastening, state of the contact surfaces, environment changes, etc.). Becaus e of the unknown coefficients, reliable simulations of fixed structure (i.e. mounted, assembled, not in a free-free state) are difficult to perform. The method serves as a tool to obtain good correlation between the FEM of a structure and the experimental data. Simple modal tests are required to estimate the first few modes of the fixed system. The FEM of the structure is considered in a free-free state and the support stiffness coefficients of the FEM are estimated by the proposed method. Further simulations with test - tuned and correlated complete FEM could be performed in time or frequency domain.
Estimation of the size of informal employment based on administrative records with non‐ignorable selection mechanism
- Maciej Berȩsewicz
- Dagmara Nikulin
2021 JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS
In this study, we used company level administrative data from the National Labour Inspectorate and The Polish Social Insurance Institution in order to estimate the prevalence of informal employment in Poland in 2016. Since the selection mechanism is non‐ignorable, we employed a generalization of Heckman’s sample selection model assuming non‐Gaussian correlation of errors and clustering by incorporation of random effects. We found that 5.7% (4.6%, 7.1%; 95% CI ) of registered enterprises in Poland, to some extent, take advantage of the informal labour force. Our study exemplifies a new approach to measuring informal employment, which can be implemented in other countries. It also contributes to the existing literature by providing, to the best of our knowledge, the first estimates of informal employment at the level of companies based solely on administrative data
Estimators of covariance matrices in Msplit(q) estimation
- Zbigniew Wiśniewski
- Marek Zienkiewicz
2021 SURVEY REVIEW
This paper proposes methods for the determination of covariance matrices of Msplit(q) estimators. The solutions presented here allow Msplit(q) estimation to be supplemented by the operations from the domain of accuracy analysis (especially that concerning estimators of parameters). Theoretical forms of covariance matrices of Msplit(q) estimators were established using the empirical influence functions and the equivalent covariance matrices of observation errors. The estimators of covariance matrices of Msplit(q) estimators were determined based on the adopted statistical observation models and their random errors. The unknown variance coefficients of these models were estimated employing the principles of square estimation.
Eurozone or National Inflation Projections: Which has Greater Impact on Consumer Expectations?
- Magdalena Szyszko
- Karolina Tura-Gawron
2021 Pełny tekst PANOECONOMICUS
We compare the dependence of consumer inflation expectations on European Central Bank (ECB) inflation projections with that on national central bank (NCB) projections in four economies: Austria, Belgium, Finland, and Germany. We aim to assess whether the information published by central banks affects consumers, and whether inflation projections published by NCBs are more relevant to consumers than those published for the entire Eurozone. Inflation expectations were obtained from the Business and Consumer Surveys conducted by the Directorate General for Economic and Financial Affairs of the European Commission and quantified using the probabilistic method. The methodology covers: (1) forecast encompassing tests, (2) the Granger causality test, and (3) impulse response analysis complemented by (4) forecast error variance decomposition. The results suggest that the ECB outlook constitutes a more important factor in expectation formation. This article adds to the existing literature by comparing the impact of common and national projections on consumer expectations.
