Search results for: draft genome sequence
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Wild oscillations in a nonlinear neuron model with resets: (I) Bursting, spike-adding and chaos
PublicationIn a series of two papers, we investigate the mechanisms by which complex oscillations are generated in a class of nonlinear dynamical systems with resets modeling the voltage and adaptation of neurons. This first paper presents mathematical analysis showing that the system can support bursts of any period as a function of model parameters, and that these are organized in a period-incrementing structure. In continuous dynamical...
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Uniwersalny program komputerowy do projektowania zmiany kierunku trasy
PublicationW pracy przedstawiono kolejny program komputerowy stanowiący implementację algorytmu obliczeniowego dotyczącego projektowania zmiany kierunku trasy kolejowej, dostosowanego do techniki ciągłych pomiarów satelitarnych. Program ten ma charakter uniwersalny, gdyż w ogólnym przypadku obejmuje wprowadzenie do układu geometrycznego dwóch łuków kołowych o różnym promieniu, czyli zastosowanie łuku koszowego. Może się to okazać szczególnie...
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Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants
PublicationThe genome feature of SARS-CoV-2 leads the virus to mutate and creates new variants of concern. Tackling viral mutations is also an important challenge for the development of a new vaccine. Accordingly, in the present study, we undertook to identify B- and T-cell epitopes with immunogenic potential for eliciting responses to SARS-CoV-2, using computational approaches and its tailoring to coronavirus variants. A total of 47 novel...
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Genetic and biochemical characterization of yeasts isolated from Antarctic soil samples
PublicationThe Polish Arctowski Station is situated in the maritime Antarctic on the western shore ot' Admiralty Bay and encompasses terrestrial habitats which are not perma-nently covered by ice, in contrast to morę than 90% of the island's surface area. Over the past several decades, stud-ies exploring the soils of those habitats have revealed a considerable diversity of bacteria, filamentous fungi, and, to a lesser extent, yeasts; however,...
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Chicken feather keratin as a source of bioactive peptides useful in prevention of metabolic disorders – in silico and in vitro hydrolysis
PublicationProtein derived bioactive peptides not only serve as nutrients but can also exert drug-like activity, e.g. antidiabetic, antihypertensive, or antimicrobial, to name a few. Most biopeptides have beneficial effects on health that make them attractive for nutraceutical applications. The majority of bioactive peptides have been obtained from food proteins, but protein-rich by-products generated by agriculture...
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On the Origin of Protein Superfamilies and Superfolds
PublicationDistributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to...
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Adaptive Sampling for Non-intrusive Reduced Order Models Using Multi-Task Variance
PublicationNon-intrusive reduced order modeling methods (ROMs) have become increasingly popular for science and engineering applications such as predicting the field-based solutions for aerodynamic flows. A large sample size is, however, required to train the models for global accuracy. In this paper, a novel adaptive sampling strategy is introduced for these models that uses field-based uncertainty as a sampling metric. The strategy uses...
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Modelling and Analysis of the Positioning Accuracy in the Loading Systems of Mobile Cranes
PublicationIn this work, the authors analyse the influence of the order and range of sequential movements of a crane's working members on the accuracy of the final cargo positioning. The analysis was conducted on the basis of a specially developed method in which the authors proposed the introduction of a geometrical indicator of positioning the load in the intermediate positions (after completing each movement sequence) and in the target...
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Storing Matter’technique in SIMS depth profile analysis
PublicationSecondary ion mass spectrometry (SIMS) is a very useful technique for the analysis of layered systems. It is based on the primary ion beam sputtering of solids and mass analysis of the emitted secondary ions. A main limitation of this technique results from the direct quantitative analysis, since the ionization efficiency of a given atom is highly influenced by the neighbouring atoms at the surface. This phenomenon is known as...
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Thermographic imaging of electrochemical double layer capacitors during cycling charging - discharging 0 - 3,3 V at 420 mA. Sample 103, run #1.
Open Research DataDataset contains thermal images of prototype electrochemical double layer capacitor taken during cyclic charging - discharging. The sample was charged to 3,3 V and discharged to 10 mV by constant current 420 mA. Sample 103, experiment run #1. Voltage was increased to accelerate the ageing process.The images were taken with thermographic camera VigoCAM...
