Wyniki wyszukiwania dla: RNASEQ
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The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L
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International Representation of S-Modular Knowledge Base in RKaSeA System
PublikacjaNiniejszy artykuł przedstawia nową metodę reprezentacji wiedzy ontologicznej wyrażonej w logice opisowej. Metoda ta, nazwana G-Cart została zaimplementowana w nowo utworzonym systemie zarządzania wiedzą RKaSeA. Artykuł opisuje podstawowe założenia metody oraz praktyczne zagadnienia związane z jej implementacją.
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Wewnętrzna reprezentacja konglomeratowej bazy wiedzy w systemie RKaSeA
PublikacjaNiniejszy artykuł prezentuje koncepcję wewnętrznej reprezentacji wiedzy ontologicznej zastosowaną w nowo opracowanym systemie zarządzania wiedzą ontologiczno-regułową RKaSeA. Reprezentacja ta stanowi praktyczne wdrożenie opublikowanej wcześniej koncepcji modularyzacji bazy wiedzy polegającej na jej podziale na semantyczne jednostki - konglomeraty. Opracowana metoda reprezentacji stanowi zarazem rozwinięcie wprowadzonej wcześniej...
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Wnioskowanie z różnych źródeł osobników w systemie RKaSeA
PublikacjaNiniejszy artykuł prezentuje koncepcję zarządzania wiedzą asercjonalną zastosowaną w systemie zarządzania wiedzą RKaSeA. Koncepcja ta traktuje opis świata jako zbiór osobników. Dzięki temu udało się objąć nią również mechanizmy obsługi reguł oraz mechanizm pozyskiwania wiedzy z zewnętrznych źródeł danych. Mechanizmy te sa traktowane jako dodatkowe typy źródeł osobników.
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Assessment of cross compatibility of pear (Pyrus communis L.) cultivars on the basis of pollen tube observations and analysis of the S-RNase gene
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Small regulatory bacterial RNAs regulating the envelope stress response
PublikacjaMost bacteria encode a large repertoire of RNA-based regulatory mechanisms. Recent discoveries have revealed that the expression of many genes is controlled by a plethora of base-pairing noncoding small regulatory RNAs (sRNAs), regulatory RNA-binding proteins and RNA-degrading enzymes. Some of these RNA-based regulated processes respond to stress conditions and are involved in the maintenance of cellular homeostasis. They achieve...
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Two small RNAs conserved in Enterobacteriaceae provide intrinsic resistance to antibiotics targeting the cell wall biosynthesis enzyme glucosamine-6-phosphate synthase
PublikacjaFormation of glucosamine-6-phosphate GlcN6P) by enzyme GlcN6P synthase (GlmS) represents the first step in bacterial cell envelope synthesis. In Escherichia coli, expression of glmS is controlled by small RNAs (sRNAs) GlmY and GlmZ. GlmZ activates the glmS mRNA by base-pairing. When not required, GlmZ is bound by adapter protein RapZ and recruited to cleavage by RNase E inactivating the sRNA. The homologous sRNA GlmY activates...
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A prototypical non-malignant epithelial model to study genome dynamics and concurrently monitor micro-RNAs and proteins in situ during oncogene-induced senescence
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Human Induced Pluripotent Stem Cell-Derived Microvesicles Transmit RNAs and Proteins to Recipient Mature Heart Cells Modulating Cell Fate and Behavior
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Correction to: A prototypical non-malignant epithelial model to study genome dynamics and concurrently monitor micro-RNAs and proteins in situ during oncogene-induced senescence
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The Toolbox of Methods for Multidirectional Characterization of Dietary Nucleic Acids; Verification for Raw and Processed Food Products
PublikacjaCurrently, the nutritional value of food is associated mainly with components such as proteins, carbohydrates, and lipids. However, another important macromolecules present in many foods are dietary nucleic acids (dietNA), i.e., DNA as well as both coding and non-coding RNAs. In the context of food chemistry and nutrition, dietNA are nowadays vastly neglected. In consequence, there are no dedicated methodologies to characterize...
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Net Object Days (Includings MATES, ENASE etc.)
