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The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana
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The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana
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SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis
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One tube mutation detection using sensitive fluorescent dyeing of MutS protected DNA
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Isolation and identification of the restriction endonuclease Ptal fromPhormidium tadzschicicum, an isoschizomer of BspMII
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Targeted DNA oxidation by LSD1–SMAD2/3 primes TGF-β1/ EMT genes for activation or repression
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Endogenous oxidative DNA base modifications analysed with repair enzymes and GC/MS technique
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
PublicationWe present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can...
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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A new Thermus sp. class-IIS enzyme subfamily: isolation of a ''twin'' endo nuclease TspDTI with a novel specificity 5´-ATGAA(N11/9)-3´, related to TspGWI, Taqll and Tth111II. 5´-ATGAA(N11/9)-3´, spokrewnionej z TspGWI, TaqII i Tth111II.
PublicationOdkryto i scharakteryzowano nową subrodzinę enzymów klasy IIS z Thermus sp.
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TspGWI, a thermophilic class-IIS restriction endonuclease from Thermus sp.,recognizes novel asymmetric sequence 5´-ACGGA(N11/9)-3
PublicationA novel prototype class-IIS restriction endonuclease, TspGWI, was isolated from the thermophilic bacterium Thermus sp. GW. The recognition sequence and cleavage positions have been established: TspGWI recognizes the non-palindromic 5-bp sequence 5′-ACGGA-3′ and cleaves the DNA 11 and 9 nt downstream in the top and bottom strand, respectively. In addition, an accompanying endonuclease, TspGWII, an isoschizomer of Pst I, was found...
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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H2AX phosphorylation, its role in DNA damage response and cancer therapy
PublicationDouble-strand breaks (DSBs) are the most deleterious DNA lesions, which, if left unrepaired, may have severe consequences for cell survival, as they lead to chromosome aberrations, genomic instability, or cell death. Various physical, chemical, and biological factors are involved in DSB induction. Cells respond to DNA damage by activating the so-called DNA damage response (DDR), a complex molecular mechanism developed to detect...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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TRWAŁOŚĆ PROJEKTU ERASMUS+ SP4CE - STUDIUM PRZYPADKU
PublicationProjekt ERASMUS+ Partnerstwo Strategiczne na Rzecz Kreatywności i Przedsiębiorczości (ang. Strategic Partnership for Creativity and Entrepreneurship - SP4CE) dotyczył wdrażania i upowszechniania innowacyjnych rozwiązań wzmacniających współpracę europejską w dziedzinie kształcenia i szkolenia zawodowego. Działania projektowe były związane z promowaniem innowacyjnych praktyk w edukacji oraz szkoleniach poprzez wspieranie spersonalizowanych...
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Platform Supporting the Esophageal Impedance Analysis
PublicationThe esophageal pH-impedance examination is one of the most popular diagnostic methods for identifying the upper gastrointestinal tract’s diseases. Inconclusive test evaluation criteria makes it difficult to state the definite diagnosis. In this paper, the computer platform supporting the research and teaching process in the area of pH-impedance analysis is presented. Users, having a variety of mathematical and statistical methods...
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Mini-Cave Automatic Virtual Environment Application in Security, Safety, and Defence Studies
PublicationThe aim of the article is to analyse the use of mini-Cave Automatic Virtual Reality Environment (mini-CAVE) in academic studies on security, safety, and defence. The literature review based on Web of Science database and the case study of the War Studies University research activities indicated the mini-CAVE can be used in two areas as a research infrastructure and as a didactic tool. It can be concluded that due to the development...
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Lifelong Learning Idea in Architectural Education
PublicationThe recent advances in IT and technology are forcing changes in the approach to educating society. In the 20th century, life-long learning was understood as educating adults in order to improve their occupational qualifications. Life-long learning allows the needs of the present-day world to be addressed through providing the individual with education at every stage of his/her life various forms. The search for a new model...
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Retrieval of Heterogeneus Sevices in C2NIWA Repository
PublicationThe paper reviews the methods used for retrieval of information and services. The selected approaches presented in the review inspired us to build retrieval mechanisms in a system for searching the resources stored in the C2NIWA repository. We describe the architecture of the system, its functions and the surrounding subsystems to which it is related. For retrieval of C2NIWA sevices we propos three approaches based on: keyword...