Evaluating architecture students' knowledge of the history of architecture by tests and by drawings: a comparative analysis
- Maria Sołtysik
2021 Pełny tekst World Transactions on Engineering and Technology Education
The methods of evaluating students’ knowledge in architectural education, and in particular in education on history of architecture, are specific in many respects. Apart from checking the general knowledge of history concerning chronology, artistic trends, styles, main objects and architects, it should also check students’ ability to analyse the historic architecture in a drawing form. Such a form of presenting architecture has proven to be the most comprehensive and aimed on understanding its development throughout the ages. Thus, the methods of evaluating students’ historical knowledge at GUT include two main methods of examination – tests and drawings. Both methods and their results were closely investigated and compared after the first semester exam in the academic year 2020/2021. A comparative analysis was conducted in context of correctness, efficiency, usefulness and difficulty, both from the perspective of the students examination results and the student questionnaire
Evaluating Industry 4.0 Implementation Challenges Using Interpretive Structural Modeling and Fuzzy Analytic Hierarchy Process
- Ahmad Reshad Bakhtari
- Mohammad Waris
- Cesar Sanin
- Edward Szczerbicki
2021 Pełny tekst CYBERNETICS AND SYSTEMS
The fourth industrial revolution known as Industry 4.0 is reshaping and evolving the way industries produce products and individuals live and work therefore, gaining massive attraction from academia, business and politics. The manufacturing industries are optimistic regarding the opportunities Industry 4.0 may offer such as, improved efficiency, productivity and customization. The present research contributes to the Industry 4.0 literature by identifying, modelling, analyzing and prioritizing the challenges in implementing Industry 4.0 in manufacturing industries. In doing so, the paper first introduces the interpretive structural modelling (ISM) to develop the hierarchical relationships among the challenges and analyzes their mutual interactions. Further, ‘Matrice d’Impacts Croises Multiplication Appliquee aun Classement’ (MICMAC) analysis is used to categorize the challenges into four categories namely, autonomous, driver, dependent and linkage based on their driving power and dependence power. Moreover, fuzzy-analytic hierarchy process (F-AHP) methodology is used to prioritize the challenges based on three criteria; driving power, dependence power and change management. The hierarchical model developed through ISM methodology shows that “lack of vision and leadership from top management (C12), lack of skills training program and education (C2) and uncertainty of return on investment (C9)” are the major challenges in implementing Industry 4.0 in manufacturing industries. The findings of F-AHP analysis suggests that “lack of vision and leadership from top management (C12), lack of skilled workforce (C3), lack of skills training program and education (C2) and uncertainty of return on investment (C9)” are some of the major challenges of implementing Industry 4.0. Finally, the obtained results show how challenges affect other so that to uncover the root cause triggering the other challenges. The industrial practitioners and managers can then take advantage of these analyzes to know which challenge acts as the main barrier in implementing Industry 4.0 and to be focused first in order to reach a solution.
Evaluating the antibacterial activity of muramyl dipeptide derivatives, retro-tuftsin derivatives, and anthraquinone oligopeptides against a range of pathogenic bacteria
- Magdalena Wysocka
- Krystyna Dzierzbicka
- Beata Krawczyk
2021 Pełny tekst Acta Biochimica Polonica
Search for new and efficient antibiotic is crucial because of microbial drug resistance and problems with side effects of the administered medication. In this study, we evaluate the in vitro microbiological activity of muramyl dipeptide derivatives, retro-tuftsin derivatives (i.e., tuftsin with reversed amino acid sequences), and combinations of retro-tuftsin derivatives with substituted anthraquinones. The potency of the investigated derivatives towards methicillin-sensitive Staphylococcus aureus (MSSA), methicillin-resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae ESBL (extended-spectrum β-lactamases) was compared based on the spectroscopically-measured minimal inhibitory concentrations (MIC values). The bacterial growth have also been studied with different concentrations of compounds. Statistical analysis of the results revealed that certain modifications lead to promising activity against S. aureus (anthraquinone analogue – 3c and retro-tuftsin derivative – 2b), while other derivatives exhibit activity against P. aeruginosa (muramyl dipeptide derivative – 1d and retro-tuftsin derivative – 2b). The obtained results of microbiological activity indicate that the structure of the tested compounds may be the basis for further modifications.
