Wyszukiwarka
Wyniki wyszukiwania dla: DRAFT GENOME SEQUENCE
-
Dorota Wojtowicz-Jankowska dr hab. inż. arch.
OsobyStarszy wykładowca na Wydziale Architektury Politechniki Gdańskiej. W latach 1996 – 2014 pracowała w Katedrze Użyteczności Publicznej, a obecnie jest zatrudniona w Katedrze Projektowania Środowiskowego. W roku 2006 uzyskała tytuł doktora. Od roku 2011 jest członkiem POIA RP. W latach 2014 – 2017 była członkiem Rady Wydziału. W pracy badawczej zajmuje się problematyką związaną z przestrzeniami ekspozycyjnymi. W obszarze jej zainteresowań...
-
Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublikacjaCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
-
Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer
Publikacja -
The Influence of the Cuboid Float’s Parameters on the Stability of a Floating Building
PublikacjaUsually, the concept of sufficient stability of a floating structure is connected with the capacity to keep a small heel angle despite the moment of heeling. The variable responsible for these characteristics is the initial metacentric height, which is the relation between the hydrostatic features of the pontoon and the mass properties of the entire object. This article answers the questions of how heavy the floating system should...
-
Genomic and Functional Characterization of the Unusual pLOCK 0919 Plasmid Harboring thespaCBAPili Cluster inLactobacillus caseiLOCK 0919
Publikacja -
Application of the Chimney Cap as a Method of Improving the Effectiveness of Natural Ventilation in Buildings
PublikacjaAdequately designed natural ventilation is the cheapest and easiest way to effectively remove indoor pollutants and keep the air inside a building fresh. A prediction of the performance and effectiveness of ventilation in order to determine the design of a ventilation system can provide real and long-term cost savings. The worst time in terms of the efficiency of natural ventilation is the spring-autumn transition period [7]. In...
-
Hybrid approach to ontology specification and development
PublikacjaIn this chapter a first draft of a hybrid ontology development approach is presented. The context of this method encompasses the multi-agent system equipped with knowledge bases and inferring engine. The process of ontology engineering appears as a complex issue, as it addresses different point-views of both, a client and a modeler with a requirements/system analyst. Regarding this, an approach based on the knowledge preprocessing...
-
Evolving gene regulatory networks controlling foraging strategies of prey and predators in an artificial ecosystem
PublikacjaCo-evolution of predators and prey is an example of an evolutionary arms race, leading in nature to selective pressures in positive feedback. We introduce here an artificial life ecosystem in which such positive feedback can emerge. This ecosystem consists of a 2-dimensional liquid environment and animats controlled by evolving artificial gene regulatory networks encoded in linear genomes. The genes in the genome encode chemical...
-
Optimal edge-coloring with edge rate constraints
PublikacjaWe consider the problem of covering the edges of a graph by a sequence of matchings subject to the constraint that each edge e appears in at least a given fraction r(e) of the matchings. Although it can be determined in polynomial time whether such a sequence of matchings exists or not [Grötschel et al., Combinatorica (1981), 169–197], we show that several questions about the length of the sequence are computationally intractable....
-
A Method for Optimising the Blade Profile in Kaplan Turbine
PublikacjaThis paper introduces a method of blade profile optimisation for Kaplan-type turbines, based on modelling the interaction between rotor and stator blades. Rotor and stator blade geometry is described mathematically by means of a midline curve and thickness distribution. Genetic algorithms are then used to find a global optimum that minimises the loss coefficient. This allows for variety of possible blade shapes and configurations....
-
Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublikacjaAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
-
A Generalized Version of the Lions-Type Lemma
PublikacjaIn this short paper, I recall the history of dealing with the lack of compactness of a sequence in the case of an unbounded domain and prove the vanishing Lions-type result for a sequence of Lebesgue-measurable functions. This lemma generalizes some results for a class of Orlicz–Sobolev spaces. What matters here is the behavior of the integral, not the space
-
Sensorless Control of Polyphase Induction Machines
PublikacjaThe basics of transformations of polyphase systems into orthogonal systems are explained. Vector models of induction machines in orthogonal planes are analysed and multiscalar models for rotor flux and main flux together with stator current are presented. A speed observer based on an extended model of the induction machine for selected variables is applied in the control system for the induction machine. On the basis of the model...
-
Equivalence of equicontinuity concepts for Markov operators derived from a Schur-like property for spaces of measures
PublikacjaVarious equicontinuity properties for families of Markov operators have been – and still are – used in the study of existence and uniqueness of invariant probability for these operators, and of asymptotic stability. We prove a general result on equivalence of equicontinuity concepts. It allows comparing results in the literature and switching from one view on equicontinuity to another, which is technically convenient in proofs....
