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Search results for: dna mismatch enrichment
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Seabed characterisation using spectral moments of the echo signal
PublicationZbadano użyteczność zastosowania momentów spektralnych obwiedni echa w rozpoznawaniu i klasyfikacji dna morskiego. Przeprowadzono obliczenia momentów spektralnych dla około 15000 ech od dna zarejestrowanych w rejonie Bałtyku Południowego i potwierdzono tezę, że wartości tych momentów skorelowane są silnie z typem dna i rodzajem osadów.
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The fate and contamination of trace metals in soils exposed to a railroad used by Diesel Multiple Units: Assessment of the railroad contribution with multi-tool source tracking
PublicationSoil samples from cut slopes from lightly loaded railway lines used by Diesel Multiple Units for 5 years in Gdansk (Poland) were collected and analyzed for trace metals (TMs): Zn, Pb, Cd, Ni, Cr, Cu, and Fe. The main aim was to assess soil enrichment, contamination status, and distribution of TMs relative to the distance from the railway track. Extensive source tracking analyses were performed using cluster analysis (CA) and the...
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Metylotransferazy ssaków – inhibitory i aktywatory
PublicationWśród metylotransferaz ssaków możemy wyróżnić metylotransferazy histonowe oraz metylotransferazy DNA. Metylacja DNA w obrębie wysp CpG oraz metylacja histonów wpływają na poziom ekspresji genów w komórkach ssaczych. Dodatkowo dzięki metylacji zapewniana jest stabilność i integralność genomu ludzkiego. Metylotransferazy DNA, będące głównym tematem tego artykułu, są często przedmiotem badań, gdyż nieprawidłowa metylacja DNA jest...
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DDLMS PCR double digestion Ligation Mediated Suppression PCR - a new technique for bacterial specific differentiation
PublicationA new diagnostic kit for K. oxytoca specific differentiation based on ddLMS PCR (ang. double digest ligation Mediated PCR) technique is shown. As a species-specific DNA fragment pehX gene, encoding the enzyme polygalactouronase, was chosen. The genome sequence of K. oxytoca is digested with two endonucleases: AclI and BclI which cut DNA before and after pehX gene. The polymorphic DNA fragments are ligated with AclI-end-specific...
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Loop-mediated isothermal amplification (LAMP) as a diagnostic tool in detection of infectious diseases
PublicationLoop-mediated isothermal amplification (LAMP) is a gene amplification method which amplifies DNA with high specificity and efficiency under isothermal conditions. Because of its rapidity and simplicity, it is a valuable diagnostic tool in the early detection and identification of infectious diseases. LAMP method is based on the use of a set of four to six specially designed primers spanning six to eight distinct sequences on the...
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Sensitivity of echo parameters to seafloor properties and depth variability.
PublicationPrzeprowadzono badanie użyteczności wybranych parametrów echa akustycznego, w szczególności wymiaru fraktalnego oraz momentów spektralnych obwiedni, w klasyfikacji dna morskiego, ze szczególnym uwzględnieniem wpływu zmieniającej się głębokości. Wykorzystano numeryczną symulację rozpraszania echa na dnie oraz innych elementów procesu akustycznego sondowania dna, w tym także procedurę kompensacji wpływu zmian głębokości dna na echo.
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Michał Szydłowski dr hab. inż.
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Multi-Decision Analysis for selection of the best procedure for PAHs determination in smoked food.
PublicationMaking a proper decision in multifacitated situation is very challenging task. Especially, if there are many alternatives and criteria, even contradictory ones. The support tools may be application of MultiCriteria Decision Analysis methods. In this study the application of PROMETHEE...
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The antioxidative properties of white cabbage (Brassica oleracea var. capitata f. alba) fresh and submitted to culinary processing
PublicationKapusta biała stanowi jeden z podstawowych składników diety w Europie centralnej. W publikacji autorzy skupili się na określeniu właściwościach przeciwutleniających kapusty świeżej, kiszonej i poddanej obróbce termicznej. Te właściwości zostały oszacowane dla soków przy wykorzystaniu systemów pozakomórkowych, w komórkach HT29 pod kątem ochrony przed utlenieniem DNA oraz poprzez symulację GSTs i naprawę DNA. Wszystkie badane soki...
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Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models
PublicationOxidative damage to DNA is widely known to contribute to aging and disease. This relationship has been extensively studied for telomeres – structures that cap chromosome ends – due to their role in cell proliferation and senescence, and exceptional susceptibility to oxidation. Indeed, the repetitive telomeric DNA sequence contains the 5′-GGG-3′ motif that has the lowest ionization potential of all trinucleotides. Accordingly, experiments...
