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Wyniki wyszukiwania dla: LIGAND/DNA INTERACTIONS
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Real-time isothermal DNA amplification monitoring in picoliter volumes using an optical fiber sensor
PublikacjaRolling circle amplification (RCA) of DNA can be considered as a great alternative to the gold standard polymerase chain reaction (PCR), especially during this pandemic period, where rapid, sensitive, and reliable test results for hundreds of thousands of samples are required daily. This work presents the first research to date on direct, real-time and label-free isothermal DNA amplification monitoring using a microcavity in-line...
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Decisional DNA based intelligent knowledge model for flexible manufacturing system
PublikacjaModeling an effective mechanism for design and control strategies for the implementation of a flexible manufacturing system (FMS) has been a challenge. Consequently, to overcome this issue various techniques have applied in the past but most of these models are effective only for some specific situation or an element of FMS. In this study, the knowledge representation technique of Decisional DNA (DDNA) is applied to FMS to develop...
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Collagen type II–hyaluronan interactions – the effect of proline hydroxylation: a molecular dynamics study
PublikacjaHyaluronan–collagen composites have been employed in numerous biomedical applications. Understanding the interactions between hyaluronan and collagen is particularly important in the context of joint cartilage function and the treatment of joint diseases. Many factors affect the affinity of collagen for hyaluronan. One of the important factors is the ratio of 3- or 4-hydroxy proline to proline residues. This article presents...
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Dysfunctional prefrontal cortical network activity and interactions following cannabinoid receptor activation.
PublikacjaCoordinated activity spanning anatomically distributed neuronal networks underpins cognition and mediates limbic-cortical interactions during learning, memory, and decision-making. We used CP55940, a potent agonist of brain cannabinoid receptors known to disrupt coordinated activity in hippocampus, to investigate the roles of network oscillations during hippocampal and medial prefrontal cortical (mPFC) interactions in rats. During...
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Aplikacja wspomagająca przetwarzanie sekwencji dna: moduł dopasowań
PublikacjaBiologia molekularna jest obecnie bardzo dynamicznie rozwijającą się dziedziną nauki. Wzrost mocy obliczeniowej komputerów pozwala na coraz szybszą i dokładniejszą analizę wielocząsteczkowych biologicznych polimerów. Poniższy artykuł przedstawia jeden z modułów programu AlignGator - modułowego systemu przeznaczonego do analizy DNA. Omawiany moduł pozwala na tworzenie, oraz edycję wielodopasowań. W początkowej części artykułu opisane...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublikacjaBrominated 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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Decisional DNA with embedded Relief-F linear regression for knowledge and experience management
PublikacjaOmowiono zastowania Decyzyjnego DNA, regresji liniowej oraz funkcji RELIEF-F w procesach formalnego modelowania i wspomagania zarzadzania wiedza oraz zarzadzania doswiadczeniem.
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Intermolecular Interactions as a Measure of Dapsone Solubility in Neat Solvents and Binary Solvent Mixtures
PublikacjaDapsone is an effective antibacterial drug used to treat a variety of conditions. However, the aqueous solubility of this drug is limited, as is its permeability. This study expands the available solubility data pool for dapsone by measuring its solubility in several pure organic solvents: N-methyl-2-pyrrolidone (CAS: 872-50-4), dimethyl sulfoxide (CAS: 67-68-5), 4-formylmorpholine (CAS: 4394-85-8), tetraethylene pentamine (CAS:...
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Efficacious Alkaline Copper Corrosion Inhibition by a Mixed Ligand Copper(II) Complex of 2,2′-Bipyridine and Glycine: Electrochemical and Theoretical Studies
PublikacjaA mixed ligand copper(II) complex, namely, [Cu(BPy)(Gly)Cl]⋅2H2O (CuC) (BPy=2,2′-bipyridine and Gly=glycine), was synthesized and characterized. The synthesized CuC complex was tested as inhibitor to effectively mitigate the corrosion of copper in alkaline solutions using the linear sweep voltammetry (LSV) and linear polarization resistance (LPR) techniques. For the sake of comparison, such two D.C. electrochemical techniques were...
