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Search results for: dna topoizomeraza ii
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Single-stranded DNA-binding proteins (SSBs) - sources and applicationsin molecular biology
PublicationBiałka wiążące się do jednoniciowego DNA (SSB) odgrywają ważną rolę w replikacji, rekombinacji i naprawie DNA u bakterii, archea i eukariota. Ostatnio wzrosło zainteresowanie białkami SSB jako przydatnymi narzędziami w metodach badawczych biologii molekularnej, analitycznych i diagnostycznych. Większość znanych prokariotycznych białek SSB zbudowanych jest z czterech podjednostek (homotetramer) z jedną domeną wiążąca (OB) jednoniciowe...
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Ruthenium(II) and Iridium(III) Complexes as Tested Materials for New Anticancer Agents
PublicationThe oncological use of cisplatin is hindered by its severe side eects and a very important resistance problem. To overcome these problems, scientists have attempted to design new generation transition-metal anticancer complexes. In this study, we present new complexes, ruthenium(II) [(6-p-cymene)RuCl(py2CO)]PF6 (1), iridium(III) [(5-Cp)IrCl(py2CO)]PF6 (2), and NH4[IrCl4(py2CO)]H2O (3), based on di-2-pyridylketone (py2CO). The prepared...
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Teloxantron inhibits the processivity of telomerase with preferential DNA damage on telomeres
PublicationTelomerase reactivation is one of the hallmarks of cancer, which plays an important role in cellular immortalization and the development and progression of the tumor. Chemical telomerase inhibitors have been shown to trigger replicative senescence and apoptotic cell death both in vitro and in vivo. Due to its upregulation in various cancers, telomerase is considered a potential target in cancer therapy. In this study, we identified...
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Data regarding a new, vector-enzymatic DNA fragment amplification-expression technology for the construction of artificial, concatemeric DNA, RNA and proteins, as well as biological effects of selected polypeptides obtained using this method
PublicationApplications of bioactive peptides and polypeptides are emerging in areas such as drug development and drug delivery systems. These compounds are bioactive, biocompatible and represent a wide range of chemical properties, enabling further adjustments of obtained biomaterials. However, delivering large quantities of peptide derivatives is still challenging. Several methods have been developed for the production of concatemers –...
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Introducing the concept of Decisional DNA-Based web content mining
PublicationPrzedstawiono koncepcje zastosowania struktury reprezentacji wiedzy opartej na decyzyjnym DNA w procesie wyszukiwania informacji w internecie. Dokonano analizy eksperymentow tak wspomaganego wyszukiwania oraz sformulowano wnioski na temat przyszlych badan prowadzacych do dalszej integracji procesu wyszukiwania z doswiadczeniami zdobytymi w trakcie tego wyszukiwania.
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Genome-Wide DNA Methylation and Gene Expression in Patients with Indolent Systemic Mastocytosis
PublicationMastocytosis is a clinically heterogenous, usually acquired disease of the mast cells with a survival time that depends on the time of onset. It ranges from skin-limited to systemic disease, including indolent and more aggressive variants. The presence of the oncogenic KIT p. D816V gene somatic mutation is a crucial element in the pathogenesis. However, further epigenetic regulation may also affect the expression of genes that...
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Molecular differences in mitochondrial DNA (mtDNA) genomes of dogs with malignant mammary tumours
Open Research DataThe aim of this study was to determine molecular defects in mitochondrial DNA with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained...
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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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Evolutionary algorithm and decisional DNA for multiple travelling salesman problem
PublicationIn the real world, it is common to face optimization problems that have two or more objectives that must be optimized at the same time, that are typically explained in different units, and are in conflict with one another. This paper presents a hybrid structure that combines set of experience knowledge structures (SOEKS) and evolutionary algorithms, NSGA-II (Non-dominated Sorting Genetic Algorithm II), to solve multiple optimization...
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Covalent DNA modification by products of myrosinase catalysed glucosinolate degradation in cell-free system
PublicationThe bioactive phytochemicals found in Brassica vegetables belonging to glucosinolates (GLS) and especially the products of their degradation isothiocyanates (ITC) and indoles are regarded as the most promising cancer chemopreventive compounds. These secondary metabolites constitute defence system repelling or preventing the development of agrophages attacking brassica plants. The antibiological properties of these compounds suggest...
