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Search results for: DNA REPAIR ENZYMES
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Towards neural knowledge DNA
PublicationIn this paper, we propose the Neural Knowledge DNA, a framework that tailors the ideas underlying the success of neural networks to the scope of knowledge representation. Knowledge representation is a fundamental field that dedicates to representing information about the world in a form that computer systems can utilize to solve complex tasks. The proposed Neural Knowledge DNA is designed to support discovering, storing, reusing,...
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Identification, cloning, expression, and characterizationof a highly thermostable single-stranded-DNA-binding protein (SSB) from Deinococcus murrayi
PublicationZidentyfikowano i scharakteryzowano białko SSB-podobne, pochodzące z Deinococcus murrayi (DmuSSB). Otrzymany w reakcji PCR fragment zawierający kompletny gen ssb sklonowano w systemie ekspresyjnym Escherichia coli. Gen składa się z 826 nt, kodujących 276 reszt aminokwasowych z wyliczoną teoretycznie masą cząsteczkową monomeru równą 30,14 kDa. DmuSSB zawiera dwie domeny wiążące jednoniciowe DNA OBna monomer I funkcjonuje jako homodimer....
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Taq DNA polymerase fused with DNA binding protein with increased resistance to inhibitors from clinical samples
PublicationNowadays PCR method is commonly used in molecular diagnostic. However, in many cases PCR is limited, by the presence of inhibitory substances in biological, soil or food samples Efficiency and fidelity of amplification is strongly connected with DNA polymerase and reaction conditions. To meet the requirements of modern diagnostic methods it is essential to seeking for new DNA polymerases with better properties useful in these field....
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Underwater Wet Repair Welding of API 5L X65M Pipeline Steel
PublicationThis paper presents results of the research of effect of polymer insulation of pipeline made of API 5L X65M steel as well as underwater wet welding parameters on properties of joints made by covered electrodes. Effect of heat input on structure and hardness of joints during repair of underwater pipeline was analyzed. Welding defects like microcracks, micro-lacks of fusion, slag inclusions, as well as HAZ hardness increase over...
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Viability of decisional DNA in robotics
PublicationThe Decisional DNA is an artificial intelligence system that uses prior experiences to shape future decisions. Decisional DNA is written in the Set Of Experience Knowledge Structure (SOEKS) and is capable of capturing and reusing a broad range of data. Decisional DNA has been implemented in several fields including Alzheimer’s diagnosis, geothermal energy and smart TV. Decisional DNA is well suited to use in robotics due to the...
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Ocena wpływu pokarmowych kwasów nukleinowych i ich komponentów na replikacyjną i naprawczą syntezę DNA w modelach komórek ludzkiego układu pokarmowego
PublicationKwasy nukleinowe, do których należą DNA i RNA, są podstawowymi elementami każdej komórki niezbędnymi do prawidłowego funkcjonowania organizmu. Pomimo, że cząsteczki te stanowią również nieodłączne składniki produktów żywnościowych spożywanych przez człowieka, to badania na temat ich zawartości w żywności oraz wartości odżywczej są ograniczone. Wyniki uzyskane w niniejszej pracy doktorskiej pokazały istotne różnice w ilości, wielkości...
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Modified DNA polymerases for PCR troubleshooting
PublicationPCR has become an essential tool in biological science. However, researchers often encounter problems with difficult targets, inhibitors accompanying the samples, or PCR trouble related to DNA polymerase. Therefore, PCR optimization is necessary to obtain better results. One solution is using modified DNA polymerases with desirable properties for the experiments. In this article, PCR troubleshooting, depending on the DNA polymerase...
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Adding Interpretability to Neural Knowledge DNA
PublicationThis paper proposes a novel approach that adds the interpretability to Neural Knowledge DNA (NK-DNA) via generating a decision tree. The NK-DNA is a promising knowledge representation approach for acquiring, storing, sharing, and reusing knowledge among machines and computing systems. We introduce the decision tree-based generative method for knowledge extraction and representation to make the NK-DNA more explainable. We examine...
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Dynamics of mechanical model of implant-tissue system in ventral hernia repair
PublicationThe paper deals with a finite element modelling of implants in the problem of ventral hernia repair. The synthetic mesh implanted in the abdomen during surgery is here modelled as a membrane structure. Thesystem undergoes the internal abdominal pressure that occurs during the postoperative cough, the load identified in the literature as the main cause of the connection failure and hernia recurrence. The model can be used to estimate...
