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Why the Solvation Water around Proteins Is More Dense than Bulk Water
PublicationThe main aim of this work is to propose a rational explanation of the commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that the geometry of the water–water hydrogen bond network within solvation layer differs from the one in bulk water, and it is the result of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the...
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Properties of water in the region between a tubulin dimer and a single motor head of kinesin
PublicationA kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin...
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Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer—the first solvation shell—around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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Ontology-based text convolution neural network (TextCNN) for prediction of construction accidents
PublicationThe construction industry suffers from workplace accidents, including injuries and fatalities, which represent a significant economic and social burden for employers, workers, and society as a whole.The existing research on construction accidents heavily relies on expert evaluations,which often suffer from issues such as low efficiency, insufficient intelligence, and subjectivity.However, expert opinions provided in construction...
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A novel microstrip dual-layer rat-race coupler with compact size and enhanced bandwidth
PublicationMicrowave hybrid couplers are crucial components of mixers, phase shifters, amplifiers and other high-frequency systems. Conventional couplers are characterized by large size which limits their usefulness in modern applications. In this work, a novel compact rat-race coupler with enhanced bandwidth has been proposed. The structure consists of six compact microstrip resonant cells. It is implemented on two separate layers which permits...
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Digital microcontroller for sonar waveform generator
PublicationGenerating sounding signals is essential for the operation of active sonar. The system should be highly reliable. This can be achieved through architecture, communication between the devices, and a well-designed and self–testing software. The system presented in the article is responsible for the generation of hydroacoustic sounding signals, and ensures proper interaction between power amplifiers and power supplies. Thanks to its...
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Genotyping of clinical isolates of fluconazole-resistant Candida albicans
PublicationThe aim of the study was to compare the discriminatory power of RAPD-PCR method with using RSD10 primer and microsatellite analysis with using (GACA)4 primer for genotyping clinical isolates of fluconazole-resistant C. albicans. Isolates were received from patients of Children's Memorial Health Institute in Warsaw. However in the case of both tested methods low number of amplified fragments was generated, nine and six different...
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Technique to improve CMRR at high frequencies in CMOS OTA-C filters
PublicationIn this paper a technique to improve the common-mode rejection ratio (CMRR) at high frequencies in the OTA-C filters is proposed. The technique is applicable to most OTA-C filters using CMOS operational transconductance amplifiers (OTA) based on differential pairs. The presented analysis shows that a significant broadening of CMRR bandwidth can be achieved by using a differential pair with the bodies of transistors connected to...
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MutS3: a MutS homologue of unknown biological function
PublicationThe homologues of MutS proteins are widespread among both Prokaryotes and Eukaryotes. MutS designated as MutS1 is a part of MMR (mismatch repair) system which is responsible for removal of mispaired bases and small insertion/deletion loops in DNA. Initially, the only MutS homologues known were those engaged in mismatch repair and these were later designated as MutS1. Subsequently, the MutS2 homologue was distinguished. MutS2 does...
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Properties of recombinant trehalose synthase from Deinococcus radiodurans expressed in Escherichia coli
PublicationA trehalose synthase gene from Deinococcus radiodurans(DSMZ 20539)containing 1659 bp reading frame encoding 552 amino acids was amplified using PCR. The gene was finally ligated into pET30Ek/LIC vector and expressed after isopropyl β-d-thiogalactopyranoside induction in Escherichia coli (DE3) Rosetta pLysS. The recombinanttrehalose synthase (DraTreS) containing a His6-tag at the C-terminus was purified by metal affinity chromatography...
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Realistic noise-tolerant randomness amplification using finite number of devices
PublicationRandomness is a fundamental concept, with implications from security of modern data systems, to fundamental laws of nature and even the philosophy of science. Randomness is called certified if it describes events that cannot be pre-determined by an external adversary. It is known that weak certified randomness can be amplified to nearly ideal randomness using quantum-mechanical systems. However, so far, it was unclear whether randomness amplification...
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Fusion of DNA-binding domain of Pyrococcus furiosus ligase with TaqStoffel DNA polymerase as a useful tool in PCR with difficult targets
PublicationThe DNA coding sequence of TaqStoffel polymer- ase was fused with the DNA-binding domain of Pyrococcus furiosus ligase. The resulting novel recombinant gene was cloned and expressed in E. coli. The recombinant enzyme was purified and its enzymatic features were studied. The fusion protein (PfuDBDlig-TaqS) was found to have enhanced processivity as a result of the conversion of the Taq DNA polymerase from a relatively low processive...
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Low cost set-up for supercapacitors parameters evaluation
PublicationSupercapacitors are capable to store relatively high amount of energy comparing to its mass. Growing number of these devices applications requires development of new testing methods. Standard methods of evaluation of supercapacitor parameters, as cycling voltammetry, CV, galvanostatic cycling with potential limitation, GCPL, impedance measurements, require equipment of high cost...