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cis-Dichloro(di-tert-butylphosphine-kappa-P)(triphenylphosphine-kappa-P)platinum(II) tetrahydrofuran hemisolvate
PublicationTytułowy związek, [cis-(t-Bu2PH)(Ph3P)PtCl2] został otrzymany w reakcji (Ph3P)2PtCl2 z 1,1,3,3-tetra-tert-butylo-2-trimetylosililotrifosfanem. Widmo 31P{1H} NMR wskazuje na tworzenie się tytułowego związku razem ze znacznymi ilościami Ph3P oraz 1,1,3,3-tetra-tert-butylotrifosfanu.
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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Set of Experience and Decisional DNA: Toward Brains for Cyber-physical Systems and Industry of the Future
PublicationThe concept of Decisional DNA is decade old. This article introduces the initial idea of Set of Experience Knowledge Structure, its advancement into Decisional DNA, and its potential for real life applications in divers domains. The most current and future research steps into Industry 4.0 are also presented and discussed
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Real-time isothermal DNA amplification monitoring in picoliter volumes using an optical fiber sensor
PublicationRolling 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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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublicationMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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Prediction based on integration of Decisional DNA and a feature selection algorithm Relief-F
PublicationThe paper presents prediction model based on Decisional DNA and Set of experienced integrated with Relief_F algorithm for feature selection
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Decisional DNA based intelligent knowledge model for flexible manufacturing system
PublicationModeling 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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Thermal decomposition of some aromatic azomonoethers. Part II. Non-isothermal study of three liquid crystals in dynamic air atmosphere
PublicationW ramach pracy zweryfikowano stabilność termiczną trzech barwników azowych o właściwościach ciekłokrystalicznych - potencjalnych prekursorów do otrzymywania warstw stosowanych w optyce nieliniowej. Zarejestrowano przebiegi TG, DTG, DTA oraz DSC jak również analizowano skład gazów powstających podczas rozpadu za pomocą przystawki FTIR. Przeprowadzono analizę kinetyki rozkładu, wyznaczając energię aktywacji procesu.
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Simple colorimetric copper(II) sensor – spectral characterization and possible applications
PublicationNew o-hydroxyazocompound L bearing pyrrole residue was obtained in the simple synthetic protocol. The structure of L was confirmed and analyzed by X-ray diffraction. It was found that new chemosensor can be successfully used as copper(II) selective spectrophotometric regent in solution and can be also applied for the preparation of sensing materials generating selective color signal upon interaction with copper(II). Selective colorimetric...
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Novel Diazocrowns with Pyrrole Residue as Lead(II) Colorimetric Probes
PublicationNovel 18- and 23-membered diazomacrocycles were obtained with satisfactory yields by diazocoupling of aromatic diamines with pyrrole in reactions carried under high dilution conditions. X-ray structure of macrocycle bearing five carbon atoms linkage was determined and described. Compounds were characterized as chromogenic heavy metal ions receptors. Selective color and spectral response for lead(II) was found in acetonitrile and...
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Aplikacja wspomagająca przetwarzanie sekwencji dna: moduł dopasowań
PublicationBiologia 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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Filozofia społeczna Jana Pawła II (krótkie wprowadzenie)
PublicationW artykule przedstawiono zarys antropologii filozoficznej oraz główne tezy filozofii społecznej Jana Pawła II wyłożone w encyklikach: ''Redemptor hominis'', ''Laborem exercens'', ''Sollicitudo rei socialis'' i ''Centesimus annus''.
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Pyrrole bearing diazocrowns: Selective chromoionophores for lead(II) optical sensing
PublicationDiazocrowns of 18-, 21- and 23-membered rings with pyrrole residue as a part of macrocycle were for the first time used as chromoionophores in lead(II) selective optodes. Sensing properties of optodes depend on the type of macrocycle, namely its size and the type of linker: oligoether or hydrocarbon chain. The best results were obtained for optode bearing 18-membered crown with oligoether linker showing linear response range of...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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(-4,4'-Bipyridyl-2N:N')bis[bis(tri-tert-butoxysilanethiolato-2S,O)cadmium(II)] toluene disolvate
PublicationW strukturze tytułowego kompleksu znajdują się oddzielne cząsteczki, w których każdy atom kadmu jest koordynowany przez dwa atomy siarki, dwa atomy tlenu i jeden atom azotu. Geometria każdego z atomów kadmu jest pośrednia pomiędzy piramidą o podstawie kwadratu a bipiramidą trygonalną. Dwie jednostki tri-tert-butoksysilanotiolanu kadmu są połączone cząsteczką 4,4'-bipirydylu. Dodatkowo w strukturze kompleksu znajduje się cząsteczka...
