2,629 research outputs found
RegEl Database: text-mined regulatory elements from the literature and their associations to genes and disease
No full text@article{garda2022regel,
title={RegEl corpus: identifying DNA regulatory elements in the scientific literature},
author={Garda, Samuele and Lenihan-Geels, Freyda and Proft, Sebastian and Hochmuth, Stefanie and Sch{\"u}lke, Markus and Seelow, Dominik and Leser, Ulf},
journal={Database},
volume={2022},
year={2022},
publisher={Oxford Academic}
}
# RegEl PubMed Database
This database contains the annotations generated by running [HunFlair](https://github.com/flairNLP/flair/blob/master/resources/docs/HUNFLAIR.md) models trained on the [RegEl corpus](https://zenodo.org/record/5776679) over >20M PubMed abstracts.
By pairing these annotations with the one provided by PubTator this generates a large text mining database of regulatory elements associated with genes (normalized to NCBI Gene ids) and disease (normalized to either MeSH or OMIM).
The tables composing the database are:
* abstracts.db:
- pmid = PubMed ID of the given abstracts
- sid = sentence ID of the given abstracts (from 0 to # of sentences)
- text = text of the given sentence
* gene.db and disease.db:
- pmid = PubMed ID of the given abstracts
- sid = sentence ID of the given abstracts (from 0 to # of sentences)
- etype = entity type (enhancer, promoter, TFBS)
- ann_text = mention of the regulatory element as found in the abstract
- start = position (# character) in which the mention begins
- end = position (# characters) in which the mention ends
- score = model's confidence
- cui = gene or disease identifier
- cui_symbol = official symbol of cui (if available
Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast
No full text18 páginas, 8 figuras, 2 tablas.Optimized nutrient utilization is crucial for the progression of microorganisms in competing communities. Here we investigate how different budding yeast species and ecological isolates have established divergent preferences for two alternative sugar substrates: Glucose, which is fermented preferentially by yeast, and galactose, which is alternatively used upon induction of the relevant GAL metabolic genes. We quantified the dose-dependent induction of the GAL1 gene encoding the central galactokinase enzyme and found that a very large diversification exists between different yeast ecotypes and species. The sensitivity of GAL1 induction correlates with the growth performance of the respective yeasts with the alternative sugar. We further define some of the mechanisms, which have established different glucose/galactose consumption strategies in representative yeast strains by modulating the activity of the Gal3 inducer. (1) Optimal galactose consumers, such as Saccharomyces uvarum, contain a hyperactive GAL3 promoter, sustaining highly sensitive GAL1 expression, which is not further improved upon repetitive galactose encounters. (2) Desensitized galactose consumers, such as S. cerevisiae Y12, contain a less sensitive Gal3 sensor, causing a shift of the galactose response towards higher sugar concentrations even in galactose experienced cells. (3) Galactose insensitive sugar consumers, such as S. cerevisiae DBVPG6044, contain an interrupted GAL3 gene, causing extremely reluctant galactose consumption, which is, however, improved upon repeated galactose availability. In summary, different yeast strains and natural isolates have evolved galactose utilization strategies, which cover the whole range of possible sensitivities by modulating the expression and/or activity of the inducible galactose sensor Gal3.This work was funded by a grant from Ministerio de Ciencia e Innovación PID2019-104214RB-I00 to AP-A and MP, and K.B.S.S. was supported by the DBT-Ramalinagaswami fellowship (AU/SAS/DBT-RLS/20-21/04_KS_03.25) and Ahmedabad University start-up grant (AU/SUG/SAS/DBLS/2019-20/01)Peer reviewe
Genomic Instability and Epigenetic Changes during Aging
No full textAging is considered the deterioration of physiological functions along with an increased mortality rate. This scientific review focuses on the central importance of genomic instability during the aging process, encompassing a range of cellular and molecular changes that occur with advancing age. In particular, this revision addresses the genetic and epigenetic alterations that contribute to genomic instability, such as telomere shortening, DNA damage accumulation, and decreased DNA repair capacity. Furthermore, the review explores the epigenetic changes that occur with aging, including modifications to histones, DNA methylation patterns, and the role of non-coding RNAs. Finally, the review discusses the organization of chromatin and its contribution to genomic instability, including heterochromatin loss, chromatin remodeling, and changes in nucleosome and histone abundance. In conclusion, this review highlights the fundamental role that genomic instability plays in the aging process and underscores the need for continued research into these complex biological mechanismsResearch of the authors was funded by grants from Ministerio de Ciencia, Innovación y Universidades PID2019-104214RB-I00 (A.P.-A., M.P.) and Agencia Valenciana de la Innovación INNEST/2021/266 (A.P.-A.)Peer reviewe
Evidence based leadership
No full textAuthor Markus PodduikinMasterarbeit Johannes Kepler Universität Linz 2024Arbeit gesperr
Improving the search for monitoring tools using recommender technology
No full textAuthor Markus Eisl BSc.Masterarbeit Universität Linz 2023Arbeit gesperr
Improving the search for monitoring tools using recommender technology
No full textAuthor Markus Eisl BSc.Masterarbeit Universität Linz 2023Arbeit gesperr
metal-organic framework 4H, 4H-octafluoroazobenezene perfluoroazobenzene
No full textauthor: Markus RödlKumulative Masterarbeit aus einem ArtikelMasterarbeit University of Innsbruck 2022Arbeit gesperr
metal-organic framework 4H, 4H-octafluoroazobenezene perfluoroazobenzene
No full textauthor: Markus RödlKumulative Masterarbeit aus einem ArtikelMasterarbeit University of Innsbruck 2022Arbeit gesperr
Strategi Pelayanan Lintas Budaya Berdasarkan Markus 4:1-34
No full textHarming & Katarina, Cross-cultural Service Strategy based on Mark 4: 1-34. The author conducted a study of the text of Mark 4: 1-34 using qualitative research literature study using the biblical hermeneutic principle. Based on the analysis of the text of Mark 4: 1-34 the authors find there are four cross-cultural service strategies namely by understanding local culture, using media. Harming & Katarina, Strategi Pelayanan Lintas budaya Berdasarkan Markus 4:1-34. Penulis melakukan penelitian terhadap teks Markus 4:1-34 dengan menggunakan penelitian kualitatif studi pustaka dengan menggunakan prinsip hermeneutik Alkitab. Berdasarkan analisis terhadap teks Markus 4:1-34 penulis menemukan ada empat strategi pelayanan lintas budaya yaitu dengan memahami budaya lokal, menggunakan media yang ada dalam budaya, memberdayakan potensi yang ada, dan menciptakan terobosan
Development of a Software Tool for Analyzing Experimental Data of a Recycling Machine
No full textAuthor DI Markus Kirchmayr, BScMasterarbeit Universität Linz 2022Arbeit nach Ablauf der Sperre auf den öffentlichen PCs in den Bibliotheken der JKU+Medizin abrufba
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