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Wyniki wyszukiwania dla: WHOLE-GENOME SEQUENCING
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Whole-genome sequencing and antimicrobial potential of bacteria isolated from Polish honey
PublikacjaThe aim of this study was the whole-genome analysis and assessment of the antimicrobial potential of bacterial isolates from honey harvested in one geographical location—the north of Poland. In total, 132 strains were derived from three honey samples, and the antimicrobial activity of CFAM (cell-free after-culture medium) was used as a criterion for strain selection and detailed genomic investigation. Two of the tested isolates...
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Whole genome sequencing of Fowl aviadenovirus A - a causative agent of gizzard erosion and ulceration, in adult laying hens
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An accurate assignment test for extremely low‐coverage whole‐genome sequence data
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An accurate assignment test for extremely low-coverage whole-genome sequence data
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Discrimination of hospital isolates of Acinetobacter baumannii using repeated sequences and whole genome alignment differential analysis
PublikacjaAn 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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The New Klebsiella pneumoniae ST152 Variants with Hypermucoviscous Phenotype Isolated from Renal Transplant Recipients with Asymptomatic Bacteriuria-Genetic Characteristics by WGS.
PublikacjaKlebsiella pneumoniae (Kp) is one of the most important etiological factors of urinary tract infections in renal transplant (RTx) recipients. We described the antimicrobial susceptibility phenotypes and genomic features of two hypermucoviscous (HM) Kp isolates recovered from RTx recipients with asymptomatic bacteriuria (ABU). Using whole genome sequencing (WGS) data, we showed that the strains belong to the ST152 lineage with the...
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Probiotic potential of Bacillus Isolates from Polish Bee Pollen and Bee Bread
PublikacjaThe main goal of this study was the evaluation of the probiotic potential of 10 Bacillus spp. strains isolated from 5 bee bread and 3 bee pollen samples. The antagonistic interaction with Staphylococcus aureus and Escherichia coli was a primary criterion for the preliminary selection of the isolates. Three out of ten strains—PY2.3 (isolated from pollen), BP20.15 and BB10.1 (both isolated from bee bread)—were found to be possible...
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Ligation Mediated PCR methods, their possibilities and limitations
PublikacjaThe application of molecular diagnostics for bacterial strain typing or identifying bacteria at the strain level is of particular importance at present. However, among the many genotyping methods that are currently available, no single one is universally ideal. In this article, we thus review the Ligation Mediated PCR group methods as prospects from which to choose. We discuss different strategies for selecting the amplified PCR...
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Fouling mechanisms in anoxic-aerobic sequencing batch membrane bioreactor based on adapted Hermia models and main foulant characteristics
PublikacjaVarious derivatives of Hermia models (complete pore blocking, intermediate pore blocking, cake layer formation, and standard pore blocking) and different assessments of foulant characteristics have long been used to determine the membrane fouling mechanisms. Accordingly, this study aims to adapt Hermia models and their combination according to the operating conditions of an anoxic-aerobic sequencing batch membrane bioreactor (A/O-SBMBR)....
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Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges
PublikacjaStaphylococci are increasingly recognized as etiological agents of many opportunistic human and animal infections, emphasizing the need for a rapid and accurate identification, even to a genotypical level of these bacteria. In the recent years, there has been a significant progress in typing and phylogenetic study of Staphylococcus species. Here, we describe molecular methods used in taxonomy as well as staphylococci characterization....
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Stardust - Investigation of Microbes in the Stratosphere
PublikacjaThe stratospheric microbiome has been investigated several times using the methods of classical microbiology. In this experiment, we have combined them with some novel approaches including whole- metagenome amplification, Maldi TOF mass spectrometry and Sanger DNA sequencing. The results of the experiment may provide the scientists with knowledge about the mechanisms of survivability of microorganisms in stratospheric conditions...
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Immunophenotyping and transcriptional profiling of in vitro cultured human adipose tissue derived stem cells
PublikacjaAdipose-derived stem cells (ASCs) have become an important research model in regenerative medicine. However, there are controversies regarding the impact of prolonged cell culture on the ASCs phenotype and their differentiation potential. Hence, we studied 10 clinical ASCs replicates from plastic and oncological surgery patients, in six-passage FBS supplemented cultures. We quantified basic mesenchymal cell surface marker transcripts...
