Search results for: site-directed mutagenesis
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Quantitative Risk Assessment in Construction Disputes Based on Machine Learning Tools
PublicationA high monetary value of the construction projects is one of the reasons of frequent disputes between a general contractor (GC) and a client. A construction site is a unique, one-time, and single-product factory with many parties involved and dependent on each other. The organizational dependencies and their complexity make any fault or mistake propagate and influence the final result (delays, cost overruns). The constant will...
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An Impact Analysis of Artificial Light at Night (ALAN) on Bats. A Case Study of the Historic Monument and Natura 2000 Wisłoujście Fortress in Gdansk, Poland
PublicationThe artificial light at night (ALAN) present in many cities and towns has a negative impact on numerous organisms that live alongside humans, including bats. Therefore, we investigated if the artificial illumination of the historic Wisłoujście Fortress in Gdańsk, Poland (part of the Natura 2000 network), during nighttime events, which included an outdoor electronic dance music (EDM) festival, might be responsible for increased...
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Incremental dynamic analysis and fragility assessment of buildings founded on different soil types experiencing structural pounding during earthquakes
PublicationThe effect of the soil type on buildings experiencing pounding during earthquakes is investigated in this study using the incremental dynamic analysis and fragility assessment methods. Three 3-D structures with different number of storeys (4, 6 and 8) were considered in this study. Three pounding scenarios between these three buildings were taken into account, i.e. pounding between 4-storey and 6-storey buildings, between 4-storey...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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Structure and water uptake in BaLnCo2O6−δ (Ln =La, Pr, Nd, Sm, Gd, Tb and Dy)
PublicationThe structure of BaLnCo2O6-δ (Ln =La, Pr, Nd, Sm, Gd, Tb and Dy) was studied by the means of synchrotron radiation powder X-ray diffraction, neutron powder diffraction and Transmission Electron Microscopy (TEM), while water uptake properties were analysed with the use of thermogravimetry (TG) and water adsorption isotherms. The structure refinement revealed that the dominant phase in all compositions was orthorhombic with an ordering...
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The Housing Pattern and Entrepreneurship in Polish Suburban Landscape
PublicationAbstract. Housing stimulates the development of SMEs (small and medium enterprises) in the suburbs. The multidisciplinary research in fields of urban planning and economics, carried out by the Authors, confirms this trend. The purpose of this paper is to present the multidisciplinary results of the research on the determinants of SME localization in the suburban areas of Gdansk, Gdynia and Sopot (the Metropolitan Area Gdansk–Gdynia-Sopot...
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Studies on the formation of formaldehyde during 2-ethylhexyl 4-(dimethylamino)benzoate demethylation in the presence of reactive oxygen and chlorine species
PublicationIn order to protect the skin from UV radiation, personal care products (PCPS) often contain chemical UV-filters. These compounds can enter the environment causing serious consequences on the water ecosystems. The aim of this study was to examine, the effect of different factors, such as UV light, the presence of NaOCl and H2O2 on the formaldehyde formation during popular UV filter, 2-ethylhexyl 4-(dimethylamino)benzoate (ODPABA)...
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From evil demiurge to caring hero: Images of geneticists in the movies
PublicationAlthough images of science and scientists depicted in popular culture have been criticized as an exaggeration and fear mongering, the cinema is an important resource that influences individuals’ beliefs about science. Because popular depictions of science play a crucial role in constructing the public’s ‘scientific imaginary’ they constitute an inherent dimension of the social understanding of science and are as important for...
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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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thestats: An Open-Data R Package for Exploring Turkish Higher Education Statistics
PublicationThere are open datasets available for official statistics, finance, education, and a variety of other domains. The open datasets are published by third-party vendors as well as official authorities. For example, The Turkish Higher Education Council maintains a web portal dedicated to higher education in Türkiye. Detailed datasets about universities, faculties, and departments can be obtained from the portal. Using the data provided...
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Investigation into MPI All-Reduce Performance in a Distributed Cluster with Consideration of Imbalanced Process Arrival Patterns
PublicationThe paper presents an evaluation of all-reduce collective MPI algorithms for an environment based on a geographically-distributed compute cluster. The testbed was split into two sites: CI TASK in Gdansk University of Technology and ICM in University of Warsaw, located about 300 km from each other, both connected by a fast optical fiber Ethernet-based 100 Gbps network (900 km part of the PIONIER backbone). Each site hosted a set...