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Macrocyclic derivatives of imidazole as chromoionophores for bismuth(III)/lead(II) pair
Publication18-membered diazomacrocycles with imidazole or 4-methylimidazole residue as a part of macrocycle were used as chromoionophores in bismuth(III) and lead(II) dual selective optodes for the first time. Cellulose triacetate membranes doped with macrocyclic chromoionophores are bismuth(III) and lead(II) selective with color change from orange/red to different shades of blue and violet, respectively. Results obtained for model and real...
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Decisional DNA with embedded Relief-F linear regression for knowledge and experience management
PublicationOmowiono zastowania Decyzyjnego DNA, regresji liniowej oraz funkcji RELIEF-F w procesach formalnego modelowania i wspomagania zarzadzania wiedza oraz zarzadzania doswiadczeniem.
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Heteroleptic cadmium(II) complex, potential precursor for semiconducting CdS layers. Thermal stability and non-isothermal decomposition kinetics
PublicationW ramach pracy zweryfikowano stabilność termiczną [Cd{SSi(OBut)3}(S2CNEt2)]2 - potencjalnego prekursora do otrzymywania warstw półprzewodnikowych CdS. Równocześnie przeprowadzono analizę kinetyki rozkładu za pomocą różnych metod izokonwersyjnych zaproponowanych przez Flynn-Wall-Ozawa, Kissinger-Akahira-Sunose i Friedmanna w wyniku czego wyznaczono całkowity tryplet kinetyczny dla omawianego kompleksu.
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DNA repair is responsible for the presence of oxidatively damaged DNA lesions in urine
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Badania spektroskopowe wybranych silanotiolanów kobaltu(II)
PublicationPodjęto próby otrzymania i scharakteryzowania tri-tert-butoksysilanotiolanowych kompleksów kobaltu(II), mogących spełnić rolę biomimetyków dla centrów katalitycznych wybranych metaloprotein. Przedstawiono wyniki analizy strukturalnej otrzymanych kompleksów uzyskanych z wykorzystaniem metod spektroskopii UV-vis i FT-IR zarówno dla roztworów jak i w ciele stałym. Skonfrontowano je z danymi uzyskanymi metodą analizy rentgenostrukturalnej...
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Low-Molecular Pyrazine-Based DNA Binders: Physicochemical and Antimicrobial Properties
PublicationPyrazine 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
Publicationnthrapyridazones, 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
PublicationABSTRACT 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
PublicationIn 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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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
PublicationBottom-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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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Effects of metallic silver particles on resonance energy transfer between fluorophores bound to DNA.
PublicationZbadano 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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Two-photon induced fluorescence of Cy5-DNA in buffer solution and on silver island film
PublicationOpisano fluorescencję barwnika CY5 połączonego z DNA w roztworze buforowym na wysepkach srebrowych.
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Mono- and polynuclear Co(II) silanethiolates with aliphatic diamines
PublicationFour Co(II) complexes, [Co{SSi(OtBu)3}2(dmpda)] 1, [Co{SSi(OtBu)3}2(bda)2]n2 [Co{SSi(OtBu)3}2(pda)2]n3 and [Co{SSi(OtBu)3}2(hda)2]n4 [dmpda = 3-(dimethylamino)-1-propylamine; bda = 1.4-butanediamine; pda = 1.5-pentanediamine; had = 1.6-hexanediamine] have been synthesized and characterized using X-ray diffraction. Complex 1 is mononuclear and contains Co(II) coordinated by dmpda molecule in chelating mode, whereas compounds 3 and...
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Principles and applications of Ligation Mediated PCR methods for DNA-based typing of microbial organisms
PublicationA 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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Coordination states and apparent molar volumes of cobalt(II) perchlorate and cobalt(II) chloride in N,N-diethylacetamide at 25 C
PublicationWyznaczono pozorne objętości molowe Co(ClO4)2 i CoCl2 oraz elektronowe widma absorpcyjne w zakresie widzialnym roztworów Co(ClO4)2, CoCl2, Co(ClO4)2 - CoCl2, CoCl2 - LiCl w N,N-dietyloacetamidzie. Analiza pozornych objętości molowych, oraz wpływu temperatury i składu roztworów umozliwiła zidentyfikowanie kompleksów chlorkowych kobaltu(II) powstających w układzie Co(2+)-Cl(-)-DEA. Wyznaczono stałe trwałości.
