- ItemOpen AccessModeling of the pathway of multiciliated cells' differentiation(2022-11-10)Multiciliogenesis constitutes an important biological process in which progenitor cells differentiate into multiciliated cells (MCCs). These cells are located in various biological systems, performing important biological functions such as: ensuring the circulation of cerebrospinal fluid in CNS (Central Nervous System), removing extraneous pollutants from the respiratory tract, transporting gametic cells during fertilization and many others. The aim of this diploma thesis is to study multiciliogenesis at the level of protein interactions. We examine whether our designed mathematical model is capable enough of describing the behavior of the proteins we have chosen as key factors of this biological phenomenon. More specifically, our mathematical model consists of ordinary differential equations (ODEs), each one expresses the rate of change in the concentration of one of the regulatory proteins: Geminin, Lynkeas, McIdas. For the parameter estimation of the model, we use experimental data and a calculated estimator as a comparison measurement. The results of the simulations we run, show that the designed for Geminin equation verifies with great precision qualitatively and quantitatively its behavior, as it is presented on the experimental data. On the other hand, the designed system of Lynkeas/McIdas equations, while qualitatively seems to follow the behavior seen in the experimental data, failed to quantitatively describe the experimental data. In this work, we decide to examine the simplest form of this mathematical model, where in the system of Lynkeas/McIdas equations, we integrate the negative effect of McIdas to Lynkeas in the simplest form. More complex forms of equations may describe more precisely the behavior of these proteins in the biological phenomenon under study.
- ItemOpen AccessSuper-resolution ultrasound imaging(2022-10-31)Recently, research studies have shown a rapid increase of several types of cancer which are attributed to many factors such as air pollution, unhealthy diet, modern living, random mutations etc. An important type of cancer among men that is clearly accused of high death rate if it is not diagnosed in time, is prostate cancer. Prostate cancer is being diagnosed after following a specific protocol which of course includes a TRUS-guided biopsy, usually after having an MRI scan. US has been undoubtedly considered as an imaging modality which can compete with MRI due to its low cost, the real-time imaging possibility, its portability, its non-radiation effects and its relatively easy user’s operation. On the other hand, its poor spatial resolution, often an MRI or CT-scan is required to make an accurate diagnosis of a disease regarding soft tissues. CEUS has come to bridge this gap, since it introduces UCAs, non-linear scatterers of the sound wave. These agents, often called MBs, are infused in the blood in a specific region to be scanned. A US transducer produces sound waves at a specific frequency. The MBs reflect the transmitted signal, since they are strong scatterers of sound waves, and the reflected signal is received by the transducer again. This procedure is based on the piezoelectric effect of certain materials. This means that when an electric field is applied to them they produce sound waves, but also the opposite. Thus, an image with high contrast can be achieved. Of course there are several methods that utilize the non-linear effect of the MBs and distinguish it from the surrounding tissues, called the contrast-specific imaging techniques. Many of them take advantage of the high mechanical index, while others use the low mechanical index, especially when continuous real-time imaging is necessary. This modality can be used for visualizing the micro-vascularity of the prostate gland in super-resolution using accurate localization-based detection procedures. Since, it is known that there is high correlation between micro-vascularity and cancer growth, it is very important to create US images which can provide the clinician with information about the vascular bed and possibly a tumor growth at early or more progressive stages. After detecting these MBs in super-resolution images, there comes the part, where the tracking procedure is taking place. Usually, a frame sequence of the contrast-enhanced images of the prostate is available and the MBs detected using localization techniques, have to be linked in sequential frames in order to create the tracks of each MB and thus the vessels in which the MBs are flowing into. Several Algorithms have been developed for dealing with the tracking problem, mainly divided in two sub-categories, the deterministic