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Search results for: transcription
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Transcription-Austin
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Methodology and technology for the polymodal allophonic speech transcription
PublicationA method for automatic audiovisual transcription of speech employing: acoustic, electromagnetical articulography and visual speech representations is developed. It adopts a combining of audio and visual modalities, which provide a synergy effect in terms of speech recognition accuracy. To establish a robust solution, basic research concerning the relation between the allophonic variation of speech, i.e., the changes in the articulatory...
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Methodology and technology for the polymodal allophonic speech transcription
PublicationA method for automatic audiovisual transcription of speech employing: acoustic and visual speech representations is developed. It adopts a combining of audio and visual modalities, which provide a synergy effect in terms of speech recognition accuracy. To establish a robust solution, basic research concerning the relation between the allophonic variation of speech, i.e. the changes in the articulatory setting of speech organs for...
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Overview of the Virtual Transcription Laboratory Usage Scenarios and Architecture
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Material for Automatic Phonetic Transcription of Speech Recorded in Various Conditions
PublicationAutomatic speech recognition (ASR) is under constant development, especially in cases when speech is casually produced or it is acquired in various environment conditions, or in the presence of background noise. Phonetic transcription is an important step in the process of full speech recognition and is discussed in the presented work as the main focus in this process. ASR is widely implemented in mobile devices technology, but...
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The role of Snail1 transcription factor in colorectal cancer progression and metastasis
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Description of the Dataset Hanow – Praecepta de Arte Disputandi – Transcription and Photographs
PublicationThis article briefly characterises the “Hanow – Praecepta de arte disputandi – transcription and photographs” research dataset. The dataset was created based on photographs and transcriptions of the manuscript of the Latin lectures on the rules of effective discussion (the title of the manuscript: Praecepta de arte disputandi) by Michael Chris-toph Hanow (1695–1773), professor of Gdańsk Academic Gymnasium. The original document...
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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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The Phytoestrogen Genistein Modulates Lysosomal Metabolism and Transcription Factor EB (TFEB) Activation
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Multiple transcriptional factors regulate transcription of the rpoE gene in Escherichia coli under different growth conditions and when the lipopolysaccharide biosynthesis is defective.
PublicationThe RpoE sigma factor is essential for the viability of Escherichia coli. RpoE regulates extracytoplasmic functions including lipopolysaccharide (LPS) translocation and some of its non-stoichiometric modifications. Transcription of the rpoE gene is positively autoregulated by EσE and by unknown mechanisms that control the expression of its distally located promoter(s). Mapping of 5′ ends of rpoE mRNA identified five new transcriptional...
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Description of the Dataset Rhetoric at School – a Selection of the Syllabi from the Academic Gymnasium in Gdańsk – Transcription and Photographs
PublicationThe research dataset described in the article was based on photographs and transcription of a textual record from Latin syllabi for classes at the Gdańsk Academic Gymnasium. The syllabi concern the years 1645/1648/1652/1653. The original document is held in the collection of the Gdańsk Library of the Polish Academy of Sciences [reference number: Ma 3920 8o]. The collected research material can be used for studying the practical...
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The effect of cabbage juice and its active components on transcription factor Nrf2 in breast cell lines
PublicationObniżenie zagrożenia chorobami nowotworowymi w przypadku diety bogatej w kapustę wiąże się ze zdolnością bioaktywnych związków tego warzywa do indukowania enzymów ochronnych 2. fazy będacych pod kontrolą czynnika transkrypcyjnego Nrf2. Zbadano wpływ soków z kapusty na poziom Nrf2 w komórkach unieśmiertelnionych i nowotworowych linii odpowiednio MCF10A i MCF-7. W obu przypadkach obserwowano wzrost poziomu tego czynnika oraz jego...
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New markers for regulation of transcription and macromolecule metabolic process in porcine oocytes during in vitro maturation
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Hyponastic Leaves 1 Interacts with RNA Pol II to Ensure Proper Transcription of MicroRNA Genes
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Excess nitrogen responsive HvMADS27 transcription factor controls barley root architecture by regulating abscisic acid level
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GlaR (YugA)—a novel RpiR‐family transcription activator of the Leloir pathway of galactose utilization in Lactococcus lactis IL 1403
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Are 8-oxoguanine (8-oxoGua) and 5-hydroxymethyluracil (5-hmUra) oxidatively damaged DNA bases or transcription (epigenetic) marks?
