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Search results for: MICROBIAL PHYLOGENETICS
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The influence of soluble microbial products on microbial community composition: hypothesis of microbial community succession
PublicationRozpuszczalne produkty mikrobiologiczne (SMP) są związkami organicznymi wytwarzanymi podczas rozkładu substratów przez mikroorganizmy osadu czynnego. Zbadano mikroskopowo zmiany składu zespołów mikrobiologicznych (organizmów jedno- i wielokomórkowych) pod wpływem obniżonego lub zwiększonego poziomu SMP. Wysoka zawartość SMP w znacznym stopniu zmieniła skład zespołów mikrobiologicznych, od orzęsków osiadłych (12-175 µm), do...
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Adaptive response of microbial communities to soluble microbial products.
PublicationBadano wpływ obecności ubocznych produktów mikroorganizmów na stężenie biomasy osadu czynnego oraz na efektywność obniżenia ładunku BZT5 i ChZT w ściekach syntetycznych. Doświadczenia prowadzono w obecności ubocznych produktów mikroorganizmów (Soluble Microbial Products) oraz w warunkach pozbawionych tych produktów.
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Behavior of microbial communities developed in the presence/reduced level of soluble microbial products.
PublicationBadano aktywność mikrobiologiczną organizmów osadu czynnego (adaptowanego i nieadaptowanego) poprzez monitorowanie zmian pH, rozpuszczonego tlenu, BZT5 oraz ChZT w ściekach syntetycznych. Obserwowano pojawianie się ubocznych produktów mikroorganizmów (Soluble Microbial Products) oraz ich wpływ na efekt oczyszczenia ścieków. Ilość obecnych ubocznych produktów mikroorganizmów w trakcie procesu zależała także od rodzaju rozkładanych...
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Construction of phylogenetic trees with topological constraints
PublicationThis paper proposes a method of reconstruction of phylogenetic trees based on heuristic search with topological constraints. Using topological constraints it is possible to reduce the set of solutions as well as to enforce that the result is consistent with a given hypothesis about the evolution process within some group of species. Along with this work a number of algorithms used for phylogenetic analysis were implemented. Those...
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Properties of the triset metric for phylogenetic trees
Publicationthe following paper presents a new polynomial time metric for unrootedphylogenetic trees (based on weighted bipartite graphs and the method ofdetermining a minimum perfect matching) and its properties. also many its properties are presented.
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Phylogenetic Placement and Taxonomy of the Genus Hederorkis (Orchidaceae)
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Analyzing sets of phylogenetic trees using metrics
PublicationThe reconstruction of evolutionary trees is one of the primary objectives in phylogenetics. Such a tree represents historical evolutionary relationships between different species or organisms. Tree comparisons are used for multiple purposes, from unveiling the history of species to deciphering evolutionary associations among organisms and geographical areas. In this paper, we describe a general method for comparing phylogenetictrees...
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Polynomial triset metric for unrooted phylogenetic trees
Publicationthe following paper presents a polynomial triset metric for unrooted phylogenetic trees (based on weighted bipartite graphs and the method of determining a minimum edge cover) and its basic characteristics. also a list of further directions of research and examples of the wider use of this metric is presented.
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On a matching distance between rooted phylogenetic trees
PublicationThe Robinson–Foulds (RF) distance is the most popular method of evaluating the dissimilarity between phylogenetic trees. In this paper, we define and explore in detail properties of the Matching Cluster (MC) distance, which can be regarded as a refinement of the RF metric for rooted trees. Similarly to RF, MC operates on clusters of compared trees, but the distance evaluation is more complex. Using the graph theoretic approach...
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Example of utilization of permeabilized microbial cells
PublicationThe benefits of using whole bacterial cells not only exclude expensive, laborious protein isolation and purification but also stabilize enzymes by cytosol components. Increase in activity of the cells can be achieved by cells permeabilization.
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
PublicationRekonstrukcja drzew ewolucji jest jednym z głównych celów w bioinformatyce. Drzewa filogenetyczne reprezentuje historię ewolucji i związki pokrewieństwa między różnymi gatunkami. W pracy proponujemy nową ogólną metodę określania odległości między nieukorzenionymi drzewami filogenetycznymi, szczególnie użyteczną dla dużych zbiorów gatunków. Następnie podajemy szczegółowe własności jednej metryki określonej przy użyciu tej metody...
