scholarly journals Detecting miRNA Mentions and Relations in Biomedical Literature

F1000Research ◽  
2015 ◽  
Vol 3 ◽  
pp. 205 ◽  
Author(s):  
Shweta Bagewadi ◽  
Tamara Bobić ◽  
Martin Hofmann-Apitius ◽  
Juliane Fluck ◽  
Roman Klinger
Keyword(s):  
Regulatory Networks ◽  
Wide Spectrum ◽  
Mirna Gene ◽  
Biomedical Literature ◽  
Entity Recognition ◽  
Lower Sensitivity ◽  
Related Information ◽  
Manual Inspection ◽  
Number Of Publications

Introduction: MicroRNAs (miRNAs) have demonstrated their potential as post-transcriptional gene expression regulators, participating in a wide spectrum of regulatory events such as apoptosis, differentiation, and stress response. Apart from the role of miRNAs in normal physiology, their dysregulation is implicated in a vast array of diseases. Dissection of miRNA-related associations are valuable for contemplating their mechanism in diseases, leading to the discovery of novel miRNAs for disease prognosis, diagnosis, and therapy.Motivation: Apart from databases and prediction tools, miRNA-related information is largely available as unstructured text. Manual retrieval of these associations can be labor-intensive due to steadily growing number of publications. Additionally, most of the published miRNA entity recognition methods are keyword based, further subjected to manual inspection for retrieval of relations. Despite the fact that several databases host miRNA-associations derived from text, lower sensitivity and lack of published details for miRNA entity recognition and associated relations identification has motivated the need for developing comprehensive methods that are freely available for the scientific community. Additionally, the lack of a standard corpus for miRNA-relations has caused difficulty in evaluating the available systems.We propose methods to automatically extract mentions of miRNAs, species, genes/proteins, disease, and relations from scientific literature. Our generated corpora, along with dictionaries, and miRNA regular expression are freely available for academic purposes. To our knowledge, these resources are the most comprehensive developed so far.Results: The identification of specific miRNA mentions reaches a recall of 0.94 and precision of 0.93.  Extraction of miRNA-disease and miRNA-gene relations lead to an F1 score of up to 0.76. A comparison of the information extracted by our approach to the databases miR2Disease and miRSel for the extraction of Alzheimer's disease related relations shows the capability of our proposed methods in identifying correct relations with improved sensitivity. The published resources and described methods can help the researchers for maximal retrieval of miRNA-relations and generation of miRNA-regulatory networks.Availability: The training and test corpora, annotation guidelines, developed dictionaries, and supplementary files are available at http://www.scai.fraunhofer.de/mirna-corpora.html

scholarly journals Detecting miRNA Mentions and Relations in Biomedical Literature

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 205 ◽  
Author(s):  
Shweta Bagewadi ◽  
Tamara Bobić ◽  
Martin Hofmann-Apitius ◽  
Juliane Fluck ◽  
Roman Klinger
Keyword(s):  
Regulatory Networks ◽  
Wide Spectrum ◽  
Mirna Gene ◽  
Biomedical Literature ◽  
Entity Recognition ◽  
Lower Sensitivity ◽  
Related Information ◽  
Manual Inspection ◽  
Number Of Publications

Introduction: MicroRNAs (miRNAs) have demonstrated their potential as post-transcriptional gene expression regulators, participating in a wide spectrum of regulatory events such as apoptosis, differentiation, and stress response. Apart from the role of miRNAs in normal physiology, their dysregulation is implicated in a vast array of diseases. Dissection of miRNA-related associations are valuable for contemplating their mechanism in diseases, leading to the discovery of novel miRNAs for disease prognosis, diagnosis, and therapy.Motivation: Apart from databases and prediction tools, miRNA-related information is largely available as unstructured text. Manual retrieval of these associations can be labor-intensive due to steadily growing number of publications. Additionally, most of the published miRNA entity recognition methods are keyword based, further subjected to manual inspection for retrieval of relations. Despite the fact that several databases host miRNA-associations derived from text, lower sensitivity and lack of published details for miRNA entity recognition and associated relations identification has motivated the need for developing comprehensive methods that are freely available for the scientific community. Additionally, the lack of a standard corpus for miRNA-relations has caused difficulty in evaluating the available systems.We propose methods to automatically extract mentions of miRNAs, species, genes/proteins, disease, and relations from scientific literature. Our generated corpora, along with dictionaries, and miRNA regular expression are freely available for academic purposes. To our knowledge, these resources are the most comprehensive developed so far.Results: The identification of specific miRNA mentions reaches a recall of 0.94 and precision of 0.93.  Extraction of miRNA-disease and miRNA-gene relations lead to an F1 score of up to 0.76. A comparison of the information extracted by our approach to the databases miR2Disease and miRSel for the extraction of Alzheimer's disease related relations shows the capability of our proposed methods in identifying correct relations with improved sensitivity. The published resources and described methods can help the researchers for maximal retrieval of miRNA-relations and generation of miRNA-regulatory networks.Availability: The training and test corpora, annotation guidelines, developed dictionaries, and supplementary files are available at http://www.scai.fraunhofer.de/mirna-corpora.html

scholarly journals Analyzing the miRNA-Gene Networks to Mine the Important miRNAs under Skin of Human and Mouse

