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Search results for: lyme disease, borrelia burgdorferi sensu lato, epitope mapping, serodiagnosis, chimeric proteins
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Comprehensive Review of Fluorescence Applications in Gynecology
PublicationSince the introduction of indocyanine green (ICG) as a fluorophore in near-infrared imaging, fluorescence visualization has become an essential tool in many fields of surgery. In the field of gynecology, recent new applications have been proposed and found their place in clinical practice. Different applications in gynecology were investigated, subcategorized, and overviewed concerning surgical applications and available dyes....
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Numerical Simulation of Catastrophic Flood: the Case Study of Hypothetical Failure of the Bielkowo Hydro–Power Plant Reservoir
PublicationThe numerical modeling of flood wave propagation following the hypo-thetical breaks of the embankments of the Bielkowo hydro–power plant storage reservoir (Kolbudy II Reservoir) on the Radunia River in Poland have been presented. The results of computations were used to estimate the parameters of the flood waves, which are indispensable for the flood zone determination and mapping and then for the flood risk analysis. When estimating...
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The Principles of Model Building Concepts Which Are Applied to the Design Patterns for Smart Cities
PublicationThe involvement of citizens into decision-making processes is one of the main features of smart cities. Such commitment is reflected in the form of requirements towards the city, and the benefits which are expected from the city. Requirements and benefits are thus the primary language of communication between decision-makers and urban residents. To develop such a language, it becomes necessary to develop design patterns for Smart...
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublicationPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
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By-Products from Food Industry as a Promising Alternative for the Conventional Fillers for Wood–Polymer Composites
PublicationThe present paper describes the application of two types of food-industry by-products, brewers’ spent grain (BSG), and coffee silverskin (ŁK) as promising alternatives for the conventional beech wood flour (WF) for wood–polymer composites. The main goal was to investigate the impact of partial and complete WF substitution by BSG and ŁK on the processing, structure, physicochemical, mechanical, and thermal properties of resulting...
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Synthesis of amides under microwave irradiation
PublicationAmides belong to the most important carboxylic acid derivatives. They are constituents of natural compounds like peptides and proteins. They found applications in many branches of science and industry, especially in pharmaceutical and polymer science. Conventional procedures for amide preparation involve reaction between amine and carboxylic acid or their more active derivatives such as acid chlorides, acid anhydrides or esters....
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Biofilm formation and its regulation in Staphylococcus aureus
PublicationInfections caused by the major human and animal pathogen, Staphylococcus aureus are becoming an important problem due to its emerging resistance mechanisms and variety of virulence factors. Biofilm formation is considered to be one of the most important factor attributed to high pathogenicity of S. aureus. Described in the literature methods used in identification of biofilm forming abilities of bacteria consist of phenotypic and...
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublicationGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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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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Cancer immune escape: the role of antigen presentation machinery
PublicationThe mechanisms of antigen processing and presentation play a crucial role in the recognition and targeting of cancer cells by the immune system. Cancer cells can evade the immune system by downregulating or losing the expression of the proteins recognized by the immune cells as antigens, creating an immunosuppressive microenvironment, and altering their ability to process and present antigens. This review focuses on the mechanisms...
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Structural changes of a simple peptide—Trpzip-1—in aqueous solutions and the corresponding hydration phenomena under the influence of temperature
PublicationTrpzip-1, a simple β-hairpin, is a rare example of peptide with stable secondary structure and can be a convenient model to study temperature-related processes that potential prion or amyloid proteins undergo. Although its sequence is simple, the exact processes which the peptide undergoes in aqueous solutions are quite complex and not well understood. The selection of well-established experimental (DSC, FTIR) and theoretical methods...
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9,10-Dioxoanthracenyldithiocarbamates effectively inhibit the proliferation of non-small cell lung cancer by targeting multiple protein tyrosine kinases
PublicationAnthraquinones have attracted considerable interest in the realm of cancer treatment owing to their potent anticancer properties. This study evaluates the potential of a series of new anthraquinone derivatives as anticancer agents for non-small-cell lung cancer (NSCLC). The compounds were subjected to a range of tests to assess their cytotoxic and apoptotic properties, ability to inhibit colony formation, pro-DNA damage functions,...