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Drastically decreased transcription from CII-activated promoters is responsible for impaired lysogenization of the Escherichia coli rpoA341 mutant by bacteriophage λ
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Recent advances in transcription regulation
e-Learning CoursesRecent advances in transcription regulation
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Can mutations in the gene encoding transcription factor EKLF (Erythroid Krüppel-Like Factor) protect us against infectious and parasitic diseases?
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Replicating DNA by cell factories: roles of central carbon metabolism and transcription in the control of DNA replication in microbes, and implications for understanding this process in human cells
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Hanow - Praecepta de arte disputandi - transcription and photographs
Open Research DataPraecepta de arte disputandi by Enlightenment Gdańsk scholar Michael Christoph Hanow (1695-1773) are a combination of rhetorical theory and practical tips on how to effectively conduct discussions.
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Impact of heat shock transcription factor 1 on global gene expression profiles in cells which induce either cytoprotective or pro-apoptotic response following hyperthermia
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Wernsdorf - a biography of an 18th century scholar - transcription, photographs and partial translation
Open Research DataThe data set contains the transcription of a large passage of the Latin biography of the eighteenth-century philologist and theologian Gottlieb Wernsdorf (1717-1774), as well as photos of the entire print. A translation from Latin into English and Polish was added to the data set as well (that is, excerpts on the education of both Gottlieb himself,...
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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
PublicationConsistent 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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Rhetoric at school - a selection of the syllabi from the Academic Gymnasium in Gdańsk - transcription and photographs
Open Research DataThe following data set comprises a transcription (in txt and docx formats) and photographs (in jpg format) of the selected records from the Latin-language teaching syllabi termed 'Typus' or 'Catalogus lectionum' (an abbreviated title). Rhetoric is the main thematic criterion behind this choice. Various topics related to rhetoric have been taught not...
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2 Latin letters by Georg Pauli (b.1586-d.1650) - transcription, translation and photographs
Open Research DataThe data set contains two Latin letters by Georg Pauli (b. 1586 – d. 1650) to his brother Adrian (d. 1622) in photographs, transcriptions, and translations into Polish and English. The first letter was sent by Georg from Gdańsk (formerly Danzig) in 1604 when he was still a student at the local Academic Gymnasium. The second one, in turn, was written...
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The database of localization and expression of aquaporin 3 (AQP3), aquaporin 7 (AQP7) and aquaporin 9 (AQP9) in the male reproductive system in cattle. Morphometric studies. Localization of zinc finger transcription factor GATA-4.
Open Research DataThe data present research results being part of the OPUS-22 project entitled “In search of new markers of male fertility in cattle. Aquaporins expression in the reproductive organs and sperm of the bulls (Bos taurus)” obtained from the National Science Center in Poland (grant no. 2021/43/B/NZ9/00204). The aim of this part of the project was (i) to determine...
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Transcriptional activity of epigenetic remodeling genes declines in keratinocytes after in vitro expansion
PublicationPURPOSE: In vitro expansion is an invaluable method to obtain keratinocytes in amounts necessary for effective transplantation therapies. In vitro cell culturing provokes questions concerning potential epigenetic alterations occurring in expanded cells in the context of usefulness for transplantation and safety. The purpose of this study was to investigate as to whether keratinocyte expansion is associated with changes in the activity...
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Is the Identification of SNP-miRNA Interactions Supporting the Prediction of Human Lymphocyte Transcriptional Radiation Responses?
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Salt Stress Reveals a New Role for ARGONAUTE1 in miRNA Biogenesis at the Transcriptional and Posttranscriptional Levels
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Immunophenotyping and transcriptional profiling of in vitro cultured human adipose tissue derived stem cells
PublicationAdipose-derived stem cells (ASCs) have become an important research model in regenerative medicine. However, there are controversies regarding the impact of prolonged cell culture on the ASCs phenotype and their differentiation potential. Hence, we studied 10 clinical ASCs replicates from plastic and oncological surgery patients, in six-passage FBS supplemented cultures. We quantified basic mesenchymal cell surface marker transcripts...
