Search results for: TIME-DOMAIN
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Karaś P., Kochanowicz K., Pitek M., Domański P., Obuchowski I., Tomiczek B., Liberek K.: Evolution towards simplicity in bacterial small heat shock protein system// eLife -, (2023), s.1-21
PublicationEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either...
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Functional safety and reliability analysis methodoloogy for hazardous industrial plants
PublicationThis monograph is devoted to current problems and methods of the functional safety and reliability analyses of the programmable control and protection systems for industrial hazardous plants. The results of these analyses are useful in the process of safety management in life cycle, for effective reducing relevant risks at the design stage, and then controlling these risks during the operation of given installation. The methodology...
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Novel single-stranded DNA-binding proteins from extreme psychrophilic bacterium Psychromonas ingrahamii 37
PublicationWe report the identification and characterization of the single-stranded DNA binding protein (SSB) from extreme psychrophilic bacterium Psychromonas ingrahamii 37 (PinSSB) that grows expotentially at -12°C and may well grow at even lower temperatures. PinSSB is one of the largest known bacterial SSB protein consisting 222 amino acid residues with a calculated molecular mass of 25.1 kDa. The analysis by gel filtration chromatography...
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Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana
PublicationBACKGROUND: In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods.RESULTS: We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino...
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Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli
PublicationDr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond...
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Automated Reasoning Based User Interface
PublicationMotivation: The ability to directly trace how requirements are implemented in a software system is crucial in domains that require a high level of trust (e.g. medicine, law, crisis management). This paper describes an approach that allows a high level of traceability to be achieved with model-driven engineering supported by automated reasoning. The paper gives an introduction to the novel, automated user interface synthesis in...
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Iron–Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein–Protein Interaction
PublicationBiogenesis of iron–sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1,...
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Computationally efficient two-objective optimization of compact microwave couplers through corrected domain patching
PublicationFinding an acceptable compromise between various objectives is a necessity in the design of contemporary microwave components and circuits. A primary reason is that most objectives are at least partially conflicting. For compact microwave structures, the design trade-offs are normally related to the circuit size and its electrical performance. In order to obtain comprehensive information about the best possible trade-offs, multi-objective...
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
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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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OrphaGPT: An Adapted Large Language Model for Orphan Diseases Classification
PublicationOrphan diseases (OD) represent a category of rare conditions that affect only a relatively small number of individuals. These conditions are often neglected in research due to the challenges posed by their scarcity, making medical advancements difficult. Then, the ever-evolving medical research and diagnosis landscape calls for more attention and innovative approaches to address the complex challenges of rare diseases and OD. Pre-trained...
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On Computationally-Efficient Reference Design Acquisition for Reduced-Cost Constrained Modeling and Re-Design of Compact Microwave Passives
PublicationFull-wave electromagnetic (EM) analysis has been playing a major role in the design of microwave components for the last few decades. In particular, EM tools allow for accurate evaluation of electrical performance of miniaturized structures where strong cross-coupling effects cannot be adequately quantified using equivalent network models. However, EM-based design procedures (parametric optimization, statistical analysis) generate...
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Modeling and simulation of blood flow under the influence of radioactive materials having slip with MHD and nonlinear mixed convection
PublicationRadioactive materials are widely in industry, nuclear plants and medical treatments. Scientists and workers in these fields are mostly exposed to such materials, and adverse effects on blood and temperature profiles are observed. In this regard, objective of the current study is to model and simulate blood based nanofluid with three very important radioactive materials, named as Uranium dioxide (UO2), Thorium dioxide (ThO2) and...
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Establishing the allosteric mechanism in CRISPR‐Cas9
PublicationAllostery 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...
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Evolution towards simplicity in bacterial small heat shock protein system
PublicationEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either two...
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Design-Oriented Two-Stage Surrogate Modeling of Miniaturized Microstrip Circuits with Dimensionality Reduction
PublicationContemporary microwave design heavily relies on full-wave electromagnetic (EM) simulation tools. This is especially the case for miniaturized devices where EM cross-coupling effects cannot be adequately accounted for using equivalent network models. Unfortunately, EM analysis incurs considerable computational expenses, which becomes a bottleneck whenever multiple evaluations are required. Common simulation-based design tasks include...
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Crystalline Silicon (c-Si)-Based Tunnel Oxide Passivated Contact (TOPCon) Solar Cells: A Review
PublicationContact selectivity is a key parameter for enhancing and improving the power conversion efficiency (PCE) of crystalline silicon (c-Si)-based solar cells. Carrier selective contacts (CSC) are the key technology which has the potential to achieve a higher PCE for c-Si-based solar cells closer to their theoretical efficiency limit. A recent and state-of-the-art approach in this domain is the tunnel oxide passivated contact (TOPCon)...