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Bioactive compounds and the antioxidant capacity in new kiwi fruit cultivars
PublicationThe aim of this investigation was to find the best among seven different kiwi fruit cultivars (‘Hayward’, ‘Daheung’, ‘Haenam’, ‘Bidan’, ‘Hort16A’, ‘Hwamei’ and ‘SKK12’) for human consumption and to classify them as groups. Therefore, the contents of bioactive compounds and the level of antioxidant capacities of these cultivars were determined in four different extracts and compared. It was found that the contents of the bioactive...
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The Energy of Finance in Refining of Medical Surge Capacity
PublicationThe availability of resources and their concentration in the place of greatest need, will not allow us to successfully overcome a medical surge without the energy required to activate these resources and activities, and increase their quantities if necessary, that is why the staff and management of healthcare institutions are forced to making ethical crisis decisions about who wins and who loses. This study highlights the versatility...
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Consequences of lysine auxotrophy for Candida albicans adherence and biofilm formation
PublicationA number of factors are known to be involved in Candida albicans virulence, although biofilm development on the surfaces of indwelling medical devices is considered to promote superficial or systemic disease. Based on previously reported up-regulation of saccharopine and acetyllysine in biofilm cells and activation of the lysine biosynthesis/degradation pathway, we investigated...
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Evaluation of Medical Staff Satisfaction for Workplace Architecture in Temporary COVID-19 Hospital: A Case Study in Gdańsk, Poland
PublicationThis article analyses the architecture that was used in the temporary AmberExpo hospital in Gdańsk, Poland which was installed during the COVID-19 pandemic. The construction of this type of facility is often based on experimental approaches, aimed at caring for patients suffering from an infectious disease in emergency conditions. In order to assess the level of employee satisfaction with the architectural and technical elements...
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Oxylipin profiling for clinical research: Current status and future perspectives
PublicationOxylipins are potent lipid mediators with increasing interest in clinical research. They are usually measured in systemic circulation and can provide a wealth of information regarding key biological processes such as inflammation, vascular tone, or blood coagulation. Although procedures still require harmonization to generate comparable oxylipin datasets, performing comprehensive profiling of circulating oxylipins in large studies...
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Chicken feather keratin as a source of bioactive peptides useful in prevention of metabolic disorders – in silico and in vitro hydrolysis
PublicationProtein derived bioactive peptides not only serve as nutrients but can also exert drug-like activity, e.g. antidiabetic, antihypertensive, or antimicrobial, to name a few. Most biopeptides have beneficial effects on health that make them attractive for nutraceutical applications. The majority of bioactive peptides have been obtained from food proteins, but protein-rich by-products generated by agriculture...
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Method-Dependent Epidemiological Cutoff Values for Detection of Triazole Resistance in Candida and Aspergillus Species for the Sensititre YeastOne Colorimetric Broth and Etest Agar Diffusion Methods
PublicationAlthough the Sensititre Yeast-One (SYO) and Etest methods are widely utilized, interpretive criteria are not available for triazole susceptibility testing of Candida or Aspergillus species. We collected fluconazole, itraconazole, posaconazole, and voriconazole SYO and Etest MICs from 39 laboratories representing all continents for (method/agent-dependent) 11,171 Candida albicans, 215 C. dubliniensis, 4,418 C. glabrata species complex,...
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Daily diet containing canned products significantly increases serum concentrations of endocrine disruptor bisphenol A in young women
PublicationNowadays, exposure to environmental factors is considered to be one of the possible causes of several lifestyle diseases, such as obesity, type 2 diabetes, cardiovascular disease, and cancer. Particularly noteworthy are endocrine‑disrupting chemicals (EDCs), which affect the metabolism of hormones and interact with their receptors, thus exerting adverse health effects. One of the most ubiquitous EDC in daily life is bisphenol A...