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Nowelizacja art. 209 kodeksu karnego. Analiza proponowanych zmian. Analysis of the Proposed Amendments to Article 209 of the Polish Criminal Code.
Publication"W niniejszym artykule rozpatrywane jest zagadnienie przestępstwa niealimentacji (zwłaszcza, gdy pokrzywdzonymi są dzieci). Artykuł dotyczy analizy nowelizacji polskiego kodeksu karnego. Przez lata ściągalność roszczeń alimentacyjnych pozostawała na niskim poziomie. Właśnie w celu poprawy skuteczności egzekucji świadczeń alimentacyjnych Ministerstwo Sprawiedliwości przygotowało zmianę w obszarze kodeksu karnego. Nieprawidłowości...
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Gasification of Densified Biomass (DB) and Municipal Solid Wastes (MSW) Using HTA/SG Technology
PublicationThe necessity of economical and rational use of natural energy sources caused a rapid development of research on the possibilities of using non‐conventional energy resources. Taking the above into account, a new technological process of thermochemical conversion of biomass and communal waste, commonly known as High Temperature Air/Steam Gasification (HTA/SG) and Multi‐Staged Enthalpy Extraction Technology (HTAG‐MEET), was developed....
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cDNA fingerprint from the hepatopancreatic glands of pond snails (Lymnaea stagnalis) exposed to benzo[a]pyrene
PublicationIdentification of differentially expressed genes that could be potentially used as biomarkers of PAH exposure of common invertebrate animal (like freshwater snail) would be a valuable resource for investigators interested in toxicology and biomonitoring of aquatic environments. Therefore, the aim of this research was to investigate effects of waterborne benzo[a]pyrene (B[a]P) exposure on mRNA expression in the pond snail’s (Lymnaea...
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Characterization of two aminotransferases from Candida albicans
PublicationAminoadipate aminotransferase (AmAA) is an enzyme of α-aminoadipate pathway (AAP) for l-lysine biosynthesis. AmAA may also participated in biosynthesis or degradation of aromatic amino acids and in d-tryptophan based pigment production. The AAP is unique for fungal microorganisms. Enzymes involved in this pathway have specific structures and properties. These features can be used as potential molecular markers. Enzymes catalyzing...
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Mono- and bi-metallic plasmonic photocatalysts for degradation of organic compounds under UV and visible light irradiation
PublicationTitania powders were surface modified with gold and/or silver nanoparticles (NPs) by photodeposition method. Gold modified titania exhibited much higher photocatalytic activity during methanol dehydrogenation under UV irradiation than titania modified with monometallic silver and bimetallic Au–Ag NPs. Bimetallic photocatalysts exhibited either enhanced or reduced visible light activity, depending on properties of noble metal NPs,...
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Computer-Aided Design of Railroad Horizontal Arc Areas in Adapting to Satellite Measurements
PublicationThis paper presents a method of designing railway sections located in horizontal arcs. The adopted procedure is universal, i.e., it creates the possibility of varying both the type and the length of the assumed transition curves. This means that the applied analytical formulas apply to the boundary conditions of the transition curves and all of the simplifications widely existing in common algorithms have been eliminated. The presented...
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A Method for Underwater Wireless Data Transmission in a Hydroacoustic Channel under NLOS Conditions
PublicationWireless data transmission in the hydroacoustic channel under non-line-of-sight (NLOS) propagation conditions, for example, during a wreck penetration, is difficult to implement reliably. This is mostly due to the multipath propagation, which causes a reduction in the quality of data reception. Therefore, in this work an attempt has been made to develop a reliable method of wireless underwater communication test it under the NLOS...
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Cyclic deformation and fracture behaviour of additive manufactured maraging steel under variable-amplitude loading
PublicationThe cyclic deformation and fracture behaviour of 18Ni300 maraging steel produced by laser beam powder bed fusion is studied under variable-amplitude loading. The tests were conducted under fully-reversed strain-controlled conditions with a loading sequence comprising three ascending cycles and three descending cycles repeated sequentially until failure. After the tests, fracture surfaces were examined using height and volume surface...