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Structural Properties and Water Uptake of SrTi1−xFexO3−x/2−δ
PublicationIn this work, Fe-doped strontium titanate SrTi1−xFexO3−x/2−δ, for x = 0–1 (STFx), has been fabricated and studied. The structure and microstructure analysis showed that the Fe amount in SrTi1−xFexO3−x/2−δ has a great influence on the lattice parameter and microstructure, including the porosity and grain size. Oxygen nonstoichiometry studies performed by thermogravimetry at different atmospheres showed that the Fe-rich compositions...
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Characterization methods of nickel nano-particles obtained by the ex-solution process on the surface of Pr, Ni-doped SrTiO3 perovskite ceramics
PublicationIn this paper, a novel electrode material based on Pr, Ni co-doped strontium titanate ( Sr0.7Pr0.3)xTi1−yNiyO3 with constant amount of 30% praseodymium dopant, different amount of nickel (y = 0.06 and y = 0.10) and additional nonstoichiometry in Sr-site (x = 1; x = 0.9 and x = 0.8) was investigated as fuel electrode for SOEC devices. A porous ceramics were prepared by solid-state reaction method. X-ray diffraction measurements...
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The early failure of the gamma nail and the dynamic hip screw in femurs with a wide medullary canal. A biomechanical study of intertrochanteric fractures
PublicationBackground: Intertrochanteric fractures may occur in a bone with a wide medullary canal that may lead to significant mobility of a intramedullary nail, contrary to an extramedullary device. This study evaluates the Dynamic Hip Screw and the gamma nail in AO 31.A2.1 fractures in these circumstances. Methods: Synthetic femora with canals drilled to 18 mm were used. Five fixation types were examined: a 2 - hole and a 4 – hole Dynamic...
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THE 3D MODEL OF WATER SUPPLY NETWORK WITH APPLICATION OF THE ELEVATION DATA
Publication3D visualization is a key element of research and analysis and as the source used by experts in various fields e.g.: experts from water and sewage systems. The aim of this study was to visualize in three-dimensional space model of water supply network with relief. The path of technological development of GESUT data (Geodezyjna Ewidencja Sieci Uzbrojenia Terenu – geodetic records of public utilities) for water supply and measurement...
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Toward Mechanosynthesis of Diamondoid Structures: X. Commercial Capped CNT SPM Tip as Nowadays Available C2 Dimer Placement Tool for Tip-Based Nanofabrication
PublicationAccording to Drexler, advanced mechanosynthesis will employ advanced nano-machines, but advanced nano-machines will themselves be products of advanced mechanosynthesis. This circular relationship must be broken via TBN technology development. In this article, the possibility of using easily available commercial CNT tips to assemble carbon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target...
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The New 3D Printed Left Atrial Appendage Closure with a Novel Holdfast Device: A Pre-Clinical Feasibility Animal Study
PublicationMany patients undergoing cardiac surgery have risk factors for both atrial fibrillation and stroke. The left atrial appendage (LAA) is the primary site for thrombi formation. Therefore LAA occlusion devices should be tested for their ability to reduce future cerebral ischemic events in patients with high-risk of haemorrhage. The aim of this study was to evaluate the safety and feasibility of a novel left atrial appendage exclusion...
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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublicationTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
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Reliability of nitrogen removal processes in multistage treatment wetlands receiving high-strength wastewater
Publicationreatment wetlands have been proved to be more effective than conventional treatment processes in case of high-strength wastewater containing high concentrations of ammonium nitrogen and recalcitrant organic matter. In this study nitrogen removal processes and reliability of nitrogen removal at two identical pilot-scale multistage treatment wetlands (MTWs) receiving real, non-synthetic wastewater were discussed. The wastewater discharged...