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The construction of bifunctional fusion proteins consisting of MutS and GFP
PublicationSkonstruowano białka chimeryczne zawierające białko MutS z Thermus thermophilus i białko zielonej fluoresceiny GFP z Aequorea victoria, posiadające dla łatwiejszego oczyszczania domeny oligo-histydynowe na N- lub C-końcu. Fuzyjne białka rozpoznawały niekomplementarności w DNA podobnie do MutS T. thermophilus. Fluorescencyjne białka rozpoznające niekomplementarne DNA mogą być użyteczne w wykrywaniu jednonukleotydowych polimorfizmów...
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PCR-ELISA: inexpensive alternative to quantitative PCR
PublicationPCR-ELISA (polymerase chain reaction-enzyme linked immunosorbent assay), a combination of PCR and ELISA methods, has been used since late 1980s. The technique is based on specially labelled DNA fragments which are captured by specific DNA sequences and detected by antibodies. The whole procedure of PCR-ELISA is divided into three steps: DNA extraction, PCR reaction and detection by ELISA. The method has been found as very specific...
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Microstructure and Electrical Properties of Fe,Cu Substituted (Co,Mn)3O4 Thin Films
PublicationIn this work, thin films (~1000 nm) of a pure MnCo2O4 spinel together with its partially substituted derivatives (MnCo1.6Cu0.2Fe0.2O4, MnCo1.6Cu0.4O4, MnCo1.6Fe0.4O4) were prepared by spray pyrolysis and were evaluated for electrical conductivity. Doping by Cu increases the electrical conductivity, whereas doping by Fe decreases the conductivity. For Cu containing samples, rapid grain growth occurs and these samples develop cracks...
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Interactions of telomeric proteins with nucleic acids: sequence recognition on intact and oxidatively damaged telomeres
PublicationTelomeres are complex nucleoprotein assemblies that play a vital role in the maintenance of functional ends of linear chromosomes. Telomeric DNA, composed of tandem repeats of the 5'-TTAGGG-3' motif, solves the so-called end replication problem: as chromosomes shorten with each cell division, no information is lost, and the telomere can be re-extended. In the cell, many protein factors regulate telomere length, nuclear positioning...
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Increasing efficiency of technological process by limiting impact of corrosive environment on operation of spiral classifiers
PublicationMost of the technological operations related to the preparation of the output to be enriched and to the production of the final copper concentrate take place with the use of water environment. Water management, besides using innovative technical and technological solutions, is a significant factor in the whole copper ore enrichment process. Mine water resources and surface water of the tailing pond named "Żelazny Most" are the...
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The effect of calcination temperature on structure and photocatalytic properties of Au/Pd nanoparticles supported on TiO2
PublicationBimetallic nanoparticles, composed of two different metal elements, can exhibit peculiar electronic, optical, and catalytic or photocatalytic properties that are absent in the corresponding monometallic nanoparticles. We show the effect of calcination temperature (from 350 to 700°C) on the structure and the photocatalytic properties of Au/Pd-modified TiO2. The composition of the bimetallic Au/Pd nanoparticles in relation to their...
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Grażyna Grelowska prof. dr hab. inż.
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Identification and cloning of C. albicans SC5314 genes encoding L-methionine biosynthetic pathway enzymes.
Open Research DataEnzymes of fungal L-methionine biosynthetic pathway: homoserine O-acetyltransferase (Met2p), O-acetylhomoserine sulfhydrylase (Met15p) and cystathionine-γ-synthase (Str2p) could be exploited as molecular targets for antifungal chemotherapy. The goal of the study was to identify and clone genes encoding mentioned above enzymes. MET2, MET15 and STR2 genes...
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Classification methods and criteria
PublicationKlasyfikacja akustyczna dna morskiego jest najnowszą metodologią zaprojektowaną w celu zdalnego wykrywania rozmaitych charakterystyk dna morskiego z informacji zawartych w echch od dna akustycznych impulsów transmitowanych z różnego typu sonarów. Poza szególnymi chrakterystykami sprzętowymi każdego systemu ASC, istotą każdej metody jest klasyfikacja modułu, który wyciąga serie cech z echa sygnału i przetwarza je aby posortować...
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X-ray and UV Radiation Damage of dsDNA/Protein Complexes
PublicationRadiation and photodynamic therapies are used for cancer treatment by targeting DNA. However, efficiency is limited due to physico-chemical processes and the insensitivity of native nucleobases to damage. Thus, incorporation of radio- and photosensitizers into these therapies should increase both efficacy and the yield of DNA damage. To date, studies of sensitization processes have been performed on simple model systems, e.g.,...
