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Search results for: MOLECULAR MODELING,MOLECULES,NEURAL NETWORKS,SOLVENTS,VISCOSITY
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On-line Search in Two-Dimensional Environment
PublicationWe consider the following on-line pursuit-evasion problem. A team of mobile agents called searchers starts at an arbitrary node of an unknown network. Their goal is to execute a search strategy that guarantees capturing a fast and invisible intruder regardless of its movements using as few searchers as possible. As a way of modeling two-dimensional shapes, we restrict our attention to networks that are embedded into partial grids:...
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A Perspective on Fast-SPICE Simulation Technology
PublicationThis chapter presents an introduction to the area of accelerated transistor-level (‘fast-SPICE’) simulation for automated verification and characterization of integrated circuits (ICs) from technologist’s perspective. It starts with outlining goals, expectations and typical usage models for fast-SPICE simulators, stressing how they differ from regular SPICE tools. It continues with presenting and classifying core technologies typically...
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Extraction pathways and purification strategies towards carminic acid as natural-based food colorant: A comprehensive review
PublicationAs a current trend of fabricating healthier products, food manufacturing companies seek for natural-based food colorant aiming to replace the synthetic ones, which apart from meeting sensorial and organoleptic aspects, they can also act as health promoters offering additional added value. Carminic acid is a natural based food colorant typically found in several insect taxa. However, there are current approaches which pursue the...
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Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations
PublicationN-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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Dynamic coloring of graphs
PublicationDynamics is an inherent feature of many real life systems so it is natural to define and investigate the properties of models that reflect their dynamic nature. Dynamic graph colorings can be naturally applied in system modeling, e.g. for scheduling threads of parallel programs, time sharing in wireless networks, session scheduling in high-speed LAN's, channel assignment in WDM optical networks as well as traffic scheduling. In...
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A Highly Selective Biosensor Based on Peptide Directly Derived from the HarmOBP7 Aldehyde Binding Site
PublicationThis paper presents the results of research on determining the optimal length of a peptide chain to eectively bind octanal molecules. Peptides that map the aldehyde binding site in HarmOBP7 were immobilized on piezoelectric transducers. Based on computational studies, four Odorant Binding Protein-derived Peptides (OBPPs) with dierent sequences were selected. Molecular modelling results of ligand docking with selected peptides were...
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Unusual Influence of Fluorinated Anions on the Stretching Vibrations of Liquid Water
PublicationInfrared (IR) spectroscopy is a commonly used and invaluable tool in the studies of solvation phenomena in aqueous solutions. Concurrently, ab initio molecular dynamics (AIMD) simulations deliver the solvation shell picture at a molecular detail level and allow for a consistent decomposition of the theoretical IR spectrum into underlying spatial correlations. Here, we demonstrate how the novel spectral decomposition techniques...
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Targeting Spike‐ACE2 Interface of SARS‐CoV‐2 and its Omicron Variant: A Comparative Screening of Potential Inhibitors for Existing and Anticipating Variants Using Molecular Modelling Approach
PublicationThe recent COVID pandemic has shown major impact on public health and economic crisis. Despite the development of many vaccines and drugs against the severe acute respiratory syndrome (SARS) coronavirus 2, the pandemic still persists. The continued spread of the virus is largely driven by the emergence of viral variants such as α, β, γ, delta, epsilon spike, omicron and its subvariants (BA.1,2,3) which can evade the current vaccines...
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Studies on applicability of new solid-phase microextraction fibers for the selective extraction and determination of short - chain monocarboksylic acids
PublicationShort-chain monocarobxylic acids, sometimes referred to as volatile fatty acids (VFA), are a group of low molecular weight alkyl monocarboxylic acids that are widely distributed within the environment. These molecules contain any from 2 to 8 carbon atoms and originate from the anaerobic biodegradation of organic matter such as carbohydrates, proteins, and fats. These compounds are commonly found in the effluents from animal farming,...
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Aggregation of imidazoacridinones - spectroscopic and microcalorimetric approach
PublicationImidazoacridinones (IA) belong to a group of polycyclic heteroaromatic antitumor compounds. IA create the aggregated form in water solution. Self-association of substances is a very important phenomenon in many fields of applied chemistry. It is also fundamental model reaction of many kinds of molecular interactions such as the micelle formation of amphiphilic substances and the binding of small organic molecules to macromolecules....
