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  • 11
    Publication Date: 2013-10-05
    Description: Background: The epithelial-to-mesenchymal transition is an important mechanism in cancer metastasis. Although transcription factors including SNAIL, SLUG, and TWIST1 regulate the epithelial-to-mesenchymal transition, other unknown transcription factors could also be involved. Identification of the full complement of transcription factors is essential for a more complete understanding of gene regulation in this process. Chromatin immunoprecipitation-sequencing (ChIP-Seq) technologies have been used to detect genome-wide binding of transcription factors; here, we developed a systematic approach to integrate existing ChIP-Seq and transcriptome data. We scanned multiple transcription factors to investigate their functional impact on the epithelial-to-mesenchymal transition in the human A549 lung adenocarcinoma cell line. Results: Among the transcription factors tested, impact scores identified the forkhead box protein A1 (FOXA1) as the most significant transcription factor in the epithelial-to-mesenchymal transition. FOXA1 physically associates with the promoters of its predicted target genes. Several critical epithelial-to-mesenchymal transition effectors involved in cellular adhesion and cellular communication were identified in the regulatory network of FOXA1, including FOXA2, FGA, FGB, FGG, and FGL1. The implication of FOXA1 in the epithelial-to-mesenchymal transition via its regulatory network indicates that FOXA1 may play an important role in the initiation of lung cancer metastasis. Conclusions: We identified FOXA1 as a potentially important transcription factor and negative regulator in the initial stages of lung cancer metastasis. FOXA1 may modulate the epithelial-to-mesenchymal transition via its transcriptional regulatory network. Further, this study demonstrates how ChIP-Seq and expression data could be integrated to delineate the impact of transcription factors on a specific biological process.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 12
    Publication Date: 2015-05-10
    Description: Background: Corals are capable of launching diverse immune defenses at the site of direct contact with pathogens, but the molecular mechanisms of this activity and the colony-wide effects of such stressors remain poorly understood. Here we compared gene expression profiles in eight healthy Acropora hyacinthus colonies against eight colonies exhibiting tissue loss commonly associated with white syndromes, all collected from a natural reef environment near Palau. Two types of tissues were sampled from diseased corals: visibly affected and apparently healthy. Results: Tag-based RNA-Seq followed by weighted gene co-expression network analysis identified groups of co-regulated differentially expressed genes between all health states (disease lesion, apparently healthy tissues of diseased colonies, and fully healthy). Differences between healthy and diseased tissues indicate activation of several innate immunity and tissue repair pathways accompanied by reduced calcification and the switch towards metabolic reliance on stored lipids. Unaffected parts of diseased colonies, although displaying a trend towards these changes, were not significantly different from fully healthy samples. Still, network analysis identified a group of genes, suggestive of altered immunity state, that were specifically up-regulated in unaffected parts of diseased colonies. Conclusions: Similarity of fully healthy samples to apparently healthy parts of diseased colonies indicates that systemic effects of white syndromes on A. hyacinthus are weak, which implies that the coral colony is largely able to sustain its physiological performance despite disease. The genes specifically up-regulated in unaffected parts of diseased colonies, instead of being the consequence of disease, might be related to the originally higher susceptibility of these colonies to naturally occurring white syndromes.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 13
    Publication Date: 2016-03-10
    Description: Pseudomonas aeruginosa, a Gram-negative, aerobic coccobacillus bacterium is an opportunistic human pathogen and worldwide the fourth most common cause of hospital-acquired infections w...
    Electronic ISSN: 1471-2091
    Topics: Chemistry and Pharmacology
    Published by BioMed Central
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  • 14
    Publication Date: 2016-03-25
    Description: A standardized imaging proposal evaluating implanted left atrial appendage (LAA) occlusion devices by cardiac computed tomography angiography (cCTA) has never been investigated.
    Electronic ISSN: 1471-2342
    Topics: Biology
    Published by BioMed Central
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  • 15
    Publication Date: 2016-06-30
    Description: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful f...
    Electronic ISSN: 1471-2148
    Topics: Biology
    Published by BioMed Central
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  • 16
    Publication Date: 2015-10-13
    Description: Background: Oral health is part of general health, and in adolescence, it represents a good individual health indicator. Three country-based oral health epidemiological studies have been developed in Brazil (1986, 2003 and 2010). The objective of this study was to analyze oral disease trends among Brazilian adolescents and to compare these trends to the World Health Organization’s goals with a focus on public health policies implemented between 1986 and 2010. Methods: This is an epidemiological observational study performed with secondary data from Brazilian Oral Health surveys (1986, 2003 and 2010). The DMFT (number of decayed, missing and filled teeth) index was used for the 12-year-old and 15- to 19-year-old groups, and periodontal disease (CPI) and the percentage of individuals who needed and/or had prostheses were evaluated in the 15- to 19-year-old group. Results: Between 1986 and 2010, DMFT decreased from 6.65 to 2.07 (68.9 % reduction) in the 12-year-old group and from 12.68 to 4.25 (66.5 % reduction) in the 15- to 19-year-old group. In all groups, the missing component had the strongest decrease. Adolescents had a reduction of 20.3 % in access to dental care. In 2003, in the 15- to 19-year-old group, 89.5 % of teenagers had at least one decayed tooth, while in 2010, the value was 76.1 %. In 2010, the percentage of adolescents without gingival problems varied among different regions of Brazil, with 30.8 % in the North and 56.8 % in the Southeast. Regarding DMFT, the difference between the North and Southeast Regions was 84 %. Conclusions: Improvement trends regarding adolescent oral health were observed, which seem to be supported by health education and promotion activities along with the reorganization of the Brazilian health system.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 17
    Publication Date: 2015-12-18
    Description: Gene expression is an inherently stochastic process, owing to its dynamic molecular nature. Protein amount distributions, which can be acquired by cytometry using a reporter gene, can inform about the mechanis...