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Application of multi-criteria methods to compare different solutions of supplying buildings in electricity from photovoltaic systems
PublicationNowadays, the technologies of electricity generation in distributed systems are usually associated with Renewable Energy Sources (RES). The choice of the construction site depends mainly on the availability of the power system. However, energy planning, especially in case of RES, is a complex process involving multiple and often conflicting objectives. The complexity of the selection of the electricity system is typically addressed...
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Numerical Methods
e-Learning CoursesNumerical Methods: for Electronics and Telecommunications students, Master's level, semester 1 Instructor: Michał Rewieński, Piotr Sypek Course description: This course provides an introduction to computational techniques for the simulation and modeling of a broad range of engineering and physical systems. Concepts and methods discussed are widely illustrated by various applications including modeling of integrated circuits,...
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Antifungal Effect of Penicillamine Due to the Selective Targeting of L-Homoserine O-Acetyltransferase
PublicationDue to the apparent similarity of fungal and mammalian metabolic pathways, the number of established antifungal targets is low, and the identification of novel ones is highly desirable. The results of our studies, presented in this work, indicate that the fungal biosynthetic pathway of L-methionine, an amino acid essential for humans, seems to be an attractive perspective. The MET2 gene from Candida albicans encoding L-homoserine...
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Informal Settlements and International Migrants: The city of Rome (Italy) as Case Study
PublicationToday, urbanization is happening at an unprecedentedly rapid rate, owing heavily to the influx of migrants. Empirical evidence shows the development of informal settlements in cities as a result of migration, including Rome. Furthermore, information on informal settlements is either insufficient or inadequate, which makes it challenging for architects, urban planners, and policymakers to form viable solutions to deal with the situations...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Game Theory Analysis of Bidding for a Construction Contract
PublicationThe authors are concerned with a bidding problem. There are two companies (P1 and P2) bidding for a highway construction project. In order to be more competitive, P1 considers buying a new gravel pit near the construction site. The basic cost of the pit is known to both companies. However, there is also an additional, hidden, cost (C) known only to P1. P2 is uncertain whether the hidden cost is C = 0 or C = x. P1 plans to bid for...
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The Comparison of the Web GIS Applications Relevant for 4D Models Sharing
PublicationThe paper presents results of the project: Cultural Heritage Through Time (CHT 2, http://cht2-project.eu) realized accomplished within the framework of the “Joint Programming Initiative in Cultural Heritage” JPI-CH (http://www.jpi-culturalheritage.eu) by an international consortium: Politecnico di Milano (IT), Newcastle University (UK), Salamanca University (ES), and Stanislaw Staszic Scientific Association SSSA (a non-profit...
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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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Singlet oxygen in the removal of organic pollutants: An updated review on the degradation pathways based on mass spectrometry and DFT calculations
PublicationThe degradation of pollutants by a non-radical pathway involving singlet oxygen (1O2) is highly relevant in advanced oxidation processes. Photosensitizers, modified photocatalysts, and activated persulfates can generate highly selective 1O2 in the medium. The selective reaction of 1O2 with organic pollutants results in the evolution of different intermediate products. While these products can be identified using mass spectrometry...
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Using creative approaches for discovering biomorphic forms for appropriate human habitation in natural environments. Case study of Kashubian Lake District
PublicationThe research process consisted of studies of natural and cultural conditions of the Kashubian Lake District This is an area of exceptional natural conditions. For centuries, it has seen human habitation with respect to landscape values. Given its extensive forest cover and the lack of heterogeneity of natural conditions, the area has become an interesting inspiration for the author’s original project. The project is aimed at searching...
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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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Reducing Monitoring Costs in Industrially Contaminated Rivers: Cluster and Regression Analysis Approach
PublicationMonitoring contamination in river water is an expensive procedure, particularly for developing countries where pollution is a significant problem. This study was conducted to provide a pollution monitoring strategy that reduces the cost of laboratory analysis. The new monitoring strategy was designed as a result of cluster and regression analysis on field data collected from an industrially influenced river. Pollution sources in...
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Silicon Oxycarbide (SiOC) Ceramic Materials as Anodes for Lithium Ion Batteries
PublicationPolymer derived ceramics (PDCs) have attracted attention as alternative anode material for Li-ion batteries. It has been found that ternary SiOC and SiCN ceramics obtained through pyrolysis of various preceramic polymers display high reversible capacities of 500 – 650 mAh/g. In this work we try to correlate the electrochemical performance of polymer derived silicon oxycarbide with its chemical composition and microstructural features....
