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Search results for: DE-CISIONAL DNA
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The New LM-PCR/Shifter Method for the Genotyping of Microorganisms Based on the Use of a Class IIS Restriction Enzyme and Ligation Mediated PCR
PublicationThis study details and examines a novel Ligation-Mediated - Polymerase Chain Reaction (LM-PCR) method. Named the LM-PCR/Shifter, it relies on the use of a Class IIS restriction enzyme giving restriction fragments with different 4 base, 5' overhangs, this being the Shifter, and the ligation of appropriate oligonucleotide adapters. A sequence of 4-base, 5' overhangs of the adapter and a 4-base sequence of the 3' end of the primer(s)...
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From tryptophan to novel mitochondria-disruptive agent, synthesis and biological evaluation of 1,2,3,6-tetrasubstituted carbazoles
PublicationMitochondrial targeting plays an important role in anticancer therapy. The Mn(III)-promoted cyclization of 5- (1H-indol-3-yl)-3-oxopentanoic acid allow to obtain novel substituted carbazole derivatives that can act as mitochondria-disruptive agents. The starting materials used for the synthesis of these new aminocarbazoles are oxopentanoate derivatives of tryptophan. The scope and limitation of this method of synthesis are determined...
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Palindromic carbazole derivatives: unveiling their antiproliferative effect via topoisomerase II catalytic inhibition and apoptosis induction
PublicationHuman DNA topoisomerases are essential for crucial cellular processes, including DNA replication, transcription, chromatin condensation, and maintenance of its structure. One of the significant strategies employed in cancer treatment involves the inhibition of a specific type of topoisomerase, known as topoisomerase II (Topo II). Carbazole derivatives, recognised for their varied biological activities, have recently become a significant...
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EASY ACCESS TOOL FOR SMALL INTERFERING RNA (siRNA) DATA
PublicationFor many decades it was an accepted dogma of molecular genetics that the expression of genes is a “one-way-road” leading only in one direction from DNA to RNA to proteins. Recent discoveries in modern molecular genetics have challenged this dogma showing that specific RNA molecules play a central role in controlling the activity of genes by changing the structure of DNA sequences, targeting other RNAs for degradation or blocking...
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Methodology of the Morphometry Study on Baltic Herring
PublicationAcoustic techniques are used in the estimation of the abundance of Baltic herring. Investigations of the relationship between the Baltic herring individual target strength TS and the total fish length L, significant in the acoustic assessment, demonstrated its de-pendence on the study area location. It motivated the detailed analysis of the relationship between herring from the southern Baltic ICES Subdivisions 24, 25, and 26,...
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Enviromental factors az the elements determingthe development of floating homes
PublicationThe popularity of Floating Homes in Western Europe and North America is noticeable. The interest in thesefacilities in Poland is also constantly growing. The popularity of Floating Homes is due to climate change, risingland prices and population density in city centers. However, environmental factors play a significant role in theirdevelopment. The publication presents the results of research on the impact of environmental factors...
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Synthesis of a state feedback controller for an averaging tank with variable filling
PublicationIn paper, a nonlinear averaging tank with variable filling is considered. The main purpose of this research work was the modelling and control system synthesis of an averaging tank. The control objectives included ensuring stability and zero steady-state error of the system and achieving settling time as short as possible, while maintaining a minimal overshoot. In order to achieve the intended purpose, firstly a mathematical model...
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Diamond investments – Is the market free from multiple price bubbles?
PublicationThe following study aims to investigate whether multiple price bubbles, in which the quoted market price of diamonds significantly deviates from their fundamental value, exist in the diamond market. It was conducted using ADF, SADF and GSADF tests, with the latter found to be an optimal form of evaluating the analysed issue. The presented results support the conclusion that the diamond market is not free from periods defined as...
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Bioconversion of waste materials to hydrogen via dark fermentation using Enterobacter aerogenes
PublicationHydrogen can be obtained via dark fermentation with the use of anaerobic Enterobacter aerogenes. The efficiency of hydrogen production by fermentation techniques is strongly dependent on the con-ditions used i.e. the pH range, temperature, composition of fermentation broths, oxygen content, or even the presence of substances with potentially inhibitory effects on the microbiological culture [1-4]. The paper describes the study...