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Analysis of odour interactions in model gas mixtures using electronic nose and fuzzy logic
PublikacjaMeasurement and monitoring of air quality in terms of odour nuisance is an important problem. Although the source of these nuisances is different (e.g. wastewater treatment plants, municipal landfills), their common feature is that they are a complex mixture of odorants with different odour thresholds. An additional problem is occurrence of the odour interactions between mixture components. From a practical point of view, it would...
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DNA repair is responsible for the presence of oxidatively damaged DNA lesions in urine
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Low-Molecular Pyrazine-Based DNA Binders: Physicochemical and Antimicrobial Properties
PublikacjaPyrazine and its derivatives are a large group of compounds that exhibit broad biological activity, the changes of which can be easily detected by a substituent effect or a change in the functional group. The present studies combined theoretical research with the density functional theory (DFT) approach (B3LYP/6-311+G**) and experimental (potentiometric and spectrophotometric) analysis for a thorough understanding of the structure...
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Molecular basis for the DNA damage induction and anticancer activity of asymmetrically substituted anthrapyridazone PDZ-7
Publikacjanthrapyridazones, imino analogues of anthraquinone, constitute a family of compounds with remarkable anti-cancer activity. To date, over 20 derivatives were studied, of which most displayed nanomolar cytotoxicity towards broad spectrum of cancer cells, including breast, prostate and leukemic ones. BS-154, the most potent derivative, had IC50 values close to 1 nM, however, it was toxic in animal studies. Here, we characterize another...
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The Neural Knowledge DNA Based Smart Internet of Things
PublikacjaABSTRACT The Internet of Things (IoT) has gained significant attention from industry as well as academia during the past decade. Smartness, however, remains a substantial challenge for IoT applications. Recent advances in networked sensor technologies, computing, and machine learning have made it possible for building new smart IoT applications. In this paper, we propose a novel approach: the Neural Knowledge DNA based Smart Internet...
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Decisional DNA based framework for representing Virtual Engineering Objects
PublikacjaIn this paper, we propose a frame-work to represent the Virtual Engineering Objects (VEO) utilizing Set of Knowledge Experience Structure (SOEKS) and Decisional DNA. A VEO will enable the discovery of new knowledge in a manufacturing unit and the generation of new rules that drive reasoning. The proposed VEO framework will not only be knowledge based representation but it will also have its associated experience embedded within...
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Effects of metallic silver particles on resonance energy transfer between fluorophores bound to DNA.
PublikacjaZbadano wpływ filmów wysepek metalicznego srebra na rezonansowe przekazywanie energii między fluoroforami związanymi z DNA. Donorem i akceptorem były odpowiednio 4´,6 diamidyno-2-fenylindon i jodek propydyny. Zmierzone dla tego układu czasy zaniku i widma fluorescencji pokazują, że sąsiedztwo cząstek srebra dramatycznie zwiększa promień Forstera, a tym samym i przekazywanie energii w znakowanym DNA.
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Interactions between polyphenolic antioxidants quercetin and naringenin dictate the distinctive redox-related chemical and biological behaviour of their mixtures
PublikacjaFood synergy concept is suggested to explain observations that isolated antioxidants are less bioactive than real foods containing them. However, mechanisms behind this discrepancy were hardly studied. Here, we demonstrate the profound impact of interactions between two common food flavonoids (individual: aglycones quercetin—Q and naringenin—N− or their glycosides rutin—R and naringin—N+ vs. mixed: QN− and RN+) on their electrochemical...
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Two-photon induced fluorescence of Cy5-DNA in buffer solution and on silver island film
PublikacjaOpisano fluorescencję barwnika CY5 połączonego z DNA w roztworze buforowym na wysepkach srebrowych.