-
Graph classes generated by Mycielskians
PublikacjaIn this paper we use the classical notion of weak Mycielskian M'(G) of a graph G and the following sequence: M'_{0}(G) =G, M'_{1}(G)=M'(G), and M'_{n}(G)=M'(M'_{n−1}(G)), to show that if G is a complete graph oforder p, then the above sequence is a generator of the class of p-colorable graphs. Similarly, using Mycielskian M(G) we show that analogously defined sequence is a generator of the class consisting of graphs for which the...
-
Evolution of chemotaxis in single-cell artificial organisms
PublikacjaThe model of a liquid two-dimensional environment, which is based on physics of diffusion, allows us to simulate the diffusion of morphogenes. Artificial organisms move using a chemotaxis reacting to concentration difference. Organisms are controlled by a gene regulatory network coded in a linear genome and reproduce by division. We made a lot of experiments presenting organisms’ behaviour in various environment conditions. We...
-
Architectural project VI 2021/2022 _Erasmus _JB
Kursy OnlineThe design task is to develop a draft revitalisation plan and a conceptual proposal for a complex of architectural objects for an area in Dolne Miasto, Gdańsk. The proposal should include spatial, social and environmental solutions to restore the attractiveness of a historical district and enhance its visual coherence and functionality. Moreover, the aim is to develop detailed architectural and functional solutions for a selected...
-
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...
-
Moments of Hermite-Gaussian functionals
PublikacjaMoments of finite products of Hermite-Gaussian functionals are expressed by covariances of Gaussian sequence.
-
Wartość miejsca w małym i średnim mieście
PublikacjaPublic space is a matter of concern for international humanitarian organisations. The paper describes the initiative of UN-Habitat organisation for the creation of Charter of Public Space and the draft of this document. Next the definition of “place” is provided and the definitions of social capital and the bond between social capital and place attachment are presented. The actions proposed nowadays to create places are described....
-
The importance of a place in a small or medium - Sized Town.- Vol. 2
PublikacjaPublic space is a matter of concern for international humanitarian organisations. The paper describes the initiative of UNHabitat organisation for the creation of Charter of Public Space and the draft of this document. Next the definition of “place” is provided and the definitions of social capital and the bond between social capital and place attachment are presented. The actions proposed nowadays to create places are described....
-
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...
-
MSP for port areas – To what extent should we interfere with governance of ports’ waters? Case study of Polish seaports
PublikacjaThe EU MSP Directive imposed the requirement to develop plans for all water areas under the jurisdiction of an EU country by the end of March 2021. Poland is the only country in the Baltic Sea Region whose maritime administration has decided to elaborate detailed maritime spatial plans for port waters. The aim of the paper is to draw conclusions from the work carried out so far on the MSP for Polish port water areas. For this purpose,...
-
In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates
PublikacjaBacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active...
-
Plasmids pMET2M1 and pMET15M1 with the SAT1 Flipper knockout cassette construction
Dane BadawczeThe goal of the study was to obtain plasmids containing the SAT1 Flipper knockout cassette along with upstream and downstream gene fragments (MET2, MET15) and to introduce a cleavage site for restriction enzymes into them.
-
Sequences of large subunit ribosomal RNA gene, partial sequence encoding D1/D2 domain of psychrotolerant pigment-producing yeast-like fungi
Dane BadawczeDNA fragments encoding D1/D2 domain of large subunit ribosomal RNA of psychrotolerant pigment-producing yeast-like fungi named Red, Pink and Black were PCR amplified using NL1 5’ GCATATCAATAAGCGGAGGAAAAG 3’ and NL4 5’ GGTCCGTGTTTCAAGACGG 3’ primers and sequenced by Sanger method using the same primers.
-
Inserts amplification for knockout cassette construction
Dane BadawczeThe goal of the study was to obtain optimal conditions for amplification of upstream and downstream genes fragments and introduce a cleavage site for restriction enzymes into them thanks to which it will be possible to clone fragments into a plasmid containing elements of the knockout cassette. The constructed cassettes will enable the removal of the...
-
Shape Optimisation of Kaplan Turbine Blades Using Genetic Algorithms
PublikacjaThis monograph is a comprehensive guide to a method of blade profile optimisation for Kaplan-type turbines. This method is based on modelling the interaction between rotor and stator blades. Additionally, the shape of the draft tube is investigated. The influence of the periodic boundary condition vs. full geometry is also discussed. Evolutionary algorithms (EA) are used as an optimisation method together with artificial neural...