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The Discrete-Continuous, Global Optimisation of an Axial Flow Blood Pump
PublicationThis paper presents the results of the discrete-continuous optimisation of an axial flow blood pump. Differential evolution (DE) is used as a global optimisation method in order to localise the optimal solution in a relatively short time. The whole optimisation process is fully automated. This also applies to geometry modelling. Numerical simulations of the flow inside the pump are performed by means of the Reynolds-Average Navier-Stokes...
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Impact of the glazed roof on acoustics of historic interiors
PublicationThe paper discusses the adverse acoustic phenomena occurring in the semi-open interiors (courtyards, yards) covered with a glass roof. Particularly negative is the rever-beration noise, which leads to the degradation of the utility functions of the resulting spaces. It involves the drastically reducing the intelligibility of speech, loss of natural sounding of music, problems with the sound system, as well as disturbances in the...
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Is This Distance Teaching Planning That Bad?
PublicationIn spring 2020, university courses were moved into the virtual space due to the Covid-19 lockdown. In this paper, we use experience from courses at Gdańsk University of Technology and ETH Zurich to identify core problems in distance teaching planning and to discuss what to do and what not to do in teaching planning after the pandemic. We conclude that we will not return to the state of (teaching) affairs that we had previously....
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Detection of Lexical Stress Errors in Non-Native (L2) English with Data Augmentation and Attention
PublicationThis paper describes two novel complementary techniques that improve the detection of lexical stress errors in non-native (L2) English speech: attention-based feature extraction and data augmentation based on Neural Text-To-Speech (TTS). In a classical approach, audio features are usually extracted from fixed regions of speech such as the syllable nucleus. We propose an attention-based deep learning model that automatically de...
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Contaminants in airport runoff water in the Vicinities of Two International Airports in Poland
PublicationThe general aim of the study was to evaluate environmental quality associated with the operations (combustion of fuels, cleaning of aircraft and airport aprons, aircraft, ground vehicle maintenance and repairs, fuelling operations, de/anti-icing operations) of international airports located in central and northern of Poland. These two monitoring areas were set up to monitor PAHs, PCBs, formaldehydes, phenols, detergents (cationic,...
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Reverse flow routing problem solved by the Space-Time Conservation Method
PublicationW artykule rozpatruje się zagadnienie odwrotnej transformacji przepływów dla przypadku przepływu nieustalonego wolno zmiennego w kanałach otwartych, opisanego układem równań de Saint Venanta. Przedstawiono specyficzne dla rozpatrywanego przypadku problemy powstające na etapie jego rozwiązywania oraz zaproponowano efektywny algorytm obliczeniowy, wykorzystujący nową, atrakcyjną metodę czasoprzestrzennych objętości skończonych. Do...
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Induction of G2/M phase arrest and apoptosis of human leukemia cells by potent antitumor triazoloacridinone C-1305
PublicationWykazaliśmy, że pochodna triazoloakrydonu C-1305 w stężeniach biologicznie istotnych indukuje blok cyklu komórkowego w fazie G2/M i apoptozę w komórkach białaczek ludzkich MOLT4 i HL60. Zjawisko apoptozy zostało określone na podstawie charakterystycznych zmian morfologicznych jak i biochemicznych tj. fragmentacji DNA, aktywacji kaspazy 3, cięcia PARP, spadku potencjału mitochondrialnego i ATP oraz eksternalizacji fosfatydyloseryny.
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Indukcja apoptozy w komórkach białaczek ludzkich molt4 i hl60 przez acyloksytriazoloakrydony - nową grupe związków o właściwościach przeciwnowotworowych
PublicationWykazazno, że acyloksytriazoloakrydony, podobnie jak badane wcześniej triazoloakrydony, indukują apoptozę w komórkach białaczek ludzkich MOLT4 i HL60 w stężeniach biologicznie istotnych, odpowiadających wartościom EC90 i EC80. Zjawisko apotozy zbadano w oparciu o zmiany morfologiczne w komórkach (ciałka apoptotyczne), międzynukleosomalną fragmentację DNA, zmiany w budowie błony cytoplazmatycznej, spadek mitochondrialnego potencjału...