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Multicopy Suppressor Analysis of Strains Lacking Cytoplasmic Peptidyl-Prolyl cis/trans Isomerases Identifies Three New PPIase Activities in Escherichia coli That Includes the DksA Transcription Factor
PublikacjaConsistent with a role in catalyzing rate-limiting step of protein folding, removal of genes encoding cytoplasmic protein folding catalysts belonging to the family of peptidyl-prolyl cis/trans isomerases (PPIs) in Escherichia coli confers conditional lethality. To address the molecular basis of the essentiality of PPIs, a multicopy suppressor approach revealed that overexpression of genes encoding chaperones (DnaK/J and GroL/S),...
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Ideologiczny i praktyczny model metaontologii
PublikacjaRozwój inicjatywy Semantic Web spowodował rozwój różnych języków definiowania wiedzy i manipulowania nią. W ramach tych języków istotnym elementem jest zaprojektowanie rozkazów terminologicznych. W artykule przedstawiono sposób realizacji zapytań terminologicznych w języku KQL (Knowledge Query Language) - języku dostępu do systemu zarządzania wiedzą RKaSeA.
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A vector-enzymatic DNA fragment amplification-expression technology for construction of artificial, concatemeric DNA, RNA and proteins for novel biomaterials, biomedical and industrial applications
PublikacjaA DNA fragment amplification/expression technology for the production of new generation biomaterials for scientific, industrial and biomedical applications is described. The technology enables the formation of artificial Open Reading Frames (ORFs) encoding concatemeric RNAs and proteins. It recruits the Type IIS SapI restriction endonuclease (REase) for an assembling of DNA fragments in an ordered head-to-tail-orientation. The...
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Ideological and Practical Model of Metaontology
PublikacjaRozwój inicjatywy Semantic Web spowodował rozwój różnych języków definiowania wiedzy i manipulowania nią. W ramach tych języków istotnym elementem jest zaprojektowanie rozkazów terminologicznych. W artykule przedstawiono sposób realizacji zapytań terminologicznych w języku KQL (Knowledge Query Language), służącym do dostępu do systemu zarządzania wiedzą RKaSeA.
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Adam Przybyłek dr
Osobystopień doktora uzyskany w grudniu 2011 od Wydziału Elektroniki, Telekomunikacji i Informatyki, PG od 2012 zatrudniony jako adiunkt w Katedrze Inżynierii Oprogramowania, WETI PG; wcześniej pracował jako asystent w Katedrze Informatyki Ekonomicznej UG oraz instruktor w Akademii CISCO zainteresowania badawcze: programowanie aspektowe, metodyki zwinne, modelowanie procesów biznesowych więcej informacji na stronie domowej: http://przybylek.wzr.pl
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The crucial contemporary problems of the computational methods for ship propulsor hydrodynamics
PublikacjaPraca przedstawia krytyczny przegląd współczesnych metod obliczeniowych stosowanych do projektowania i analizy pracy pędników okretowych. Omówiono modele linii nośnej i powierzchni nośnej, a także metody elementów brzegowych i metody RANSE oraz LES. Przedstawiono przykładowe wyniki obliczeń oraz oceniono i porównano dokładność opisywanych metod.
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Triazoloacridone C-1305 impairs XBP1 splicing by acting as a potential IRE1α endoribonuclease inhibitor
PublikacjaInositol requiring enzyme 1 alpha (IRE1α) is one of three signaling sensors in the unfolding protein response (UPR) that alleviates endoplasmic reticulum (ER) stress in cells and functions to promote cell survival. During conditions of irrevocable stress, proapoptotic gene expression is induced to promote cell death. One of the three signaling stressors, IRE1α is an serine/threonine-protein kinase/endoribonuclease (RNase) that...
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S-Modules - An Approach to Capture Semantics fo Modularized DL Knowledge Bases
PublikacjaModularity of ontologies has been recently recognized as a key requirement for collaborative ontology engineering and distributed ontology reuse. Partitioning of an ontology into modules naturally gives rise to development of module processing methods. In this paper we describe an algebra of ontology modules developed during our work on a Knowledge Base Management System called RKaSeA. The idea differs from other algebras in the...