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Integrated Control in High-Speed Networks Using Constrained Model Predictive Control
PublicationThis paper studies congestion control in high-speed communication networks using Model Predictive Control (MPC). Network traffic is assumed to consist of best-effort and priority traffic sources. An integrated controller consisting of two control parts is designed. The controller calculates the capacity for priority sources and the input rate of best-effort sources. MPC is desirable as it can take into account the constraints on...
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The shallow sea experiment with usage of linear hydrophone array
PublicationPurpose of this article is to present designed and made linear hydrophone array and the results obtained during in situ trails on Gulf of Gdańsk. The measuring system allowed to localize hydrophones in the selected points and perform measurements in both the horizontal antenna positioning and vertical. Made in this way recordings allow creating accurate 3D imaging of sound intensity/propagation. During research three floating objects...
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Acetate-Induced Disassembly of Spherical Iron Oxide Nanoparticle Clusters into Monodispersed Core−Shell Structures upon Nanoemulsion Fusion
PublicationIt has been long known that the physical encapsulation of oleic acid-capped iron oxide nanoparticles (OA−IONPs) with the etyltrimethylammonium (CTA+) surfactant induces the formation of spherical iron oxide nanoparticle clusters (IONPCs). However, the behavior and functional properties of IONPCs in chemical reactions have been largely neglected and are still not well-understood. Herein, we report an unconventional ligand-exchange...
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Entrepreneurship Today: Selected Aspects
PublicationAt its very beginning, entrepreneurship was a purely economic notion. However, this growing interest in entrepreneurship-related problems prompted other sciences to participate in explaining the entrepreneurship phenomenon. Nowadays, entrepreneurship is analyzed through multiple theoretical lenses of economics, management, psychology, sociology – just to name a few. Therefore, it would be difficult to find a notion that could be...
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Warstwy funkcjonalne tlenkowych ogniw paliwowych
PublicationIn this paper, results describing current research on solid oxide fuel cells conducted at Gdańsk University of Technology, Faculty of Electronics, Telecommunications and Informatics are presented. The results are related to three kinds of functional layers: a thin cathode layer between the porous cathode layer and the electrolyte to improve the cathode performance, a buffer layer between the electrolyte and the cathode to slow...
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Beyond Traditional Learning: The LLM Revolution in BPM Education at University
PublicationLarge Language Models (LLMs) significantly impact higher education, requiring changes in educational processes, especially in Business Process Management (BPM) practical exercises. The research aims to evaluate the effectiveness of LLMs in BPM education to determine if LLMs can supplement educators. The study involved 33 master’s degree students. Students’ works were manually evaluated and compared to LLM-generated responses. Results...
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Charakterystyka otoczki solwatacyjnej białka przeciwdziałającego zamarzaniu wody
PublicationWiele organizmów rozwinęło oryginalne sposoby na radzenie sobie z niebezpieczeństwami związanymi z narażaniem na niskie temperatury. Istnieje np. szczególna grupa białek powstrzymujących wzrost zarodków krystalizacji wody. W budowie analizowanego tu białka wskazać można trzy powierzchnie: jedną wiążącą się do lodu oraz dwie pozostające w kontakcie z wodą w stanie ciekłym. Przedmiotem tej pracy było opisanie struktury wody sąsiadującej...
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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Theoretical Investigation of the Electron-Transfer Dynamics and Photodegradation Pathways in a Hydrogen-Evolving Ruthenium-Palladium Photocatalyst
PublicationTime-dependent density functional theory calcula- tions combinedwith the Marcus theory of electron transfer (ET) were app lied on the molecular photocatalys t [(tbbpy) 2 Ru(tpph z)PdC l 2 ] 2 + in order to elucidate thelight-in- duced relaxation pathways populated upon excitation in the longer wavelength range of its absorption spectrum. The computational resultsshow that after the initial excitation, metal (Ru) to ligand (tpphz)chargetransfer...
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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublicationMost protein molecules do not adsorb onto ice, one of the exceptions being so-called antifreeze proteins. In this paper, we describe that there is a force pushing an antifreeze protein molecule away from the ice surface when it is not oriented with its ice-binding plane toward the ice and that this pushing force may be also present even when the protein is oriented with its ice-binding plane toward the ice. This force is absent...
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Interfacial water controls the process of adsorption of hyperactive antifreeze proteins onto the ice surface
PublicationA mechanism of interactions between the ice-binding surface of a hyperactive antifreeze protein molecule and the ice surface is proposed, involving the influence of water present between the two surfaces on the behavior of the approaching molecule. It is demonstrated that the interfacial water, even before its full solidification, can act as a factor that pushes away or pulls nearer the protein molecule to ensure its proper positioning....