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Salt melt synthesis of curved nitrogen-doped carbon nanostructures: ORR kinetics boost
PublicationImplementing metal-free electrocatalysts for the oxygen reduction reaction (ORR) and revealing crucial chemical or topographical parameters driving their activity are vital for the development of power cells. The carbon-based catalysts are very often synthesized through carbonization of biopolymers, in particular, those one containing nitrogen groups such as chitosan. Unfortunately, the resulting carbonaceous materials usually...
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NEW EXPERIENCES IN DIKE CONSTRUCTION WITH SOIL-ASH COMPOSITESAND FINE-GRAINED DREDGED MATERIALS
PublicationThe supporting structure inside a coastal dike is often made of dredged non-uniform sand with good compaction proper-ties. Due to the shortage of natural construction material for both coastal and river dikes and the surplus of different processed mate-rials, new experiments were made with sand-ash mixtures and fine-grained dredged materials to replace both dike core and dikecover materials resulting in economical, environmentally...
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Organic carbon fluxes of a glacier surface: a case study of Foxfonna, a small Arctic glacier
PublicationArctic glaciers are rapidly responding to global warming by releasing organic carbon (OC) to downstream ecosystems. The glacier surface is arguably the most biologically active and biodiverse glacial habitat and therefore the site of important OC transformation and storage, although rates and magnitudes are poorly constrained. In this paper, we present measurements of OC fluxes associated with atmospheric deposition, ice melt,...
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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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Tree rings as an indicator of atmospheric pollutant deposition to subalpine spruce forests in the Sudetes (Southern Poland)
PublicationIn spite of their moderate altitude (1000–1600m a.s.l.), the Western SudetyMountains belong to areas with the most efficient fog precipitation in Europe. Intense industrial activity in the area of windward western foothills caused an exceptional intensification of atmospheric pollutant deposition via precipitation and fog to take place since the 1950s. In the second half of the 1970s a massive spruce forest dieback began affecting...
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Atmospheric opacity estimation based on IWV derived from GNSS observations for VLBI applications
PublicationThermal emission of atmospheric water vapor has a great influence on the calibration of radio astronomical observations at millimeter wavelengths. The phenomenon of an atmospheric water vapor emits noise signal and attenuates astronomical emission. At 22 GHz, integrated water vapor (IWV) obtained from global navigation satellite systems (GNSS) is strictly related to atmospheric opacity (τ0), which is a crucial parameter for data...
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Urban dew formation efficiency and chemistry in Poland
PublicationThe measurements of dew formation efficiency and chemistry were performed in Poland in September 2009, as a part of a longer, two-year sampling campaign. Pairs of sites, representing centers of major Polish cities and rural conditions in three different regions, were compared. With the aim to get more detailed landuse-oriented characteristics of dew, two additional sites were set close to Wroclaw. Collection of dew at each site...
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APPLICATION OF CHEMOMETRIC ANALYSIS TO THE STUDY OF SNOW AT THE SUDETY MOUNTAINS, POLAND
PublicationSnow samples were collected during winter 2011/2012 in three posts in the Western Sudety Mountains (Poland) in 3 consecutive phases of snow cover development, i.e. stabilisation (Feb 1st), growth (Mar 15th) and its ablation (Mar 27th). To maintain a fixed number of samples, each snow profile has been divided into six layers, but hydrochemical indications were made for each 10 cm section of core. The complete data set was subjected...
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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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Synthesis and biological evaluation of fluorinated N-benzoyl and N-phenylacetoyl derivatives of 3-(4-aminophenyl)-coumarin-7-O-sulfamate as steroid sulfatase inhibitors
PublicationIn the present work, we report convenient methods for the synthesis of 3-(4-aminophenyl)-coumarin-7-O-sulfamate derivatives N-acylated with fluorinated analogues of benzoic or phenylacetic acid as steroid sulfatase (STS) inhibitors. The design of these potential STS inhibitors was supported by molecular modeling techniques. Additionally, computational docking methods were used to determine the binding modes of the synthesized inhibitors...
