ABSTRACT
Breast cancer (BC) remains the most diagnosed cancer in women, accounting for 12% of new annual cancer cases in Europe and worldwide. Advances in surgery, radiotherapy and systemic treatment have resulted in improved clinical outcomes and increased survival rates in recent years. However, BC therapy-related cardiotoxicity, may severely impact short- and long-term quality of life and survival. This study presents the CARDIOCARE platform and its main components, which by integrating patient-specific data from different categories, data from patient-oriented eHealth applications and wearable devices, and by employing advanced data mining and machine learning approaches, provides the healthcare professionals with a valuable tool for effectively managing BC patients and preventing or alleviating treatment induced cardiotoxicity.Clinical Relevance- Through the adoption of CARDIOCARE platform healthcare professionals are able to stratify patients for their risk for cardiotoxicity and timely apply adequate interventions to prevent its onset.
Subject(s)
Breast Neoplasms , Humans , Female , Aged , Breast Neoplasms/drug therapy , Cardiotoxicity/etiology , Cardiotoxicity/prevention & control , Quality of Life , EuropeABSTRACT
With the completion of the Human Genome Project and the emergence of high-throughput technologies, a vast amount of molecular and biological data are being produced. Two of the most important and significant data sources come from microarray gene-expression experiments and respective databanks (e,g., Gene Expression Omnibus-GEO (http://www.ncbi.nlm.nih.gov/geo)), and from molecular pathways and Gene Regulatory Networks (GRNs) stored and curated in public (e.g., Kyoto Encyclopedia of Genes and Genomes-KEGG (http://www.genome.jp/kegg/pathway.html), Reactome (http://www.reactome.org/ReactomeGWT/entrypoint.html)) as well as in commercial repositories (e.g., Ingenuity IPA (http://www.ingenuity.com/products/ipa)). The association of these two sources aims to give new insight in disease understanding and reveal new molecular targets in the treatment of specific phenotypes.Three major research lines and respective efforts that try to utilize and combine data from both of these sources could be identified, namely: (1) de novo reconstruction of GRNs, (2) identification of Gene-signatures, and (3) identification of differentially expressed GRN functional paths (i.e., sub-GRN paths that distinguish between different phenotypes). In this chapter, we give an overview of the existing methods that support the different types of gene-expression and GRN integration with a focus on methodologies that aim to identify phenotype-discriminant GRNs or subnetworks, and we also present our methodology.
Subject(s)
Computational Biology/methods , Gene Regulatory Networks , Oligonucleotide Array Sequence Analysis , Signal Transduction , Databases, Genetic , Gene Expression Profiling/methods , Humans , Molecular Sequence Annotation , Systems Biology/methodsABSTRACT
Chronic inflammatory diseases like periodontitis have a complex pathogenesis and a multifactorial etiology, involving complex interactions between multiple genetic loci and infectious agents. We aimed to investigate the influence of genetic polymorphisms and bacteria on chronic periodontitis risk. We determined the prevalence of 12 single-nucleotide polymorphisms (SNPs) in immune response candidate genes and 7 bacterial species of potential relevance to periodontitis etiology, in chronic periodontitis patients and non-periodontitis control individuals (N = 385). Using decision tree analysis, we identified the presence of bacterial species Tannerella forsythia, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and SNPs TNF -857 and IL-1A -889 as discriminators between periodontitis and non-periodontitis. The model reached an accuracy of 80%, sensitivity of 85%, specificity of 73%, and AUC of 73%. This pilot study shows that, on the basis of 3 periodontal pathogens and SNPs, patterns may be recognized to identify patients at risk for periodontitis. Modern bioinformatics tools are valuable in modeling the multifactorial and complex nature of periodontitis.
Subject(s)
Chronic Periodontitis/genetics , Genes, MHC Class II/genetics , Genetic Predisposition to Disease/genetics , Gram-Negative Bacteria/physiology , Polymorphism, Single Nucleotide/genetics , Adult , Aged , Aggregatibacter actinomycetemcomitans/physiology , Alveolar Bone Loss/genetics , Alveolar Bone Loss/microbiology , Area Under Curve , Bacteroides/physiology , Chronic Periodontitis/microbiology , Computational Biology , Decision Support Techniques , Decision Trees , Female , Humans , Interleukin-1alpha/genetics , Male , Middle Aged , Models, Genetic , Pilot Projects , Porphyromonas gingivalis/physiology , Risk Factors , Sensitivity and Specificity , Tumor Necrosis Factor-alpha/genetics , Young AdultABSTRACT
In order to diagnose epilepsy, neurologists rely on their experience, performing an equal assessment of the electroencephalogram and the clinical image. Since misdiagnosis reaches a rate of 30% and more than one-third of all epilepsies are poorly understood, a need for leveraging diagnostic precision is obvious. With the aim at enhancing the clinical image assessment procedure, this paper evaluates the suitability of certain facial expression features for detecting and quantifying absence seizures. These features are extracted by means of time-varying signal analysis from signals that are gained by applying computer vision techniques, such as face detection, dense optical flow computation and averaging background subtraction. For the evaluation, video sequences of four patients with absence seizures are used. The classification performance of a C4.5 decision tree shows accuracies of up to 99.96% with a worst percentage of incorrectly classified instances of 0.14%.