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Experience-Oriented Knowledge Management for Internet of Things
PublicationIn this paper, we propose a novel approach for knowledge management in Internet of Things. By utilizing Decisional DNA and deep learning technologies, our approach enables Internet of Things of experiential knowledge discovery, representation, reuse, and sharing among each other. Rather than using traditional machine learning and knowledge discovery methods, this approach focuses on capturing domain’s decisional events via Decisional...
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Benzonaza(R): możliwości praktycznych zastosowań.
PublicationBenzonaza znajduje zastosowanie w efektywnym obniżaniu lepkości i usuwaniu kwasów nukleinowych z roztworów białkowych. Zbadano w praktyce jej możliwości aplikacyjne w oczyszczaniu białek rekombinantowych wiążących jednoniciowe DNA (ang. SSB - single stranded DNA binding protein).
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Polychlorinated Biphenyls (PCBs) and Polycyclic Aromatic Hydrocarbons (PAHs): Sediments and Water Analysis
PublicationUnfavorable side effects of different forms of anthropogenic activities can be found anywhere in the world. One of the basic characteristics of pollutants entering marine and ocean waters is their spread and movement in the global ocean. A portion of the substances entering the marine environment is rapidly degraded by chemical processes occurring in the air, sediments, and water, thereby losing their toxic properties. The biggest...
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Genotyping Techniques for Determining the Diversity of Microorganisms
PublicationTyping of microbial pathogens, or identifying bacteria at the strain level, is particularly important for diagnosis, treatment, and epidemiological surveillance of bacterial infections. This is especially the case for bacteria exhibiting high levels of antibiotic resistance or virulence, and those involved in nosocomial or pandemic infections. Strain typing also has applications in studying bacterial population dynamics. The part...
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Projektowanie Konstrukcji Okrętu, P, BOiJ, sem7 DS - studia niestacjonarne, zimowy 21/22, (PG_00046546)
e-Learning CoursesWykonanie metodą MES w oprogramowaniu MSC Patran/Nastran 2021.1 Student Edition analizy obciążenia fragmentu sekcji dna podwójnego i pokładu promu pasażersko-samochodowego.
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A simple modification to improve the accuracy of methylation-sensitive restriction enzyme quantitative polymerase chain reaction
PublicationDNA digestion with endonucleases sensitive to CpG methylation such as HpaII followed by polymerase chain reaction (PCR) quantitation is commonly used in molecular studies as a simple and inexpensive solution for assessment of region-specific DNA methylation. We observed that the results of such analyses were highly overestimated if mock-digested samples were applied as the reference.We determined DNA methylation levels in several...
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Monitoring of volatile organic compounds (VOCs) in atmospheric air. Part II. Sample collection and preparation
PublicationThe paper reviews literature information on air sampling techniques commonly used for monitoring volatile organic compounds (VOCs) levels in atmospheric air. It describes containers for collecting samples of atmospheric air, such as vacuum canisters and bags made from synthetic materials. It discusses dynamic, passive and denudational techniques for sampling analytes from air combining isolation with preliminary enrichment, and...
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The smoothness test for a density function
PublicationThe problem of testing hypothesis that a density function has no more than μ derivatives versus it has more than μ derivatives is considered. For a solution, the L2 norms of wavelet orthogonal projections on some orthogonal ‘‘differences’’ of spaces from a multiresolution analysis is used. For the construction of the smoothness test an asymptotic distribution of a smoothness estimator is used. To analyze that asymptotic distribution,...
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Możliwości zastosowań, potencjalne źródła oraz ewolucja technologiczna sposobu otrzymywania trehalozy ze szczególnym uwzględnieniem enzymu syntazy trehalozy [EC 5.4.99.16]
PublicationJedna z wiodących gałęzi współczesnej biotechnologii opiera się na produkcji białek – przede wszystkim enzymów. Są one powszechnie wykorzystywane: od przemysłu chemicznego poprzez przemysł spożywczy aż po medycynę i życie codzienne (czy ktoś wyobraża sobie w dzisiejszych czasach proszek do prania „bez enzymu”). Przed rozwojem nowoczesnych metod biologii molekularnej i inżynierii genetycznej pozyskiwano interesujące substancje z...