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DNA and its Metaphors
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Selective Cytostatic and Cytotoxic Anticancer Effects of Bisfunctional Agents: A Strategy for the Design of DNA Binding Agents
PublikacjaVarious agents have been synthesized and proved useful for the National Cancer Institute's anticancer testing as potential new drugs, but most agents suffer side effects from their limited selectivity against cancer cells over healthy ones. Therefore, this paper attempts to describe drugs in terms of the level of tumor cell selectivity which they possess to define the features of mols. that are essential for useful cytotoxicity....
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
PublikacjaRNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA....
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Principles and applications of Ligation Mediated PCR methods for DNA-based typing of microbial organisms
PublikacjaA significant number of DNA-based techniques has been introduced into the field of microorganisms’ characterization and taxonomy. These genomic fingerprinting methods were developed to detect DNA sequence polymorphisms by using general principles, such as restriction endonuclease analysis, molecular hybridization, and PCR amplification. In recent years, some alternative techniques based on ligation of oligonucleotide adapters before...
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Vasopressin V2 receptor/bioligand interactions
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Ln2(SeO3)2(SO4)(H2O)2 (Ln=Sm, Dy, Yb): A Mixed‐Ligand Pathway to New Lanthanide(III) Multifunctional Materials Featuring Nonlinear Optical and Magnetic Anisotropy Properties
PublikacjaBottom-up assembly of optically nonlinear and magnetically anisotropic lanthanide materials involving precisely placed spin carriers and optimized metal-ligand coordination offers a potential route to developing electronic architectures for coherent radiation generation and spin-based technologies, but the chemical design historically has been extremely hard to achieve. To address this, we developed a worthwhile avenue for creating...
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Supramolecular Synthesis Based on a Combination of Se···N Secondary Bonding Interactions with Hydrogen and Halogen Bonds
PublikacjaExamination of the solid state structures of 2,1,3-benzoselenadiazole complexes with hydrogen or halogen bond donors has demonstrated that the 2,1,3-benzoselenadiazole molecules preferably form centrosymmetric dimers with use of [Se–N]2 supramolecular synthon, whereas the two remaining nitrogen atoms not involved in the [Se–N]2 supramolecular interactions can act as acceptors of hydrogen or halogen bonds. Cocrystallization of selenadiazoles...
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Increased concentration of Taq DNA polymerase as a solution for GC-rich templates from clinical and environmental samples
PublikacjaDNA polymerase is an enzyme which plays crucial role in replication and DNA repair. It found application in PCR (polymerase chain reaction) where catalyses process of in vitro DNA synthesis. To meet the demands posed by mod- ern diagnostic, molecular biology or genetic engineering it is necessary to improve DNA polymerases to obtain new or better features useful in these fields. So far implemented modifications in majority are...
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Analysis of the influence of polystyrene microplastics and their derivatives on the DNA of human colon epithelial cells HT29 with the comet assay
PublikacjaWe have been using plastic for almost a century and nowadays a lot of them circulates as pollutants in the environment and still defragmenting to micro and nanoscale. The exposition through the food chain and its precise impact on human health is still not clear. In our study, we tested real food packaging after contact with food products and real thermoinsulation and environmental samples of polystyrene in different model liquids,...
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Study of the ability of TXT-compounds to promote telomeric G4 DNA thermal stabilization using FRET melting assay
Dane BadawczeThe data set contains a DNA melting screen obtained from the FRET melting assay. Thermal stabilities of G-quadruplex structures were analysed in the presence and in absence of ligands. TMPyP4 and MTX were used as references. Measurements were carried out in triplicate using a LightCycler 480 thermocycler (Roche Life Science) with a filter setting of...
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Klasyfikacja dna morskiego na podstawie kątowej zależności cech echa z sonaru wielowiązkowego
PublikacjaPrzedstawiono metodę rozpoznawania i klasyfikacji rodzaju dna morskiego opartą na przetwarzaniu echa z sonaru wielowiązkowego. Metoda ta polega na obliczaniu zbioru parametrów obwiedni ech dla poszczególnych wiązek, podobnie jak w metodach wykorzystujących echosondy jednowiązkowe. Następnie estymowana jest zależność wartości poszczególnych parametrów od kąta wiązki oraz badane jest powiązanie otrzymanej zależności z rodzajem dna...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublikacjaTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Silver nanoparticles induce premutagenic DNA oxidation that can be prevented by phytochemicals from Gentiana asclepiadea
PublikacjaAmong nanomaterials, silver nanoparticles (AgNPs) have the broadest and most commercial applications due to their antibacterial properties, highlighting the need for exploring their potential toxicity and underlying mechanisms of action. Our main aim was to investigate whether AgNPs exert toxicity by inducing oxidative damage to DNA in human kidney HEK 293 cells. In addition, we tested whether this damage could be counteracted...
