Emmanouil Sifakis

... Andriana Prentza, Senior Member, IEEE, Aristotelis Chatziioannou, Member , IEEE, Dimitris Koutsouris, Senior Member , IEEE, Eleftheria Koultouki, Fotini ... EG Sifakis is with the Biomedical Engineering Laboratory, National Technical University of Athens, Zografou, Athens, 15773 ...

Automatic segmentation of the arterial lumen from ultrasound images is an important task in clinical diagnosis. Carotid artery recognition, the first task in lumen segmentation, should be performed in a fully automated, fast, and reliable way to further facilitate the low-level task of arterial delineation. In this paper, a user-independent, real-time algorithm is introduced for carotid artery localization in longitudinal B-mode ultrasound images. The proposed technique acts directly on the raw image, and exploits basic statistics along with anatomical knowledge. The method's evaluation and parameter value optimization were performed on a threefold cross validation basis. In addition, the introduced algorithm was systematically compared with another algorithm for common carotid artery recognition in B-mode scans, separately for multi-frame and single-frame data. The data sets used included 2,149 images from 100 subjects taken from three different institutions and covering a wide...

High-throughput DNA methylation profiling exploits microarray technologies thus providing a wealth of data, which however solicits rigorous, generic, and analytical pipelines for an efficient systems level analysis and interpretation. In this study, we utilize the Illumina's Infinium Human Methylation 450K BeadChip platform in an epidemiological cohort, targeting to associate interesting methylation patterns with breast cancer predisposition. The computational framework proposed here extends the--established in transcriptomic microarrays--logarithmic ratio of the methylated versus the unmethylated signal intensities, quoted as M-value. Moreover, intensity-based correction of the M-signal distribution is introduced in order to correct for batch effects and probe-specific errors in intensity measurements. This is accomplished through the estimation of intensity-related error measures from quality control samples included in each chip. Moreover, robust statistical measures exploiti...

Transcriptionally active and inactive chromatin domains tend to segregate into separate sub-nuclear compartments to maintain stable expression patterns. However, here we uncovered an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains (LADs). The interactome is regulated by PARP1 and its co-factor CTCF. They not only mediate chromatin fiber interactions but also promote the recruitment of circadian genes to the lamina. Synchronization of the circadian rhythm by serum shock induces oscillations in PARP1-CTCF interactions, which is accompanied by oscillating recruitment of circadian loci to the lamina, followed by the acquisition of repressive H3K9me2 marks and transcriptional attenuation. Furthermore, depletion of H3K9me2/3, inhibition of PARP activity by olaparib, or downregulation of PARP1 or CTCF expression counteracts both recruitment to the envelope and circadian transcription. PARP1- and CTCF-regulated contacts bet...