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Technological Considerations of Periodic Repair Works of Concrete Industrial Floors
PublicationConcrete floors are among the elements in construction facilities whose design requires engineering experience, workmanship requires the maintenance of a technological regime, while during their operation it is necessary to conduct periodic repairs. Concrete floors are most often used as working and communication space in industrial facilities, and very often they are also a functional element in objects that are immovable monuments....
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Behaviour of orthotropic surgical implant in hernia repair due to the material orientation and abdomen surface deformation
Publicationrelation to the different range of typical deformations observed in different directions and zones of abdomen surface due to the patients’ life activities, has a significant influence on the extreme junction forces in the mesh–tissue connections and hence the repair persistence. The finite element model of the orthotropic implant was developed, and the junction forces in the connections of tissue and mesh were studied. The kinematical...
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Green engineered biomaterials for bone repair and regeneration: Printing technologies and fracture analysis
PublicationDespite the exceptional self-regeneration properties of bone, severe injuries often require additional surgical intervention such as using artificial bone constructs. These structures need to meet a number of criteria regarding their structure, performance, alongside the rate and the mechanism of erosion and fracture when implanted, for stimulating the regeneration of defected bone and, more critically providing support in the...
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SIMULATION OF PROCEED® SURGICAL MESH APPLIED TO VENTRAL HERNIA REPAIR
PublicationIn the present research, Proceed® implant is considered. The system is subjected to short-time dynamic pressure load, similar to post-operative cough naturally occurring in human abdomen. The model refers to a clinical case of 5cm of hernia operated by Proceed implant fixed by 15 joints every 3cm around the orifice. The simulations of the implanted mesh are performed by means of the Finite Element Method. The implant is modelled...
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Cough influence on fascia-mesh system built for a hernia repair - an experimental research
PublicationAn experimental approach to identify stronger and weaker fixation schemes in laparoscopic ventral hernia repair is presented in the paper. Two types of implants, whose mechanical properties are significantly different and five kinds of connectors are considered. Physical models of operated hernia have been built using those materials and porcine abdominal tissue. The models have been subjected to dynamic impulse load, similar to...
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Enzymes of UDP-GlcNAc biosynthesis in yeast
PublicationD-glukozamina stanowi ważny składnik budulcowy głównych elementów strukturalnych grzybowej ściany komórkowej: chityny, chitozanu i mannoprotein. Inne aminocukry, takie jak D-mannozamina i D-galaktozamina, stosunkowo powszechne w komórkach wyższych organizmów eukariotycznych, rzadko występują u grzybów i są praktycznie nieobecne w komórkach drożdży i drożdżaków. Zawierający glukozaminę nukleotyd cukrowy UDP-GlcNAc jest syntezowany...
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Dual inhibition of PI3K/Akt signaling and the DNA damage checkpoint in p53-deficient cells with strong survival signaling: implications for cancer therapy
PublicationOporność komórek nowotworowych na leki uszkadzjące DNA związana jest ściśle ze zdolnością do utrzymywania blok z fazie G2 cyklu komórkowego. Blok ten regulowany jest przez mechanizmy punktu kontrolnego G2/M oraz szlaki przeżycia komórkowego. W pracy badaliśmy rolę szlaku kinazy PI3K/Akt w funkcjonowaniu punktu kontrolnego cyklu komórkowego i wpływ na przeżycie komórek traktowanych lekiem przeciwnowotworowym - cisplatyną. Nasze...
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Naprawa przegubów Estakady Kwiatkowskiego w Gdyni = Hinges repair og the E. Kwiatkowskiego trestle bridge in Gdynia
PublicationE. Kwiatkowskiego trestle bridge is one of the main parts of road infrastructure that connects sea transport (container terminal BTC) national roads A1,1,7. Every limitation of motor traffic causes many problems for Gdynia inhabitants and moreover economical loss in transport economy. In recent two years there were expertise and repair project of hinges carried out. Paper presents genesis and reasons of hinges damages, theoretical...