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Methodology of generation of CFD meshes and 4D shape reconstruction of coronary arteries from patient-specific dynamic CT
PublicationDue to the difficulties in retrieving both the time‑dependent shapes of the vessels and the generation of numerical meshes for such cases, most of the simulations of blood flow in the cardiac arteries use static geometry. The article describes a methodology for generating a sequence of time‑dependent 3D shapes based on images of different resolutions and qualities acquired from ECG‑gated coronary artery CT angiography. The precision...
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Automatic labeling of traffic sound recordings using autoencoder-derived features
PublicationAn approach to detection of events occurring in road traffic using autoencoders is presented. Extensions of existing algorithms of acoustic road events detection employing Mel Frequency Cepstral Coefficients combined with classifiers based on k nearest neighbors, Support Vector Machines, and random forests are used. In our research, the acoustic signal gathered from the microphone placed near the road is split into frames and converted...
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Odnowa modelu biznesu
PublicationW artykule przedstawiono wyniki badań teoretycznych nad istotą odnowy strategicznej biznesu. Odnowę tę oparto na restauracji ciągu zarządzania strategicznego.
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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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Endoscopic Video Classification with the Consideration of Temporal Patterns
PublicationThe article describes a novel approach to automatic recognition and classification of diseases in endoscopic videos. Current directions of research in this field are discussed. Most presented methods focus on processing single frames and do not take into consideration the temporal relationship between continuous classifications. Existing approaches that consider the temporal structure of an incoming frame sequence are focused on...
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Implementacja odbiornika RAKE w technologii SDR (Software Defined Radio)
PublicationRóżnorodność standardów systemów radiokomunikacyjnych, w tym telefonii komórkowej i bezprzewodowej, przy dużej ruchliwości ich abonentów, powoduje, że niezbędne jest skonstruowanie wielosystemowego terminala ruchomego, mającego techniczne możliwości współpracy z systemami radiokomunikacyjnymi działającymi w różnych standardach. W ten sposób zrodziła się idea radia definiowanego programowego SDR (Software Define Radio), bazująca...
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Study of the Layer-Type BST Thin Film with X-ray Diffraction and X-ray Photoelectron Spectroscopy
PublicationIn the present paper, results of X-ray photoelectron studies of electroceramic thin films of barium strontium titanate, Ba1xSrxTiO3 (BST), composition deposited on stainless-steel substrates are presented. The thin films were prepared by the sol-gel method. A spin-coating deposition of BST layers with different chemical compositions was utilized so the layer-type structure of (0-2) connectivity was formed. After the deposition,...
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Non-Linear Analysis of Structures Utilizing Load-Discretization of Stiffness Matrix Method with Coordinate Update
PublicationThis paper proposes a stiffness method based structural analysis algorithm for geometrically non-linear structures. In this study, the applied load on the joints has been discretized to a sequence of a few loadings applied. Each loading step produces incremental external nodal displacements, which are added to the corresponding coordinates to get a new geometrical shape of the structure. This process is iteratively repeated until...
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Application of safirinium N-hydroxysuccinimide esters to derivatization of peptides for high-resolution mass spectrometry, tandem mass spectrometry, and fluorescent labeling of bacterial cells
PublicationMass spectrometry methods are commonly used in the identification of peptides and biomarkers. Due to a relatively low abundance of proteins in biological samples, there is a need for the development of novel derivatization methods that would improve MS detection limits. Hence, novel fluorescent N-hydroxysuccinimide esters of dihydro-[1,2,4]triazolo[4,3-a]pyridin-2-ium carboxylates (Safirinium P dyes) have been synthesized. The...
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Deep Instance Segmentation of Laboratory Animals in Thermal Images
PublicationIn this paper we focus on the role of deep instance segmentation of laboratory rodents in thermal images. Thermal imaging is very suitable to observe the behaviour of laboratory animals, especially in low light conditions. It is an non-intrusive method allowing to monitor the activity of animals and potentially observe some physiological changes expressed in dynamic thermal patterns. The analysis of the recorded sequence of thermal...
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Simulation model for evaluation of QOS dynamic routing
PublicationCurrent informational networks use a large variety of technologies to support data exchange. Most of them are focused on IP protocol and include mechanisms which by definition should supply demanded QoS. One of those mechanisms is efficient path calculation - routing. Traffic offered to the network can change very rapidly in short term. Routing should support such traffic changes and all the time calculate valid paths in terms...