and the probabilistic. The deterministic approach is assumed to be a more conservative method for dealing with tracking and it is based on the optimization of the assignment problem like the Nearest-Neighbor algorithm, after having accurately localized the targets. The probabilistic approaches, on the other hand, have been recently introduced to deal with the tracking problems and it seems that they lead to more accurate and reliable results than the previous ones, since they are based on the prediction of the trajectory using the prior knowledge of measurements like locations or velocities, thus creating realistic probabilities of a certain MB to be linked with another MB. In this study a new tracking algorithm is introduced, the BM3D plus Rho, which utilizes the correlation between MBs in sequential frames to form links inside tracks. Of course, a thorough investigation of MB size and other characteristics is preceded. The new algorithm uses data taken from manually collected tracks in a sample of the population in order to optimize the linking procedure on a link-based level. A new detection filter is also added which leads to even more accurate localizations. During the analysis, an evaluation procedure is taking place using synthetic data produced by an algorithm, and thus a more robust comparison can be achieved. In this study, It was found that the vector angle correlation between MBs inside the same track range from 0 to 23 (angle in degrees) for the sample and dataset SRI001, which of course can be used in other datasets such as SRI010, in which the resulting maps were clearly improved even if the maximum correlation value is not know from a respective sample, like in SRI001. Resulting track number maps, velocity maps and blood flow maps show that the vessels can be clearly separated and the noisy areas have been reduced compared to the previous version of the algorithm. Thus the micro-vascularity of the prostate in both datasets with different MB size distributions and PSFs is depicted clearly, and of course enhanced correctly in the expected areas. It was found also, that the long tracks which the algorithm calculated do not locate inside the cancer area, but in the healthy regions, and this information is important for assessing also the differences between the cancer and the healthy area. The detection due to the filter showed an almost 2% improvement in the detection part. The tracking was improved by a significant percent since the vessels in the maps are very well structured and also the areas which contain already confirmed vessels have greater amplitude than before. The mean link per track has risen about 6% while the total tracks and links formed have risen in SRI001 by 5.2% and 11.9% respectively, and the fact that the high density areas are enhanced, is a strong indicator that these rise in links and tracks includes correct additions.
- ItemOpen AccessΜελέτη και προσομοίωση λειτουργίας ηλεκτρονικών μετατροπέων ισχύος για μικροδίκτυα συνεχούς τάσηςΤο μέλλον των συστημάτων ενέργειας διαγράφει εδώ και καιρό μια τροχιά αποκεντροποίησης και μετάβασης από την κάθετη και μονοσήμαντη κατεύθυνση τόσο των στρατηγικών ελέγχου, όσο και του τρόπου της πολιτικής λειτουργίας του, σε μια κατάσταση που χαρακτηρίζεται από την κατανεμημένη φιλοσοφία της, καθώς και τον πολυεπίπεδο και αμφίδρομο τρόπο της ροής της ισχύος μέσα στα επιμέρους συστήματα του. Σε αυτή τη μετάβαση τα μικροδίκτυα κατέχουν ιδιάζουσα θέση, καθώς όντας μικρά, τοπικά συστήματα ενέργειας, τα οποία ενσωματώνουν παραγωγή, αποθήκευση και κατανάλωση, μπορούν να λειτουργούν είτε διασυνδεδεμένα με το κυρίως δίκτυο, είτε νησιδοποιημένα, είτε υπό μεταβατικές συνθήκες μεταξύ νησιδοποίησης και μη. Λόγω αυτών των δυνατοτήτων λειτουργίας τους, τα μικροδίκτυα συνεισφέρουν στην πραγμάτωση του μετασχηματισμού του υπάρχοντος συμβατικού δικτύου ενέργειας, σε ένα σύστημα με αποκεντροποιημένο χαρακτήρα και τρόπο λειτουργίας. Με την παρούσα μελέτη εξετάζονται οι ηλεκτρονικοί μετατροπείς ισχύος, οι οποίοι θα χρησιμοποιηθούν για να ενσωματωθούν ένα μικροδίκτυο συνεχούς τάσης, ανεξάρτητο ως προς τη λειτουργία του από το κυρίως δίκτυο, όντας ενεργειακά αυτόνομο μέσω της χρήσης αποθηκευτικών μέσων ενέργειας. Στην παρούσα εργασία γίνεται παρουσίαση και προσομοίωση ενός αυτόνομου μικροδικτύου συνεχούς τάσης. Το υπό μελέτη μικροδίκτυο αποτελείται από μια μονάδα αποθήκευσης ενέργειας, είτε υπό τη μορφή ηλεκτρικής είτε θερμικής ενέργειας, καθώς και από κατανεμημένες μονάδες παραγωγής, οι οποίες κάνουν χρήση ανανεώσιμων πηγών ενέργειας. Συγκεκριμένα οι μονάδες αυτές αποτελούνται από μια φωτοβολταϊκή και μια αιολική μονάδα παραγωγής ενέργειας. Κατά τη διάρκεια της εργασίας γίνεται προσομοίωση τόσο της λειτουργίας των μετατροπέων