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Regulacja topologii DNA przez topoizomerazę typu II, czyli jak struktura DNA wpływa na funkcjonowanie genów
PublicationW wielu ważnych procesach jakie zachodzą w komórce zmienia się topologia DNA i struktura chromatyny. Enzym, topoizomeraza typu II, jest jednym z ważnych czynników, który reguluje zmiany topologiczne i strukturalne w jądrze, przez co ma bezpośredni lub pośredni wpływ na takie procesy jak uporządkowanie struktury chromatyny poprzez wiązanie pętli chromatyny do szkieletu jądrowego, transkrypcję i replikację DNA, reperację uszkodzeń...
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The influence of fresh cabbage and sauerkraut juices on the activity of protective enzymes in human cell lines
PublicationMechanizmami przeciwrakotwórczego działania związków zawartych w kapuście jest m.in. metaboliczna aktywacja enzymów II fazy detoksykacji, indukcja enzymów naprawczych DNA oraz aktywnośc przeciwutleniająca. Do enzymów II fazy odtruwania należą m.in. S-transferazy glutationowe (GST) oraz oksydoreduktaza chinonowa NQO1 zwana też DT-diaforazą. GST katalizują reakcję sprzęgania glutationu z wieloma różnymi typami ksenobiotyków, ułatwiając...
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Development of polyurethanes for bone repair
PublicationThe purpose of this paper is to review recent developments on polyurethanes aimed at the design, synthesis, modifications, and biological properties in the field of bone tissue engineering. Different polyurethane systems are presented and discussed in terms of biodegradation, biocompatibility and bioactivity. A comprehensive discussion is provided of the influence of hard to soft segments ratio, catalysts, stiffness and hydrophilicity...
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The development of Decisional DNA digital TV
PublicationZaproponowano koncepcje opartej na wiedzy i doswiadczeniu telewizji cyfrowej z wbudowanym decyzyjnym DNA.
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Decisional DNA applied to digital TV
PublicationPrzedstawiono nowoczesną koncepcje integracji decyzyjnego DNA z telewizją cyfrową w celu pozyskiwania wiedzy o oglądalności poszczególnych programów.
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Fusion of DNA-binding domain of Pyrococcus furiosus ligase with TaqStoffel DNA polymerase as a useful tool in PCR with difficult targets
PublicationThe DNA coding sequence of TaqStoffel polymer- ase was fused with the DNA-binding domain of Pyrococcus furiosus ligase. The resulting novel recombinant gene was cloned and expressed in E. coli. The recombinant enzyme was purified and its enzymatic features were studied. The fusion protein (PfuDBDlig-TaqS) was found to have enhanced processivity as a result of the conversion of the Taq DNA polymerase from a relatively low processive...
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Testing the usability of decisional DNA in robotics
PublicationW pracy poddano dyskusji i nalizie obszary mozliwych zastowac reprezentacji wiedzy zwanej Decisional DNA w zagadnieniach zwiazanych z robotyka.
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Preparation of DNA films for studies under vacuum conditions
PublicationExperiments were carried out to determine the optimum conditions required for the preparation of uniform films of supercoiled plasmid DNA to be used in irradiation experiments under high vacuum conditions. Investigations reveal that significant damage to the DNA molecules occurs due to the evacuation process when films were formed from DNA samples in ultra high purity water only. A variety of bases were tested for their possible...
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Thermodynamics aspects of interactions between acridine derivatives and DNA
PublicationDNA is a molecular target for many anticancer and antiviral drugs. Therefore, a clear understanding of the interaction of small molecules with DNA is important in the rational design of ligands that can bind to DNA with high affinity and selectivity. There are several methods to investigate interactions between drug and DNA. Some of them measure changing into DNA structures, such as lengthening and untwisting of helix of DNA. Other...
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Assessment of technical condition and repair of steel structure elements on the example of fire damage in a warehouse building
PublicationThe paper analyses a case study on the structural assessment of warehouse building partially damaged by fire caused by external source (fire of lorries close to the building). The authors focus on the site investigations and laboratory test results prior to assessing actual condition of the structural elements. Both strengthening concept and repair procedure of a steel column are addressed here. A short literature survey in the...
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Isoform-specific inhibition of DNA topoisomerase II as the mechanism of action of novel anticancer agent C-1305
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Early models of DNA damage formation
PublicationPrzeanalizowano jedne z pierwszych modeli opisujących uszkodzenia nici DNA. Przeanalizowano uszkodzenia powstające w pojedynczych i podwójnych niciach, pod wpływem czynników fizycznych i chemicznych.