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Genome Sequence of the Probiotic Strain Lactobacillus rhamnosus (Formerly Lactobacillus casei) LOCK900
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Genome Sequence of the Probiotic Strain Lactobacillus rhamnosus (Formerly Lactobacillus casei) LOCK908
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Complete Genome Sequence of the Probiotic Strain Lactobacillus casei (Formerly Lactobacillus paracasei) LOCK919
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Genome-Wide DNA Methylation and Gene Expression in Patients with Indolent Systemic Mastocytosis
PublikacjaMastocytosis is a clinically heterogenous, usually acquired disease of the mast cells with a survival time that depends on the time of onset. It ranges from skin-limited to systemic disease, including indolent and more aggressive variants. The presence of the oncogenic KIT p. D816V gene somatic mutation is a crucial element in the pathogenesis. However, further epigenetic regulation may also affect the expression of genes that...
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Bioaugmentation of a sequencing batch reactor with Archaea for the treatment of reject water
PublikacjaIn this study, the bioaugmentation of a sequencing batch reactor (SBR) for the treatment of reject water from wastewater treatment plant was evaluated. For the bioaugmentation step a product containing an enrichment of microorganisms from the Archaea domain was used to enhance the performance of the reactor for treating reject water. The experiment was carried out in two parallel lab-scale sequencing batch reactors. The first one...
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Draft genome sequence of antimicrobial producing Paenibacillus alvei strain MP1 reveals putative novel antimicrobials
PublikacjaA Paenibacillus strain isolated in previous research exhibited antimicrobial activity against relevant human pathogens including Staphylococcus aureus and Listeria monocytogenes. In this study, the genome of the aforementioned strain, designated as MP1, was shotgun sequenced. The draft genome of strain MP1 was subject to multiple genomic analyses to taxonomically characterize it and identify the genes potentially responsible for...
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Platelet RNA Sequencing Data Through the Lens of Machine Learning
PublikacjaLiquid biopsies offer minimally invasive diagnosis and monitoring of cancer disease. This biosource is often analyzed using sequencing, which generates highly complex data that can be used using machine learning tools. Nevertheless, validating the clinical applications of such methods is challenging. It requires: (a) using data from many patients; (b) verifying potential bias concerning sample collection; and (c) adding interpretability...
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Removal of Pharmaceutically Active Compounds in Sequencing Batch Reactor
PublikacjaIn recent years, considerable attention was paid to the presence of organic micro-pollutants such as Active Pharmaceutical Ingredients (API) in the aquatic environment due to their negative impact on public health and aquatic ecosystems. Numerous papers have pointed out API presence as common constituents of effluents from Wastewater Treatment Plants (WWTPs). This is the result of various efficiencies of API removal by conventional...
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Detection of circulating tumor cells by means of machine learning using Smart-Seq2 sequencing
PublikacjaCirculating tumor cells (CTCs) are tumor cells that separate from the solid tumor and enter the bloodstream, which can cause metastasis. Detection and enumeration of CTCs show promising potential as a predictor for prognosis in cancer patients. Furthermore, single-cells sequencing is a technique that provides genetic information from individual cells and allows to classify them precisely and reliably. Sequencing data typically...
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Pilot- scale plant for material recycling of whole waste tires
PublikacjaContinously growing demad for all kinds of vehicles and general tendency to regular exchange of tires are causing growth of scrap tires which need management. A risings of large quantities of used rubber products, especially used tires has been increasing every year in Poland, in 2006 it was 160 thousand. The waste management and recycling of used tires become a major environmental problem. It is worth noticing that tires which...
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Pyrolysis Process of Whole Waste Tires as a Biomass Energy Recycling
PublikacjaThe article is devoted to the description of material recycling of whole waste tires, including a new method of pyrolysis process, resulting in the final products: technically oil fractions (rubber plasticizer of rubber compounds) or diesel fuels (light, medium and heavy), activated carbon, gas fuel and steel scrap. Operational and performance tests of the first version of the pilot plant, consisting of three contributions cooperating...
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Blood equivalent phantom vs whole human blood, a comparative study
PublikacjaPreclinical research of biomedical optoelectronic devices is often performed with the use of blood phantoms — a simpli¯ed physical model of blood. The aim of this study is the comparison and distinction between blood phantoms as well as whole human blood measurements. We show how the use of such phantoms may in°uence the incorrect interpretation of measured signal. On the other hand, we highlight how the use of blood phantoms enables...
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Supervisory fuzzy control system for biological processes in sequencing wastewater batch reactor
PublikacjaThe paper proposes the design of the supervisory heuristic fuzzy control system applied to a Sequencing Batch Reactor (SBR) in the Wastewater Treatment Plant (WWTP). Based on real data records and the biological process and aeration system models, a control system for biological processes has been designed. The supervisory control system performs management of the reactor work cycle, determines the phase length, controls the sludge...
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Modelling of sequencing batch reactor operating at various aeration modes
PublikacjaThe presented study involved designing a computer model of a sequencing batch reactor (SBR) at laboratory scale. The data pertaining to the technical aspects of the bioreactor and quality indicators of wastewater constituted the input for the employed simulation tool, i.e. GPS-X software package. The results of a simulation involving a 12-hour operation cycle are presented in this work; each cycle included 6 phases: filling, mixing,...