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Nonlocal nonlinear bending of rectangular nanoscale plate including central hole via complex differential quadrature method
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Digital Signal Processing for Hydroacoustic System in Biomimetic Underwater Vehicle
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Maintenance Interval Adjustment Based on the Experience, Case Study of Marine Air Compressor System
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Maritime Communications Network Development Using Virtualised Network Slicing of 5G Network
PublikacjaThe paper presents the review on perspectives of maritime systems development at the context of 5G systems implementation and their main properties. Firstly, 5G systems requirements and principles are discussed, which can be important for maritime applications. Secondly, the problems of network softwarisation, virtualisation and slicing, and possible types of services for potential implementation in 5G marine applications are described....
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Fire Protection and Materials Flammability Control by Artificial Intelligence
PublikacjaFire safety has become a major challenge of materials developers because of the massive production of organic materials, often combustibles, and their use for different purposes. In this sense, fire safety is critically considered in the development of engineering materials [1, 2]. The multiplicity of parameters contributing to the development of formulation of flame-retardant materials from one side and the sustainability concerns...
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Generation and Characterization of a DNA-GCN4 Oligonucleotide-Peptide Conjugate: The Impact DNA/Protein Interactions on the Sensitization of DNA
PublikacjaRadiotherapy, the most common therapy for the treatment of solid tumors, exerts its effects by inducing DNA damage. To fully understand the extent and nature of this damage, DNA models that mimic the in vivo situation should be utilized. In a cellular context, genomic DNA constantly interacts with proteins and these interactions could influence both the primary radical processes (triggered by ionizing radiation) and secondary reactions,...
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Analysis of the process of water entry of an amphibious vehicle
PublikacjaThe paper presents a method of computational and experimental analysis of the process of water entry of an amphibious vehicle. The computational method is based on the Reynolds Averaged Navier-Stokes Equations (RANSE) solver and the xperiment was carried out in the towing tank at Ship Design and Research Centre S.A. with the use of a scale model. The analysis was focused on the safety of water entry, i.e. the maximum pitch and...
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EASY ACCESS TOOL FOR SMALL INTERFERING RNA (siRNA) DATA
PublikacjaFor 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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Cząsteczki mikroRNA - nowy biologicznie aktywny składnik mleka kobiecego
PublikacjaCząsteczki mikroRNA są krótkimi, niekodującymi oligonukleotydami odpowiadającymi za potranskrypcyjną regulację ekspresji genów. W wyniku ich aktywności kontrolowanych jest wiele procesów komórkowych oraz szlaków sygnalizacyjnych. Od 2010 roku wiadomo, że wchodzą one w skład mleka kobiecego, które obecnie uznaje się za jedno z najbogatszych pokarmowych źródeł mikroRNA. Funkcje tych cząsteczek w organizmie karmionego mlekiem matki...
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Development of globalization in culture on the example of Europe
PublikacjaThis article attempts to reflect on the consequences of cultural globalization i.e. the opporturnities and threats that exist it brings with it for existing local cultures. As we know, The processes of globalization contribute to the emergence of any, often contradictory phenomena in the field of culture which influence the existing local cultural systems in various ways. It is assumed that the most important consequence of cultural...
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The Essential Oils Composition ofSalvia mirzayanii
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Synthesis, characteristics, and photocatalytic activity of zinc oxide nanoparticles stabilized on the stone surface for degradation of metronidazole from aqueous solution
PublikacjaAbstract Background: The presence of antibiotics such as metronidazole in wastewater even at low concentrations requires searching for a suitable process such as advanced oxidation process (AOP) to reduce the level of pollutants to a standard level in water. Methods: In this study, zinc oxide (ZnO) nanoparticles were synthesized by thermal method using zinc sulfate (ZnSO4) as a precursor, then, stabilized on stone and was used...