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Targeting DNA Topoisomerase II in Antifungal Chemotherapy.
PublicationTopoisomerase inhibitors have been in use clinically for the treatment of several diseases for decades. Although those enzymes are significant molecular targets in antibacterial and anticancer chemotherapy very little is known about the possibilities to target fungal topoisomerase II (topo II). Raising concern for the fungal infections, lack of effective drugs and a phenomenon of multidrug resistance underlie a strong need to expand...
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Reduced-cost constrained miniaturization of wideband antennas using improved trust-region gradient search with repair step
PublicationIn the letter, an improved algorithm for electromagnetic (EM)-driven size reduction of wideband antennas is proposed. Our methodology utilizes variable-fidelity EM simulation models, auxiliary polynomial regression surrogates, as well as multi-point response correction. The constraint handling is implicit, using penalty functions. The core optimization algorithm is a trust-region gradient search with a repair step added in order...
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Some applications of thermophiles and their enzymes for protein processing
PublicationPrzedstawiono charakterystykę, właściwości oraz możliwości zastosowań enzymów proteolitycznych wytwarzanych przez termofile. Zaletą tych biokatalizatorów jest między innymi duża odporność na działanie rozpuszczalników organicznych, detergentów i innych czynników denaturujących białka oraz mała wrażliwość na zmiany pH. Dokonano też przeglądu czynników powodujących dużą stabilność proteaz z termofili.
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Pegylated Fluorescent Peptides as Substrates of Proteolytic Enzymes
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[Chapter] 2. Thermostable enzymes in food processing
PublicationW rozdziale przedstawiono charakterystykę termostabilnych hydrolaz glikozydów, izomeraz, transferaz,lipaz i enzymów proteolitycznych w przetwórstwie rozmaitych surowców źywnościowych. Podano przyczyny termostabilności tych enzymów oraz wymieniono korzyści wynikające z ich stosowania.
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Toward Intelligent Recommendations Using the Neural Knowledge DNA
PublicationIn this paper we propose a novel recommendation approach using past news click data and the Neural Knowledge DNA (NK-DNA). The Neural Knowledge DNA is a novel knowledge representation method designed to support discovering, storing, reusing, improving, and sharing knowledge among machines and computing systems. We examine our approach for news recommendation tasks on the MIND benchmark dataset. By taking advantages of NK-DNA, deep...
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An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublicationAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
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Safety assessment of a concrete viaduct damaged by vehicle impact and an evaluation of the repair
PublicationDamage to lower parts of viaducts caused by impact from under-passing high vehicles is relatively frequent. One such incident, in which a viaduct was damaged by the impact from a truck with an improperly assembled hydraulic crane, is considered in this work. The analysis is based on a detailed object damage evaluation, 3D laser scanning, and numerical simulations. The aim of the study is to accurately model the vehicle impact into...
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The Decisional DNA-Based Smart Bike for Internet of Things
PublicationIn this paper, we introduce a novel application of the Internet of Things, the Decisional DNAbased Smart Bike. The Decisional DNA is a domain-independent, flexible and standard knowledge representation structure; it allows its domains to acquire and store experiential knowledge and formal decision events in an explicit way. By using Decisional DNA, the sensor-equipped bicycle is able to learn its user’s weight, riding habits, etc....
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Measuring the density of DNA films using ultraviolet-visible interferometry
PublicationIn order to determine a proper value for the density of dry DNA films we have used a method based upon the measurement of interference effects in transmission spectra of thin DNA layers. Our results show that the methodology is effective and the density of DNA in this state, 1.407 g/cm3, is much lower than the commonly used 1.7 g/cm3. Obtaining accurate values for the DNA film density will allow the optical constants for DNA to...
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Badanie i porównanie zdolności wybranych leków i związków przeciwnowotworowych do międzyłańcuchowego sieciowania DNA mitochondrialnego i jądrowego w komórkach nowotworowych
PublicationCelem pracy było zbadanie zdolności przeciwnowotworowych związków do indukowania międzyłańcuchowych wiązań sieciujących DNA mitochondrialne w ludzkich komórkach nowotworowych oraz porównanie ze zdolnością do sieciowania DNA jądrowego. Pochodna 4-metylo-1-nitroakrydyny C-1748, Ledakrin i mitomycyna C wykazują zdolność do sieciowania mtDNA i jDNA w komórkach raka okrężnicy HCT-8 w sposób zależny od dawki; C-1748 w komórkach raka...