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Effect of Acetylation and Beta‐Amylase Treatment on Complexation of Debranched Starch with Naringenin
PublicationStarch inclusion complexation has been shown to improve solubility of water insoluble molecules. Potato starch and Hylon VII are acetylated at two levels and then debranched alone or combined with β‐amylase hydrolysis, and its complexes with naringenin are prepared in aqueous conditions and characterized in this study. Both soluble and insoluble complexes are formed with the soluble complex present in the supernatant and the insoluble...
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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L1 Cell Adhesion Molecule Overexpression Down Regulates Phosphacan and Up Regulates Structural Plasticity-Related Genes Rostral and Caudal to the Complete Spinal Cord Transection
PublicationL1 cell adhesion molecule (L1CAM) supports spinal cord cellular milieu after contusion and compression lesions, contributing to neuroprotection, promoting axonal outgrowth, and reducing outgrowth-inhibitory molecules in lesion proximity. We extended investigations into L1CAM molecular targets and explored long-distance effects of L1CAM rostral and caudal to complete spinal cord transection (SCT) in...
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Autonomous pick-and-place system based on multiple 3Dsensors and deep learning
PublicationGrasping objects and manipulating them is the main way the robot interacts with its environment. However, for robots to operate in a dynamic environment, a system for determining the gripping position for objects in the scene is also required. For this purpose, neural networks segmenting the point cloud are usually applied. However, training such networks is very complex and their results are unsatisfactory. Therefore, we propose...
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Autonomous Perception and Grasp Generation Based on Multiple 3D Sensors and Deep Learning
PublicationGrasping objects and manipulating them is the main way the robot interacts with its environment. However, for robots to operate in a dynamic environment, a system for determining the gripping position for objects in the scene is also required. For this purpose, neural networks segmenting the point cloud are usually applied. However, training such networks is very complex and their results are unsatisfactory. Therefore, we propose...
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How to Sort Them? A Network for LEGO Bricks Classification
PublicationLEGO bricks are highly popular due to the ability to build almost any type of creation. This is possible thanks to availability of multiple shapes and colors of the bricks. For the smooth build process the bricks need to properly sorted and arranged. In our work we aim at creating an automated LEGO bricks sorter. With over 3700 different LEGO parts bricks classification has to be done with deep neural networks. The question arises...
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MobileNet family tailored for Raspberry Pi
PublicationWith the advances in systems-on-a-chip technologies, there is a growing demand to deploy intelligent vision systems on low-cost microcomputers. To address this challenge, much of the recent research has focused on reducing the model size and computational complexity of contemporary convolutional neural networks (CNNs). The state-of-the-art lightweight CNN is MobileNetV3. However, it was designed to achieve a good trade-off between...
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Playback detection using machine learning with spectrogram features approach
PublicationThis paper presents 2D image processing approach to playback detection in automatic speaker verification (ASV) systems using spectrograms as speech signal representation. Three feature extraction and classification methods: histograms of oriented gradients (HOG) with support vector machines (SVM), HAAR wavelets with AdaBoost classifier and deep convolutional neural networks (CNN) were compared on different data partitions in respect...
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Performance and Energy Aware Training of a Deep Neural Network in a Multi-GPU Environment with Power Capping
PublicationIn this paper we demonstrate that it is possible to obtain considerable improvement of performance and energy aware metrics for training of deep neural networks using a modern parallel multi-GPU system, by enforcing selected, non-default power caps on the GPUs. We measure the power and energy consumption of the whole node using a professional, certified hardware power meter. For a high performance workstation with 8 GPUs, we were...
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Performance tuning of chitosan-based membranes by protonated 2-Pyrrolidone-5-carboxylic acid-sulfolane DES for effective water/ethanol separation by pervaporation
PublicationToday, the applicability of deep eutectic solvents (DES) in various fields, including membrane science and technology, is extensively investigated. In pioneering works, we have implemented different DES as a component of chitosan (CS)-based flat membranes for pervaporation (PV) separation. Herein, we present a new protonated (by sulphuric acid) 2-Pyrrolidone-5-carboxylic acid: sulfolane DES, as a green additive for its chemical...
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On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
PublicationAmphotericin B (AmB) is a well-known membrane-active antibiotic that has been used to treat systemicfungal infections for more than 45 years. Therapeutic application of AmB is based on the fact that it is moreactive against ergosterol-containing membranes of fungal cells than against mammalian membranes withcholesterol. In this paper, we examine the hypothesis according to which the selectivity of the AmB's membraneaction originates...