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Electron ionization and low energy electron attachment to molecules of biological interest
PublicationEthylenediaminetetraacetic acid (EDTA) and 2-amino-2-(hydroxymethyl)-1,3-propanediol (TRIS) were investigated by electron impact ionization and low energy electron attachment. Both compounds are components of biological buffers and often are used as DNA stabilizers in irradiation studies. hus it is of a great importance to understand their potential interactions with radiation. Our results revealed that at least one of them, EDTA, may...
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Electron ionization and low energy electron attachment to molecules of biological interest
PublicationEthylenediaminetetraacetic acid (EDTA) and 2-amino-2-(hydroxymethyl)-1,3-propanediol (TRIS) were investigated by electron impact ionization and low energy electron attachment. Both compounds are components of biological buffers and often are used as DNA stabilizers in irradiation studies. hus it is of a great importance to understand their potential interactions with radiation. Our results revealed that at least one of them, EDTA, may...
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Cardinal regenerative features of the MRL mouse
PublicationIn this review, we discuss recent studies relating to major features of adult MRL mouse biology that contribute to the regenerative responses seen. These include an increased inflammatory cell profile, a unique glycolytic metabolic state typically found during embryogenesis, and a cell cycle phenotype of DNA damage and G2/M arrest. These traits have been found in other mammalian and non-mammalian regenerative systems. How these...
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Analysis of a gene expression model
PublicationWe study a mathematical model of gene transcription and protein synthesis with negative feedback. We consider a system of equations taking into account the number of active binding sites, the way in which dimers bind to DNA and time delay in translation process. For a simplified model that consist of three ordinary differential equations with time delay we derive conditions for stability of the positive steady state and for the...
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Seafloor backscattering: numerical simulation vs. filter theory approach.
PublicationPrzedstawiono model opisujący rozpraszanie sygnału akustycznego na nierównomiernej, regularnie sfalowanej powierzchni dna morskiego jako filtr liniowy z odpowiedzią impulsową o zmieniającej się w czasie chwilowej dominującej częstotliwości. Porównano przewidywania modelu z wynikami otrzymanymi w wyniku złożonych obliczeniowo symulacji numerycznych opartych na fizycznym modelu zjawiska wykorzystującym aproksymację Kirchhoffa. Wstępnie...
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Projektowanie tras tramwajowych przy wykorzystaniu Mobilnych Pomiarów Satelitarnych
PublicationW pracy przedstawiono metodykę projektowania tras tramwajowych dostosowaną do rozwijanej w Zespole Naukowym metody Mobilnych Pomiarów Satelitarnych. Opisano badania inwentaryzacyjne wykonane na torach tramwajowych, których wyniki posłużyły jako dane wejściowe w procesie projektowania. Pokazano, w jaki sposób dostosowano analityczne algorytmy projektowania tras kolejowych do specyfiki układów geometrycz-nych występujących w torach...
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Metody zwiększania dostępności i efektywności informatycznej infrastruktury w inteligentnym mieście
PublicationW pracy omówiono metody zwiększania dostępności i efektywności informatycznej infrastruktury w inteligentnym mieście. Sformułowano dwa kryteria do oceny rozmieszczenia kluczowych zasobów w systemie smart city. Zobrazowano proces wyznaczania rozwiązań kompromisowych spośród rozwiązań Pareto-optymalnych. Omówiono metaheurystyki inteligencji zbiorowej, w tym roju cząstek, kolonii mrówek, roju pszczół oraz ewolucji różnicowej, za pomocą...
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Diagnostic Accuracy of Liquid Biopsy in Endometrial Cancer
PublicationBackground: Liquid biopsy is a minimally invasive collection of a patient body fluid sample. In oncology, they offer several advantages compared to traditional tissue biopsies. However, the potential of this method in endometrial cancer (EC) remains poorly explored. We studied the utility of tumor educated platelets (TEPs) and circulating tumor DNA (ctDNA) for preoperative EC diagnosis, including histology determination. Methods:...