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Scaling scrum with a customized nexus framework: A report from a joint industry‐academia research project
Publicationespite a wide range of scaling frameworks available, large-scale agile transformations are not straightforward undertakings. Few organizations have structures in place that fit the predefined workflows – while once one applies an off-the-shelf framework outside of its prescribed process, guidance quickly runs out. In this paper, we demonstrate how to instantiate a method configuration process using a lightweight experimental approach...
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Robot-Based Intervention for Children With Autism Spectrum Disorder: A Systematic Literature Review
PublicationChildren with autism spectrum disorder (ASD) have deficits in the socio-communicative domain and frequently face severe difficulties in the recognition and expression of emotions. Existing literature suggested that children with ASD benefit from robot-based interventions. However, studies varied considerably in participant characteristics, applied robots, and trained skills. Here, we reviewed robot-based interventions targeting...
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Review of Selected Methods for Prediction of Added Resistance in Following Waves
PublicationThe added resistance in waves is a mean value of non-linear, second order reaction of a ship to incoming waves. In the beginning of the 20th century, the experimental methods for investigation of ship hydrodynamics at model scale were developed. They allowed the evaluation of added resistance by measurements in irregular waves (directly) or by measurements in regular waves (in-direct method). The main goal was to find more precise...
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A Parallel Corpus-Based Approach to the Crime Event Extraction for Low-Resource Languages
PublicationThese days, a lot of crime-related events take place all over the world. Most of them are reported in news portals and social media. Crime-related event extraction from the published texts can allow monitoring, analysis, and comparison of police or criminal activities in different countries or regions. Existing approaches to event extraction mainly suggest processing texts in English, French, Chinese, and some other resource-rich...
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Implementation of Hermite-Ritz method and Navier’s Technique for Vibration of Functionally Graded Porous Nanobeam Embedded in Winkler-Pasternak Elastic Foundation Using bi-Helmholtz type of nonlocal elasticity
PublicationPresent study is devoted to investigating the vibration characteristics of Functionally Graded (FG) porous nanobeam embedded in an elastic substrate of Winkler-Pasternak type. Classical beam theory (CBT) or Euler-Bernoulli beam theory (EBT) has been incorporated to address the displacement of the FG nanobeam. Bi-Helmholtz type of nonlocal elasticity is being used to capture the small scale effect of the FG nanobeam. Further, the...
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Improved Modeling of Microwave Structures Using Performance-Driven Fully-Connected Regression Surrogate
PublicationFast replacement models (or surrogates) have been widely applied in the recent years to accelerate simulation-driven design procedures in microwave engineering. The fundamental reason is a considerable—and often prohibitive—CPU cost of massive full-wave electromagnetic (EM) analyses related to solving common tasks such as parametric optimization or uncertainty quantification. The most popular class of surrogates are data-driven...
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Assembly of Lipopolysaccharide in Escherichia coli Requires the Essential LapB Heat Shock Protein
PublicationHere, we describe two new heat shock proteins involved in the assembly of LPS in Escherichia coli, LapA and LapB (lipopolysaccharide assembly protein A and B). lapB mutants were identified based on an increased envelope stress response. Envelope stress responsive pathways control key steps in LPS biogenesis and respond to defects in the LPS assembly. Accordingly, the LPS content in ΔlapB or Δ(lapA lapB) mutants was elevated, with...
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Audio content analysis in the urban area telemonitoring system
PublicationArtykuł przedstawia możliwości rozwinięcie monitoringu miejskiego o automatyczną analizę dźwięku. Przedstawiono metody parametryzacji dźwięku, które możliwe są do zastosowania w takim systemie oraz omówiono aspekty techniczne implementacji. W kolejnej części przedstawiono system decyzyjny oparty na drzewach zastosowany w systemie. System ten rozpoznaje dźwięki niebezpieczne (strzał, rozbita szyba, krzyk) wśród dźwięków zarejestrowanych...
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How to Design Affect-aware Educational Systems – the AFFINT Process Approach
PublicationComputer systems, that support learning processes, can adapt to the needs and states of a learner. The adaptation might directly address the knowledge deficits and most tutoring systems apply an adaptable learning path of that kind. Apart from a preliminary knowledge state, there are more factors, that influence education effectiveness and among those there are fluctuating emotional states. The tutoring systems may recognize or...
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Long range molecular dynamics study of regulation of eukaryotic glucosamine-6-phosphate synthase activity by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase catalyses the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5' diphospho N-acetyl-D-glucosamine (UDPGlcNAc), is an essential substrate for assembly of bacterialand fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which makes it a potential target...