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Arctic catchment as a sensitive indicator of the environmental changes: distribution and migration of metals (Svalbard)
PublicationArctic regions experience metal pollution, despite their remote location, and the distribution and migration of those metals determine their potential impact on the local environment. Here, a High-Arctic catchment (Revelva, Svalbard) located remotely from human-induced pollution sources is studied with respect to the distribution and migration of chosen trace elements (Ag, Al, As, B, Ba, Bi, Ca, Cd, Co, Cr, Cu, Cs, Mo, Ni, Pb,...
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Interactive and Media Architecture – From Social Encounters to City Planning Strategies
PublicationThe paper searches into the potential of media and interactive projects to support participation and generate social encounters in public spaces. Moreover, it proposes implementation of media and interactive projects into city planning processes. On the basis of theoretical approaches, case studies and interdisciplinary surveys the paper gives insight how interactive and media architecture can engage people in activities in urban...
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Development of biocompatible iron oxide-silicon oxide core-shell nanoparticles as subcellular delivery platform for glucosamine-6-phosphate synthase inhibitors
PublicationIn order to develop the preparation of iron oxide-silica coreshell nanoparticles (CSNPs), thesis deeply explores the cetyltrimethylammonium (CTA+) directed silica coating methods of the oleic-acid capped iron oxide nanoparticles (OA-IONPs) initialized under near-neutral pH conditions. It is demonstrated that the initial alkaline hydrolysis of ethyl acetate in the presence of CTA+ and OA-IONPs induces an unusual ligand exchange...
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The particle method for simulation of self-organization phenomena
PublicationThe aim of the work was to design, implement, and use, in a number of experiments, an abstract software environment (an artificial world)suitable for modelling systems consisting of many moving and interactingobjects distributed in space. The environment, named DigiHive, is directed towards modeling of complex systems manifested by processes of self-organization, self-reproduction and self modifications. The environment is mainly...
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Conley-Morse graphs for a two-patch vaccination model
Open Research DataThis dataset contains selected results of rigorous numerical computations described in Section 5 of the paper "Rich bifurcation structure in a two-patch vaccination model" by D.H. Knipl, P. Pilarczyk, G. Röst, published in SIAM Journal on Applied Dynamical Systems (SIADS), Vol. 14, No. 2 (2015), pp. 980–1017, doi: 10.1137/140993934.
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Electrochemical oxidation of landfill leachate using boron-doped diamond anodes: pollution degradation rate, energy efficiency and toxicity assessment
PublicationElectrochemical oxidation (EO), due to high efficiency and small carbon footprint, is regarded as an attractive option for on-site treatment of highly contaminated wastewater. This work shows the effectiveness of EO using three boron-doped diamond electrodes (BDDs) in sustainable management of landfill leachate (LL). The effect of the applied current density (25–100 mA cm−2) and boron doping concentration (B/C ratio: 500 ppm, 10,000...
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The Distribution of Glucosinolates in Different Phenotypes of Lepidium peruvianum and Their Role as Acetyl- and Butyrylcholinesterase Inhibitors—In Silico and In Vitro Studies
PublicationThe aim of the study was to present the fingerprint of different Lepidium peruvianum tu- ber extracts showing glucosinolates-containing substances possibly playing an important role in preventinting dementia and other memory disorders. Different phenotypes of Lepidium peruvianum (Brassicaceae) tubers were analysed for their glucosinolate profile using a liquid chromatograph coupled with mass spectrometer (HPLC-ESI-QTOF-MS/MS platform)....
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An Overview of Treatment Approaches for Octahydro-1, 3, 5, 7-tetranitro-1, 3, 5, 7-tetrazocine (HMX) Explosive in Soil, Groundwater, and Wastewater
PublicationOctahydro-1, 3, 5, 7-tetranitro-1, 3, 5, 7-tetrazocine (HMX) is extensively exploited in the manufacturing of explosives; therefore, a significant level of HMX contamination can be encountered near explosive production plants. For instance, up to 12 ppm HMX concentrations have been observed in the wastewater effluent of a munitions manufacturing facility, while up to 45,000 mg/kg of HMX has been found in a soil sample taken from...