7 results on '"A. Tsakalidis"'
Search Results
2. The omega-3 and retinopathy of prematurity relationship
- Author
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Angeliki Chranioti, Christos Tsakalidis, Stavros A. Dimitrakos, Asimina Mataftsi, and Angelakis Malamas
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chemistry.chemical_classification ,Retina ,business.industry ,Cellular differentiation ,Inflammation ,Retinal ,Retinopathy of prematurity ,Review ,medicine.disease_cause ,medicine.disease ,Bioinformatics ,Neuroprotection ,03 medical and health sciences ,Ophthalmology ,chemistry.chemical_compound ,0302 clinical medicine ,medicine.anatomical_structure ,chemistry ,030221 ophthalmology & optometry ,medicine ,medicine.symptom ,business ,030217 neurology & neurosurgery ,Oxidative stress ,Polyunsaturated fatty acid - Abstract
The aim of this article is to examine the effect of omega-3 (ω-3) long-chain polyunsaturated fatty acids (LCPUFAs) intake on retinopathy of prematurity (ROP) by reviewing the experimental and clinical trials conducted on animal models and infants. LCPUFAs demonstrate cytoprotective and cytotherapeutic actions contributing to a number of anti-angiogenic and neuroprotective mechanisms within the retina. Their intake appears to have a beneficial effect on ischemia, oxidative stress, inflammation and cellular signaling mechanisms, influencing retinal cell gene expression and cellular differentiation. ω-3 LCPUFAs may modulate metabolic processes that activate molecules implicated in the pathogenesis of vasoproliferative and neurodegenerative retinal diseases such as ROP.
- Published
- 2016
3. Netherton Syndrome in a Neonate with Possible Growth Hormone Deficiency and Transient Hyperaldosteronism
- Author
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Sarri Constantina, Babatseva Evgenia, Chatziioannidis Ilias, Karagianni Paraskevi, Mamuris Zissis, Tsakalidis Christos, Lithoxopoulou Maria, Patsatsi Aikaterini, Mitsiakos George, Nikolaidis Nikolaos, and Galli-Tsinopoulou Asimina
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medicine.medical_specialty ,business.industry ,Genetic disorder ,lcsh:RJ1-570 ,Case Report ,lcsh:Pediatrics ,General Medicine ,medicine.disease ,Bioinformatics ,Hyperaldosteronism ,Frameshift mutation ,Growth hormone deficiency ,Endocrinology ,Internal medicine ,Medicine ,Missense mutation ,Netherton syndrome ,Hypernatremia ,Allele ,business - Abstract
Netherton syndrome, a rare autosomal recessive genetic disorder, is classified as an ichthyosiform syndrome. In this report we present the case of a neonate with erythroderma shortly after birth, accompanied by severe hypernatremia, recurrent infections, transient hyperaldosteronism, and signs of growth hormone (GH) deficiency. DNA molecular analysis in theSPINK5gene revealed heterozygosity in our index patient for 238insG and 2468delA frameshift mutations in exons 4 and 26, respectively, in the maternal allele and 1431-12G>A splice-site mutation in intron 15 in the paternal allele as well as the missense variation E420K in homozygous state. Combination of the identified mutations along with transient hyperaldosteronism and possible GH deficiency have not been described before. Accordingly, the importance of early multidisciplinary approach is highlighted, in order to reach accurate diagnosis, initiate prompt treatment, and ensure survival with fewer disease complications.
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- 2015
4. CHRONOS: a time-varying method for microRNA-mediated subpathway enrichment analysis.
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Vrahatis, Aristidis G., Dimitrakopoulou, Konstantina, Balomenos, Panos, Tsakalidis, Athanasios K., and Bezerianos, Anastasios
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BIOINFORMATICS ,MESSENGER RNA ,MICRORNA genetics ,GENE expression ,NEURAL circuitry ,FUNCTIONAL analysis - Abstract
Motivation: In the era of network medicine and the rapid growth of paired time series mRNA/ microRNA expression experiments, there is an urgent need for pathway enrichment analysis methods able to capture the time- and condition-specific 'active parts' of the biological circuitry as well as the microRNA impact. Current methods ignore the multiple dynamical 'themes'—in the form of enriched biologically relevant microRNA-mediated subpathways—that determine the functionality of signaling networks across time. Results: To address these challenges, we developed time-vaRying enriCHment integrOmics Subpathway aNalysis tOol (CHRONOS) by integrating time series mRNA/microRNA expression data with KEGG pathway maps and microRNA-target interactions. Specifically, microRNAmediated subpathway topologies are extracted and evaluated based on the temporal transition and the fold change activity of the linked genes/microRNAs. Further, we provide measures that capture the structural and functional features of subpathways in relation to the complete organism pathway atlas. Our application to synthetic and real data shows that CHRONOS outperforms current subpathway-based methods into unraveling the inherent dynamic properties of pathways. [ABSTRACT FROM AUTHOR]