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FLOOD MANAGEMENT IN URBAN BASINS OF THE CITY OF GDAŃSK
PublicationOver the last years, the City of Gdańsk suffers twice from flash floods. Both events were caused by intense storms which produced significant surface runoff and caused inundation private and cities properties. The first case of July 2001 flood [3], [9] was the turning point for the city authorities, who decide to look close on the flood management in small urban catchments. The aim of research projects was to establish technical...
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On a 3D material modelling of smart nanocomposite structures
PublicationSmart composites (SCs) are utilized in electro-mechanical systems such as actuators and energy harvesters. Typically, thin-walled components such as beams, plates, and shells are employed as structural elements to achieve the mechanical behavior desired in these composites. SCs exhibit various advanced properties, ranging from lower order phenomena like piezoelectricity and piezomagneticity, to higher order effects including flexoelectricity...
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S09-4 The development of the Physical Activity Environment Policy Index (PA-EPI): a tool for monitoring and benchmarking government policies and actions to improve physical activity
PublicationBackground Insufficient physical activity (PA) is a global issue for health. A multifaceted response, including government action, is essential to improve population levels of PA. The purpose of this study was to develop the ‘Physical Activity Environment Policy Index’ (PA-EPI) monitoring framework to assess government policies and actions for creating a healthy PA environment. Methods An iterative process was undertaken. This...
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The Physical Activity Environment Policy Index for monitoring government policies and actions to improve physical activity
PublicationBackground A multifaceted response, including government action, is essential to improve population levels of physical activity (PA). This article describes the development process of the ‘Physical Activity Environment Policy Index’ (PA-EPI) monitoring framework, a tool to assess government policies and actions for creating a healthy PA environment. Methods An iterative process was undertaken. This involved a review of policy...
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Globalized Simulation-Driven Miniaturization of Microwave Circuits by Means of Dimensionality-Reduced Constrained Surrogates
PublicationSmall size has become a crucial prerequisite in the design of modern microwave components. Miniaturized devices are essential for a number of application areas, including wireless communications, 5G/6G technology, wearable devices, or the internet of things. Notwithstanding, size reduction generally degrades the electrical performance of microwave systems. Therefore, trade-off solutions have to be sought that represent acceptable...
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Smart Knowledge Engineering for Cognitive Systems: A Brief Overview
PublicationCognition in computer sciences refers to the ability of a system to learn at scale, reason with purpose, and naturally interact with humans and other smart systems, such as humans do. To enhance intelligence, as well as to introduce cognitive functions into machines, recent studies have brought humans into the loop, turning the system into a human–AI hybrid. To effectively integrate and manipulate hybrid knowledge, suitable technologies...
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Low-cost performance-driven modelling of compact microwave components with two-layer surrogates and gradient kriging
PublicationUtilization of electromagnetic (EM) simulation tools has become indispensable for reliable evaluation of microwave components. As the cost of an individual analysis may already be considerable, the computational overhead associated with EM-driven tasks that require massive simulations (e.g., optimization) may turn prohibitive. One of mitigation methods is the employment of equivalent network models. Yet, they are incapable of accounting...
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Low-cost multi-criterial design optimization of compact microwave passives using constrained surrogates and dimensionality reduction
PublicationDesign of contemporary microwave circuits is a challenging task. Typically, it has to take into account several performance requirements and constraints. The design objectives are often conflicting and their simultaneous improvement may not be possible; instead, compromise solutions are to be sought. Representative examples are miniaturized microwave passives where reduction of the circuit size has a detrimental effect on its electrical...
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Time-domine Dipole Fields in acoustic and Elektromagnetics
PublicationThe ultrawideband (UWB) radio technique presents a challenge not just for technology. The UWB carrier-free pulses act at a close distance, their electromagnetic fields being very different from classic monochromatic plane wave. The author proposes to adapt a time-domian approach to analysis of broadband spherical fields, both acoustic and electromagnetic, in fundamental cases of quasi-point physical sources.
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Glucosamine-6-phosphate synthase with an oligoHis insert
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase known also as L-Glutamine: D-fructose-6-phosphate aminotransferase (EC 2.6.1.16), catalyzes the first committed step in the amino sugar biosynthetic pathway in prokaryotic and eukaryotic organisms. The final product of this pathway is an activated precursor of numerous macromolecules containing amino sugars, including chitin and mannproteins in fungi, peptydoglican and lipopolysaccharides...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria Desulfotalea psychrophila, Flavobacterium psychrophilum, Psychrobacter arcticus, Psychrobacter cryohalolentis, Psychromonas ingrahamii, Psychroflexus torquis, and Photobacterium profundum
PublicationBackground: Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombination and repair in Bacteria, Archaea and Eukarya. In recent years, there has been an increasing interest in SSBs, since they find numerous applications in diverse molecular biology and analytical methods. Results: We report the characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria Desulfotalea...