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The comparison of cytotoxic and genotoxic activities of glucosinolates, isothiocyanates, and indoles
PublicationChemopreventive properties of Brassica vegetables are attributed mainly to their characteristic compounds—glucosinolates (GLs) and their main hydrolysis products—isothiocyanates (ITCs) and indoles. In this study, we compared antiproliferative activity (MTT test in HT29 cells) and genotoxic effects (comet assay in HT29 cells and restriction analysis in a cell-free system) of three GLs (sinigrin (SIN), glucotropaeolin (GTL), and...
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Targeting yeast topoisomerase II by imidazo and triazoloacridinone derivatives resulting in their antifungal activity
PublicationFungal pathogens are considered as serious factors for deadly diseases and are a case of medical concern. Invasive fungal infections also complicate the clinical course of COVID-19, leading to a significant increase in mortality. Furthermore, fungal strains' multidrug resistance has increased the demand for antifungals with a different mechanism of action. The present study aimed to identify antifungal compounds targeting yeast...
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Anticancer Imidazoacridinone C-1311 is Effective in Androgen-Dependent and Androgen-Independent Prostate Cancer Cells
PublicationAndrogen receptor (AR) plays a crutial role in prostate cancer (PCa) development and metastasis. Here, we reported potent anti-PCa activity of a small molecule imidazoacridinone C-1311. In AR-positive PCa cells, C-1311 was found to inhibit the transcriptional activity of AR uncovering a novel mechanism that may be relevant for its anticancer effect. Mechanistically, C-1311 decreased AR binding to prostate-specific antigen (PSA)...
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Results from a Genome-Wide Association Study (GWAS) in Mastocytosis Reveal New Gene Polymorphisms Associated with WHO Subgroups
PublicationMastocytosis is rare disease in which genetic predisposition is not fully understood. The aim of this study was to analyze associations between mastocytosis and single nucleotide polymorphisms (SNPs) by a genome-wide association study (GWAS) approach. A total of 234 patients were enrolled in our study, including 141 with cutaneous mastocytosis (CM; 78 children and 63 adults) and 93 with systemic mastocytosis (SM, all adults)....
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A first-principles study of electron attachment to the fully hydrated bromonucleobases
PublicationDegradation mechanism of four brominated nucleobases (BrX), potential DNA radiosensitizers, is studied in explicit water solution, using ab initio molecular dynamics. Several fs long dynamics is needed to localize an electron on the nucleobase. Produced by electron attachment BrX anion radical degrades through the bromide anion abstraction, barrier-free (purines) or with low barrier (pyrimidines), to a reactive nucleobase radical....
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Charakterystyka bakterii rodzaju Thermus i ich przydatność w biotechnologii
PublicationGram ujemne, termofilne bakterie rodzaju Thermus o optymalnych temperaturach wzrostu mieszczących się w zakresie 55-85 C są przydatne jako źródło nukleaz, polimeraz DNA oraz wielu innych termostabilnych enzymów. W przedstawionym artykule wymieniono występowanie i morfologię bakterii rodzaju Thermus, sposoby odżywiania i warunki ich wzrostu, budowę struktur powierzchniowych, sposoby adaptacji do wzrostu w podwyższonej temperaturze...
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Molecular detection of Candida krusei
PublicationThe species identification of fungi belonging to genus Candida is an important issue as this genus becomes the emerging problem of nosocomial infections. As Candida krusei presents intrinsicresistance to the fluconazole that is the drug of the first choice in case of invasive candidiasis the PCR identifying the DNA of C. krusei was elaborated. The analytical sensitivity of the assay on spiked blood samples was estimated at 3-5...
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PCR detection of Scopulariopsis brevicaulis
PublicationScopulariopsis brevicaulis is known as a most common etiological factor of the mould toenail infections. There are also reports indicating that S. brevicaulis could cause organ and disseminated infections. Nowadays microscopic observations from the direct sample and culture are crucial for the appropriate recognition of the infection. In this paper is presented a PCR-based method for S. brevicaulis detection. The specificity of...