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Structural insights, biocatalytic characteristics, and application prospects of lignin-modifying enzymes for sustainable biotechnology
PublicationLignin modifying enzymes (LMEs) have gained widespread recognition in depolymerization of lignin polymers by oxidative cleavage. LMEs are a robust class of biocatalysts that include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), laccase (LAC), and dye-decolorizing peroxidase (DyP). Members of the LMEs family act on phenolic, non-phenolic substrates and have been widely researched for valorization...
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Damage repair of the double shell tank
PublicationPłaszcz wewnętrzny stalowego zbiornika dwupłaszczowego o pojemności 10000 m3 został zdeformowany w wyniku błędu popełnionego podczas próby wodnej przy odbiorze zbiornika. W referacie omówiono technologię naprawy silnie zdeformowanego płaszcza zbiornika. Stosowano roztłaczanie hydrauliczne, prostowanie mechaniczne i termiczne oraz wymianę najbardziej uszkodzonych blach.
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A case study of constructing decisional DNA on finanse
PublicationPrzedstawiono koncepcję i rozwiązanie analityczne opisu rynku finansowego przy pomocy reprezentacji wiedzy zwanej ''decyzyjne DNA''.
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Safety of erection and repair of steel tanks with geometric imperfections using heavylift jack-up system
PublicationSafety analysis is performed of cylindrical vertical steel tanks during erection using heavylift jack up system. During an assembly or repair process a set of hydraulic supports is used. It allows to use the in-place lifting of heavy steel constructions on the required height. Wind can strongly influence stability of the lifted tank. Any geometric imperfections can reduce the critical or limit load. In the work failures of the...
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Problem of aggregation in dye-DNA interaction, calorimetry studies
PublicationNucleic acids are the biological target for many antimicrobial, antitumor and antiviral drugs. Ligand-DNA interactions can be classified into two major categories: 1. covalent binding, which can provide to intermolecular adducts, 2. physico-chemical interactions, which can be divided into intercalation (e.g. adriamycin) or groove binding (e.g. dystamycin). There are several methods to investigate interactions between drug and DNA....
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Termodynamika niekowalencyjnego oddziaływania małocząsteczkowych ligandów z dna
PublicationKwasy nukleinowe są jednym z głównych celów biologicznych dla wielu antybiotyków oraz leków przeciwnowotworowych i przeciwwirusowych. Podczas tworzenia nowych farmaceutyków ważna jest dokładna wiedza na temat sposobu wiązania się leku do DNA. Oddziaływanie ligand-DNA można podzielić na dwie grupy: 1. wiązanie kowalencyjne, które często prowadzi do utworzenie trwałych wiązań pomiędzy nićmi DNA, 2. fizykochemiczne wiązanie, które...
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Enzymes of the L-methionine biosynthesis pathway in Candida albicans as potential novel targets for antifungal chemotherapy
PublicationFungal pathways of essential amino acids biosynthesis provide an abundant source of molecular targets for new antifungal compounds, among which the L-methionine biosynthesis pathway (MBP) may be promising. In this dissertation I characterized three C. albicans enzymes involved in MBP: homoserine O-acetyltransferase (CaMet2p), O-acetyl-L-homoserine sulfhydrylase (CaMet15p), and cystathionine-γ-synthase (CaStr2p). I performed crystallization...
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Decisional DNA and Optimization Problem
PublicationMany researchers have proved that Decisional DNA (DDNA) and Set of Experience Knowledge Structure (SOEKS or SOE) is a technology capable of gathering information and converting it into knowledge to help decision-makers to make precise decisions in many ways. These techniques have a feature to combine with different tools, such as data mining techniques and web crawlers, helping organization collect information from different sources...
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Decisional DNA: the concept and its implementation platforms
PublicationOmowiono kopncepcje zarzadzania wiedza oparta na decyzyjnym DNA gdzie wiedza jest reprezentowana poprzez zbiory doswiadczen. Przedstawiono obecne oraz przyszle zastosowania omawianej koncepcji.