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
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Visual TreeCmp : Comprehensive Comparison of Phylogenetic Trees on the Web
Publication1. We present Visual TreeCmp—a package of applications for comparing phylogenetic tree sets. 2. Visual TreeCmp includes a graphical web interface allowing the visualization of compared trees and command line application extended by comparison methods recently proposed in the literature. 3. The phylogenetic tree similarity analysis in Visual TreeCmp can be performed using eighteen metrics, of which 11 are dedicated to rooted trees...
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Degradation of xylose using a microbial fuel cell
PublicationIt is generally known, that many kind of microorganisms are capable of using carbohydrates as a source of carbon and energy in an environment. The biodegradation process of monosaccharides from pentoses (in this case- racemic mixture of D - and L – xylose) is an immense opportunity for an entire reduction of biological contamination to neutral compounds through MFC. The process is occurred in a single-chamber MFC, which is contained...
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The use of the electromagnetic field in microbial process bioengineering
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Heterotrophic Anodic Denitrification in Microbial Fuel Cells
PublicationNowadays, pollution caused by energy production systems is a major environmental concern. Therefore, the development of sustainable energy sources is required. Amongst others, the microbial fuel cell (MFC) seems to be a possible solution because it can produce clean energy at the same time that waste is stabilized. Unfortunately, mainly due to industrial discharges, the wastes could contain nitrates, or nitrates precursors such...
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Microbial risks in mild hot smoking of fish
PublicationGorące wędzenie ryb w łagodnych warunkach, w temperaturze nie przekraczającej 65 stopni Celsjusza wewnątrz ryby i przy niskiej zawartości soli w mięsie tylko częściowo inaktywuje bakterie chorobotwórcze oraz w niewystarczającym stopniu hamuje wzrost drobnoustrojów podczas przechowywania produktu. Wymagane bezpieczeństwo można osiągnąć tylko w przypadku bardzo świeżego surowca i wysokiej higieny podczas jego przetwarzania oraz przechowywania...
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Analyzing sets of phylogenetic trees obtained from bayesian MCMC process using topology metrics
PublicationThe reconstruction of evolutionary trees is one of the primary objectives in phylogenetics. Such a tree represents historical evolutionary relationship between different species or organisms. Tree comparisons are used for multiple purposes, from unveiling the history of species to deciphering evolutionary associations amongorganisms and geographical areas.In the paper, we describe a general method for comparing hylogenetic trees....
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Comparing phylogenetic trees using a minimum weight perfect matching
PublicationA phylogenetic tree represents historical evolutionary relationshipbetween different species or organisms. There are various methods for reconstructing phylogenetic trees.Applying those techniques usually results in different treesfor the same input data. An important problem is to determinehow distant two trees reconstructed in such a wayare from each other. Comparing phylogenetic trees is alsouseful in mining phylogenetic information...
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Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages
PublicationThe ability to quantify a dissimilarity of different phylogenetic trees is required in various types of phylogenetic studies, for example, such metrics are used to assess the quality of phylogeny construction methods and to define optimization criteria in supertree building algorithms. In this article, starting from the already described concept of matching metrics, we define three new metrics for rooted phylogenetic trees. One...
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Sample preparation procedures utilized in microbial metabolomics: An overview
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AGAR a Microbial Colony Dataset for Deep Learning Detection
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Microbial and Endotoxin Contamination of Water-Soluble Metalworking Fluids
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Microbial response of the anammox process to trace antibiotic concentration
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The Influence of External Load on the Performance of Microbial Fuel Cells
PublicationIn this work, the effect of the external load on the current and power generation, as well as on the pollutant removal by microbial fuel cells (MFCs), has been studied by step-wise modifying the external load. The load changes included a direct scan, in which the external resistance was increased from 120 Ω to 3300 Ω, and a subsequent reverse scan, in which the external resistance was decreased back to 120 Ω. The reduction in the...
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Into the Unknown: Microbial Communities in Caves, Their Role, and Potential Use
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Critical Case Stochastic Phylogenetic Tree Model via the Laplace Transform
PublicationBirth–and–death models are now a common mathematical tool to describe branching patterns observed in real–world phylogenetic trees. Liggett and Schinazi (2009) is one such example. The authors propose a simple birth–and–death model that is compatible with phylogenetic trees of both influenza and HIV, depending on the birth rate parameter. An interesting special case of this model is the critical case where the birth rate equals the...