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Photostability pf Cy3 and Cy5-labeled DNA in the presence of metallic silver particles
PublikacjaZbadano wpływ cząstek metalicznego srebra na fotostabilność oligomerów DNA kowalencyjnie związanych z Cy3 lub Cy5. Zbliżenie fluoroforów do cząstek srebra powodowało zwiększenie intensywności fluorescencji i pojawienie się frakcji emisji bardziej odpornej na wybielanie.
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The influence of the substrate temperature on the preparation of DNA films for studies under vacuum conditions
PublikacjaPrzeanalizowano wpływ temperatury na formowanie warstw DNA. Sprawdzono wpływ stabilizatorów na jakość otrzymanych próbek. Stwierdzono, że optymalnymi warunkami przygotowywania filmów do badań w warunkach próżniowych jest - 10 st. C przy minimalnej zawartości NaOH.
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DNA adduct formation by C-1748, a potent antitumor 4-methyl-1-nitroacridine of lowered toxicity.
Publikacja4-podstawione 1-nitroakrydyny reprezentują nową grupę pochodnych zsyntetyzowanych na Politechnice Gdańskiej. W porównaniu do macierzystych 1-nitroakrydyn związki te wykazują obniżoną toksyczność i podwyższoną aktywność przeciwnowotworową. Wiodąca pochodna 4-metylo-1-nitroakrydyna o symbolu C-1748 jest obecnie w przygotowaniu do I fazy badań klinicznych w leczeniu raka okrężnicy. Wprowadzenie elektrodonorowej grupy metylowej w...
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Antioxidant Interactions between Major Phenolic Compounds Found in 'Ataulfo' Mango Pulp: Chlorogenic, Gallic, Protocatechuic and Vanillic Acids
PublikacjaPhenolic compounds are known to have antioxidant capacity; however, there is little information about molecular interactions between particular phenolics found in fruits at different developmental stages. Therefore, the total antioxidant capacity of the phenolic compounds of a fruit may not correspond to the sum of individual antioxidant capacity given by antioxidants from that tissue. In this study, individual antioxidant capacity...
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Fluorescence of nanodiamond cocktails: pH-induced effects through interactions with comestible liquids
PublikacjaFluorescent nanodiamonds with nitrogen-vacancy centers have become important nanoscale probes for sensing and imaging. The surface chemistry of the nanodiamonds influences their emission, interactions, and quantum properties. In this work, we propose to utilize fluorescent nanodiamonds as photostable markers for investigation of comestible liquids. We prepared nanodiamond/comestibles suspensions/cocktails with a wide range of pH...
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Determination of Odour Interactions of Three-Component Gas Mixtures Using an Electronic Nose
PublikacjaThe paper presents an application of an electronic nose prototype comprised of six TGS-type sensors and one PID-type sensor to identify odour interaction phenomena in odorous three-component mixtures. The investigation encompassed eight odorous mixtures—toluene-acetone-triethylamine and formaldehyde-butyric acid-pinene — characterized by different odour intensity and hedonic tone. A principal component regression (PCR) calibration...
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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublikacjaIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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Toward Smart Innovation Engineering: Decisional DNA-Based Conceptual Approach
PublikacjaABSTRACT Knowledge and experience are essential requirements for product innovation. The presented paper proposes a systematic approach for product innovation support using a Smart Knowledge Management System comprising a Set of Experience Knowledge Structure (SOEKS) and Decisional DNA (DDNA). This proposed system is dynamic in nature because it updates itself every time a new decision related to innovation is made. Through this...