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Jianghong Wu ◽  
Husile Gong ◽  
Yongsheng Bai ◽  
Wenguang Zhang
Keyword(s):  
Gene Networks ◽  
Regulatory Networks ◽  
Mirna Gene ◽  
Genetic Regulatory Networks ◽  
Host Immunity ◽  
Genetic Networks ◽  
Target Sites ◽  
Enormous Number ◽  
Human And Mouse

Genetic networks provide new mechanistic insights into the diversity of species morphology. In this study, we have integrated the MGI, GEO, and miRNA database to analyze the genetic regulatory networks under morphology difference of integument of humans and mice. We found that the gene expression network in the skin is highly divergent between human and mouse. The GO term of secretion was highly enriched, and this category was specific in human compared to mouse. These secretion genes might be involved in eccrine system evolution in human. In addition, total 62,637 miRNA binding target sites were predicted in human integument genes (IGs), while 26,280 miRNA binding target sites were predicted in mouse IGs. The interactions between miRNAs and IGs in human are more complex than those in mouse. Furthermore,hsa-miR-548,mmu-miR-466, andmmu-miR-467have an enormous number of targets on IGs, which both have the role of inhibition of host immunity response. The pattern of distribution on the chromosome of these three miRNAs families is very different. The interaction of miRNA/IGs has added the new dimension in traditional gene regulation networks of skin. Our results are generating new insights into the gene networks basis of skin difference between human and mouse.

scholarly journals A Knowledge-Driven Approach to Extract Disease-Related Biomarkers from the Literature

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
À. Bravo ◽  
M. Cases ◽  
N. Queralt-Rosinach ◽  
F. Sanz ◽  
L. I. Furlong
Keyword(s):  
Text Mining ◽  
Named Entity Recognition ◽  
Relation Extraction ◽  
Recognition System ◽  
Biomedical Literature ◽  
Entity Recognition ◽  
Scientific Publications ◽  
Positive Ratio ◽  
Related Information ◽  
Mesh Terms

The biomedical literature represents a rich source of biomarker information. However, both the size of literature databases and their lack of standardization hamper the automatic exploitation of the information contained in these resources. Text mining approaches have proven to be useful for the exploitation of information contained in the scientific publications. Here, we show that a knowledge-driven text mining approach can exploit a large literature database to extract a dataset of biomarkers related to diseases covering all therapeutic areas. Our methodology takes advantage of the annotation of MEDLINE publications pertaining to biomarkers with MeSH terms, narrowing the search to specific publications and, therefore, minimizing the false positive ratio. It is based on a dictionary-based named entity recognition system and a relation extraction module. The application of this methodology resulted in the identification of 131,012 disease-biomarker associations between 2,803 genes and 2,751 diseases, and represents a valuable knowledge base for those interested in disease-related biomarkers. Additionally, we present a bibliometric analysis of the journals reporting biomarker related information during the last 40 years.

The potential role of tea in periodontal therapy: An updated review

2020 ◽  
Vol 17 ◽  
Author(s):  
Ali Forouzanfar ◽  
Hamideh Sadat Mohammadipour ◽  
Fatemeh Forouzanfar
Keyword(s):  
Green Tea ◽  
Potential Role ◽  
Wide Spectrum ◽  
Periodontal Diseases ◽  
Herbal Remedies ◽  
World Population ◽  
Tea Leaves ◽  
The World ◽  
Green Tea Leaves

: Periodontal diseases are highly prevalent and can affect high percentage of the world population. Oxidative stress and inflammation plays an important role in the pathogenesis of periodontal diseases. Nowadays, more attention has been focused on the herbal remedies in the field of drug discovery. Green tea is an important source of polyphenol antioxidants, it has long been used as a beverage worldwide. The most interesting polyphenol components of green tea leaves that are related with health benefits are the catechins. Taken together this review suggested that green tea with its wide spectrum of activities could be a healthy alternative for controlling the damaging reactions seen in periodontal diseases.