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INFLUENCE OF CERAMIC COATING ON MECHANICAL PROPERTIES OF STAINLESS STEEL
PublicationCrystal structure and phase composition of stainless steel substrates (AISI 304 type) was studied and it was found that they adopted the cubic symmetry. The calculated elementary cell parameter for the mayor Fe-Ni phase (weight fraction 99%) was a = 3.593 Å, whereas the mean grain size was = 2932 Å. Morphology of the stainless steel substrate surface was studied with profilometry. Mechanical properties of the stainless steel...
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A study of the kinetics of bismuth telluride synthesis by an oxide reduction method
PublicationThe kinetics of a reduction of bismuth and tellurium oxides in a hydrogen atmosphere, leading to the formation of thermoelectric bismuth telluride is investigated. The evaluation of the reaction kinetics was based on a thermogravimetric analysis performed in non-isothermal conditions. A non-parametric analysis method and the Friedman method were used for the evaluation of the data. Additionally, for a better understanding of the...
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Rapid Microwave Design Optimization in Frequency Domain Using Adaptive Response Scaling
PublicationIn this paper, a novel methodology for cost-efficient microwave design optimization in the frequency domain is proposed. Our technique, referred to as adaptive response scaling (ARS), has been developed for constructing a fast replacement model (surrogate) of the high-fidelity electromagnetic-simulated model of the microwave structure under design using its equivalent circuit (low-fidelity model). The basic principle of ARS is...
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KernelHive: a new workflow-based framework for multilevel high performance computing using clusters and workstations with CPUs and GPUs
PublicationThe paper presents a new open-source framework called KernelHive for multilevel parallelization of computations among various clusters, cluster nodes, and finally, among both CPUs and GPUs for a particular application. An application is modeled as an acyclic directed graph with a possibility to run nodes in parallel and automatic expansion of nodes (called node unrolling) depending on the number of computation units available....
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Low-power microwave-induced fabrication of functionalised few-layer black phosphorus electrodes: A novel route towards Haemophilus Influenzae pathogen biosensing devices
PublicationIn this paper, various passivation schemes were applied at few-layer black phosphorus (FLBP) to achieve covalent functionalisation with 4-azidobenzoic acid, improving its electrochemical response intended for analytical and biosensing applications. The thermal and microwave assisted modification procedures in toluene and dime-thylformamide resulted in high reversibility of reactions on functionalised FLBP using a ferricyanide/ferrocya-nide...
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MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences
Publication—Machine Learning (ML) methods have been used with varying degrees of success on protein prediction tasks, with two inherent limitations. First, prediction performance often depends upon the features extracted from the proteins. Second, experimental data may be insufficient to construct reliable ML models. Here we introduce MP3vec, a transferable representation for protein sequences that is designed to be used specifically for sequence-to-sequence...
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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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Phosphorylation‐mediated regulation of heat shock response in Escherichia coli
PublicationEscherichia coli has two heat shock regulons under the transcriptional control of Esigma(32) and Esigma(E) RNA polymerases. These polymerases control the expression of genes, the products of which are needed for correct folding of proteins in the cytoplasm and the extracytoplasm respectively. In this study, we report that mutations in a tyrosine phosphatase-encoding gene led to decreased activity of these heat shock regulons. The...
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Design, synthesis, and biological evaluation of tetrahydroquinolinones and tetrahydroquinolines with anticancer activity
PublicationColorectal cancer (CRC) is the most commonly diagnosed cancer in Europe and the United States and the second leading cause of cancer related mortality. A therapeutic strategy used for the treatment of CRC involves targeting the intracellular levels of reactive oxygen species (ROS). In this study, we synthesized a series of novel tetrahydroquinolinones and assessed their ability to inhibit CRC growth and proliferation by evoking...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
PublicationThe structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA...
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In vitro antioxidative and binding properties of phenolics in traditional, citrus and exotic fruits
PublicationMany polyphenols bind proteins, therefore our research was focused on the potential of protein binding to polyphenols of investigated fruits and their health-related effects. The contents of polyphenols and related antioxidant activities of traditional, citrus and exotic fruits were compared. The presence of polyphenols (flavonoids and phenolic acids) in the investigated samples and their interaction with human serum albumin (HSA)...