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Three-fast-searchable graphs
PublicationIn the edge searching problem, searchers move from vertex to vertex in a graph to capture an invisible, fast intruder that may occupy either vertices or edges. Fast searching is a monotonic internal model in which, at every move, a new edge of the graph G must be guaranteed to be free of the intruder. That is, once all searchers are placed the graph G is cleared in exactly |E(G)| moves. Such a restriction obviously necessitates...
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Multiregional PI control strategy for dissolved oxygen and aeration system control at biological wastewater treatment plant
PublicationThe dissolved oxygen is a key parameter for biological processes at wastewater treatment plant. The dissolved oxygen tracking problem is one of the most complex and fundamental issue of biological processes. The paper proposes a new multiregional control strategy for dissolved oxygen tracking problem. The aeration system is included in overall control structure. The control mechanism within the operating point area is based on...
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Improvement of time difference of arrival measurements resolution by using fractional delay filters in a direct sequence-code division multiple access radionavigation system
PublicationThis study presents a method of improving time measurements resolution in a direct sequence-code division multiple access receiver by using a fine code tracking loop based on fractional delay filtering of a despreading sequence. It briefly describes the structure of a generic digital code tracking loop and the proposed modification which allows to measure time difference of arrival values with the subsample resolution, together...
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Hedging with derivatives - Case of Polish market
PublicationThis paper attempts to show the ways of reaching the competitive advantage by hedging with derivatives in Poland. It shows the results of investigation of 50 Polish companies and comparison to the situation in high developed countries. Through broad review of relevant literature, the authors presented the correlation between hedging and competitive advantage. Moreover, paper shows the reasons, of differences between Poland and...
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Maternal smoking Modulates Fatty Acid Profile of Breast Milk
PublicationAIM: We hypothesized that the fatty acid composition of breast milk can be affected by a smoking habit in the mother. Consequently, this study verified whether maternal smoking modulates, and if so to what extent, the breast milk fatty acid profile. METHODS: The study included 20 postpartum women who declared smoking more than five cigarettes daily throughout a period of pregnancy and lactation, and 136 non-smoking postpartum women....
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Hybrid Laboratory of Radio Communication With Online Simulators and Remote Access
PublicationContribution: Two toolsets for the remote teaching of radio communication laboratory classes: 1) online simulators for individual work of students and 2) a remote access system to laboratory workstations for group work. Initial assumptions and method of implementation of both tools are presented. Background: The COVID-19 pandemic has forced a change in teaching at all levels of education. The specificity of practical classes, such...
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Photovoltaic Maximum Power Point Technique based on Incremental Conductance (INCON) control algorithm
PublicationMaximum output power status can significantly improve the deployment rate of solar energy system. In order to get the maximum power output, issue of tracking maximum power point (MPP), reduced harmonics around MPP and improve efficiency of the solar power energy system, this paper presents the improved maximum power point tracking (MPPT) control...
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Semantic modeling of contextual augmented reality environments
PublicationDespite significant progress in the field of augmented reality (AR), regarding both hardware and software, there is still a lack of universal models and methods that would enable building ubiquitous AR systems that could be used anywhere and anytime, covering different application areas. This dissertation describes a new approach to building AR systems, called the Contextual Augmented Reality Environment (CARE). The CARE approach...
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Chapel at St. Joseph's Church in Gdańsk
PublicationThe subject of this article is the chapel located in the former Gdańsk Carmelite monastery complex. The results of the architectural research carried out in it in 2014–2015 are presented. As a result, the time and purpose of the building’s construction were established. The original appearance and traces of later alterations were also recognised. The recesses found on the longitudinal walls, of similar dimensions, not reaching...
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Total impact of oxidative stress genes on cardiovascular events—a 7-year follow-up study
PublicationCardiovascular (CV) events are the number one cause of lifetime disability and deaths worldwide. It is well known that traditional risk factors do not fully correlate with clinical outcomes; therefore, searching for other markers that would explain CV events occurrence seems essential. Of importance, one of the main factors at the origin of CV events is oxidative stress, causing inflammation and atherosclerotic plaque instability....
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Application of Fast Cameras to String Vibrations Recording
PublicationA hardware and software solution for guitar string vibration measurement by fast cameras is described. Orthogonal setup for 3D image acquisition is proposed capable to capture several thousand image frames per second. Dedicated image processing algorithm was developed and described in the paper, aimed at tracking the movement of some selected points along the string. Fast and accurate tracking results provided a detailed information...