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BETWEEN IDEA AND INTERPRETATION - DESIGN PROCESS AUGMENTATION
PublicationThe following paper investigates the idea of reducing the human digital intervention to a minimum during the advanced design process. Augmenting the outcome attributes beyond the designer's capabilities by computational design methods, data collection, data computing and digital fabrication, altogether imitating the human design process. The primary technical goal of the research was verification of restrictions and abilities used...
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Prediction of maximum tensile stress in plain-weave composite laminates with interacting holes via stacked machine learning algorithms: A comparative study
PublicationPlain weave composite is a long-lasting type of fabric composite that is stable enough when being handled. Open-hole composites have been widely used in industry, though they have weak structural performance and complex design processes. An extensive number of material/geometry parameters have been utilized for designing these composites, thereby an efficient computational tool is essential for that purpose. Different Machine Learning...
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Soft X-ray Induced Production of Neutral Fragments in High-Rydberg States at the O 1s Ionization Threshold of the Water Molecule
PublicationDissociation of water molecules after soft X-ray absorption can yield neutral fragments in high-Rydberg (HR) states. We have studied the production of such fragments by field ionization and ion time-of-flight (TOF) spectrometry. Neutral HR fragments are created at all resonances below the O 1s ionization potential (IP) and particularly within 1 eV above the O 1s IP. The latter effect is due to the recapture of the O 1s photoelectrons...
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublicationShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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Generation-recombination and 1/f noise in carbon nanotube networks
PublicationThe low-frequency noise is of special interest for carbon nanotubes devices, which are building blocks for a variety of sensors, including radio frequency and terahertz detectors. We studied noise in as-fabricated and aged carbon nanotube networks (CNNs) field-effect transistors. Contrary to the majority of previous publications, as-fabricated devices demonstrated the superposition of generation-recombination (GR) and 1/f noise...
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Automatic Emotion Recognition in Children with Autism: A Systematic Literature Review
PublicationThe automatic emotion recognition domain brings new methods and technologies that might be used to enhance therapy of children with autism. The paper aims at the exploration of methods and tools used to recognize emotions in children. It presents a literature review study that was performed using a systematic approach and PRISMA methodology for reporting quantitative and qualitative results. Diverse observation channels and modalities...
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Predictions of cervical cancer identification by photonic method combined with machine learning
PublicationCervical cancer is one of the most commonly appearing cancers, which early diagnosis is of greatest importance. Unfortunately, many diagnoses are based on subjective opinions of doctors—to date, there is no general measurement method with a calibrated standard. The problem can be solved with the measurement system being a fusion of an optoelectronic sensor and machine learning algorithm to provide reliable assistance for doctors...
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Performance Analysis of the OpenCL Environment on Mobile Platforms
PublicationToday’s smartphones have more and more features that so far were only assigned to personal computers. Every year these devices are composed of better and more efficient components. Everything indicates that modern smartphones are replacing ordinary computers in various activities. High computing power is required for tasks such as image processing, speech recognition and object detection. This paper analyses the performance of...
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Soft Sensor Application in Identification of the Activated Sludge Bulking Considering the Technological and Economical Aspects of Smart Systems Functioning
PublicationThe paper presented the methodology for the construction of a soft sensor used for activated sludge bulking identification. Devising such solutions fits within the current trends and development of a smart system and infrastructure within smart cities. In order to optimize the selection of the data-mining method depending on the data collected within a wastewater treatment plant (WWTP), a number of methods were considered, including:...
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A comparative analysis of the effectiveness of corporate bankruptcy prediction models based on financial ratios: Evidence from Colombia, 2008 to 2015
PublicationLogit and discriminant analyses have been used for corporate bankruptcy prediction in several studies since the last century. In recent years there have been dozens of studies comparing the several models available, including the ones mentioned above and also probit, artificial neural networks, support vector machines, among others. For the first time for Colombia, this paper presents a comparative analysis of the effectiveness...
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Rapid Surrogate-Aided Multi-Criterial Optimization of Compact Microwave Passives Employing Machine Learning and ANNs
PublicationThis article introduces an innovative method for achieving low-cost and reliable multi-objective optimization (MO) of microwave passive circuits. The technique capitalizes on the attributes of surrogate models, specifically artificial neural networks (ANNs), and multi-resolution electromagnetic (EM) analysis. We integrate the search process into a machine learning (ML) framework, where each iteration produces multiple infill points...