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Improvement of derivatized amino acid detection sensitivity in micellar electrokinetic capillary chromatography by means of acid-induced pH-mediated stacking technique
PublicationDerivatization is a frequently used sample prepara-tion procedure applicable to the enhancement of analyte de-tection sensitivity. Amino acids mostly require derivatization prior to electrophoretic or chromatographic analysis, especial-ly if spectrophotometric detection is used. This study presents an on-line preconcentration technique for derivatized amino acids. The sensitivity of the method was improved by the utilization of...
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Numeryczna analiza zagrożenia powodziowego na odcinku starego koryta Raduni w Kolbudach
PublicationPodczas pracy nad określeniem zagrożenia powodziowego w Kolbudach przeanalizowano nieustalony proces transformacji fali powodziowej na starym odcinku Raduni. W tym celu określono hydrogram hipotetycznej fali wezbraniowej o określonym prawdopodobieństwie występowania (p=1%) w przekroju jazu Kolbudy. Przemieszczająca się w korycie rzeki fala wezbraniowa jest zjawiskiem zmiennym w czasie, do opisu, której stosuje się równania nieustalonego...
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Roughness evaluation of turned composite surfaces by analysis of the shape of Autocorrelation Function
PublicationIn this paper, the application of an Autocorrelation Function for the characterisation of surface topography was validated. The roughness evaluation of turned composite surfaces was supported by sophisticated studies of the Autocorrelation Function properties, considering especially the shape of the function. Details were measured with the optical method. The selection of the surface roughness evaluation procedures was carried...
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The LaPdIn 4 indide and elementary properties of the LaTIn 4 ( T = Ni, Pd, Pt) materials family
PublicationThe indium-rich intermetallic compound LaPdIn4 is reported, prepared by arc-melting and annealing at 600 C. Single crystal X-ray diffraction found the material to be orthorhombic, space group Cmcm (No. 63), with lattice parameters a ¼ 4.5462(3) Å, b ¼ 16.9208(10) Å, and c ¼ 7.3100(5) Å. This previously unreported indide is isostructural with LaNiIn4 and LaPtIn4. It is demonstrated that all three compounds in the LaTIn4 (T ¼ Ni,...
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Modeling Object Oriented Systems via Controlled English Verbalization of Description Logic
PublicationThe need for formal methods for Object Oriented (OO) systems resulted in methods like UML and Lepus3 that are de-facto graphical languages equipped with formal tools that are able to handle the design of OO systems. However, they lack precise semantics which might lead to problems, such as inconsistencies or redundancies. On the other hand, to our knowledge, there is no approach that allows one to understand and follow the requirements...
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The effect of beech wood (Fagus sylvatica L.) steaming process on the colour change versus depth of tested wood layer
PublicationThe results of experimental research on the colour changes of beech wood at different depths of the tested layer are presented. Beech wood (Fagus sylvatica L.) dried in a conventional kiln was tested. Half of the wood samples were steamed prior to the drying process. Colour changes were measured at various depths after the face milling process was used to remove the material to expose to the deeper surface. The colour changes were...
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Specification-Oriented Automatic Design of Topologically Agnostic Antenna Structure
PublicationDesign of antennas for modern applications is a challenging task that combines cognition-driven development of topology intertwined with tuning of its parameters using rigorous numerical optimization. However, the process can be streamlined by neglecting the engineering insight in favor of automatic de-termination of structure geometry. In this work, a specification-oriented design of topologically agnostic antenna is considered....
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Stable isotopes unveil one millennium of domestic cat paleoecology in Europe
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Nowoczesne metody diagnostyki zakażeń dermatofitowych
PublicationGrzyby należące do rodzajów Microsporum, Trichophyton i Epidermophyton są główną przyczyną powierzchownych zakażeń grzybiczych. Klasyczna identyfikacja gatunkowa czynnika etiologicznego tych grzybic oparta na obserwacjach mikro- i makroskopowych możliwa jest dopiero po uzyskaniu czystej hodowli dermatofitów. W związku z powolnym tempem wzrostu jest ona możliwa po dwóch, trzech tygodniach po pobrania próbki. Molekularne metody diagnostyczne...