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Konstrukcja Okrętu II , W, BOiJ, sem 5 - studia niestacjonarne , zimowy 21/22 (PG_00046526)
e-Learning CoursesOgólne zasady konstrukcji kadłubów statkówCz. I Ruszty, odstęp elementów zładu, krzyżowanie się usztywnień, otwory, luzy i naddatki, węzłówkiCz. II Nazwy płatów poszycia, usztywnień i wiązarów elementów kadłubaDna pojedynczegoDna podwójnegoPokładów Burty pojedynczejBurty podwójnejGrodzi i przegródRufyDziobuFundamenty SG, SP oraz innych urządzeńZbiornikówNadbudówki, pokładówki
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Tuning the extraction properties of ionogel-coated Solid-phase microextraction fibers based on the solvation properties of the ionic liquids
PublicationA silica-based network was used to immobilize ionic liquid-based ionogels and applied as a fiber coating forsolid-phase microextraction (SPME). The ionogels were prepared by a sol–gel process, using two ionic liquids,triethylsulfonium bis(trifluoromethylsulfonyl)imide ([Set3][TFSI]) and 1-butyl-1-methylpiperidinium bis(tri-fluoromethylsulfonyl)imide ([C4C1Pip][TFSI]), as well as their equimolar mixture. Methyltrimethoxysilane wasused...
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Virtual Engineering Objects: Effective Way of Knowledge Representation and Decision Making
PublicationThis paper presents a knowledge representation case study by constructing Decisional DNA of engineering objects. Decisional DNA, as a knowledge representation structure not only offers great possibilities on gathering explicit knowledge of formal decision events but also it is a powerful tool for decision-making process. The concept of Virtual engineering Object (VEO), which is a knowledge and experience representation of engineering...
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Data on solutions of Hes1 system
Open Research DataHes1 protein (hairy and enhancer of split 1) belongs to the helix-loop-helix (bHLH) family of transcription proteins, i.e. DNA-binding proteins in the promoter region or in another region where regulation of transcription processes occurs. The database collects data on solutions of the Hes1 systems with multiple binding sites and the dimer formation...
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A 1-nS 1-V Sub-1-µW Linear CMOS OTA with Rail-to-Rail Input for Hz-Band Sensory Interfaces
PublicationThe paper presents an operational transconductance amplifier (OTA) with low transconductance (0.62–6.28 nS) and low power consumption (28–270 nW) for the low-frequency analog front-ends in biomedical sensor interfaces. The proposed OTA implements an innovative, highly linear voltage-to-current converter based on the channel-length-modulation effect, which can be rail-to-rail driven. At 1-V supply and 1-Vpp asymmetrical input driving,...
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Assessment of E-government inclusion policies toward seniors: A framework and case study
PublicationDigital exclusion of seniors covers both social and technical drivers that affect the magnitude of this phenomenon. It arises from the fear of technology, reduced manual and mental abilities, socio-economic status, and also the mismatch between the technological environment and the needs of the elderly. The consideration of the needs of seniors are mainly implemented through social policies while the provision of government services...
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VOLTAMMETRIC DETERMINATION OF DEOXYRIBONUCLEIC ACID PRESENCE ON A CARBON ELECTRODE
PublicationThis paper presents a voltammetry as a useful method to analyse DNA from different species. This electrochemical method is well know and used in different analyses. The influence of an area of working electrode and the capacity component, is shown at equals and the measurement. In voltammetry DNA measurement the capacity component is very important and must be taken into consideration. All mathematical analyses were verify at laboratory.
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Wiązanie się do DNA pochodnych 4-metylo-1-nitroakrydyny wykazujących właś-ciwości przeciwnowotworowe.**2003, 116 s. 23 rys. 12 tab. bibliogr. 163 poz. maszyn. Rozprawa doktorska /09.05.2003/ P. Gdań. Wydz. Chem. Promotor: prof. dr hab. inż. J. Konopa.
Publication.
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Novel primosomal protein B from Clostridium pastuerianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Multisine impedimetric probing of biocatalytic reactions for label-free detection of DEFB1 gene: How to verify that your dog is not human?
PublicationAlbert is a dog (Canis familiaris), but he does not realize this. Albert loves human food (and beer), watching movies on the internet, sleeping in bed, and more. But he should not do all these things. To convince him that, we have desinged a test procedure. The DEFB1 gene is unique to human species. Detecting its presence from saliva and in short periods may offer an advantage in the field of forensic medicine, and influence Albert’s...