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An Assessment of RASSCF and TDDFT Energies and Gradients on an Organic Donor−Acceptor Dye Assisted by Resonance Raman Spectroscopy
PublicationThe excitation energies and gradients in the ground and the first excited state of a novel donor−(π- bridge)−acceptor 4-methoxy-1,3-thiazole-based chromophore were investigated by means of MS-RASPT2/RASSCF and TDDFT in solution. Within both methods, the excitation energies strongly depend on the employed equilibrium structures, whose differences can be rationalized in terms of bond length alternation indexes. It is shown that functionals with...
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Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublicationWater molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel...
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The accretion of the new ice layer on the surface of hexagonal ice crystal and the influence of the local electric field on this process
PublicationThe process of creation of a new layer of ice on the basal plane and on the prism plane of a hexagonal ice crystal is analyzed. It is demonstrated that the ordering of water molecules in the already existing crystal affects the freezing. On the basal plane, when the orientations of water molecules in the ice block are random, the arrangement of the new layer in a cubic manner is observed more frequently — approximately 1.7 times...
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Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein
PublicationMany hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were...
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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublicationThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
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Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublicationUsing molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation...
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Light‐Driven Multi‐Charge Separation in a Push‐Pull Ruthenium‐Based Photosensitizer – Assessed by RASSCF and TDDFT Simulations
PublicationThe performance of photosensitizers in the field of, for example, solar energy conversion, relies on their light-harvesting efficiency in the visible region, population of long-lived charge separated intermediates, as well as their charge-accumulation capacity amongst other properties. In this computational study, we investigate the photophysical properties of a bis(bipyridyl)ruthenium(II)-based black dye (Ru) incorporating a chromophoric...
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Revealing the Frank–Evans “Iceberg” Structures within the Solvation Layer around Hydrophobic Solutes
PublicationUsing computer simulations, the structural properties of solvation water of three model hydrophobic molecules, methane and two fullerenes (C60 and C80), were studied. Systems were simulated at temperatures in the range of 250−298 K. By analyzing both the local ordering of the molecules of water in the solvation layers and the structure of hydrogen bond network, it is shown that in the solvation layer of hydrophobic molecules, ordered...
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Effect of the Catalytic Center on the Electron Transfer Dynamics in Hydrogen-Evolving Ruthenium-Based Photocatalysts Investigated by Theoretical Calculations
PublicationThe light-induced relaxation pathways in the molecular photocatalyst [(tbbpy)2Ru(tpphz)PtCl2]2+ are investigated with time-dependent density functional theory calculations together with the Marcus theory of electron transfer (ET). The calculations show that metal (Ru) to ligand (tpphz) charge transfer (MLCT) triplet states are populated following an excitation in the longer wavelength range of the absorption spectrum, but that an...
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A universal method for the identification of genes encoding amatoxins and phallotoxins in poisonous mushrooms
PublicationABSTRACT Background. As the currently known diagnostic DNA targets amplified in the PCR assays for detection of poisonous mushrooms have their counterparts in edible species, there is a need to design PCR primers specific to the genes encoding amanitins and phallotoxins, which occur only in poisonous mushrooms. Objective. The aim of the study was testing of PCR-based method for detection of all genes encoding hepatotoxic cyclic...
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Tailoring the electrochemical degradation of iron protected with polypyrrole films for biodegradable cardiovascular stents
PublicationThe degradation of polypyrrole (PPy) coated iron is studied in phosphate buffer saline solution at 37 °C by odd random phase multisine electrochemical impedance spectroscopy (ORP-EIS). PPy is electropolymerized with anti-inflammatory salicylates incorporated in the film, as a drug release system. The modelling of EIS over time provides the quantitative description of the corrosion behaviour of the material. Thus, the reliable...
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Investigating lubricants behaviour in microgravity for vibration damping purposes
PublicationVibration is one of the harshest environments an object is exposed to during and after launch into space on a launch vehicle. Such vibrations should be damped to avoid destruction of the spacecraft or its elements. Currently, active and material damping is used. A possibility of using lubrication as the damping factor is suggested by some research. MoS2 is a typical solid lubricant used in space applications. Its properties vary...
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Energy efficient indoor localisation for narrowband internet of things
PublicationThere are an increasing number of Narrow Band IoT devices being manufactured as the technology behind them develops quickly. The high co-channel interference and signal attenuation was seen in edge Narrow Band IoT devices make it challenging to guarantee the service quality of these devices. To maximize the data rate fairness of Narrow Band IoT devices, a multi-dimensional indoor localization model is devised, consisting of...
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Adaptive Method of Raster Images Compression and Examples of Its Applications in the Transport Telematic Systems
PublicationThe paper presents a concept and exemplary application of an adaptive method of compression of raster images which may be applied, i.a. in ITS systems. The described method allows to improve the efficiency of systems belonging to ITS category, which require transmission of large volumes of image data through telecommunications networks. The concept of the adaptive method of compression of raster images described in the paper uses...