Evaluating the convenience and safety effects of bicycle lanes in Gdańsk
- Romanika Okraszewska
- Karolina Kijewska
- Joanna Wachnicka
- Miroslava Mikusova
2021 Pełny tekst Archives of Civil Engineering
Bicycle lanes are lanes marked on a road and dedicated for exclusive use for cyclists.. Because they combine bike and motor traffic they provide directness and flow. However, a shared use of streets could result in bicycle-car accidents. Following up on the good practice Western countries have in planning cycle infrastructure, Gdańsk has recently introduced bike lanes on a few streets. The aim of the research was to assess the attractiveness and safety of bike lanes as a relatively new and rare solution in Gdansk. The attractiveness was assessed using the multi-criteria method. The data for the assessment came from surveys and fieldwork (inventory, observation of cyclist behaviour, traffic counts). Additionally, safety information was supplemented with police statistics on collisions and accidents. The results show that the level of bike lane usage is rather high (more than 70%). However, 80% of the respondents do not find them as attractive as separated bike paths. The advantages indicated by bike lane users included speed, surface quality, and comfort. Those who avoiding bike lanes have pointed to insufficient sense of safety. The main problems were identified such as speed and volume of motor traffic, width of bicycle lane, surface quality and parking places located next to bike lanes. The conclusions from the research are consistent with the literature. The findings could improve the attractiveness and safety of bike lanes in Gdańsk if implemented by bike infrastructure planners and designers
Evaluating the influence of radiative heat flux on convective heat transfer from a vertical plate in air using an improved heating plate
- Michał Ryms
- Witold Lewandowski
2021 INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
This article examines the influence of radiative heat flux on the accuracy of the results of free convective heat transfer in air. In order to carry out these tests, based on the experience gained during the operation of a plate heated on one side, compensated by a reverse heat loss flux counter-heater, a unique double-sided heating sandwich plate was designed and built, consisting of three thin epoxy resin plates reinforced with glass fibre. The paths of surface resistance thermometers were etched using photolithography on the two outer plates laminated on one side with copper. The traces of two resistance heaters were etched on both sides of the third, bilaterally laminated middle plate. This paper provides a detailed technical description of the new type of plate, the method of its implementation and determination of its operational range, calibration procedures (separately for integrated thermometers and heaters). Also described are the methods for conducting experimental tests in the vertical using the balance method in air and in water, and the gradient method using a thermal imaging camera and a detection mesh in order to validate the results obtained.
Evaluating the Internal and External Usability of Mobile Technologies in Facilitating Knowledge Transfer
- Michał Kuciapski
- Paweł Weichbroth
2021 Pełny tekst
A worker’s performance and productivity depend on a variety of factors including knowledge, to be essential for self-effectiveness and self-efficacy. In the literature, knowledge transfer is argued to enhance the quality of work, and therefore, its value. When addressing this issue, the latest studies have considered and evaluated the use of mobile technologies, which are evidenced to improve a worker’s capacity and skills. However, only a few have investigated the impact of the internal and external usability of mobile technologies in facilitating knowledge transfer. This study draws upon evidence from a survey (n = 237) which shows that both internal and external usability positively influence knowledge transfer. The results of this research shed new light on the importance of mobile technology acceptance by employees, providing a better understanding of how and why rich usability facilitates knowledge transfer and eventually impacts their performance and productivity.
Evaluation and start-up of an electro-Fenton-sequencing batch reactor for dairy wastewater treatment
- Mohammad Reza Heidari
- Mohammad Malakootian
- Grzegorz Boczkaj
- Xun Sun
- Yang Tao
- Shirish H. Sonawane
- Hakimeh Mehdizadeh
2021 Pełny tekst Water Resources and Industry
This study examined the performance of an integrated wastewater (WW) treatment system, namely an electro-Fenton (EF)-sequencing batch reactor (SBR), for dairy industry WW. The EF process was used as the first stage of the SBR. It degrades bio-refractory compounds via advanced oxidation processes, thereby resulting in the formation of simple biodegradable intermediates. Several factors, including the hydraulic retention time (HRT), sludge volume index (SVI), and sludge retention time (SRT) of the EFSBR, were optimized. The effectiveness was studied for 1 y laboratory-scale experiments under stable conditions (HRT of 10 h, SRT of 15 d, mixed liquor suspended solids concentration of 3500 mg/L, and SVI of 89), which revealed 99% chemical oxygen demand, 97% total nitrogen, and 95% total phosphorus removal. Thus, the developed system is economically feasible and superior to other conventional biological treatment systems.