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The Escherichia coli RNA polymerase alpha subunit and transcriptional activation by bacteriophage lambda CII protein.
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Transcriptional profile of in vitro expanded human epidermal progenitor cells for the treatment of non-healing wounds
PublicationBackground Epidermal progenitor cells (EPCs) have been under extensive investigation due to their increasing potential of application in medicine and biotechnology. Cultured human EPCs are used in the treatment of chronic wounds and have recently became a target for gene therapy and toxicological studies. One of the challenges in EPCs culture is to provide a high number of undifferentiated, progenitor cells displaying high viability...
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Modelling gene expression of a self-regulating protein
PublicationWe analyze a model of gene transcription and protein synthesis. We take into account the number of sites on the protein’s promoter at which the protein’s dimers can bind blocking transcription of protein mRNA.
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Optimizing Medical Personnel Speech Recognition Models Using Speech Synthesis and Reinforcement Learning
PublicationText-to-Speech synthesis (TTS) can be used to generate training data for building Automatic Speech Recognition models (ASR). Access to medical speech data is because it is sensitive data that is difficult to obtain for privacy reasons; TTS can help expand the data set. Speech can be synthesized by mimicking different accents, dialects, and speaking styles that may occur in a medical language. Reinforcement Learning (RL), in the...
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Hopf bifurcation in time‐delayed gene expression model with dimers
PublicationWe study a mathematical model of gene transcription and protein synthesis with negative feedback. We consider a system of equations taking into account the formation of dimers (i.e., complex formed by two protein monomers), the way in which dimers bind to DNA and time delay in translation process. For the model consisting of three ordinary differential equations with time delay, we derive conditions for stability of the positive...
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Regulated assembly of lipopolysaccharide and sensing of its alterations in Escherichia coli
PublicationThis 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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Data on solutions of Hes1 system
Open Research DataHes1 protein (hairy and enhancer of split 1) belongs to the helix-loop-helix (bHLH) family of transcription proteins, i.e. DNA-binding proteins in the promoter region or in another region where regulation of transcription processes occurs. The database collects data on solutions of the Hes1 systems with multiple binding sites and the dimer formation...
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Interaction of the conserved region 4.2 of sigma(E) with the RseA anti-sigma factor
PublicationEo-E RNA polymerase transcribes a regulon of folding factors for the bacterial envelope and is induced by physical and chemical stresses. The RseA anti-sigma factor inhibits the activity of Esigma(E) RNA, polymerase. It is shown here that the N-terminal portion of sigma(E), residues 1-153, binds core RNA polymerase. RseA interacts with residues 154-191 of sigma(E), a site that is homologous to region 4, the sigma factor binding...
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Bimodal classification of English allophones employing acoustic speech signal and facial motion capture
PublicationA method for automatic transcription of English speech into International Phonetic Alphabet (IPA) system is developed and studied. The principal objective of the study is to evaluate to what extent the visual data related to lip reading can enhance recognition accuracy of the transcription of English consonantal and vocalic allophones. To this end, motion capture markers were placed on the faces of seven speakers to obtain lip...
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Epitaph of Bartholomew Wagner in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to Bartholomew Wagner, city physician from 1562, who came to Gdańsk from Konigsberg. Data set contains one general photo of the epitaph, transcription of its text in Latin, its translation in Polish, and the biography of the deceased, also...
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Foundation text of St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the medieval foundation preserved on the wall above the sacristy entrance in St. Mary’s Church in Gdańsk, which confirms that the foundation stone of the temple was laid on 28th of March 1343. The data set contains one general photo of the foundation text, transcription of its text in Latin and its Polish...
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Epitaph of John Schroeder in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to John Schröder, son of Simon. John, as he was a single, erected this epitaph for himself. Data set contains one general photo of the epitaph, transcription of its text in Latin, its translation in Polish, and the biography of the deceased,...