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Modelling of Objects Behaviour for Their Re-identification in Multi-camera Surveillance System Employing Particle Filters and Flow Graphs
PublicationAn extension of the re-identification method of modeling objects behavior in muti-camera surveillance systems, related to adding a particle filter to the decision-making algorithm is covered by the paper. A variety of tracking methods related to a single FOV (Field of Vision) are known, proven to be quite different for inter-camera tracking, especially in case of non-overlapping FOVs. The re-identification methods refer to the...
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Student competitions as a socio-spatial tool for planning urban structures
PublicationThe aim of the article is to show the interdependencies between theory and practice based on the example of the student competitions at the Faculty of Architecture at the Gdańsk University of Technology. These competitions, on the one hand, broaden the spectrum of issues related to design and, on the other hand, contribute to the better recognition of problems related to tasks to be solved. Both the teaching and applicational aspects...
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The reactions of dialkyl phosphites and phosphine oxides with iodosylbenzene
PublicationThe reaction of iodosylbenzene with >P(O)H type of acids (dialkyl phosphites, secondary phosphine oxides) was studied. The acids of >P(O)H type add to iodosylbenzene to yield intermediate 6 which in the aprotic solvents yields oxidation products, it means >P(O)OH acids and/or anhydride of >P(O)OP(O)< type. On the other hand if the reaction is performed in alcohol as a solvent in the presence of sodium alcoholate >P(O)OR ester is...
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User Authentication by Eye Movement Features Employing SVM and XGBoost Classifiers
PublicationDevices capable of tracking the user’s gaze have become significantly more affordable over the past few years, thus broadening their application, including in-home and office computers and various customer service equipment. Although such devices have comparatively low operating frequencies and limited resolution, they are sufficient to supplement or replace classic input interfaces, such as the keyboard and mouse. The biometric...
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Soil and groundwater contamination as a result of sewage sludge land application
PublicationThe leaching of chemical compounds (N-NO3, N-NH4, Norg, P-PO4, Ptot) and trace elements (Cd, Cu, Cr, Ni, Zn, and Pb) from sewage sludge and their migration through the soil profile was the subject of the study. The column experiments were carried out under atmospheric conditions corresponding to naturally occurring storm events - sewage sludge amended soil was irrigated with high rates of water. The column filter media used in...
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The influence of humic substances in treated sewage on the quality of surface waters
PublicationAt present the evaluation of WWTP effectiveness is based upon organic matter and nutrients removal. Recently it was found out that sewage treatment leads to formation of resistant to biochemical degradation organic compounds, similar to humic acids. The humic acids formed during sewage treatment process play diversified functions when discharged to surface waters - for instance they can act as carriers of hydrophobic organic pollutants...
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ABSORPCJA, METABOLIZM I ROLA BIOLOGICZNA KWASÓW NUKLEINOWYCH OBECNYCH W ŻYWNOŚCI
PublicationKwasy nukleinowe należą do niedocenianych składników żywności, szczególnie surowej lub nisko przetworzonej. W niniejszej publikacji skupiono się na omówieniu przemian, jakim podlegają kwasy nukleinowe w przewodzie pokarmowym człowieka, procesie absorpcji nukleotydów oraz nukleozydów z przewodu pokarmowego, a także przedstawiono podstawowe etapy ich metabolizmu w komórkach organizmu. Produkty trawienia kwasów nukleinowych stanowią...
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Surface Treatment of Rubber Waste
PublicationThis chapter deals with the study of different approaches to improve the compatibility of waste rubber with polymeric matrixes of high density polyethylene (HDPE) by using surface treatments to increase adhesion. Different surface treatments such as etching with sulphuric and nitric acids, the use of a silane as a coupling agent and chlorination with trichloroisocyanuric acid (TCI) have been applied. The modification of waste rubber...
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Treated wasetewater as a source of humic substances in surface waters
PublicationHumic substances impose substantial effect on the aquatic environment as well as the water organisms and human health. Among other features, the humic acids determine organoleptic properties of surface waters. Therefore explanation of the origin and properties of humic acids in surface waters is one of the priorities of water technology.Recently it was pointed out that in the wastewater treatment process organic compounds characterized...