Evaluation of antimicrobial activities of powdered cuttlebone against Klebsiella oxytoca, Staphylococcus aureus, and Aspergillus flavus
- Ghazal Yazdanpanah
- Neda Javid
- Zhila Honarmandrad
- Najmeh Amirmahani
- Alireza Nasiri
2021 Pełny tekst Environmental Health Engineering and Management Journal
Background: The presence of medicines in the environment is considered as a serious threat to the human health. The entrance of these substances into the water sources causes soil pollution, which eventually leads to the environmental pollution and it creates some problems for the public health. Also, increasing antibiotic resistant bacteria has attracted the attention of researchers to the use of natural resources such as marine products, for producing new antibiotics. The aim of this study was to evaluate antimicrobial activities of powdered cuttlebone against Klebsiella oxytoca, Staphylococcus aureus, and Aspergillus flavus. Methods: At first, cuttlebones were washed, dried, and powdered. Then, the powdered cuttlebone was characterized. In the next step, its antimicrobial activities were evaluated using agar well diffusion technique, and minimum inhibitory concentration (MIC) was calculated. Results: The powdered cuttlebone was found to be effective against K. oxytoca (24 mm, MIC: 10-1 mg/mL), but no antimicrobial response was found against S. aureus. Also, the powdered cuttlebone antifungal activity and MIC against A. flavus were recorded 23 mm and 10-1 mg/mL, respectively. Conclusion: The obtained results suggest antimicrobial activities of powdered cuttlebone, which are concentration dependent. Furthermore, cuttlebone can be used as an accessible natural source to provide novel, low cost, and safe antimicrobial agents.
Evaluation of aspiration problems in L2 English pronunciation employing machine learning
- Magdalena Piotrowska
- Andrzej Czyżewski
- Tomasz Ciszewski
- Grazina Korvel
- Adam Kurowski
- Bożena Kostek
2021 Pełny tekst Journal of the Acoustical Society of America
The approach proposed in this study includes methods specifically dedicated to the detection of allophonic variation in English. This study aims to find an efficient method for automatic evaluation of aspiration in the case of Polish second-language (L2) English speakers’ pronunciation when whole words are analyzed instead of particular allophones extracted from words. Sample words including aspirated and unaspirated allophones were prepared by experts in English phonetics and phonology. The datasets created include recordings of words pronounced by nine native English speakers of standard southern British accent and 20 Polish L2 English users. Complete unedited words are treated as input data for feature extraction and classification algorithms such as k-nearest neighbors, naive Bayes method, long-short term memory, and convolutional neural network (CNN). Various signal representations, including low-level audio features, the so-called mid-term and feature trajectory, and spectrograms, are tested in the context of their usability for the detection of aspiration. The results obtained show high potential for an automated evaluation of pronunciation focused on a particular phonological feature (aspiration) when classifiers analyze whole words. Additionally, CNN returns satisfying results for the automated classification of words containing aspirated and unaspirated allophones produced by Polish L2 speakers.
EVALUATION OF EFFECTIVENESS OF WATERJET PROPULSOR FOR A SMALL UNDERWATER VEHICLE
- Lech Rowiński
2021 Pełny tekst Polish Maritime Research
T he goal of the project described is to replace the existing propulsion system of a small underwater vehicle with a solution less prone to mechanical damage and ensuring a lower risk of the entanglement of fibrous objects suspended in the body of water. Four typical marine screws are utilised in the current design of the vehicle. One possible solution of the problem is the application of waterjet propulsors located inside the body of the vehicle instead. The general condition of the application of the new solution was to secure at least the same motion control capabilities of the vehicle while the basic capability is its propulsion effectiveness at the required speed. Specific features of the considered waterjet propulsor, when compared with their application in surface vessel propulsion, are the lack of the head losses and the low significance of cavitation issues. One of the difficulties in the considered case is the small diameter of the propulsor in comparison to commercially available waterjet units, which have diameters between 0.1 [m] and 1.0 [m]. There is very little data regarding the design and performance of devices in the 0.02 to 0.05 [m] range. Methods utilised to forecast the performance of the new propulsion system are presented and results compared. These were semi-empirical calculations, numerical calculations and tests of real devices. The algorithm that is based on semi-empirical calculations is of particular interest while it offers possibility quick assessment of performance of a propulsor composed of several well defined components. The results indicate the feasibility of modification of the propulsion system for the considered vehicle if all the existing circumstances are taken into account.