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Nonlinear Fuzzy Control System for Dissolved Oxygen with Aeration System in Sequencing Batch Reactor
PublikacjaBiological processes at a wastewater treatment plant are complex, multivariable, time varying and nonlinear. Moreover, interactions between the components are very strong. Control of dissolved oxygen is one of most important task at the plant. The level of dissolved oxygen in aerobic tanks has significant influence on behaviour and activity of microorganisms at the plant. Air for aerated tanks is supplied by the aeration system...
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The Influence of Sulfate on Anaerobic Ammonium Oxidation in a Sequencing Batch Reactor
PublikacjaAnaerobic ammonia-oxidizing bacteria have a more comprehensive metabolism than expected - there may be other electron acceptors that oxidize ammonium nitrogen under anaerobic conditions, in addition to the well-known nitrite nitrogen, one of which is sulfate in the sulfammox process. Sulfate-containing compounds are part of the medium for the anammox process, but their concentrations are not particularly high (0.2 g MgSO4 ∙ 7H2O/dm3...
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Modeling sequencing batch reactor operational conditions depending on oxygen concentration
PublikacjaSequencing batch reactors (SBR) can be used as a fill-and draw activated sludge system for wastewater treatment with considerable operating flexibility and the possibility to conduct experiments under standard conditions and extreme case scenarios. Mathematical modeling and computer simulations provide an opportunity to implement existing wastewater processes in modeling software and evaluate different modifications at low costs...
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Possibilities of utilizing used tires in whole
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Combinated treatment of landfill leachates with wastewater in a sequencing batch reactor (SBR)
PublikacjaSanitary landfill leachates are treated usually by multistage systems using physical, chemical and biological processes. One of the most economic and efficient method is combined treatment of landfill leachates with municipal wastewater in a sequencing batch reactor (SBR. The main advantage of such co-treatment is that landfill leachates variability (in quality and quantity) do not influence the effectiveness of biological processes....
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Expression of goose parvovirus whole VP3 protein and its epitopes in Escherichia coli cells
PublikacjaThe aim of this study was the expression of goose parvovirus capsid protein (VP3) and its epitopes in Escherichia coli cells. Expression of the whole VP3 protein provided an insufficient amount of protein. In contrast, the expression of two VP3 epitopes (VP3ep4, VP3ep6) in E. coli, resulted in very high expression levels. This may suggest that smaller parts of the GPV antigenic determinants are more efficiently expressed than the...
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Machining process sequencing and machine assignment in generative feature-based CAPP for mill-turn parts
PublikacjaProcess selection and sequencing, as one of the most complex issues when evaluated from a mathematical point of view and crucial in CAPP, still attract research attention. For the current trend of intelligent manufacturing, machining features (MFs) are the information carriers for workpiece geometry and topology representation. They are basically derived from CAD models and are used by downstream engineering applications. A feature-based...
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A Model-Based Improved Control of Dissolved Oxygen Concentration in Sequencing Wastewater Batch Reactor
PublikacjaBiochemical processes at wastewater treatment plant are complex, nonlinear, time varying and multivariable. Moreover, relationships between processes are very strong. One of the most important issues is exerting proper control over dissolved oxygen levels during nitrification phase. This parameter has a very large impact on activity of microorganisms in activated sludge and on quality of pollution removal processes. Oxygen is supplied...
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Evaluation and start-up of an electro-Fenton-sequencing batch reactor for dairy wastewater treatment
PublikacjaThis study examined the performance of an integrated wastewater (WW) treatment system, namely an electro-Fenton (EF)-sequencing batch reactor (SBR), for dairy industry WW. The EF process was used as the first stage of the SBR. It degrades bio-refractory compounds via advanced oxidation processes, thereby resulting in the formation of simple biodegradable intermediates. Several factors, including the hydraulic retention time (HRT),...
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Absorption spectroscopy setup for determination of whole human blood and blood–derived materials spectral characteristics
PublikacjaA dedicated absorption spectroscopy system was set up using tungsten-halogen broadband source, optical fibers, sample holder, and a commercial spectrometer with CCD array. Analysis of noise present in the setup was carried out. Data processing was applied to the absorption spectra to reduce spectral noise, and improve the quality of the spectra and to remove the baseline level. The absorption spectra were measured for whole blood...
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Mixed integer nonlinear optimization of biological processes in wastewater sequencing batch reactor
PublikacjaWastewater treatment plays a key role for humanity. The waste entering lakes, rivers, and seas deteriorates daily quality of life. Therefore, it is very important to improve the efficiency of wastewater treatment. From a control point of view, a biological wastewater treatment plant is a complex, non-linear, multidimensional, hybrid control system. The paper presents the design of the optimizing hierarchical control system applied...