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Novel primosomal protein B from Clostridium pasteurianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Real-Time PCR: molecular technique of many applications
PublicationReal-Time PCR is a sensitive DNA amplification technique initially applied in genetics and molecular biology. It enables in vivo copying of the selected DNA fragment (flanked by two primers) by the thermostable polymerase (in the presence of magnesium ions and deoxynucleotide triphosphates) and simultaneous measurement of the fluorescence. For one or more specific sequences in a DNA sample, real-time PCR enables both detection...
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Diagnostyka molekularna w medycynie 2023
e-Learning CoursesCelem przedmiotu jest zapoznanie studenta z nowoczesnymi, molekularnymi metodami stosowanymi w diagnostyce medycznej oraz nabycie umiejętności posługiwania się programami do obróbki danych z poziomu DNA.
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ALIS-FLP: amplified ligation selected fragment-length polymorphism method for microbial genotyping
PublicationA DNA fingerprinting method known as ALIS-FLP (amplified ligation selected fragment-length polymorphism) has been developed for selective and specific amplification of restriction fragments from TspRI restriction endonuclease digested genomic DNA. The method is similar to AFLP, but differs in that only one specific restriction enzyme (TspRI) is used. The cohesive ends of the DNA fragments are ligated with two types of oligonucleotide....
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Spectroelectroanalytical properties of antitumor agent C1311
PublicationZastosowano kilka metod woltamperometrycznych dla charakterystyki właściwości elektrochemicznych przeciwnowotworowej pochodnej imidazoakrydonu o symbolu C-1311. Wyniki wskazały, że możliwym będzie zastosowanie metod elektrochemicznych do badania oddziaływań badanego związku z DNA. Badania spektroelektrochemiczne ujawniły, że oscylacyjne zmiany absorbcji związku obserwowane po cyklicznej polaryzacji elektrody. Oscylacje te znikały...
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MutL protein as a constituent of vsp, ner and mmr repair systems
PublicationMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mis- match repair system (MMR). However, there is growing evidence that MMR system is not the only field of action for these pro- teins. Moreover, the participation in MMR does not even have to be their primary function. There are some reports indicat- ing involvement of MutL in BER, NER and VSP (very short patch repair)....
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The role of epigenetics in regeneration
PublicationComplex changes in chromatin structure and at the transcriptional level occur from the creation of a single parental gamete throughout fertilization, embryo development and the life of an adult organism. Epigenetic changes, such as methylation and hydroxymethylation of DNA or histone methylation and acetylation, are an important part of these processes. Epigenetic regulation has an essential influence on gene expression level. DNA...
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Instalacja i wstępna analiza danych batymetrycznych pochodzących z echosondy wielowiązkowej
PublicationW akustycznym telemonitoringu środowiska morskiego stosowane są dwa rodzaje sonarów, a mianowicie: sonary boczne i echosondy wielowiązkowe. Oba systemy dostarczają danych zarówno dla batymetrii, jak i dla akustycznego obrazowania dna morskiego. Echosondy wielowiązkowe są zaawansowanymi technologicznie urządzeniami, które dzięki wielokierunkowej obserwacji szerokokątnej dna, przy jednoczesnym utrzymaniu wysokiej rozdzielczości kątowej,...
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Discrimination of hospital isolates of Acinetobacter baumannii using repeated sequences and whole genome alignment differential analysis
PublicationAn optimized method for bacterial strain differentiation, based on combination of Repeated Sequences and Whole Genome Alignment Differential Analysis (RS&WGADA), is presented in this report. In this analysis, 51 Acinetobacter baumannii multidrug-resistance strains from one hospital environment and patients from 14 hospital wards were classified on the basis of polymorphisms of repeated sequences located in CRISPR region, variation...
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Adaptive neuro fuzzy and fuzzy decision tree classifiers as applied to sea floor characterization.
PublicationPrzedstawiono wyniki badań wpływu różnych parametrów echa odbitego od dna morskiego na dokładność klasyfikacji typu dna przy pomocy sieci neuronowej z logiką rozmytą i przy pomocy drzew decyzyjnych. W szczególności uwzględniono takie parametry echa jak: energia, amplituda i nachylenie opadającego zbocza, wzbogacone o współczynniki falkowe otrzymane z dyskretnej transformacji falkowej (DWT).
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RECSYS CHALLENGE 2015: a BUY EVENT PREDICTION IN THE E-COMMERCE DOMAIN
PublicationIn this paper we present our approach to RecSys Challenge 2015. Given a set of e-commerce events, the task is to predict whether a user will buy something in the current session and, if yes, which of the item will be bought. We show that the data preparation and enrichment are very important in finding the solution for the challenge and that simple ideas and intuitions could lead to satisfactory results. We also show that simple...