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- 2016
- Full Text
- View/download PDF
5. DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments.
- Author
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Vrahatis, Aristidis G., Balomenos, Panos, Tsakalidis, Athanasios K., and Bezerianos, Anastasios
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BIOINFORMATICS ,PHARMACOLOGY ,VISUALIZATION ,TARGETED drug delivery ,DISEASES - Abstract
Summary: DEsubs is a network-based systems biology R package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customized framework with a broad range of operation modes at all stages of the subpathway analysis, enabling so a case-specific approach. The operation modes include pathway network construction and processing, subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render DEsubs a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level drug targets and biomarkers for complex diseases. [ABSTRACT FROM AUTHOR]
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- 2016
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6. EnsembleGASVR: a novel ensemble method for classifying missense single nucleotide polymorphisms.
- Author
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Rapakoulia, Trisevgeni, Theofilatos, Konstantinos, Kleftogiannis, Dimitrios, Likothanasis, Spiros, Tsakalidis, Athanasios, and Mavroudi, Seferina
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SINGLE nucleotide polymorphisms ,GENETIC polymorphism research ,NUCLEOTIDE sequence ,BIOINFORMATICS ,STATISTICAL ensembles - Abstract
Motivation: Single nucleotide polymorphisms (SNPs) are considered the most frequently occurring DNA sequence variations. Several computational methods have been proposed for the classification of missense SNPs to neutral and disease associated. However, existing computational approaches fail to select relevant features by choosing them arbitrarily without sufficient documentation. Moreover, they are limited to the problem of missing values, imbalance between the learning datasets and most of them do not support their predictions with confidence scores.Results: To overcome these limitations, a novel ensemble computational methodology is proposed. EnsembleGASVR facilitates a two-step algorithm, which in its first step applies a novel evolutionary embedded algorithm to locate close to optimal Support Vector Regression models. In its second step, these models are combined to extract a universal predictor, which is less prone to overfitting issues, systematizes the rebalancing of the learning sets and uses an internal approach for solving the missing values problem without loss of information. Confidence scores support all the predictions and the model becomes tunable by modifying the classification thresholds. An extensive study was performed for collecting the most relevant features for the problem of classifying SNPs, and a superset of 88 features was constructed. Experimental results show that the proposed framework outperforms well-known algorithms in terms of classification performance in the examined datasets. Finally, the proposed algorithmic framework was able to uncover the significant role of certain features such as the solvent accessibility feature, and the top-scored predictions were further validated by linking them with disease phenotypes.Availability and implementation: Datasets and codes are freely available on the Web at http://prlab.ceid.upatras.gr/EnsembleGASVR/dataset-codes.zip. All the required information about the article is available through http://prlab.ceid.upatras.gr/EnsembleGASVR/site.htmlContact: mavroudi@ceid.upatras.grSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM PUBLISHER]
- Published
- 2014
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7. SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis.
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Tsagrasoulis, Dimosthenis, Danos, Vasilis, Kissa, Maria, Trimpalis, Philip, Koumandou, V. Lila, Karagouni, Amalia D., Tsakalidis, Athanasios, and Kossida, Sophia
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CHIMERIC proteins ,DATABASES ,COMPUTERS in biology ,GENOMIC information retrieval ,BIOINFORMATICS - Abstract
Domain Fusion Analysis takes advantage of the fact that certain proteins in a given proteome A, are found to have statistically significant similarity with two separate proteins in another proteome B. In other words, the result of a fusion event between two separate proteins in proteome B is a specific full-length protein in proteome A. In such a case, it can be safely concluded that the protein pair has a common biological function or even interacts physically. In this paper, we present the Fusion Events Database (FED), a database for the maintenance and retrieval of fusion data both in prokaryotic and eukaryotic organisms and the Software for the Analysis of Fusion Events (SAFE), a computational platform implemented for the automated detection, filtering and visualization of fusion events (both available at: http://www.bioacademy.gr/bioinformatics/projects/ProteinFusion/index.htm). Finally, we analyze the proteomes of three microorganisms using these tools in order to demonstrate their functionality. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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