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Experimental and numerical investigation of crosstalk effect in coupled coplanar waveguides - part II: Multimode coupled line representation
PublicationW pracy przedstawiono metodę analizy nieidealności połączenia poszczegółnych fragmentów rozłożonego ekranu na zjawisko przesłuchu w strukturze sprzężonych falowodów koplanarnych z uziemionym centralnym paskiem. Analiza bierze pod uwagę efekty dyspersji oraz wielorodzajową naturę rozchodzenia się fali elektromagnetycznej w strukturze wieloprzewodowej. Teorię zweryfikowano praktycznie uzyskując bardzo dobrą zgodność pomiędzy wynikami...
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DNA and its Metaphors
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Selectivity of Pb(II) transport across polymer inclusion membranes doped with imidazole azothiacrown ethers
PublicationMembrany wykonane z trioctanu celulozy zawierające jako jonofor 18 i 21-członowe azotiakorony z resztą imidazolu w makropierścieniu przebadano pod kątem transportu jonów Zn(II), Cd(II) i Pb(II) z wodnego roztworu soli (pH ~5.5, cMe = 0,001 M). W wyniku badań ustalono, że jon Pb(II) może być efektywnie wydzielony z roztworu mieszaniny jonów Pb(II), Zn(II), Co(II), Ni(II), Cu(II) i Cd(II).Sekwencja selektywności transportu dla 18-członowej...
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The Reactivity of the Imine Bond within Polynuclear Nickel(II) Complexes
PublicationThree novel Ni complexes with the Schiff base ligand 2-methoxy-6-(E-2-pyridyliminomethyl)-phenol (L1) are described. In comparison with the similar 2-(pyridine-2-ylimino-methyl)phenol (pymp), the mode of coordination of L1 is altered due to the presence of methoxy substituent introducing the sterical hindrance. During the synthesis of the complexes, partial hydrolysis of the ligand was observed. Since such immediate hydrolysis...
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Metody bezsiatkowe - nowe perspektywy zastosowania w geoinżynierii.Część II. Rozwiązanie zagadnienia Flamanta z zastosowaniem metody MLPG
PublicationW artykule przedstawiono praktyczny przykład zastosowania metody MLPG do klasycznego zagadnienia mechaniki gruntów. Rozważanym zagadnieniem jest fundament pasmowy na podłożu sprężystym (uogólnione zagadnienie Flamanta). Dla rozważanego problemu dobrano optymalne parametry funkcji multikwadratowych z bazą radialną, na których oparta jest interpolacja. Zbadano również dokładność obliczeniową w zależności od parametrów definiujących...
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(μ2-4,4'-Bipyridyl-κ2N:N')bis[bis(tri-tert-butoxysilanothiolato- κ2S,O)cadmium(II)] tetrahydrofuran disolvate
PublicationW strukturze tytułowego kompleksu znajdują się oddzielne cząsteczki, w których każdy atom kadmu jest koordynowany przez dwa atomy siarki, dwa atomy tlenu i jeden atom azotu. Geometria każdego z atomów kadmu jest pośrednia pomiędzy piramidą o podstawie kwadratu a bipiramidą trygonalną. Dwie jednostki tri-tert-butoksysilanotiolanu kadmu są połączone cząsteczką 4,4'-bipirydylu. Dodaktowo w strukturze kompleksu znajdują się dwie cząsteczki...
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Increased concentration of Taq DNA polymerase as a solution for GC-rich templates from clinical and environmental samples
PublicationDNA 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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Structural Variety of Cobalt(II), Nickel(II), Zinc(II), and Cadmium(II) Complexes with 4,4′-Azopyridine: Synthesis, Structure and Luminescence Properties
PublicationSelf-assembled bi- and polymetallic complexes of CoII, NiII, ZnII, and CdII were obtained by the reaction of 4,4′-azopyridine (azpy) with metal tri-tert-butoxysilanethiolates (Co, 1; Cd, 2), acetylacetonates (Ni, 3; Zn, 4), and acetates (Cd, 5). All compounds were characterized by single-crystal X-ray structure analysis, elemental analysis, FTIR spectroscopy, and thermogravimetry. Complexes 1, 2 and 4, 5 exhibit diverse structural...
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Klasyfikacja dna morskiego na podstawie kątowej zależności cech echa z sonaru wielowiązkowego
PublicationPrzedstawiono 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...