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Recovery and re-use of photovoltaic solar cells from crystalline silicon
PublicationCrystalline silicon-type PV modules consist, in order of mass, of glass, an aluminium frame, an EVA coating, solar cells, a terminal box, back film and tapping screws. From the economic point of view, pure silicon, recoverable from spent cells, is the most important material owing to its cost and shortage. For crystalline, silicon-based PV cells, the following chemical treatments were performed: removal of the metal coating, followed...
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Recovery of silver metallization from damaged silicon cells
PublicationMetallization is one of the key process steps to fabricate solar cells with high performance in a cost-effective way. Majority of photovoltaic solar cell manufacturing uses thick film screen print metallization with Ag containing paste to produce solar cells. The average lifetime of PV modules can be expected to be more than 25 years. The disposal of PV systems will become a problem in view of the continually increasing production...
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Beyond Traditional Learning: The LLM Revolution in BPM Education at University
PublicationLarge Language Models (LLMs) significantly impact higher education, requiring changes in educational processes, especially in Business Process Management (BPM) practical exercises. The research aims to evaluate the effectiveness of LLMs in BPM education to determine if LLMs can supplement educators. The study involved 33 master’s degree students. Students’ works were manually evaluated and compared to LLM-generated responses. Results...
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Chlorine-free extraction and structural characterization of cellulose nanofibers from waste husk of millet (Pennisetum glaucum)
PublicationThis study aims to extract cellulose nanofibers (CNFs) from a sustainable source, i.e. millet husk, which is an agro-waste worthy of consideration. Pre-treatments such as mercerisation, steam explosion, and peroxide bleaching (chlorine-free) were applied for the removal of non-cellulosic components. The bleached millet husk pulp was subjected to acid hydrolysis (5% oxalic acid) followed by homogenization to extract CNFs. The extracted...
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A new look at the statistical identification of nonstationary systems
PublicationThe paper presents a new, two-stage approach to identification of linear time-varying stochastic systems, based on the concepts of preestimation and postfiltering. The proposed preestimated parameter trajectories are unbiased but have large variability. Hence, to obtain reliable estimates of system parameters, the preestimated trajectories must be further filtered (postfiltered). It is shown how one can design and optimize such...
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Post-comatose patients with minimal consciousness tend to preserve reading comprehension skills but neglect syntax and spelling
PublicationModern eye tracking technology provides a means for communication with patients suffering from disorders of consciousness (DoC) or remaining in locked-in-state. However, being able to use an eye tracker for controlling text-based contents by such patients requires preserved reading ability in the first place. To our knowledge, this aspect, although of great social importance, so far has seemed to be neglected. In the paper, we...
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Narzędzia treningu twórczości jako pomoc w kształceniu projektantów
PublicationKreatywność rozwijać. Na tym założeniu opiera się międzynarodowy program edukacyjny Odyssey of the Mind (Odyseja Umysłu). W programie zespoły młodych osób pracują metodą projektową, wykorzystując różnorodne techniki treningu twórczości, nad rozwiązaniem abstrakcyjnego problemu rozbieżnego. Część absolwentów programu wybiera kierunki kreatywne jako naturalną kontynuację procesu edukacji. Elementy treningu twórczości można wykorzystać...
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Systems of Public Higher Education in Poland and Germany. Evidence from Institution Level Data
PublicationThe chapter presents a comparative analysis of public higher education systems (HES) in Germany and Poland. Instead of limiting our study to macro indicators such as gross expenditure on higher education or R&D as per cent of GDP, we draw on the evidence based on micro data especially collected for this study and concerning individual higher education institutions (HEIs). Comparative analysis is based on a sample of 71 public...
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Chitosan-protein scaffolds loaded with lysostaphin as potential antistaphylococcal wound dressing materials.
PublicationAIMS: The development of technology for preparing chitosan-protein scaffolds loaded with lysostaphin, which potentially could be used as dressing for wound treatment and soft tissue infections caused by Staphylococcus aureus. METHODS AND RESULTS: The unique technology of chitosan solubilization using gaseous CO(2) instead of organic or inorganic acids was used for the incorporation of lysostaphin, the enzyme that exhibits bactericidal...
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Variable-structure algorithm for identification of quasi-periodically varying systems
PublicationThe paper presents a variable-structure version of a generalized notchfiltering (GANF) algorithm. Generalized notch filters are used for identification of quasi-periodically varying dynamic systems and can be considered an extension, to the system case, of classical adaptive notch filters. The proposed algorithm is a cascade of two GANF filters: a multiple-frequency "precise" filter bank, used for precise system tracking, and a...