Gut Mycobiota and Fungal Metabolites in Human Homeostasis

2018 ◽  
Vol 20 (2) ◽  
pp. 232-240 ◽  
Author(s):  
Izabella Mogilnicka ◽  
Marcin Ufnal
Keyword(s):  
Wide Spectrum ◽  
Biological Effects ◽  
Fungal Species ◽  
Fungal Metabolites ◽  
Human Gut ◽  
Fecal Transplantation ◽  
Bacterial Microbiota ◽  
Bowel Diseases ◽  
Inflammatory Bowel

Background:Accumulating evidence suggests that microbiota play an important role in host’s homeostasis. Thus far, researchers have mostly focused on the role of bacterial microbiota. However, human gut is a habitat for several fungal species, which produce numerous metabolites. Furthermore, various types of food and beverages are rich in a wide spectrum of fungi and their metabolites.Methods:We searched PUBMED and Google Scholar databases to identify clinical and pre-clinical studies on fungal metabolites, composition of human mycobiota and fungal dysbiosis.Results:Fungal metabolites may serve as signaling molecules and exert significant biological effects including trophic, anti-inflammatory or antibacterial actions. Finally, research suggests an association between shifts in gut fungi composition and human health. Changes in mycobiota composition have been found in obesity, hepatitis and inflammatory bowel diseases.Conclusion:The influence of mycobiota and dietary fungi on homeostasis in mammals suggests a pharmacotherapeutic potential of modulating the mycobiota which may include treatment with probiotics and fecal transplantation. Furthermore, antibacterial action of fungi-derived molecules may be considered as a substitution for currently used antibacterial agents and preservatives in food industry.

scholarly journals Quantifying Media Effects, Its Content, and Role in Promoting Community Awareness of Chikungunya Epidemic in Bangladesh

Epidemiologia ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 84-94
Author(s):  
Mst. Marium Begum ◽  
Osman Ulvi ◽  
Ajlina Karamehic-Muratovic ◽  
Mallory R. Walsh ◽  
Hasan Tarek ◽  
...  
Keyword(s):  
Social Media ◽  
Web Based ◽  
Study Objective ◽  
The Public ◽  
Mainstream Media ◽  
Related Information ◽  
Vector Borne ◽  
Media Outlet ◽  
And Control

Background: Chikungunya is a vector-borne disease, mostly present in tropical and subtropical regions. The virus is spread by Ae. aegypti and Ae. albopictus mosquitos and symptoms include high fever to severe joint pain. Dhaka, Bangladesh, suffered an outbreak of chikungunya in 2017 lasting from April to September. With the goal of reducing cases, social media was at the forefront during this outbreak and educated the public about symptoms, prevention, and control of the virus. Popular web-based sources such as the top dailies in Bangladesh, local news outlets, and Facebook spread awareness of the outbreak. Objective: This study sought to investigate the role of social and mainstream media during the chikungunya epidemic. The study objective was to determine if social media can improve awareness of and practice associated with reducing cases of chikungunya. Methods: We collected chikungunya-related information circulated from the top nine television channels in Dhaka, Bangladesh, airing from 1st April–20th August 2017. All the news published in the top six dailies in Bangladesh were also compiled. The 50 most viewed chikungunya-related Bengali videos were manually coded and analyzed. Other social media outlets, such as Facebook, were also analyzed to determine the number of chikungunya-related posts and responses to these posts. Results: Our study showed that media outlets were associated with reducing cases of chikungunya, indicating that media has the potential to impact future outbreaks of these alpha viruses. Each media outlet (e.g., web, television) had an impact on the human response to an individual’s healthcare during this outbreak. Conclusions: To prevent future outbreaks of chikungunya, media outlets and social media can be used to educate the public regarding prevention strategies such as encouraging safe travel, removing stagnant water sources, and assisting with tracking cases globally to determine where future outbreaks may occur.

scholarly journals Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hong Wang ◽  
Aiping Duan ◽  
Jing Zhang ◽  
Qi Wang ◽  
Yuexian Xing ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Glucocorticoid Receptor ◽  
Protective Effect ◽  
Histone Modification ◽  
Regulatory Networks ◽  
Target Gene ◽  
Regulatory Elements ◽  
Chromatin Interactions ◽  
Super Enhancer

AbstractElucidating transcription mediated by the glucocorticoid receptor (GR) is crucial for understanding the role of glucocorticoids (GCs) in the treatment of diseases. Podocyte is a useful model for studying GR regulation because GCs are the primary medication for podocytopathy. In this study, we integrated data from transcriptome, transcription factor binding, histone modification, and genome topology. Our data reveals that the GR binds and activates selective regulatory elements in podocyte. The 3D interactome captured by HiChIP facilitates the identification of remote targets of GR. We found that GR in podocyte is enriched at transcriptional interaction hubs and super-enhancers. We further demonstrate that the target gene of the top GR-associated super-enhancer is indispensable to the effective functioning of GC in podocyte. Our findings provided insights into the mechanisms underlying the protective effect of GCs on podocyte, and demonstrate the importance of considering transcriptional interactions in order to fine-map regulatory networks of GR.

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