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Gracjana Klein-Raina dr hab.
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Epitaph of Henry Giese in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to Henry Giese, a member of merchant family that came from Germany and settled down in Gdańsk in XVI century. Data set contains one general photo of the epitaph, transcription of its text in Latin, its translation in Polish, and the biography...
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Epitaph of Oehm family in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to Öhm family, rather unknown to Gdańsk. The epitaph was erected by two latest representatives of family – John and Andrew. Data set contains one general photo of the epitaph, transcription of its text in Latin, its translation in Polish,...
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Alms-panel of Anton Moeller in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the Alms-panel placed in St. Mary’s Church in Gdańsk, that is the work of Gdańsk painter Antoni Moller, made in 1607, or rather – to be more specific – to lower part of this work, which are the verses from Holy Bible. Data set contains one general photo of the inscription, transcription of its text in Latin...
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Epitaph of Anna Loitz in St. Mary's Church in Gdansk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk which is dedicated to Anna Loitz, daughter of the well-known merchant Michał Loitz, wife of the juror and councilor Jan Konnert the Younger. The data set contains one general photo of the epitaph, transcription of its text in Latin, its Polish translation,...
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Plaque of Dorothy and John Brandes in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the plaque placed in St. Mary’s Church in Gdańsk, that is dedicated to John Brandes, highly influential citizen of Gdańsk, whose official career was crowned with the function of mayor, and his wife Dorothy née Zimmermann. The plaque was placed in the church in 1586. Data set contains two photos of the plaque,...
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Epitaph of Martin Ramus in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk which is dedicated to Martin Ramus, teacher of the parochial school at the St. Mary church in Gdansk who died on 24th of June 1631 in Gdańsk. The data set contains one general photo of the epitaph, transcription of its text in Latin, its Polish translation,...
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Epitaph of Guldenstern family in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to family Guldenstern, very noble family that came to Poland with the king of Sweden and Poland – Sigismund III Vasa, and to representatives of Swedish emigration. Data set contains one general photo of the epitaph, transcription of its...
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Epitaph of Clemens and Gabriel Coelmer in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk which is dedicated to Clemens and Gabiel Coelmer, sons of a Gdańsk merchant; Clemens devoted himself to a clerical career in Gdańsk and became a councilor. The data set contains one general photo of the epitaph, transcription of its text in Latin, its Polish...
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Sepulchral plate of Dorothy and Matthias Zimmermann in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the sepulchral plate placed in St. Mary’s Church in Gdańsk which is dedicated to Dorothy and Matthias Zimmermann, a wealthy merchant and Gdańsk mayor, trusted courtier of King Alexander Jagiellon. The data set contains one general photo of the sepulchral plate, transcription of its text in Latin, its Polish...
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Cabbage Juices and Indoles Modulate the Expression Profile of AhR, ERα, and Nrf2 in Human Breast Cell Lines
PublicationOur previous studies showed the diversified effect of cabbage juices and indoles on the estrogen metabolism key enzymes (CYP1A1, CYP1A2, CYP1B1) in breast epithelial cells differing in ER status, i.e., in tumorigenic—MCF7, MDA-MB-231 and non-tumorigenic—MCF10A cells. The aim of the present study was to further investigate the mechanism of chemopreventive action of cabbage juice and its active components by evaluating their effect...
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Epitaph of Bartholomew Schachmann in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk which is dedicated to Bartholomew Schachmann, the mayor to whom Gdańsk owes, among others, the creation of the Neptune Fountain and the decoration of the Red Hall in the New Town Hall. The data set contains one general photo of the epitaph, transcription...
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Epitaph of George Wildtberger in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk which is dedicated to George Wildtberger, personal secretary to king Sigismund III Vasa of Sweden and Poland who died on 8th of February 1593 in Gdańsk. The data set contains one general photo of the epitaph, transcription of its text in Latin, its Polish...