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Desensitization of glucosamine-6-phosphate synthase to inhibition by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase, known also as L-Glutamine: D-fructose-6-phosphate amidotransferase, catalyzes the first committed step in the pathway leading to the ultimate formation of UDP-GlcNAc. The final product of this pathway is an activated precursor of numerous macromolecules containing amino sugars, including chitin and mannproteins in fungi, peptidoglycan and lipopolysaccharides in bacteria, and glycoproteins...
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Knowledge engineer – more than only technical position. The concept of knowledge engineering education at the Faculty of Management and Economics
PublicationOrganizational learning means an effective knowledge management. Management is nothing more than the constant decision-making. Therefore organizational learning must be seen through the prism of decisions taken at all levels. Unfortunately decisions are never taken within comfortable conditions. Decision maker suffers from a lack of any support. There is often a problem with human resources having right skills, sometimes they do...
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Recent advances in high-frequency modeling by means of domain confinement and nested kriging
PublicationDevelopment of modern high-frequency components and circuits is heavily based on full-wave electromagnetic (EM) simulation tools. Some phenomena, although important from the point of view of the system performance, e.g., EM cross-coupling effects, feed radiation in antenna arrays, substrate anisotropy, cannot be adequately accounted for using simpler means such as equivalent network representations. Consequently, the involvement...
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Recent Advances in Accelerated Multi-Objective Design of High-Frequency Structures using Knowledge-Based Constrained Modeling Approach
PublicationDesign automation, including reliable optimization of engineering systems, is of paramount importance for both academia and industry. This includes the design of high-frequency structures (antennas, microwave circuits, integrated photonic components), where the appropriate adjustment of geometry and material parameters is crucial to meet stringent performance requirements dictated by practical applications. Realistic design has...
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Muramyl dipeptide-based analogs as potential anticancer compounds: Strategies to improve selectivity, biocompatibility, and efficiency
PublicationAccording to the WHO, cancer is the second leading cause of death in the world. This is an important global problem and a major challenge for researchers who have been trying to find an effective anticancer therapy. A large number of newly discovered compounds do not exert selective cytotoxic activity against tumorigenic cells and have too many side effects. Therefore, research on muramyl dipeptide (MDP) analogs has attracted interest...
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Cost-Efficient Two-Level Modeling of Microwave Passives Using Feature-Based Surrogates and Domain Confinement
PublicationA variety of surrogate modelling techniques has been utilized in high-frequency design over the last two decades. Yet, the curse of dimensionality still poses a serious challenge in setting up re-liable design-ready surrogates of modern microwave components. The difficulty of the model-ing task is only aggravated by nonlinearity of circuit responses. Consequently, constructing a practically usable surrogate model, valid across...
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Verification of the Parameterization Methods in the Context of Automatic Recognition of Sounds Related to Danger
PublicationW artykule opisano aplikację, która automatycznie wykrywa zdarzenia dźwiękowe takie jak: rozbita szyba, wystrzał, wybuch i krzyk. Opisany system składa się z bloku parametryzacji i klasyfikatora. W artykule dokonano porównania parametrów dedykowanych dla tego zastosowania oraz standardowych deskryptorów MPEG-7. Porównano też dwa klasyfikatory: Jeden oparty o Percetron (sieci neuronowe) i drugi oparty o Maszynę wektorów wspierających....
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Fusion of Taq DNA polymerase with single-stranded DNA binding-like protein of Nanoarchaeum equitans—Expression and characterization
PublicationDNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the...
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Bismuth-based nanomaterials-assisted photocatalytic water splitting for sustainable hydrogen production
PublicationThe rapidly increase in the world's population has resulted in a corresponding increase in the energy demand. This demand is largely being met by fossil fuels for power generation, industrial fuel and transportation. However, due to the limited availability of fossil fuels and their negative effects on the environment. The use of fossil fuels results in by-products such as carbon, nitrogen and sulfur oxides which have negative...
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Bismuth-based nanomaterials-assisted photocatalytic water splitting for sustainable hydrogen production
PublicationThe rapidly increase in the world's population has resulted in a corresponding increase in the energy demand. This demand is largely being met by fossil fuels for power generation, industrial fuel and transportation. However, due to the limited availability of fossil fuels and their negative effects on the environment. The use of fossil fuels results in by-products such as carbon, nitrogen and sulfur oxides which have negative...
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublicationNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublicationSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNA insequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination. Although there are differences in amino...