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Mitochondrial DNA Part B-Resources
Czasopisma -
Recent Advances in DNA and Gene Sequences
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Aplikacja wspomagająca przetwarzanie sekwencji dna: moduł edycji chromatogramu
PublikacjaModuł edycji chromatogramu jest częścią większej aplikacji, służącej do wspomagania przetwarzania danych pochodzących z sekwencjonowania DNA. Aplikacja skonstruowana jest z odrębnych, samodzielnych programów, które współpracują dwiema drogami - poprzez popularne formaty plików, co umożliwia wprowadzenie do modułów danych opracowanych częściowo w aplikacjach zewnętrznych, oraz poprzez przesyłanie danych pomiędzy modułami, co usprawnia...
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Decisional-DNA Based Smart Production Performance Analysis Model
Publikacjan order to allocate resources effectively according to the production plan and to reduce disturbances, a framework for smart production performance analysis is proposed in this article. Decisional DNA based knowledge models of engineering objects, processes and factory are developed within the proposed framework. These models are the virtual representation of manufacturing resources, and with help of Internet of Things, are capable...
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Interplay between Aryl···Perfluoroaryl and Hydrogen Bonding Interactions in Cocrystals of Pentafluorophenol with Molecules of Trigonal Symmetry
PublikacjaCocrystals of seven star-shaped triaryl compounds with pentafluorophenol (pfp) were prepared and structurally characterized by the single-crystal X-ray diffraction method. Cocrystallization of pfp with planar (or almost planar) compounds gave six 3:1 molecular complexes with well-defined layered structures. The layers are composed of alternating pfp3 trimers, linked by hydrogen bonding, and triaryl molecules held together in planes...
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Total DNA Methylation Changes Reflect Random Oxidative DNA Damage in Gliomas
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Total DNA methylation as a biomarker of DNA damage and tumor malignancy in intracranial meningiomas
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DNA methylation in cancer development, diagnosis and therapy-multiple opportunities for genotoxic agents to act as methylome disruptors or remediators
PublikacjaThe role of DNA methylation and recently discovered hydroxymethylation in the function of the human epigenome is currently one of the hottest topics in the life sciences. Progress in this field of research has been further accelerated by the discovery that alterations in the methylome are not only associated with key functions of cells and organisms, such as development, differentiation and gene expression, but may underlie a number...
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From Individual to Collective: Intelligence Amplification with Bio-Inspired Decisional DNA and its Extensions
PublikacjaIn nature, deoxyribonucleic acid (DNA) contains the genetic instructions used in the development and functioning of all known living organisms. The idea behind our vision is to develop an artificial system, an architecture that would support discovering, adding, storing, improving and sharing information and knowledge among agents and organizations through experience. We propose a novel Knowledge Representation (KR) approach in...
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π-Stacking attraction vs. electrostatic repulsion: competing supramolecular interactions in a tpphz-bridged Ru(ii)/Au(iii) complex
PublikacjaThe synthesis and characterization of a mixed metal ruthenium(II)/gold(III) complex bridged by tetrapyridophenazine (tpphz) are described. It is isostructural and isoelectronic to the well-known photocatalysts with palladium(II) or platinum(II). Concentration dependent 1H-NMR spectroscopy and XRD studies show that the electrostatic repulsion between the gold(III) moieties exceeds the attractive π-stacking interaction. Theoretical...
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Wpływ warunków naturalnych na zobrazowanie dna Zatoki Gdańskiej przy użyciu sonaru bocznego
PublikacjaGłównym celem artykułu jest przedstawienie wpływu warunków środowiskowych na dokładność zobrazowania dna morza za pomocą systemów hydroakustycznych. Czynniki naturalne, przede wszystkim falowanie powierzchni morza i niejednorodny rozkład prędkości dźwięku w wodzie, mają wpływ na zmianę toru promieni akustycznych. Choć w obu przypadkach mechanizm zjawisk jest zupełnie odmienny, odgrywają one decydującą rolę w odwzorowaniu dna i...