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Epitaph of John Sinclair in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, which is dedicated to John Sinclair, an Scottish nobleman, the 6th count of Caithness. He was general and from 1716 was chief commandant of the defenses in Gdańsk. He died in 1731 in Gdańsk. Data set contains one general photo of the epitaph, transcription...
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Epitaph of Gabriel Schumann and his son Gabriel in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to Gabriel Schumann, a noble citizen of Gdańsk, who was a juror and finally councilor of Gdańsk, and his son Gabriel, who was not only juror and councilor, but also a city treasurer. Data set contains one general photo of the epitaph, transcription...
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Analysis of a gene expression model
PublicationWe study a mathematical model of gene transcription and protein synthesis with negative feedback. We consider a system of equations taking into account the number of active binding sites, the way in which dimers bind to DNA and time delay in translation process. For a simplified model that consist of three ordinary differential equations with time delay we derive conditions for stability of the positive steady state and for the...
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Epitaph of Edward Blemke in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to Edward Blemke, a citizen of Gdańsk who was in city council as a juror, almost till his death in 1593. The epitaph, made in 1591, is one of the greatest and the most beautiful in the whole basilica. Data set contains one general photo...
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Epitaph of George Hojer in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to George Hojer, a citizen of Stralsund, who was travelling all over the Europe and unexpectedly died in Gdańsk in 1585 at the age of 25 during his way back home from Riga. Data set contains one general photo of the epitaph, transcription...
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Sepulchral plate of James von Werden in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the It refers to the sepulchral plate placed in St. Mary’s Church in Gdańsk which is dedicated to James von Werden, a rich merchant, a provisor of St. Mary Church in Gdańsk, father of Mayor John von Werden, a founder of this sepulchral plate. The data set contains one general photo of the sepulchral plate,...
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Epitaph of George Posse in St. Mary's Church in Gdańsk
Open Research DataData set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to George Posse, a Swedish nobleman who came to Poland with the king of Sweden and Poland – Sigismund III Vasa, and died in Gdańsk on 8th of March 1616. The epitaph was erected by his son Gabriel. Data set contains one general photo of the...
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Epitaph of Anna and Daniel Zierenberg in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to Anna and Daniel Zierenberg. Daniel was particularly interested in activities for the education of Gdańsk and was one of those mayors who in 1596 established the foundation called Bibliotheca Senatus Gedanensis (today PAN BG). Data set...
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Epitaph of Choene-Jaski family in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to family Chöne-Jaski, that came to Poland from Moldavia at the beginning of XVI century and was engaged in trade in amber. Later on, the representatives of the family were in city council as jurors, councilors, judges and city treasurers....
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Epitaph of James Schadius in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to James Schadius city doctor of Gdańsk, who, after he had studied medicine in Italy, stayed in Gdańsk till his death on 7th of June 1588. The epitaph was erected by his wife and son. Data set contains one general photo of the epitaph,...
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Mathematical analysis of a generalised p53-Mdm2 protein gene expression model
PublicationWe propose the generalisation of the p53-Mdm2 protein gene expression model introduced by Monk (2003). We investigate the stability of a unique positive steady state and formulate conditions which guarantee the occurrence of the Hopf bifurcation. We show that oscillatory behaviour can be caused not only by time lag in protein transcription process, but also can be present in the model without time delay. Moreover, we investigate...
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Building Knowledge for the Purpose of Lip Speech Identification
PublicationConsecutive stages of building knowledge for automatic lip speech identification are shown in this study. The main objective is to prepare audio-visual material for phonetic analysis and transcription. First, approximately 260 sentences of natural English were prepared taking into account the frequencies of occurrence of all English phonemes. Five native speakers from different countries read the selected sentences in front of...
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Epitaph of Eggert von Kempen in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk which is dedicated to Eggert von Kempen, the progenitor of the von Kempen family, a wealthy Gdańsk merchant, alderman and councilor, and to his son John, an alderman and councilor who, due to unsuccessful financial operations, significantly depleted family...
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Epitaph of John Botsack in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk which is dedicated to John Botsack, esteemed professor and rector of the Gdańsk Academic Gymnasium, Lutheran pastor of the St. Mary church in Gdańsk, author of many theological dissertations, polemical writings and sermons written in both Latin and German....
