Search
Search results for: TRANSCRIPT
-
Detecting coupling directions with transcript mutual information: A comparative study
PublicationCausal relationships are important to understand the dynamics of coupled processes and, moreover, to influence or control the effects by acting on the causes. Among the different approaches to determine cause-effect relationships and, in particular, coupling directions in interacting random or deterministic processes, we focus in this paper on information-theoretic measures. So, we study in the theoretical part the difference between...
-
Novel TG‐FGFR1 and TRIM33‐NTRK1 transcript fusions in papillary thyroid carcinoma
Publication -
Recent advances in transcription regulation
e-Learning CoursesRecent advances in transcription regulation
-
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...
-
Transcription-Austin
Journals -
Computing algebraic transfer entropy and coupling directions via transcripts
PublicationMost random processes studied in nonlinear time series analysis take values on sets endowed with a group structure, e.g., the real and rational numbers, and the integers. This fact allows to associate with each pair of group elements a third element, called their transcript, which is defined as the product of the second element in the pair times the first one. The transfer entropy of two such processes is called algebraic transfer...
-
The methylome and transcriptome of fetal skin: implications for scarless healing
PublicationAim: Fetal skin is known to heal without scarring. In mice, the phenomenon is observed until the 16–17 day of gestation – the day of transition from scarless to normal healing. The study aims to identify key methylome and transcriptome changes following the transition. Materials & methods: Methylome and transcriptome profiles were analyzed in murine dorsal skin using microarray approach. Results & conclusion: The genes associated...
-
HPV16 E6 Gene Transcripts in Primary Type II Endometrial Carcinomas
Publication -
Transcriptomic Pattern of Genes Regulating Protein Response and Status of Mitochondrial Activity Are Related to Oocyte Maturational Competence—A Transcriptomic Study
Publication -
Transcriptomic landscape of blood platelets in healthy donors
PublicationBlood platelet RNA-sequencing is increasingly used among the scientific community. Aberrant platelet transcriptome is common in cancer or cardiovascular disease, but reference data on platelet RNA content in healthy individuals are scarce and merit complex investigation. We sought to explore the dynamics of platelet transcriptome. Datasets from 204 healthy donors were used for the analysis of splice variants, particularly with...
-
Transcriptomic landscape of blood platelets in healthy donors
PublicationBACKGROUND Blood platelet RNA-sequencing is increasingly used among the scientific community. Aberrant platelet transcriptome is common in cancer or cardiovascular disease, but reference data on platelet RNA content in healthy individuals are scarce and merit complex investigation. METHODS We sought to explore the dynamics of platelet transcriptome. Datasets from 204 healthy donors were used for the analysis of splice variants,...
-
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...
-
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...
-
Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data
Publication -
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...
-
Robustness of Pathway Enrichment Analysis to Transcriptome-Wide Gene Expression Platform
Publication -
Transcriptome profiling and environmental linkage to salinity across Salicornia europaea vegetation
Publication -
Overview of the Virtual Transcription Laboratory Usage Scenarios and Architecture
Publication -
Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects
Publication -
Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
-
Comparison of Language Models Trained on Written Texts and Speech Transcripts in the Context of Automatic Speech Recognition
Publication -
The role of Snail1 transcription factor in colorectal cancer progression and metastasis
Publication -
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...
-
Is the Identification of SNP-miRNA Interactions Supporting the Prediction of Human Lymphocyte Transcriptional Radiation Responses?
Publication -
Salt Stress Reveals a New Role for ARGONAUTE1 in miRNA Biogenesis at the Transcriptional and Posttranscriptional Levels
Publication -
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...
-
Non-steroidal anti-inflammatory drugs are safe with respect to the transcriptome of human dermal fibroblasts
Publication -
Transcriptome sequencing of Brassica napus highlights the complex issues with soil supplementation with sewage sludge
Publication -
Coordinated reprogramming of renal cancer transcriptome, metabolome and secretome associates with immune tumor infiltration
Publication -
The molecular mechanism of genistein action in lysosomal storage diseases: A transcriptomic approach
Publication -
Transcriptomic responses to wounding: meta-analysis of gene expression microarray data
PublicationBackground A vast amount of microarray data on transcriptomic response to injury has been collected so far. We designed the analysis in order to identify the genes displaying significant changes in expression after wounding in different organisms and tissues. This meta-analysis is the first study to compare gene expression profiles in response to wounding in as different tissues as heart, liver, skin, bones, and spinal cord, and...
-
Transcriptomics‐Based and AOP‐Informed Structure–Activity Relationships to Predict Pulmonary Pathology Induced by Multiwalled Carbon Nanotubes
Publication -
The Escherichia coli RNA polymerase alpha subunit and transcriptional activation by bacteriophage lambda CII protein.
Publication -
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...
-
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...
-
Transcriptome profiling reveals distinctive traits of retinol metabolism and neonatal parallels in the MRL/MpJ mouse
PublicationBackground: The MRL/MpJ mouse is a laboratory inbred strain known for regenerative abilities which are manifested by scarless closure of ear pinna punch holes. Enhanced healing responses have been reported in other organs. A remarkable feature of the strain is that the adult MRL/MpJ mouse retains several embryonic biochemical characteristics, including increased expression of stem cell markers. Results: We explored the transcriptome...
-
Inhibiting Activity of HIV-1: Protease, Reverse Transcriptase and Integrase All Together by Novel Compounds Using Computational Approaches
Publication -
Transcriptomic and proteomic analysis of mouse radiation-induced acute myeloid leukaemia (AML)
Publication -
The Phytoestrogen Genistein Modulates Lysosomal Metabolism and Transcription Factor EB (TFEB) Activation
Publication -
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...
-
Transcriptome Changes in Three Brain Regions during Chronic Lithium Administration in the Rat Models of Mania and Depression
Publication -
Transcriptomic Effects of Estrogen Starvation and Induction in the MCF7 Cells. The Meta-analysis of Microarray Results
PublicationEstrogen is one of the most important signaling molecules which targets a number of genes. Estrogen levels regulate cell proliferation and a plethora of metabolic processes, which may interfere with a range of medical conditions and drug metabolism. The MCF7 breast cancer cell line, expressing the estrogen receptor α, is a well-studied model of cellular answer to estrogen. The aim of this study was to characterize transcriptomic...
-
Bystander Effects Induced by Medium From Irradiated Cells: Similar Transcriptome Responses in Irradiated and Bystander K562 Cells
Publication -
Human sperm proteins identified by 2-dimensional electrophoresis and mass spectrometry and their relevance to a transcriptomic analysis
Publication -
Transcriptomic profiling of the salt stress response in excised leaves of the halophyte Beta vulgaris ssp. maritima
Publication -
New markers for regulation of transcription and macromolecule metabolic process in porcine oocytes during in vitro maturation
Publication -
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...
-
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...
-
Hyponastic Leaves 1 Interacts with RNA Pol II to Ensure Proper Transcription of MicroRNA Genes
Publication -
Inhibiting activity of HIV-1: protease, reverse transcriptase and integrase all together by novel compounds using computational approaches (flexible and rigid docking)
PublicationAcquired immunodeficiency syndrome (AIDS), caused by human immunodeficiency virus type 1 (HIV-1) infection, is one of the most challenging diseases in recent decades. Nevertheless the shortcomings of chemical drugs such as toxicity, lack of curative effects, the search for more potent anti-HIV agents have been focused in our study. In current study, novel scaffold was designed having a benzyl and imidazole in it which are very...