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Identification and molecular modeling of a novel lipase from an Antarctic soil metagenomic library.
PublicationIn this work, we present the construction of a metagenomic library in Escherichia coli using pUC19 vector and environmental DNA directly isolated from Antarctic topsoil and screened for lipolytic enzymes. The screening on agar supplemented with olive oil and rhodamine B revealed one clone with lipolytic activity (Lip1) out of 11,000 E. coli clones. This clone harbored a plasmid, pLip1, which has an insert of 4722 bp that has been...
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A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library.
PublicationThe presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B. For this purpose, an rsfp gene was cloned and expressed in an LMG194 E. coli strain using an arabinose promoter. The resulting RSFP protein was purified...
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Ribosomal intergenic spacer analysis as a tool for monitoring methanogenic archaea changes in an anaerobic digester
PublicationThe applicability of a newly-designed PCR primer pair in examination of methanogenic Archaea in a digester treating plant biomass was evaluated by Ribosmal Intergenic Spacer Analysis (RISA). To find a suitable approach, three variants of RISA were tested: (1) standard, polyacrylamide gel-based, (2) automated, utilized capillary electrophoresis (GA-ARISA), and (3) automated microfluidics-based (MF-ARISA). All three techniques yielded...
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Analysis of Floodplain Inundation Using 2D Nonlinear Diffusive Wave Equation Solved with Splitting Technique
PublicationIn the paper a solution of two-dimensional (2D) nonlinear diffusive wave equation in a partially dry and wet domain is considered. The splitting technique which allows to reduce 2D problem into the sequence of one-dimensional (1D) problems is applied. The obtained 1D equations with regard to x and y are spatially discretized using the modified finite element method with the linear shape functions. The applied modification referring...
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Sprzętowa realizacja odbiornika sygnałów DS-CDMA w technice radia programowalnego
PublicationRóżnorodność standardów systemów radiokomunikacyjnych, powoduje, że niezbędne jest skonstruowanie wielosystemowego terminala ruchomego, mającego techniczne możliwości współpracy z systemami radiokomunikacyjnymi działającymi w różnych standardach. W ten sposób zrodziła się idea radia definiowanego programowego SDR (Software Defined Radio), bazująca na uniwersalnej warstwie sprzętowej, o funkcjonalności której decyduje jedynie warstwa...
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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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Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublicationPriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the...
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Modular Approach for Modelling Warming Up Process in Water Installations with Flow-Regulating Elements
PublicationThe paper presents a new method for modelling the warming up process of a water system with elements regulating the flow in a stochastic manner. The paper presents the basic equations describing the work of typical elements which the water installation is composed of. In the proposed method, a new computational algorithm was used in the form of an iterative procedure enabling the use of boundary conditions that can be stochastically...
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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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The thermal effort during marine steam turbine flooding with water
PublicationThe work discussed an extreme case of cooling a steam turbine. The ship's steam turbine was used as an example. In marine transport units with low-speed engines dominate, however, there are also units with steam turbines. An example of analysed marine steam turbine is shown in Fig. 1. When considering the issue of cooling steam turbines, it is necessary to estimate the extreme conditions that may occur during operation of the turbine....
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IDENTYFIKACJA CZYNNIKÓW WPŁYWAJĄCYCH NA BEZPIECZEŃSTWO EKSPLOATACJI STATKU NA ŚRÓDLĄDOWEJ DRODZE WODNEJ W DELCIE WISŁY
PublicationKażdego roku w Polsce, na śródlądowych drogach wodnych rejestrowane są przez Urzędy Żeglugi Śródlądowej, Państwową Straż Pożarną i Policję wypadki i incydenty, prowadzące zarówno do uszkodzenia infrastruktury jak i uszczerbku na zdrowiu. Poprawa poziomu bezpieczeństwa wymaga dogłębnej analizy i wyciągania wniosków z zaistniałych sytuacji awaryjnych. Istotną rzeczą jest identyfikacja i usystematyzowanie zagrożeń występujących w...