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Epitaph of Ferber family in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to one of the greatest family in Gdańsk – family Ferber, and one of its member – Konstantin Ferber, whose official career was crowned with the function of mayor of city. The epitaph was erected by his brother John Ferber, the juror, councilor...
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Molecular and structural basis of inner core lipopolysaccharide alterations in Escherichia coli: incorporation of glucuronic acid and phosphoethanolamine in the heptose region.
PublicationIt is well established that lipopolysaccharide (LPS) often carries nonstoichiometric substitutions in lipid A and in the inner core. In this work, the molecular basis of inner core alterations and their physiological significance are addressed. A new inner core modification of LPS is described, which arises due to the addition of glucuronic acid on the third heptose with a concomitant loss of phosphate on the second heptose. This...
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Neotenic phenomenon in gene expression in the skin of Foxn1- deficient (nude) mice - a projection for regenerative skin wound healing
PublicationMouse fetuses up to 16 day of embryonic development and nude (Foxn1- deficient) mice are examples of animals that undergo regenerative (scar-free) skin healing. The expression of transcription factor Foxn1 in the epidermis of mouse fetuses begins at embryonic day 16.5 which coincides with the transition point from scar-free to scar-forming skin wound healing. In the present study, we tested the hypothesis that Foxn1 expression...
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Tombstone of Simon Bahr in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the tombstone placed in St. Mary’s Church in Gdańsk which is dedicated to Simon Bahr, the merchant and banker of the Swedish King John III Vasa and his son, Sigismund III Vasa, king of Poland and Sweden. Simon formed powerful alliances by marrying his numerous offspring into the finest Gdańsk families. The...
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Epitaph of Dorothy and John Brandes in St. Mary's Church in Gdansk
Open Research DataThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to John Brandes, highly influential citizen of Gdańsk, whose official career was crowned with the function of mayor, and his wife Dorothy née Zimmermann. The epitaph was founded by their family, and especially by their grandson John Speymann,...
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Effect of new bisacridines IKE16, IKE18 and IE10 on the yeast topoisomerase II relaxation activity
Open Research DataThe datasets contain the results of new bisacridines IKE16, IKE18 and IE10 inhibition activity against yeast topoisomerase II. DNA topoisomerases (Topo) are enzymes that catalyze changes in the spatial structure of DNA and play an important role in replication, transcription and recombination. Beyond their normal functions, DNA topo are significant...
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Sepulchral plate of Thomas Tympfius in St. Mary's Church in Gdańsk
Open Research DataThe data set concerns epigraphy. It refers to the sepulchral plate placed in St. Mary’s Church in Gdańsk which is dedicated to Thomas Tympfius, a minter who, together with his brother Andrew, rented several mints in the Kingdom of Poland, and gave his name to the timpf - the silver zloty released by the Tympfius mint. Unfortunately, as a result of...
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The role of epigenetics in regeneration
PublicationComplex changes in chromatin structure and at the transcriptional level occur from the creation of a single parental gamete throughout fertilization, embryo development and the life of an adult organism. Epigenetic changes, such as methylation and hydroxymethylation of DNA or histone methylation and acetylation, are an important part of these processes. Epigenetic regulation has an essential influence on gene expression level. DNA...
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Anticancer imidazoacridinone C-1311 inhibits hypoxia-inducible factor-1α (HIF-1α), vascular endothelial growth factor (VEGF) and angiogenesis
PublicationAntitumor imidazoacridinone C-1311 is a DNA-reactive topoisomerase II and FLT3 receptor tyrosine kinase inhibitor. Here, we demonstrate the mechanism of C-1311 inhibitory action on novel targets: hypoxia-inducible factor-1α (HIF-1α), vascular-endothelial growth factor (VEGF), and angiogenesis. In a cell-free system, C-1311 prevented HIF-1α binding to an oligonucleotide encompassing a canonical hypoxia-responsive element (HRE),...