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Smart Email - Almost an Agent Platform
PublicationNetwork organizations suffer today of information overload and strain that rise their operational costs. One of the reasons of that is the dominance of email messaging as the princi-pal means of document exchange between their workers. Proac-tive documents can rationalize these costs and augment email systems with a process view based on collaboration patterns.
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Influence of CeO2 and TiO2 Particles on Physicochemical Properties of Composite Nickel Coatings Electrodeposited at Ambient Temperature
PublicationThe Ni-TiO2 and Ni-CeO2 composite coatings with varying hydrophilic/hydrophobic characteristics were fabricated by the electrodeposition method from a tartrate electrolyte at ambient temperature. To meet the requirements of tight regulation by the European Chemicals Agency classifying H3BO3 as a substance of very high concern, Rochelle salt was utilized as a buffer solution instead. The novelty of this study was to implement a...
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Expression of Deinococcus geothermalis Trehalose Synthase Gene in Escherichia coli and Its Enzymatic Properties
PublicationA novel trehalose synthase gene from Deinococcus geothermalis (DSMZ 11300) containing 1,692 bp reading-frame encoding 564 amino acids was amplified using PCR. The gene was ligated into pET30Ek/LIC vector and expressed after isopropyl alfa-D-thiogalactopyranoside induction in Escherichia coli BL21(DE3)pLysS. The recombinant trehalose synthase (DgeoTreS) containing a His6 tag at the C-terminus was purified by metal affinity chromatography...
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Portable exhaled breath analyzer employing fluctuation-enhanced gas sensing method in resistive gas sensors
PublicationThis paper presents a portable exhaled breath analyser, developed to detect selected diseases. The set-up employs resistive gas sensors: commercial MEMS sensors and prototype gas sensors made of WO3 gas sensing layers doped with various metal ingredients. The set-up can modulate the gas sensors by applying UV light to induce physical changes of the gas sensing layers. The sensors are placed in a tiny gas chamber of a volume...
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NOWE TRENDY I KIERUNKI BADAŃ W MARKETINGU USŁUG
PublicationOd momentu pojawienia się koncepcji marketingu usług przechodzi ona nieustającą ewolucję. Pojawiające się nowe trendy (m.in. Service-Dominant Logic, Service Logic, New Service Marketing) i obszary badań marketingu usług (np. Transformative Service Research) skłaniają do dokonywania podsumowań pewnego etapu rozwoju i stawiania pytań, w którym kierunku powinny podążać badania marketingu usług w przyszłości. Celem artykułu jest przedstawienie...
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Preparation of porous TiO2 films by means of pulsed laser deposition for photocatalytic applications
PublicationIn this work the preparation and structure properties of porous thin films of TiO2 were investigated. The films were produced by means of the pulsed laser deposition technique using laser pulses at 266nm (10Hz) and at fluencies of 1-3.5J/cm2. The process was performed in vacuum using O2 buffer gas and films were deposited on the SiO2 glass or Si substrate. X-ray diffraction (XRD) and Raman analysis of the structure and chemical...
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Interpretable deep learning approach for classification of breast cancer - a comparative analysis of multiple instance learning models
PublicationBreast cancer is the most frequent female cancer. Its early diagnosis increases the chances of a complete cure for the patient. Suitably designed deep learning algorithms can be an excellent tool for quick screening analysis and support radiologists and oncologists in diagnosing breast cancer.The design of a deep learning-based system for automated breast cancer diagnosis is not easy due to the lack of annotated data, especially...
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The New LM-PCR/Shifter Method for the Genotyping of Microorganisms Based on the Use of a Class IIS Restriction Enzyme and Ligation Mediated PCR
PublicationThis study details and examines a novel Ligation-Mediated - Polymerase Chain Reaction (LM-PCR) method. Named the LM-PCR/Shifter, it relies on the use of a Class IIS restriction enzyme giving restriction fragments with different 4 base, 5' overhangs, this being the Shifter, and the ligation of appropriate oligonucleotide adapters. A sequence of 4-base, 5' overhangs of the adapter and a 4-base sequence of the 3' end of the primer(s)...
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Highly Reliable Passive RFID-Based Inductor–Capacitor Sensory System Strengthened by Solvatochromism for Fast and Wide-Range Lactate Detection
PublicationA passive radio frequency-identification-based inductor-capacitor (LC) lactate sensory system with a specific dye-containing interdigitated capacitor (IDC) in which the sensing signal is amplified by the solvatochromic effect is proposed. When a lactate solution contacts the IDC of the LC lactate sensor, the capacitance of the IDC changes, changing the resonance frequency of the sensor. This changes the oscillation frequency of...
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<title>Recurrent neural network application to image filtering: 2-D Kalman filtering approach</title>
Publication