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Structure-property relationships in peroxide-assisted blends of poly(ε-caprolactone) and poly(3-hydroxybutyrate)
PublicationPoly(ε-caprolactone) and poly(3-hydroxybutyrate) (PCL/PHB) blends in two weight ratios (75/25 and 50/50) were reactively compatibilized in the presence of di-(2-tert-butyl-peroxyisopropyl)-benzene and dicumyl peroxide as free radical initiators. Rheological, mechanical, thermal properties and morphological features, as well as the chemical structure of PCL/PHB blends were investigated. It was found that regardless of PCL/PHB blend...
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Single-phase product obtained via crude glycerine depolymerisation of polyurethane elastomer: structure characterisation and rheological behaviour
PublicationPolyurethane recycling is a topic of growing interest due to the increasing amount of polyurethanewaste. The main purpose of polyurethane feedstock recycling is to recover the starting polyol, a valuable material. In thiswork, amethod of polyurethane thermo-chemical recycling, glycerolysisbymeansof crude glycerine, is proposed. Themaineffort is focusedonthe employment of crude glycerine without purification from biodiesel production...
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Diamine derivatives of dimerized fatty acids and bio-based polyether polyol as sustainable platforms for the synthesis of non-isocyanate polyurethanes
PublicationA series of environmentally friendly non-isocyanate polyurethanes (NIPUs) were successfully prepared via the polyaddition reaction of bio-based polyether polyol-based cyclic carbonate with diamine derivative of dimerized fatty acids. The syntheses of NIPUs were realized by the three-step method in the absence of toxic solvents and, importantly, the process of carbonation did not require the use of elevated pressure. The effect...
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Influence of S-Oxidation on Cytotoxic Activity of Oxathiole-Fused Chalcones
PublicationSynthesis, in vitro cytotoxic activity, and interaction with tubulin of oxidized, isomeric 1-(5-alkoxybenzo[d] [1,3]oxathiol-6-yl)-3-phenylprop-2-en-1-ones and 1-(6- alkoxybenzo[d][1,3]oxathiol-5-yl)-3-phenylprop-2-en-1- ones are described. Most of the compounds demonstrated cytotoxic activity at submicromolar concentrations. It was found that oxidation of sulfur atom of the oxathiole-fused chalcones strongly influenced activity...
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Combining Road Network Data from OpenStreetMap with an Authoritative Database
PublicationComputer modeling of road networks requires detailed and up-to-date dataset. This paper proposes a method of combining authoritative databases with OpenStreetMap (OSM) system. The complete route is established by finding paths in the graph constructed from partial data obtained from OSM. In order to correlate data from both sources, a method of coordinate conversion is proposed. The algorithm queries road data from OSM and provides...
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Predicting Ice Phenomena in a River Using the Artificial Neural Network and Extreme Gradient Boosting
PublicationForecasting ice phenomena in river systems is of great importance because these phenomena are a fundamental part of the hydrological regime. Due to the stochasticity of ice phenomena, their prediction is a difficult process, especially when data sets are sparse or incomplete. In this study, two machine learning models—Multilayer Perceptron Neural Network (MLPNN) and Extreme Gradient Boosting (XGBoost)—were developed to predict...
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A new multi-process collaborative architecture for time series classification
PublicationTime series classification (TSC) is the problem of categorizing time series data by using machine learning techniques. Its applications vary from cybersecurity and health care to remote sensing and human activity recognition. In this paper, we propose a novel multi-process collaborative architecture for TSC. The propositioned method amalgamates multi-head convolutional neural networks and capsule mechanism. In addition to the discovery...
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Data governance: Organizing data for trustworthy Artificial Intelligence
PublicationThe rise of Big, Open and Linked Data (BOLD) enables Big Data Algorithmic Systems (BDAS) which are often based on machine learning, neural networks and other forms of Artificial Intelligence (AI). As such systems are increasingly requested to make decisions that are consequential to individuals, communities and society at large, their failures cannot be tolerated, and they are subject to stringent regulatory and ethical requirements....
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Computed aided system for separation and classification of the abnormal erythrocytes in human blood
PublicationThe human peripheral blood consists of cells (red cells, white cells, and platelets) suspended in plasma. In the following research the team assessed an influence of nanodiamond particles on blood elements over various periods of time. The material used in the study consisted of samples taken from ten healthy humans of various age, different blood types and both sexes. The markings were leaded by adding to the blood unmodified...