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Analysis of the complete genome sequence of the lactococcal bacteriophage bIBB29
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Effect of Overloaded Vehicles on Whole Life Cycle Cost of Flexible Pavements
PublikacjaThe phenomenon of vehicle overloading—illegal exceeding of maximum legal weight of vehicles, is a serious problem both in developing and developed countries around the world. Overloaded vehicles occur less frequently in comparison to properly loaded vehicles but due to their greater potential to cause damage they significantly contribute to distress of pavement structure. As studies show, the number of overloaded vehicles increases...
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Supervisory Control System for Adaptive Phase and Work Cycle Management of Sequencing Wastewater Treatment Plant
PublikacjaThe paper presents the design of the integrated control system applied to Sequencing Batch Reactor (SBR) in a biological Wastewater Treatment Plant (WWTP) in Swarzewo, which operates under activated sludge technology. Based on the real data records, ASM2d biological processes model and aeration system model, hierarchical control system for dissolved oxygen tracking and cycle management is designed. Internal Model Controller (IMC)...
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Reassesing whole tooth electrical impedance spectroscopy measurements
PublikacjaW pracy dokonano krytycznej oceny wyników wcześniejszych badań spektorskopowych zębów przeprowadzonych w innych ośrodkach i porównano je z własnymi. Wskazano na trudności występujące podczas pomiarów.
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Utilizing Genome-Wide mRNA Profiling to Identify the Cytotoxic Chemotherapeutic Mechanism of Triazoloacridone C-1305 as Direct Microtubule Stabilization
PublikacjaRational drug design and in vitro pharmacology profiling constitute the gold standard in drug development pipelines. Problems arise, however, because this process is often dicult due to limited information regarding the complete identification of a molecule’s biological activities. The increasing aordability of genome-wide next-generation technologies now provides an excellent opportunity to understand a compound’s diverse eects...
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Which transport policies increase physical activity of the whole of society? A systematic review
PublikacjaPurpose: There is strong evidence of the links between car-dependence and the physical inactivity pandemic. Physical inactivity accounts for 6–10% of major non-communicable diseases. Research consistently shows that unlike passive transport, active transport is associated with higher total daily physical activity (PA). While there are public policies that support PA in transport and, as a result, overall PA levels, the specific...
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Efficient Agrobacterium-mediated transformation and genome editing of Fagopyrum tataricum
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Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia magna
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Two-Step Model Based Adaptive Controller for Dissolved Oxygen Control in Sequencing Wastewater Batch Reactor
PublikacjaDissolved Oxygen (DO) concentration is a crucial parameter for efficient operation of biological processes taking place in the activated sludge Wastewater Treatment Plant (WWTP). High-quality DO control is difficult to achieve because of complex nonlinear behavior of the plant and substantial influent disturbances. A method to improve the Direct Model Reference Adaptive Control (DMRAC) technology in application to DO tracking for...
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Results from a Genome-Wide Association Study (GWAS) in Mastocytosis Reveal New Gene Polymorphisms Associated with WHO Subgroups
PublikacjaMastocytosis 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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Effect of operating conditions on N 2 O production in an anammox sequencing batch reactor containing granular sludge
PublikacjaNitrous oxide (N2O) is one of the gases with the greatest impact in the atmosphere due to its persistence and significant contribution to the greenhouse effect. This study provides an insight into the dynamics of N2O production in wastewater nitrogen removal systems. A 10 L sequencing batch reactor containing enriched anammox biomass was subjected to different operational conditions, i.e., temperature, feed time, NO2 /NH4 þ ratio...
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A stochastic approach for the solution of single and multi – objective optimisation problems of biological processes in sequencing batch reactor
PublikacjaThis paper investigates the impact of implementing single and multi-optimisation solutions on the biological treatment process in a sequencing batch reactor (SBR). The research is based on a case study of the water resource recovery facility (WRRF) in Swarzewo, Northern Poland. The paper introduces the adaptive extremum seeking control (ESC) method for dissolved oxygen (DO) concentration control and places it in a layered control structure....
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Comparison of the Efficiency of Deammonification under Different DO Concentrations in a Laboratory-Scale Sequencing Batch Reactor
PublikacjaThe efficiency of deammonification depends on the cooperation of ammonium oxidizing bacteria and archaea (AOB/AOA), anaerobic ammonium oxidizing bacteria (AnAOB) and the effective suppression of nitrite oxidizing bacteria (NOB) that compete with AnAOB for nitrite (NO2 -N). One of the effective NOB suppression strategies is intermittent aeration. However, it is important to have a good understanding of the optimum dissolved oxygen...