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Epigenetic inhibitor zebularine activates ear pinna wound closure in the mouse
PublicationBackground:Most studies on regenerative medicine focus on cell-based therapies and transplantations.Small-molecule therapeutics, though proved effective in different medical conditions, have not been extensivelyinvestigated in regenerative research. It is known that healing potential decreases with development and devel-opmental changes are driven by epigenetic mechanisms, which suggests epigenetic repression of regenerativecapacity.Methods:We...
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Relation of the polymorphism of cyp51A sequence and the susceptibility of Aspergillus fumigatus isolates to triazoles determined by commercial gradient test (Etest) and by reference methods
PublicationThe aim of this study was to evaluate the accuracy of commercial gradient test (Etest) in the detection of triazole resistant Aspergillus fumigatus isolates using reference microdilution methods and the analysis of sequences of the cyp 51A gene. The study was performed on twenty clinical isolates which were identified as Aspergillus fumigatus based on the DNA sequences of the ITS1-2 fragment of ribosomal DNA and the β-tubulin gene,...
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Relationship between conversion rate of glucosinolates to isothiocyanates/indoles and genotoxicity of individual parts of Brassica vegetables
PublicationThe studies on the characterisation of glucosinolates (GLs) and their breakdown products in Brassicaceae species focus mainly on the edible parts. However, other products, e.g., dietary supplements, may be produced also from non-edible parts such as roots or early forms of growth: seeds or sprouts. Biological activity of these products depends on quantitative and qualitative GL composition, but is also strictly determined by GL...
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Epigenetic regulation and regeneration: the search for differentially methylated genes in the MRL mouse
PublicationThe MRL mouse is an inbred laboratory strain, which was developed in the 60’s of the 20th century and has been extensively used as a model of lupus erythematosus. The regenerative abilities of the strain were discovered in the 90' when the MRL mouse was shown to close 2 mm hole punches made in the ear pinnae four weeks after injury without scarring. The phenomenon has not been observed in other mouse strains, where the holes...
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Diagnostyka molekularna w zakażeniach szpitalnych
PublicationOpisano najczęściej wykorzystywane techniki genotypowania w badaniach zakażeń szpitalnych z uwzględnieniem ich powtarzalności i potencjału różnicującego oraz problemów technicznych i ponoszonych kosztów. Makrorestrykcyjna analiza genomowego DNA z wykorzystaniem PFGE (ang. Pulsed Field Gel Electrophoresis)jest uważana za ''złoty standard'' w typowaniu molekularnym. Jednak jest ona czasochłonna, pracochłonna i dlatego nie nadaje...
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Genotoxic effects of antitumor 1-nitroacridines C-857 and its novel analoque 4-methyl-1-nitroacridine C-1748
Publication4-podstawione 1-nitroakrydyny reprezentują nową grupę pochodnych akrydyny zsyntetyzowanych na Politechnice Gdańskiej. W przeprowadzonych badaniach nad pochodnymi C-1748 i C-857 zastosowano dwie metody badawcze: test kometowy oraz zmodyfikowany test mikrojąderkowy (CBMN assay). W teście kometowym wykazano wzrost uszkodzeń DNA w zależności od czasu i stężenia badanych pochodnych 1-nitroakrydyny. Badania aberracji chromosomalnych...
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Valence and ionic lowest-lying electronic states of small esters studied by high resolution vacuum ultraviolet photoabsorption, photoelectron spectroscopy and ab initio calculations
PublicationEsters are an important class of oxygenated volatile organic compounds used in food flavorings, perfumes and other cosmetic products. They are present in fruits and pheromones and are emitted to the atmosphere naturally. Esters are also formed in the atmosphere as a product of the oxidation of ethers. Some of them form poly-molecule chains and are used in plastics. Phosphoesters form DNA backbone, while nitroesters are known for...
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Smart Innovation Management in Product Life Cycle
PublicationThe present paper proposes a framework for smart innovation management of the product using a Smart Knowledge Management System comprising Set of Experience Knowledge Structure (SOEKS) and Decisional DNA. This proposed system will allow the entrepreneurs and organizations to perform the innovation process technically and quickly as this framework will store knowledge as well as experiences of the past innovations done in various...