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The Influence of Selecting Regions from Endoscopic Video Frames on The Efficiency of Large Bowel Disease Recognition Algorithms
PublicationThe article presents our research in the field of the automatic diagnosis of large intestine diseases on endoscopic video. It focuses on the methods of selecting regions of interest from endoscopic video frames for further analysis by specialized disease recognition algorithms. Four methods of selecting regions of interest have been discussed: a. trivial, b. with the deletion of characteristic, endoscope specific additions to the...
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Online sound restoration system for digital library applications
PublicationAudio signal processing algorithms were introduced to the new online non-commercial service for audio restoration intended to enhance the content of digitized audio repositories. Missing or distorted audio samples are predicted using neural networks and a specific implementation of the Jannsen interpolation method based on the autoregressive model (AR) combined with the iterative restoring of missing signal samples. Since the distortion...
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Prognozowanie wpływu drgań komunikacyjnych na budynki mieszkalne za pomocą sztucznych sieci neuronowych i maszyn wektorów wspierających
PublicationDrgania komunikacyjne mogą stanowić duże obciążenie eksploatacyjne budynku, powodując zarysowania i spękania tynków, odpadanie wypraw, zarysowania konstrukcji, pękanie elementów konstrukcji lub nawet zawalenie się budynku. Pomiary drgań na rzeczywistych konstrukcjach są pracochłonne i kosztowne, a co ważne nie w każdym przypadku są one uzasadnione. Celem pracy jest analiza autorskiego algorytmu, dzięki któremu z dużym prawdopodobieństwem...
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Diagnostyka łożysk silnika indukcyjnego na podstawie prądu zasilającego przy użyciu sztucznych sieci neuronowych
PublicationW artykule zawarto wyniki badań dotyczące diagnostyki łożysk silnika indukcyjnego na podstawie pomiarów prądu zasilającego z wyko-rzystaniem sztucznych sieci neuronowych. Zaprezentowano wyniki uczenia sieci oraz rezultaty testów przeprowadzonych na danych spoza zbioru uczącego. Badania wykonane zostały na obiektach z celowo wprowadzonymi uszkodzeniami łożysk. Przedstawiona nowa koncepcja zakłada użycie zestawu sieci neuronowych...
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Novel chalcone-derived pyrazoles as potential therapeutic agents for the treatment of non-small cell lung cancer
PublicationLung cancer is considered to account for approximately one-fifth of all malignant tumor-related deaths worldwide and is therefore one of the most lethal malignancies. Pyrazole scaffold possesses a wide range of biological and pharmacological activities, which play important roles in medicinal chemistry. The present study reports the synthesis and in vitro biological characterization of nine pyrazoles derived from chalcones as potential...
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Intramolecular Proton Transfer in the Radical Anion of Cytidine Monophosphate Sheds Light on the Sensitivities of Dry vs Wet DNA to Electron Attachment-Induced Damage
PublicationSingle-strand breaks (SSBs) induced via electron attachment were previously observed in dry DNA under ultrahigh vacuum (UHV), while hydrated electrons were found not able to induce this DNA damage in an aqueous solution. To explain these findings, crossed electron-molecular beam (CEMB) and anion photoelectron spectroscopy (aPES) experiments coupled to density functional theory (DFT) modeling were used to demonstrate the fundamental...
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Interaction of 4-nitrothiophenol with low energy electrons: Implications for plasmon mediated reactions
PublicationThe reduction of 4-nitrothiophenol (NTP) to 4-4′-dimercaptoazobenzene (DMAB) on laser illuminated noble metal nanoparticles is one of the most widely studied plasmon mediated reactions. The reaction is most likely triggered by a transfer of low energy electrons from the nanoparticle to the adsorbed molecules. Besides the formation of DMAB, dissociative side reactions of NTP have also been observed. Here, we present a crossed electron-molecular...
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Cooperativity of Halogen- and Chalcogen-Bonding Interactions in the Self-Assembly of 4‑Iodoethynyl- and 4,7-Bis(iodoethynyl)benzo-2,1,3-chalcogenadiazoles: Crystal Structures, Hirshfeld Surface Analyses, and Crystal Lattice Energy Calculations
PublicationSeveral new 4-iodoethynyl- and 4,7-bis- (iodoethynyl)benzo-2,1,3-chalcogenadiazoles were prepared, and a comprehensive analysis of the most prominent secondary bonding interactions responsible for the crystal self-assembly was performed using X-ray diffraction. The presence of both the iodoethynyl and chalcogenadiazole moieties allows an evaluation of the preference of these molecules to aggregate through either chalcogen- or halogen-bonding...