ανεξάρτητα ανά μονάδα παραγωγής, όσο και της συνολικής λειτουργίας του μικροδικτύου. Η εύρυθμη λειτουργία του μικροδικτύου συνεχούς τάσης εξετάζεται για διάφορα σενάρια λειτουργίας, τα οποία καθορίζονται από την έλλειψη ή την περίσσεια της παραγόμενης ισχύος. Ο έλεγχος των μετατροπέων γίνεται πρωτογενώς και περιλαμβάνει την υλοποίηση της τεχνικής MPPT σε φωτοβολταϊκή συστοιχία, καθώς και σε σύστημα ανεμογεννήτριας μέσω του ελέγχου της εικονικής εμπέδησης στην έξοδο των μετατροπέων. Το μικροδίκτυο εξετάζεται ως ενεργειακά αυτόνομο, σε όλα τα πιθανά σενάρια λειτουργίας του και με τον κατάλληλο έλεγχο επιτυγχάνεται η διατήρηση σταθερής τάσης, ακολουθώντας στενά την τάση αναφοράς του, παρά τις διακυμάνσεις στην παραγωγή και τα ηλεκτρικά και θερμικά του φορτία, κάνοντας χρήση των αποθηκευτικών του διατάξεων για την απαλοιφή οποιωνδήποτε διαταραχών ισχύος.
- ItemOpen AccessSuper-resolution ultrasound Imaging of the ovine corpus luteum vascular regulation modelUltrasound is a well-established medical imaging modality competing more advanced methods such as MRI and CT, while the recent advancements in super-resolution imaging have increased its usefulness even more. Super resolution ultrasound is frequently used in tumor detection applications, since micro-bubble tracking provides information of tissue perfusion and local haemodynamic characteristics. The particles are inserted into the blood stream via an intravenous injection and due to their mm dimensions they can reach even the smallest capillaries. Usually, they are fabricated with an gaseous inner layer and an outer shell composed by various materials such as lipids, polymers and proteins. Replacing the inner layer with chemotherapeutic drugs, targeted tumor treatment is possible. The super-resolution imaging approach is based upon the tracking of the particles as they travel in the bloodstream. To achieve that a two-step algorithm is employed which includes the segmentation and localization of the bubble and its tracing in the temporal domain. Since in the tracking the particle is considered as a single point object, replaced by its center of mass, the accuracy of the segmentation and localization determines the success of the entire algorithm. The current method includes a simple averaging filter to remove any artefacts from the image and through a probabilistic approach distinguish the pixels to those that belong to a particle and those that belong to the background. This thesis addresses some of the misconceptions of the already developed algorithm and presents a comparative study between the above segmentation and two new approaches. Firstly, the averaging filter is replaced with more proper enhancing methods such as adaptive wiener filter, non-local means or bilateral filter, replacing a simple smoothing filter with edge-preserving filters. The analysis of the original algorithm revealed an ill-defined step using the Haar-Like features, which in the new approaches is removed, while an entirely new method based on the maximization of the cross correlation between an investigated bubble and a theoretical template is used. After describing thoroughly the principles of each filter and each method, this study presents a detailed evaluation of each proposed algorithm via a synthetic data set and several feature maps produced from real US videos. The utilization of synthetic data is critical since they provide information of ground truth events and thus measurements of wrong or missed detections can be made. However, due to specific limitations of the synthetic data. an extensive assessment on real data, on both sheep ovaries and patients with prostate cancer, is necessary. Considering the same linking algorithm, any difference in the feature maps is attributed to the segmentation algorithm.
- ItemOpen AccessSeparating a mixture of quasi-periodic componetsIn many biomedical engineering applications that involve simultaneous recordings of multiple biological signals we want to extract the original signals from the observed mixtures. Due to the quasi-periodic nature of many of these biological processes, such as the heart and lung activity, we inevitable arrive to the problem of Periodic Component Analysis. We will show that this is a very special case of a broad spectrum of problems, what is known for decades as Blind Source Separation (BSS). We developed methods that attempt to solve this problem by taking into account the periodic nature of the signals as well as the realistic limitations when attempting to solve this problem in real life scenarios, specifically in the case of simultaneous recordings of heart and lung acoustic signals , where the nature of signal transmission in the human body requires a more sophisticated model.