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Bacteriophages as potential tools for use in antimicrobial therapy and vaccine development
PublicationThe constantly growing number of people suffering from bacterial, viral, or fungal infections, parasitic diseases, and cancers prompts the search for innovative methods of disease prevention and treatment, especially based on vaccines and targeted therapy. An additional problem is the global threat to humanity resulting from the increasing resistance of bacteria to commonly used antibiotics. Conventional vaccines based on bacteria...
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Prediction of metal deformation due to line heating; an alternative method of mechanical bending, based on artificial neural network approach
PublicationLine heating is one of the alternative methods of forming metals and this kind of forming uses the heating torch as a source of heat input. During the process, many parameters are considered like the size of the substrate, thickness, cooling method, source power intensity, the travel speed of the power source, the sequence of heating, and so on. It is important to analyze the factors affecting the...
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Improving the Accuracy of Automatic Reconstruction of 3D Complex Buildings Models from Airborne Lidar Point Clouds
PublicationDue to high requirements of variety of 3D spatial data applications with respect to data amount and quality, automatized, effcient and reliable data acquisition and preprocessing methods are needed. The use of photogrammetry techniques—as well as the light detection and ranging (LiDAR) automatic scanners—are among attractive solutions. However, measurement data are in the form of unorganized point clouds, usually requiring transformation...
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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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Identification and properties of the psychrophilic bacterium Desulfolatea psychrophila single-stranded DNA binding proteins
PublicationTo study the biochemical properties of SSB from Desulfolatea psychrophila (DpsSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 426 nucleotides encoding SSB protein of 142 amino acids with a calculated molecular mass of 15.6 kDa and it is the smallest known bacterial SSB protein indentified to date. The amino-acid sequence...
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Localization of impulsive disturbances in audio signals using template matching
PublicationIn this paper, a new solution to the problem of elimination of impulsive disturbances from audio signals, based on the matched filtering technique, is proposed. The new approach stems from the observation that a large proportion of noise pulses corrupting audio recordings have highly repetitive shapes that match several typical “patterns”. In many cases a representative set of exemplary pulse waveforms can be extracted from the...
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Substancje biogenne i inne problemy w zarządzaniu wodami opadowymi w portach
PublicationDo niedawna uważano, że substancjami zanieczyszczającymi wody portowe są głównie substancje ropopochodne. Ich rozlewy powstawały najczęściej w wyniku awarii, nieuwagi lub np. zatonięcia statku. W ostatnich latach jednak organizacja HELCOM w roboczych dokumentach pt.: „Draft Report on potentialsources of nutrientinputs: Baltic Sea portshandlingfertilizers” (HOD 52-2017) oraz „Results of the questionnaire on fertilizer cargo handling...
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A new B-D-galactosidase with a low temperature optimum isolated from the Antarctic Arthrobacter sp. 20B: gene cloning, purification and characterization.
PublicationA psychrotrophic bacterium producing a coldadaptedB-galactosidase upon growth at low temperatureswas classiWed as Arthrobacter sp. 20B. A genomic DNAlibrary of strain 20B introduced into Escherichia coliTOP10F' and screening on X-Gal (5-bromo-4-chloro-3-indolyl-B-D-galactopyranoside)-containing agar plates ledto the isolation of B-galactosidase gene. The B-galactosidasegene (bgaS) encoding a protein of 1,053 amino acids,with a...
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A nosocomial outbreak of Candida parapsilosis in southern Sweden verified by genotyping
PublicationIn a haematology ward, Candida parapsilosis was found in blood cultures from 4 patients within a month. As C. parapsilosis is known to have a restricted genetic diversity, a combined methodological approach was adopted to establish a possible epidemiological relationship among the isolates (n = 9). Multilocus sequence typing and random amplified polymorphic DNA analysis suggested a clonal origin of the isolates. The clonal origin...
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Molecular and structural basis of inner core lipopolysaccharide alterations in Escherichia coli: incorporation of glucuronic acid and phosphoethanolamine in the heptose region.
PublicationIt is well established that lipopolysaccharide (LPS) often carries nonstoichiometric substitutions in lipid A and in the inner core. In this work, the molecular basis of inner core alterations and their physiological significance are addressed. A new inner core modification of LPS is described, which arises due to the addition of glucuronic acid on the third heptose with a concomitant loss of phosphate on the second heptose. This...