    Electronic ISSN: 1471-2199
    Topics: Biology
    Published by BioMed Central
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  • 18
    Publication Date: 2015-04-18
    Description: Background: The widespread use of electronic health records (EHRs) has generated massive clinical data storage. Association rules mining is a feasible technique to convert this large amount of data into usable knowledge for clinical decision making, research or billing. We present a data driven method to create a knowledge base linking medications to pathological conditions through their therapeutic indications from elements within the EHRs. Methods: Association rules were created from the data of patients hospitalised between May 2012 and May 2013 in the department of Cardiology at the University Hospital of Strasbourg. Medications were extracted from the medication list, and the pathological conditions were extracted from the discharge summaries using a natural language processing tool. Association rules were generated along with different interestingness measures: chi square, lift, conviction, dependency, novelty and satisfaction. All medication-disease pairs were compared to the Summary of Product Characteristics, which is the gold standard. A score based on the other interestingness measures was created to filter the best rules, and the indices were calculated for the different interestingness measures. Results: After the evaluation against the gold standard, a list of accurate association rules was successfully retrieved. Dependency represents the best recall (0.76). Our score exhibited higher exactness (0.84) and precision (0.27) than all of the others interestingness measures. Further reductions in noise produced by this method must be performed to improve the classification precision. Conclusions: Association rules mining using the unstructured elements of the EHR is a feasible technique to identify clinically accurate associations between medications and pathological conditions.
    Electronic ISSN: 1472-6947
    Topics: Computer Science , Medicine
    Published by BioMed Central
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  • 19
    Publication Date: 2015-06-16
    Description: Background: Interleukin-27 (IL-27) has been described to be highly expressed during the very first days after birth, but secretion of IL-27 by dendritic cells during the course of childhood has not been described.FindingsIn our present study we enrolled children (n = 55) in the range from 1 day of to 18 years of age and asked for a small whole blood sample. The capacity of dendritic cells to produce IL-27 during childhood was measured after whole blood culture with or without inflammatory stimuli. Results support recent findings of high IL-27 levels after birth and lowest levels in adults. Interestingly, we detected an interim peak production level at early adolescence. Conclusion: These data hint to prominent roles of IL-27 at the very start of post-natal life. Furthermore, a link has been given to so far not described immunological events during puberty.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 20
    Publication Date: 2015-02-01
    Description: Background: Over the last decade genetic marker-based plant breeding strategies have gained increasing attention because genotyping technologies are no longer limiting. Now the challenge is to optimally use genetic markers in practical breeding schemes. For simple traits such as some disease resistances it is possible to target a fixed multi-locus allele configuration at a small number of causal or linked loci. Efficiently obtaining this genetic ideotype from a given set of parental genotypes is known as the marker-assisted gene pyramiding problem. Previous methods either imposed strong restrictions or used black box integer programming solutions, while this paper explores the power of an explicit heuristic approach that exploits the underlying genetic structure to prune the search space. Results: Gene Stacker is introduced as a novel approach to marker-assisted gene pyramiding, combining an explicit directed acyclic graph model with a pruned generation algorithm inspired by a simple exhaustive search. Both exact and heuristic pruning criteria are applied to reduce the number of generated schedules. It is shown that this approach can effectively be used to obtain good solutions for stacking problems of varying complexity. For more complex problems, the heuristics allow to obtain valuable approximations. For smaller problems, fewer heuristics can be applied, resulting in an interesting quality-runtime tradeoff. Gene Stacker is competitive with previous methods and often finds better and/or additional solutions within reasonable time, because of the powerful heuristics. Conclusions: The proposed approach was confirmed to be feasible in combination with heuristics to cope with realistic, complex stacking problems. The inherent flexibility of this approach allows to easily address important breeding constraints so that the obtained schedules can be widely used in practice without major modifications. In addition, the ideas applied for Gene Stacker can be incorporated in and extended for a plant breeding context that e.g. also addresses complex quantitative traits or conservation of genetic background.AvailabilityGene Stacker is freely available as open source software at http://genestacker.ugent.be. The website also provides documentation and examples of how to use Gene Stacker.
    Electronic ISSN: 1471-2156
    Topics: Biology
    Published by BioMed Central
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