-
Analysis of Interspike-Intervals for the General Class of Integrate-and-Fire Models with Periodic Drive
PublikacjaWe study one-dimensional integrate-and-fire models of the general type x˙=F (t, x) and analyze properties of the firing map which iterations recover consecutive spike timings. We impose very week constraints for the regularity of the function F (t, x), e.g. often it suffices to assume that F is continuous. If additionally F is periodic in t, using mathematical study of the displacement sequence of an orientation preserving circle...
-
DETERMINING THE TIME CONSTANT USING TWO METHODS AND DEFINING THE THERMOCOUPLE RESPONSE TO SINE EXCITATION OF GAS TEMPERATURE
PublikacjaThis paper describes the two methods of determining the time constant of type K thermocouple, for two construction solutions: the exposed weld and the mantle fillet weld. This is an important parameter indicating the response time of the thermocouple on the recorded signal. The first method consists of determining the value of τ in the way of numerical simulation of heat exchange between the thermocouple and the current of gas...
-
Experiments on Preserving Pieces of Information in a Given Order in Holographic Reduced Representations and the Continuous Geometric Algebra Model
PublikacjaGeometric Analogues of Holographic Reduced Representations (GAc, which is the continuous version of the previously developed discrete GA model) employ role-filler binding based on geometric products.Atomic objects are real-valued vectors in n-dimensional Euclidean space and complex statements belong to a hierarchy of multivectors. The property of GAc and HRR studied here is the ability to store pieces of information in a given...
-
Image Classification Based on Video Segments
PublikacjaIn the dissertation a new method for improving the quality of classifications of images in video streams has been proposed and analyzed. In multiple fields concerning such a classification, the proposed algorithms focus on the analysis of single frames. This class of algorithms has been named OFA (One Frame Analyzed).In the dissertation, small segments of the video are considered and each image is analyzed in the context of its...
-
Establishing the allosteric mechanism in CRISPR‐Cas9
PublikacjaAllostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR‐Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three...
-
Lekka obudowa w nadbudowach i renowacjach
PublikacjaNadbudowy i renowacje – wykorzystanie technologii lekkiej obudowy. W artykule przedstawiono możliwości wykorzystania technologii lekkiej obudowy do nadbudowy i renowacji obiektów budowlanych. Opisano kolejne kroki przygotowania inwestycji dotyczącej projektowania i realizacji nadbudowy obiektu budowlanego.
-
Hydrographic Multisensory Unmanned Watercraft
PublikacjaThis article describes the design of the unmanned surface vessel (USV) and the algorithms for planning the trajectories to be followed on measurement missions. The algorithms take account of the dynamically varying impacts of external forces (wind and surface current) on the vessel's motion. Feedback loops enable the counteraction of external factors that cause disturbance to the desired trajectory. The sensors installed on the...
-
Influence of Escherichia coli on Expression of Selected Human Drug Addiction Genes
PublikacjaThe impact of enteric microflora on the expression of genes associated with cocaine and amphetamine addiction was described. Human genome-wide experiments on RNA transcripts expressed in response to three selected Escherichia coli strains allowed for significant alteration (p > 0.05) of the linear regression model between HT-29 RNA transcripts associated with the KEGG pathway:hsa05030:Cocaine addiction after 3 h stimulation with...
-
Wykorzystanie słabych sygnałów, foresightu i ciągu zarządzania strategicznego w konfiguracji biznesu przyszłości
PublikacjaBurzliwość współczesnego otoczenia wyostrza zagadnienie przystosowania prowadzonej działalności gospodarczej do funkcjonowania w przyszłości. Do osiągnięcia sukcesu w biznesie przyszłości przyczynić się może wykorzystanie dostępnej już obecnie wiedzy. Na szczególną uwagę zasługuje teoria słabych sygnałów, metoda foresight oraz ciąg zarządzania strategicznego, które w połączeniu umożliwiają wypracowanie stanowiska w sprawie kształtu...
-
On the interspike-intervals of periodically-driven integrate-and-fire models
PublikacjaWe analyze properties of the firing map, which iterations give information about consecutive spikes, for periodically driven linear integrate-and-fire models. By considering locally integrable (thus in general not continuous) input functions, we generalize some results of other authors. In particular, we prove theorems concerning continuous dependence of the firing map on the input in suitable function spaces. Using mathematical...