Evaluation of Langmuir and Freundlich Isotherms for Removal of Cephalexin and Tetracycline Antibiotics By Sistan Sand from Water and Wastewater Samples
- Massoud Kaykhaii
- Sayedeh Samaneh Hasheminasab
- Sayyed Hossein Hashemi
- Mojtaba Sasani
2021 Iranian Journal of Analytical Chemistry
In this research, Sistan sand was used as a natural and inexpensive sorbent for removal of cephalexin and tetracycline antibiotics from water and wastewater samples. For a concentration 60.0 mg L-1 of cephalexin, optimum removal conditions were: pH of the sample 3.0, adsorbent amount 1.0 g, contact time 20.0 min, added amount of sodium chloride to adjust the ionic strength of the solution 7.0 g L-1. Langmuir isotherm was the best fitted model for this adsorption process and adsorbent capacity was calculated to be 0.26 g g-1. This adsorbent was able to remove up to 68.1% of cephalexin from wastewater. In case of tetracycline, for a 90.0 mg L-1 of the analyte, the optimum adsorption conditions were achieved at pH 8.0, 1.0 g of sorbent, contact time of 35.0 min and ionic strength of the solution as sodium chloride of 7.0 g L-1. The isotherm was best in agreement with Freundlich model. Adsorbent capacity was 0.76 g g-1 and up to 76.2% of this antibiotic could be removed from wastewater.
EVALUATION OF LIQUID-GAS FLOW IN PIPELINE USING GAMMA-RAY ABSORPTION TECHNIQUE AND ADVANCED SIGNAL PROCESSING
- Robert Hanus
- Marcin Zych
- Volodymyr Mosorov
- Anna Golijanek-Jędrzejczyk
- Marek Jaszczur
- Artur Andruszkiewicz
2021 Pełny tekst Metrology and Measurement Systems
Liquid-gas flows in pipelines appear in many industrial processes, e.g. in the nuclear, mining, and oil industry. The gamma-absorption technique is one of the methods that can be successfully applied to study such flows. This paper presents the use of thegamma-absorption method to determine the water-air flow parameters in a horizontal pipeline. Three flow types were studied in this work: plug, transitional plug-bubble, and bubble one. In the research, a radiometric set consisting of two sources Am-241 and two Nal(Tl) scintillation detectors have been applied. Based on the analysis of the signals from both scintillation detectors, the gas phase velocity was calculated using the cross-correlation method (CCM). The signal from one detector was used to determine the void fraction and to recognise the flow regime. In the latter case, Multi-Layer Perceptron type artificial neural network (ANN) was applied. To reduce the number of signal features, the principal component analysis (PCA) was used. The expanded uncertainties of gas velocity and void fraction obtained for the flow types studied in this paper did not exceed 4.3% and 7.4% respectively. All three types of analyzed flows were recognised with 100% accuracy. Results of the experiments confirm the usefulnessof gamma-ray absorption method in combination with radiometric signal analysis by CCM and ANN with PCA for comprehensive analysis of liquid-gas flow in the pipeline.
Evaluation of Six Degrees of Freedom 3D Audio Orchestra Recording and Playback using multi-point Ambisonic interpolation
- Tomasz Ciotucha
- Andrzej Rumiński
- Tomasz Żernicki
- Bartłomiej Mróz
2021 Scopus
This paper describes a strategy for recording sound and enabling six-degrees-of-freedom playback, making use of multiple simultaneous and synchronized Higher Order Ambisonics (HOA) recordings. Such a strategy enables users to navigate in a simulated 3D space and listen to the six-degrees-of-freedom recordings from different perspectives. For the evaluation of the proposed approach, an Unreal Engine-based navigable 3D audiovisual playback system was implemented. Subjective listening tests were conducted which compare the quality of the prepared walk-through.