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Palicella, a new genus of lichenized fungi and its phylogenetic position withinLecanoraceae
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Generation of microbial colonies dataset with deep learning style transfer
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Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters
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Health-promoting potential and microbial composition of fermented drink tepache
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Performance of microbial fuel cells operated under anoxic conditions
PublicationNowadays, microbial fuel cells (MFC) stand up as a promising renewable energy source. Due to the ability of the MFC to oxidize a wide spectrum of substrates, wastewater seems to be one of the most interesting fuels. Unfortunately, wastewater could contain electron acceptors such as nitrate, which could interfere with the electrical performance of the MFC. In this work, the influence of oxidised nitrogen forms on the electricity...
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The microbial and sensory quality of mackerel hot smoked in mild conditions
PublicationThe quality indices of Atlantic mackerel, hot smoked at core temperature not exceeding 60°C, containing 14–27 g salt and 580–670 g water per kg meat, was determined just after smoking and during storage. The aerobic plate count after smoking, chilling and packing in cardboard boxes was 0–12 cfu/25 cm2of the skin of the smoked fish and 10–240 cfu/g of flesh. It was 1.9 log cycle lower than that in the frozen raw material. At 2°C,...
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Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia
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Comparing Arbitrary Unrooted Phylogenetic Trees Using Generalized Matching Split Distance
PublicationIn the paper, we describe a method for comparing arbitrary, not necessary fully resolved, unrooted phylogenetic trees. Proposed method is based on finding a minimum weight matching in bipartite graphs and can be regarded as a generalization of well-known Robinson-Foulds distance. We present some properties and advantages of the new distance. We also investigate some properties of presented distance in a common biological problem...
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Morphologic, Phylogenetic and Chemical Characterization of a Brackish Colonial Picocyanobacterium (Coelosphaeriaceae) with Bioactive Properties
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Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions
PublicationAbility to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in...
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Benzalkonium Salts of Amino Acids – Physicochemical Properties and Anti-Microbial Activity
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Sludge multifunctions in a phytobiome—Forest and plantation application including microbial aspects
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Chapter 4. Electricity generation from glucose microbial fuel cell
PublicationThe microbial fuel cell was constructed to generate electricity with simultaneous digestion of a glucose fuel by a bacterial biofilm. The decomposition of glucose resulted in releasing of electrons to an anode and to production of some by-products, e.g. metane or organic acids. It was found that maximum electric power density strongly depended on the proton transport through the proton exchange membrane seperating the anolyte and...
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Microbial fuel cell applications for removal of petroleum hydrocarbon pollutants: A review
PublicationBioelectrochemical systems (BESs) are considered as the potential approaches to remediate the environments contaminated by hydrocarbons. This review addresses the application of BESs particularly microbial fuel cells (MFCs) in degradation of petroleum hydrocarbons, including BTEXs, from soil, water, wastewater and sediments. Details on reactor design and critical issues are discussed. Aspects on electrodes, redox mediators and...
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Development of an Autochthonous Microbial Consortium for Enhanced Bioremediation of PAH-Contaminated Soil
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Generating amplicon reads for microbial community assessment with next‐generation sequencing
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Reduced colonic microbial diversity is associated with colitis in NHE3-deficient mice
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Phylogenetic and geographic analysis of fowl adenovirus field strains isolated from poultry in Poland
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Phylogenetic analysis of mysterious burials revealed in the former penal labor camp Treblinka I
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Effects of climate change on microbial community structure and function in Antarctic Glacier Lagoon
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Electricity generation from rapeseed straw hydrolysates using microbial fuel cells
PublicationRapeseed straw is an attractive fuel material for microbial fuel cells (MFCs) due to its high content of carbohydrates (more than 60% carbohydrates). This study has demonstrated that reducing sugars can be efficiently extracted from raw rapeseed straw by combination of hydrothermal pretreatment and enzymatic hydrolysis followed by utilization as a fuel in two-chamber MFCs for electrical power generation. The most efficient method...
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Microbial community development on the surface of Hans and Werenskiold Glaciers (Svalbard, Arctic): a comparison
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Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition
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