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Cyanogenic Compounds and Estrogen Disruptors
PublicationBalanced diet consists largely of plants containing cyanogenic compounds in the form of the more common cyanogenic glycosides and sometimes lipids. Maize, wheat, rye, apples, barley, oats, sugar cane and yet many other plants consumed by humans contain cyanogenic compounds. However the risk of poisoning is negligible as it is very easy to remove the toxic HCN by grinding and drying in air or soaking in water and an additional...
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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Iranian future healthcare professionals’ knowledge and opinions about rare diseases: cross‑sectional study
PublicationBackground: Rare diseases are a new global health priority, requiring evidence-based estimates of the global prevalenceof diseases to inform public policymakers and provide a serious challenge to the healthcare system that must not be ignored. The purpose of this study is to investigate Iranian future healthcare professionals’ knowledge and opinions about rare diseases.Results: A total of 6838 students responded...
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Role of cholesterol in substrate recognition by -secretase
Publication-Secretase is an enzyme known to cleave multiple substrates within their transmembrane domains, with the amyloid precursor protein of Alzheimer’s Disease among the most prominent examples. The activity of -secretase strictly depends on the membrane cholesterol content, yet the mechanistic role of cholesterol in the substrate binding and cleavage remains unclear. In this work, we used all-atom molecular dynamics simulations to examine...
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Abilities, Motivations, and Opportunities of Furloughed Employees in the Context of Covid-19: Preliminary Evidence From the UK
PublicationThe Covid-19 global pandemic is a crisis like no other, forcing governments to implement prolonged national lockdowns in an effort to limit the spread of the disease. As organizations aim to adapt and remain operational, employers can suspend or reduce work activity for events related to Covid-19 and claim government support to subsidize employee wages. In this way, some employees are placed on furlough (i.e., temporary unemployment)...
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Magnetic nanocomposites for biomedical applications
PublicationTissue engineering and regenerative medicine have solved numerous problems related to the repair and regeneration of damaged organs and tissues arising from aging, illnesses, and injuries. Nanotechnology has further aided tissue regeneration science and has provided outstanding opportunities to help disease diagnosis as well as treat damaged tissues. Based on the most recent findings, magnetic nanostructures (MNSs), in particular,...
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In silico assessment and sonochemical synthesis of 2-alkynyl 3-chloropyrazines as prospective ligands for SARS-CoV-2
PublicationThe recent global pandemic caused by COVID-19 has triggered an intense effort worldwide towards the development of an effective cure for this disease. In our effort we have explored the 2-alkynyl substituted 3-chloropyrazine framework as a potential template for the design of molecules for this purpose. Our strategy was supported by the in silico studies of representative compounds to assess their binding affinities via docking...
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Możliwości zastosowań, potencjalne źródła oraz ewolucja technologiczna sposobu otrzymywania trehalozy ze szczególnym uwzględnieniem enzymu syntazy trehalozy [EC 5.4.99.16]
PublicationJedna z wiodących gałęzi współczesnej biotechnologii opiera się na produkcji białek – przede wszystkim enzymów. Są one powszechnie wykorzystywane: od przemysłu chemicznego poprzez przemysł spożywczy aż po medycynę i życie codzienne (czy ktoś wyobraża sobie w dzisiejszych czasach proszek do prania „bez enzymu”). Przed rozwojem nowoczesnych metod biologii molekularnej i inżynierii genetycznej pozyskiwano interesujące substancje z...
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Computationally Efficient Multi-Objective Optimization of and Experimental Validation of Yagi-Uda Antenna
PublicationIn this paper, computationally efficient multi-objective optimization of antenna structures is discussed. As a design case, we consider a multi-parameter planar Yagi-Uda antenna structure, featuring a driven element, three directors, and a feeding structure. Direct optimization of the high-fidelity electromagnetic (EM) antenna model is prohibitive in computational terms. Instead, our design methodology exploits response surface...