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Epigenetic Basis of Regeneration: Analysis of Genomic DNA Methylation Profiles in the MRL/MpJ Mouse
PublikacjaEpigenetic regulation plays essential role in cell differentiation and dedifferentiation, which are the intrinsic processes involved in regeneration. To investigate the epigenetic basis of regeneration capacity, we choose DNA methylation as one of the most important epigenetic mechanisms and the MRL/MpJ mouse as a model of mammalian regeneration known to exhibit enhanced regeneration response in different organs. We report the...
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The chemistry, properties and performance of flame-retardant rubber composites: Collecting, analyzing, categorizing, machine learning modeling, and visualizing
PublikacjaRubbers combine the flexibility with mechanical strength, supporting myriad applications, but suffer from inherent flammability. Formulation and production of flame-retardant rubber composites (FRRCs) have intensively been practiced over years, but not comprehensively reviewed. This necessity has outlined collecting, analyzing, screening, classifying, and interpreting the literature with the aim of classifying the FRRCs. We quantified...
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Effective method for determining environmental loads on supporting structures for offshore wind turbines
PublikacjaThis paper presents a description of an effective method for determining loads due to waves, current and wind acting on the supporting structures of the offshore wind turbines. This method is dedicated to the structures consisting of the cylindrical or conical elements as well as (truncates) pyramids of polygon with a large number of sides (8 or more). The presented computational method is based on the Morison equation, which was...
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Effective method for determining environmental loads on supporting structures for offshore wind turbines
PublikacjaThis paper presents a description of an effective method for determining loads due to waves and current acting on the supporting structures of the offshore wind turbines. This method is dedicated to the structures consisting of the cylindrical or conical elements as well as (truncates) pyramids of polygon with a large number of sides (8 or more). The presented computational method is based on the Morison equation, which was originally...
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Badanie dynamiki platform pływających morskich turbin wiatrowych z zastosowaniem metod numerycznej mechaniki płynów
PublikacjaPraca dotyczy badania ruchu platform pływających pod morskie turbiny wiatrowe. Przedstawiono w niej główne metody obliczeń i przedyskutowano ich zastosowanie. Na przykładzie koncepcji konstrukcji 3-kolumnowej platformy typu Spar przedstawiono metodykę wykonywania obliczeń z zastosowaniem programu AQWA opartego na metodzie dyfrakcyjnej, rozszerzonego o współczynniki wynikające z lepkości wyznaczone za pomocą obliczeń RANSE-CFD....
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Genetic and Epigenetic Aspects of Atopic Dermatitis
PublikacjaAtopic dermatitis is a heterogeneous disease, in which the pathogenesis is associated with mutations in genes encoding epidermal structural proteins, barrier enzymes, and their inhibitors; the role of genes regulating innate and adaptive immune responses and environmental factors inducing the disease is also noted. Recent studies point to the key role of epigenetic changes in the development of the disease. Epigenetic modifications...
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Transport of Particles in Intestinal Mucus under Simulated Infant and Adult Physiological Conditions: Impact of Mucus Structure and Extracellular DNA
PublikacjaThe final boundary between digested food and the cells that take up nutrients in the small intestine is a protective layer of mucus. In this work, the microstructural organization and permeability of the intestinal mucus have been determined under conditions simulating those of infant and adult human small intestines. As a model, we used the mucus from the proximal (jejunal) small intestines of piglets and adult pigs. Confocal...
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Regulated Control of the Assembly and Diversity of LPS by Noncoding sRNAs
PublikacjaThe outer membrane (OM) of Gram-negative bacteria is asymmetric due to the presence of lipopolysaccharide (LPS) facing the outer leaflet of the OM and phospholipids facing the periplasmic side. LPS is essential for bacterial viability, since it provides a permeability barrier and is a major virulence determinant in pathogenic bacteria. In Escherichia coli, several steps of LPS biosynthesis and assembly are regulated by the RpoE...
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Progress in module design for membrane distillation
PublikacjaThere have been tremendous advances in membrane distillation (MD) since the concept was introduced in 1961: new membrane designs and process configurations have emerged, and its commercial viability has been evaluated in several pilot-scale studies. However, its high energy consumption has hindered its commercialization. One of the most promising ways to overcome this obstacle is to develop more energy-efficient membrane modules....