-
Characterization of a cryptic plasmid pSFKW33 from Shewanella sp. 33b
PublikacjaA cryptic plasmid pSFKW33 from psychrotrophic bacterium Shewanella sp. 33B, an isolate from the Gulf of Gdansk (the Baltic Sea), was sequenced and characterized. It is an 8021 bpcircular molecule with 38% GC content, which shows a distinctive nucleotide sequence without homology to other known plasmids. The nucleotide sequence analysis predicts eight open reading frames. The deduced amino acid sequence of ORF-1 shared significant...
-
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...
-
Typing of Candida isolates from patients with invasive infection and concomitant colonization
PublikacjaWe investigated the relationship between colonizing and invasive isolates from patients with candidaemia. Molecular typing was performed using random amplification of polymorphic DNA (RAPD) and multilocus sequence typing (MLST). We found MLST to be sufficient for typing Candida isolates, and that surveillance cultures are helpful in predicting concomitant invasive isolates, but not necessarily the pathogen involved in subsequent...
-
Computing dynamical curlicues
Dane BadawczeA curlicue is a piece-wise linear curve in the complex plane which can be generated by an arbitrary sequence of real numbers u_n. It can be interpreted as a trajectory of a particle in the plane which starts in the origin at time t=0 and moves with a constant velocity, changing its direction at instances t=0,1,2,3,..., where the new direction is given...
-
─ Formation of a state institution on the basis of a process analysis - The concept of the institution of cadastre
PublikacjaModification of the structures of public administration encounters major obstacles. Institutional changes are difficult to introduce due to their complexity and broad impact. Non-substantial (political) factors are of importance as well. The resistance to change is aggravated by how difficult it is for decision-makers to assess the impact of the changes that are proposed. We present a method of handling such issues based on the...
-
Analysis of the Hydrodynamic Properties of the 3-Column Spar Platform for Offshore Wind Turbines
PublikacjaThe article presents a design of a floating platform for offshore wind turbines. The concept is a modification of the Spar design and consists of three variable section columns connected to each other by a ballast tank in the lower part of the platform. This solution makes it possible to influence the position of the centre of buoyancy and the centre of mass of the structure. Compared to the classic Spar platform structure, the...
-
On the existence of homoclinic type solutions of inhomogenous Lagrangian systems
PublikacjaWe study the existence of homoclinic type solutions for a class of inhomogenous Lagrangian systems with a potential satisfying the Ambrosetti-Rabinowitz superquadratic growth condition and a square integrable forcing term. A homoclinic type solution is obtained as a limit of periodic solutions of an approximative sequence of second order differential equations.
-
Evolution of artificial single-cell organisms foraging for resources in a 3-dimensional environment
PublikacjaForaging for resources is a simple cognitive task that even one-celled biological organisms can ac- complish. We present an Artificial Life system in which artificial unicellular organisms (animats) forage for food in a 3-dimensional simulated liquid environment. The movement of animats is controlled by evolving artificial gene regulatory networks encoded in linear genomes. When an animat consumes enough food, it produces offspring...
-
Biomimetic torene shells
PublikacjaThe genome inside the eukaryotic cells is guarded by a unique shell structure, called the nuclear envelope (NE), made of lipid membranes. This structure has an ultra torus topology with thousands of torus-shaped holes that imparts the structure a high flexural stiffness. Inspired from this biological design, here we present a novel ‘‘torene’’ architecture to design lightweight shell structures with ultra-stiffness for engineering...
-
In vitro studies of antimicrobial activity of Gly-His-Lys conjugates as potential and promising candidates for therapeutics in skin and tissue infections
PublikacjaWe presented in vitro studies of antimicrobial activity of Gly-His-Lys conjugates that are important point in preliminary biological evaluation of their potential application in skin and tissue therapy. The novel compounds include the conjugation of fatty acids with a modification of the amino acid sequence in the primary structure of Gly-His-Lys.
-
Structural changes of a simple peptide—Trpzip-1—in aqueous solutions and the corresponding hydration phenomena under the influence of temperature
PublikacjaTrpzip-1, a simple β-hairpin, is a rare example of peptide with stable secondary structure and can be a convenient model to study temperature-related processes that potential prion or amyloid proteins undergo. Although its sequence is simple, the exact processes which the peptide undergoes in aqueous solutions are quite complex and not well understood. The selection of well-established experimental (DSC, FTIR) and theoretical methods...
-
NASBA – IZOTERMICZNA AMPLIFIKACJA RNA
PublikacjaNASBA (ang. Nucleic Acid Sequence-Based Amplification) jest skuteczną i czułą techniką izotermicznej amplifikacji opartej na transkrypcji, służąca głównie do detekcji cząsteczek RNA. Znalazła ona zastosowanie do wykrywania RNA wirusowego, bakteryjnego i grzybiczego w próbkach klinicznych oraz żywości.