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Non-Destructive Testing of the Longest Span Soil-Steel Bridge in Europe—Field Measurements and FEM Calculations
PublicationThe article describes interdisciplinary and comprehensive non-destructive diagnostic tests of final bridge inspection and acceptance proposed for a soil-steel bridge made of corrugated sheets, being the European span length record holder (25.74 m). As an effect of an original concept a detailed and precise information about the structure short-term response was collected. Periodic diagnostics of bridge deformations was done one...
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Domain segmentation for low-cost surrogate-assisted multi-objective design optimisation of antennas
PublicationAbstract: Information regarding the best possible design trade-offs of an antenna structure can be obtained through multiobjective optimisation (MO). Unfortunately, MO is extremely challenging if full-wave electromagnetic (EM) simulation models are used for performance evaluation. Yet, for the majority of contemporary antennas, EM analysis is the only tool that ensures reliability. This study introduces a procedure for accelerated...
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Low-strain sensor based on the flexible boron-doped diamond-polymer structures
PublicationA free-standing high boron-doped diamond nanosheet (BDDNS) has been fabricated for the development of a flexible BDDNS strain senor. High boron-doped diamond was initially grown on a tantalum substrate in a microwave plasma-assisted chemical vapor deposition method, and was then transferred to a Kapton polymer substrate to fabricate the flexible BDDNS/Kapton device. Before performing the transfer process, the thin BDDNS’s morphology...
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Numerically Efficient Miniaturization-Oriented Optimization of an Ultra-Wideband Spline-Parameterized Antenna
PublicationDesign of ultra-wideband radiators for modern handheld applications is a challenging task that involves not only selection of an appropriate topology, but also its tuning oriented towards balancing the electrical performance and size. In this work, a low-cost design of a compact, broadband, spline-parameterized monopole antenna has been considered. The framework used for the structure design implements trust-region-based methods,...
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Volumetric incorporation of NV diamond emitters in nanostructured F2 glass magneto-optical fiber probes
PublicationIntegration of optically-active diamond particles with glass fibers is a powerful method of scaling diamond's magnetic sensing functionality. We propose a novel approach for the integration of diamond particles containing nitrogen-vacancy centers directly into the fiber core. The core is fabricated by stacking the preform from 790 soft glass canes, drawn from a single rod dip-coated with submicron diamond particles suspended in...
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How Can We Identify Electrophysiological iEEG Activities Associated with Cognitive Functions?
PublicationElectrophysiological activities of the brain are engaged in its various functions and give rise to a wide spectrum of low and high frequency oscillations in the intracranial EEG (iEEG) signals, commonly known as the brain waves. The iEEG spectral activities are distributed across networks of cortical and subcortical areas arranged into hierarchical processing streams. It remains a major challenge to identify these activities in...
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Using Isolation Forest and Alternative Data Products to Overcome Ground Truth Data Scarcity for Improved Deep Learning-based Agricultural Land Use Classification Models
PublicationHigh-quality labelled datasets represent a cornerstone in the development of deep learning models for land use classification. The high cost of data collection, the inherent errors introduced during data mapping efforts, the lack of local knowledge, and the spatial variability of the data hinder the development of accurate and spatially-transferable deep learning models in the context of agriculture. In this paper, we investigate...
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Reliable Microwave Modeling By Means of Variable-Fidelity Response Features
PublicationIn this work, methodologies for low-cost and reliable microwave modeling are presented using variable-fidelity response features. The two key components of our approach are: (i) a realization of the modeling process at the level of suitably selected feature points of the responses (e.g., S-parameters vs. frequency) of the structure at hand, and (ii) the exploitation of variable-fidelity EM simulation data, also for the response...
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Rapid Simulation-Driven Multiobjective Design Optimization of Decomposable Compact Microwave Passives
PublicationIn this paper, a methodology for fast multiobjective optimization of the miniaturized microwave passives has been presented. Our approach is applicable to circuits that can be decomposed into individual cells [e.g., compact microstrip resonant cells (CMRCs)]. The structures are individually modeled using their corresponding equivalent circuits and aligned with their accurate, EM simulated...