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Dissection of σE‐dependent cell lysis in Escherichia coli: roles of RpoE regulators RseA, RseB and periplasmic folding catalyst PpiD
PublikacjaTo understand the mechanism of sigma(E)-dependent cell lysis, we examined the consequences of deletion derivatives of rpoE regulators rseA, rseB and rseC on sigma(E) transcription, on levels of free versus membrane-bound sigma(E) and on OMP-biogenesis limiting factor(s) that could impact cell lysis. RT-PCR showed that individual nonpolar DeltarseA and DeltarseB increased the rpoE expression to varying extents, with pronounced induction...
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SiMiSnoRNA: Collection of siRNA, miRNA, and snoRNA database for RNA Interference
PublikacjaObjective:The discovery of sequence specific gene silencing which occurs due to the presence of double-stranded RNAs has considerable impact on biology, revealing an unknown level of regulation of gene expression. This process is known as RNA interference (RNAi) or RNA silencing in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecule. Two types of small RNA molecules - small...
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Checkpoints that regulate balanced biosynthesis of lipopolysaccharide and its essentiality in Escherichia coli
PublikacjaThe outer membrane (OM) of Gram-negative bacteria, such as Escherichia coli, is essential for their viability. Lipopolysaccharide (LPS) constitutes the major component of OM, providing the permeability barrier, and a tight balance exists between LPS and phospholipids amounts as both of these essential components use a common metabolic precursor. Hence, checkpoints are in place, right from the regulation of the first committed step...
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Joanna Raczek dr inż.
OsobyWykształcenie 1997 -- 2001 Studia inżynierskie, Wydział Fizyki Technicznej i Matematyki Stosowanej, Politechnika Gdańska. Kierunek: Matematyka, specjalność: Matematyka Stosowana. 2001 -- 2003 Studia magisterskie, Wydział Fizyki Technicznej i Matematyki Stosowanej, Politechnika Gdańska. Kierunek: Matematyka, specjalność: Matematyka Stosowana. 2000 -- 2004 Studia inżynierskie, Wydział Elektroniki, Informatyki i Telekomunikacji,...
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A Comprehensive Survey on Antennas On-Chip Based on Metamaterial, Metasurface, and Substrate Integrated Waveguide Principles for Millimeter-Waves and Terahertz Integrated Circuits and Systems
PublikacjaAntennas on-chip are a particular type of radiating elements valued for their small footprint. They are most commonly integrated in circuit boards to electromagnetically interface free space, which is necessary for wireless communications. Antennas on-chip radiate and receive electromagnetic (EM) energy as any conventional antennas, but what distinguishes them is their miniaturized size. This means they can be integrated inside...
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An Innovative Antenna Array with High Inter Element Isolation for Sub-6 GHz 5G MIMO Communication Systems
PublikacjaA novel technique is shown to improve the isolation between radiators in antenna arrays. The proposed technique suppresses the surface-wave propagation and reduces substrate loss thereby enhancing the overall performance of the array. This is achieved without affecting the antenna’s footprint. The proposed approach is demonstrated on a four-element array for 5G MIMO applications. Each radiating element in the array is constituted...
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Regulated assembly of lipopolysaccharide and sensing of its alterations in Escherichia coli
PublikacjaThis thesis describes mechanism of the regulation of the transcription of the rpoE gene encoding an essential RNA polymerase subunit in Escherichia coli. The RpoE regulates extracytoplasmic stress response regulon and is required to initiate transcription of genes, whose products are involvedin the folding of periplasmic proteins and synthesis and transport of outer membrane components. The transcriptional regulation of the rpoE...
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High gain/bandwidth off‑chip antenna loaded with metamaterial unit‑cell impedance matching circuit for sub‑terahertz near‑field electronic systems
PublikacjaAn innovative off-chip antenna (OCA) is presented that exhibits high gain and efficiency performance at the terahertz (THz) band and has a wide operational bandwidth. The proposed OCA is implemented on stacked silicon layers and consists of an open circuit meandering line. It is shown that by loading the antenna with an array of subwavelength circular dielectric slots and terminating it with a metamaterial unit cell, its impedance...