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Promocja zasobów Pomorskiej Biblioteki Cyfrowej na przykładzie XVIII-wiecznego rękopisu
PublicationCelem artykułu jest przedstawienie sposobu udostępniania i promocji zbiorów rękopiśmiennych na przykładzie XVIII-wiecznego rękopisu Christiana Gabriela Fishera dostępnego w Pomorskiej Bibliotece Cyfrowej (dalej: PBC). Rękopis ten stał się inspiracją do podjęcia współpracy Biblioteki Politechniki Gdańskiej oraz Instytutu Kultury Miejskiej w Gdańsku. Dzięki wspólnej inicjatywie rozpoczęto prace nad transkrypcją niemieckiego tekstu...
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HDAC Inhibitors: Innovative Strategies for Their Design and Applications
PublicationHistone deacetylases (HDACs) are a large family of epigenetic metalloenzymes that are involved in gene transcription and regulation, cell proliferation, differentiation, migration, and death, as well as angiogenesis. Particularly, disorders of the HDACs expression are linked to the development of many types of cancer and neurodegenerative diseases, making them interesting molecular targets for the design of new efficient drugs...
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Triazoloacridone C-1305 impairs XBP1 splicing by acting as a potential IRE1α endoribonuclease inhibitor
PublicationInositol 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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Justification of quasi-stationary approximation in models of gene expression of a self-regulating protein
PublicationWe analyse a model of Hes1 gene transcription and protein synthesis with a negative feedback loop. The effect of multiple binding sites in the Hes1 promoter as well as the dimer formation process are taken into account. We consider three, possibly different, time scales connected with: (i) the process of binding to/dissolving from a binding site, (ii) formation and dissociation of dimers, (iii) production and degradation of Hes1...
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Sound engineering as our commitment to its creators in Poland
PublicationSound engineering is an interdisciplinary and rapidly expanding domain. It covers many aspects, such as sound perception, studio and sound mastering technology, music information retrieval including content-based search systems and automatic music transcription frameworks, sound synthesis, sound restoration, electroacoustics, and other ones constituting multimedia technology. Moreover, machine learning methods applied to the topics...
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Analysis of allophones based on audio signal recordings and parameterization
PublicationThe aim of this study is to develop an allophonic description of English plosive consonants based on recordings of 600 specially selected words. Allophonic variations addressed in the study may have two sources: positional and contextual. The former one depends on the syllabic or prosodic position in which a particular phoneme occurs. Contextual allophony is conditioned by the local phonetic environment. Co-articulation overlapping...
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Cytokine IL6, but not IL-1β, TNF-α and NF-κB is increased in paediatric cancer patients
PublicationCytokines are responsible for maintaining homeostasis as cell growth, differentiation, migration and apoptosis mediators. They play a pivotal role in immune responses to inflammatory reactions. In oncological diseases, the cross-talk between cells of the immunological system and cells of the tumour microenvironment is led by cytokines. Also, the overproduction of cytokines may change the tumour microenvironment and stimulate tumour...
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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Palindromic carbazole derivatives: unveiling their antiproliferative effect via topoisomerase II catalytic inhibition and apoptosis induction
PublicationHuman DNA topoisomerases are essential for crucial cellular processes, including DNA replication, transcription, chromatin condensation, and maintenance of its structure. One of the significant strategies employed in cancer treatment involves the inhibition of a specific type of topoisomerase, known as topoisomerase II (Topo II). Carbazole derivatives, recognised for their varied biological activities, have recently become a significant...
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Chemical Aspects of Biological Activity of Isothiocyanates and Indoles, the Products of Glucosinolate Decomposition
PublicationThere is growing evidence that cancer chemoprevention employing natural, bioactive compounds may halt or at least slow down the different stages of carcinogenesis. A particularly advantageous effect is attributed to derivatives of sulfur-organic phytochemicals, such as glucosinolates (GLs) synthesized mainly in Brassicaceae plant family. GLs are hydrolysed enzymatically to bioactive isothiocyanates (ITC) and indoles, which exhibit strong...
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Dissection of σE‐dependent cell lysis in Escherichia coli: roles of RpoE regulators RseA, RseB and periplasmic folding catalyst PpiD
PublicationTo 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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Changes in Epigenetic Patterns Related to DNA Replication in Vicia faba Root Meristem Cells under Cadmium-Induced Stress Conditions
PublicationExperiments on Vicia faba root meristem cells exposed to 150 µM cadmium chloride (CdCl2) were undertaken to analyse epigenetic changes, mainly with respect to DNA replication stress. Histone modifications examined by means of immunofluorescence labeling included: (1) acetylation of histone H3 on lysine 56 (H3K56Ac), involved in transcription, S phase, and response to DNA damage during DNA biosynthesis; (2) dimethylation of histone...
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Regulation of the First Committed Step in Lipopolysaccharide Biosynthesis Catalyzed by LpxC Requires the Essential Protein LapC (YejM) and HslVU Protease
PublicationWe previously showed that lipopolysaccharide (LPS) assembly requires the essential LapB protein to regulate FtsH-mediated proteolysis of LpxC protein that catalyzes the first committed step in the LPS synthesis. To further understand the essential function of LapB and its role in LpxC turnover, multicopy suppressors of ΔlapB revealed that overproduction of HslV protease subunit prevents its lethality by proteolytic degradation...
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IFI16 Impacts Metabolic Reprogramming during Human Cytomegalovirus Infection
PublicationCellular lipid metabolism plays a pivotal role in human cytomegalovirus (HCMV) infection, as increased lipogenesis in HCMV-infected cells favors the envelopment of newly synthesized viral particles. As all cells are equipped with restriction factors (RFs) able to exert a protective effect against invading pathogens, we asked whether a similar defense mechanism would also be in place to preserve the metabolic compartment from HCMV...
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Checkpoints that regulate balanced biosynthesis of lipopolysaccharide and its essentiality in Escherichia coli
PublicationThe 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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CHEMOTHERAPY-MEDIATED COMPLICATIONS OF WOUND HEALING. AN UNDERSTUDIED SIDE EFFECT
PublicationSignificance: Chemotherapy is a primary method to treat cancer, but while cytotoxic drugs are designed to target rapidly dividing cancer cells, they can also affect other cell types, including dermal cells and macrophages involved in wound healing, which often leads to the development of chronic wounds. The situation becomes even more severe when chemotherapy is combined with surgical tumor excision. Recent advances: Despite its...
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Marking the Allophones Boundaries Based on the DTW Algorithm
PublicationThe paper presents an approach to marking the boundaries of allophones in the speech signal based on the Dynamic Time Warping (DTW) algorithm. Setting and marking of allophones boundaries in continuous speech is a difficult issue due to the mutual influence of adjacent phonemes on each other. It is this neighborhood on the one hand that creates variants of phonemes that is allophones, and on the other hand it affects that the border...
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The role of glucuronidation in drug resistance
PublicationThe final therapeutic effect of a drug candidate, which is directed to a specific molecular target strongly depends on its absorption, distribution, metabolism and excretion (ADME). The disruption of at least one element of ADME may result in serious drug resistance. In this work we described the role of one element of this resistance: phase II metabolism with UDP-glucuronosyltransferases (UGTs). UGT function is the transformation...
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D-loop sequences retrieved from Canis lupus familiaris mitochondrial genome
Open Research DataCanine mitochondrial genome is built of 16727 bp. Non-coding control region (mtCR), called also D-loop, begins with 15458 nucleotide and ends with 16727 nucleotide. The length of this fragment is 1270 bp (Kim et al., 1998). D-loop region is responsible for replication and transcription of mitochondrial DNA. Mutations that occur within it may cause irregularity...
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Fluconazole resistant Candida auris clinical isolates have increased levels of cell wall chitin and increased susceptibility to a glucosamine-6-phosphate synthase inhibitor
PublicationIn 2009 Candida auris was first isolated as fungal pathogen of human disease from ear canal of a patient in Japan. In less than a decade, this pathogen has rapidly spread around the world and has now become a major health challenge that is of particular concern because many strains are resistant to multiple class of antifungal drugs. The lack of available antifungals and rapid increase of this fungal pathogen provides an incentive...