Morphological, histochemical, and interstitial pressure changes in the tibialis anterior muscle before and after aortofemoral bypass in patients with peripheral arterial occlusive disease

BACKGROUND: Morphological and electrophysiological studies of ischemic muscles in peripheral arterial disease disclosed evidence of denervation and fibre atrophy. The purpose of the present study is to describe morphological changes in ischemic muscles before and after reperfusion surgery in patients with peripheral occlusive arterial disease, and to provide an insight into the effect of reperfusion on the histochemistry of the reperfused muscle. METHODS: Muscle biopsies were obtained from the tibialis anterior of 9 patients with chronic peripheral arterial occlusive disease of the lower extremities, before and after aortofemoral bypass, in order to evaluate the extent and type of muscle fibre changes during ischemia and after revascularization. Fibre type content and muscle fibre areas were quantified using standard histological and histochemical methods and morphometric analysis. Each patient underwent concentric needle electromyography, nerve conduction velocity studies, and interstitial pressure measurements. RESULTS: Preoperatively all patients showed muscle fibre atrophy of both types, type II fibre area being more affected. The mean fibre cross sectional area of type I was 3,745 μm(2) and of type II 4,654 μm(2) . Fibre-type grouping, great variation in fibre size and angular fibres were indicative of chronic dennervation-reinnervation, in the absence of any clinical evidence of a neuropathic process. Seven days after the reperfusion the areas of both fibre types were even more reduced, being 3,086 μm(2) for type I and 4,009 μm(2) for type II, the proportion of type I fibres, and the interstitial pressure of tibialis anterior were increased. CONCLUSIONS: The findings suggest that chronic ischemia of the leg muscles causes compensatory histochemical changes in muscle fibres resulting from muscle hypoxia, and chronic dennervation-reinnervation changes, resulting possibly from ischemic neuropathy. Reperfusion seems to bring the oxidative capacity of the previously ischemic muscle closer to normal

DIANA-miRGen v4 : indexing promoters and regulators for more than 1500 microRNAs

Deregulation of microRNA (miRNA) expression plays a critical role in the transition from a physiological to a pathological state. The accurate miRNA promoter identification in multiple cell types is a fundamental endeavor towards understanding and characterizing the underlying mechanisms of both physiological as well as pathological conditions. DIANA-miRGen v4 (www.microrna.gr/mirgenv4) provides cell type specific miRNA transcription start sites (TSSs) for over 1500 miRNAs retrieved from the analysis of >1000 cap analysis of gene expression (CAGE) samples corresponding to 133 tissues, cell lines and primary cells available in FANTOM repository. MiRNA TSS locations were associated with transcription factor binding site (TFBSs) annotation, for >280 TFs, derived from analyzing the majority of ENCODE ChIP-Seq datasets. For the first time, clusters of cell types having common miRNA TSSs are characterized and provided through a user friendly interface with multiple layers of customization. DIANA-miRGen v4 significantly improves our understanding of miRNA biogenesis regulation at the transcriptional level by providing a unique integration of high-quality annotations for hundreds of cell specific miRNA promoters with experimentally derived TFBSs.peer-reviewe

A method for identifying TSS from CAGE data using a Genomic Signal Processing approach

Η επεξεργασία σήματος σε επίπεδο γονιδιώματος μπορεί να λύσει διάφορα βιολογικά προβλήματα με χαμηλό υπολογιστικό κόστος. Υπάρχουν πολλοί μαθηματικοί αλγόριθμοι οι οποίοι χρησιμοποιούνται κυρίως για την αναγνώριση των γονιδίων και τη σύγκριση μεταξύ ακολουθιών, χρησιμοποιώντας αρκετές αναπαραστάσεις του DNA που δεν εξελίχθηκαν λόγω έλλειψης αποτελεσματικότητας. Η γνώση της ακριβούς θέσης των θέσεων έναρξης μεταγραφής (TSS), εκεί δηλαδή όπου ξεκινά η μεταγραφή στο 5'- άκρο μιας αλληλουχίας γονιδίου σε ένα RNA μόριο, είναι απαραίτητη για την αναγνώριση των ρυθμιστικών περιοχών που το επηρεάζουν. Στη βιβλιογραφία έχουν αναφερθεί πολλές προσεγγίσεις σχετικά με τον εντοπισμό των θέσεων έναρξης της μεταγραφής. Αυτή η μελέτη παρουσιάζει μια νέα μέθοδο για την αναγνώριση των θέσεων έναρξης μεταγραφής (TSS) από τα δεδομένα CAGE (Cap Analysis of Gene Expression) και την εφαρμογή χαρακτηριστικών και τεχνικών δανεισμένων από την επεξεργασία σήματος, που αποσκοπούν επίσης στην αναγνώριση σημείων έναρξης της μεταγραφής. Παρουσιάζεται μία νέα μέθοδος για την αναπαράσταση των νουκλεοτιδίων ικανή να εξάγει και να παρουσιάσει την πληροφορία σε μορφή σήματος στο πεδίο του χρόνου. Τα σήματα μεταφέρθηκαν από το πεδίο του χρόνου στο πεδίο των συχνοτήτων, οπού μπορεί να γίνει φιλτράρισμα αυτών και να απομακρυνθεί ο θόρυβος με αποτελεσματικό τρόπο. Ύστερα τα σήματα επανήλθαν στο πεδίο του χρόνου. Χρησιμοποιήθηκαν αρκετά φίλτρα και οι παράμετροί τους βελτιστοποιήθηκαν για να μεγιστοποιήσουν την ακρίβεια και την απόδοση των αποτελεσμάτων. Στα πλαίσια αυτής της εργασίας έχει σχεδιαστεί και υλοποιηθεί ένα πλήρως παραμετροποιήσιμο υπολογιστικό εργαλείο με τη χρήση τεχνικών επεξεργασίας σήματος και μαθηματικών αλγορίθμων ικανών να ανιχνεύουν θέσεις έναρξης μεταγραφής με υψηλή ακρίβεια. Η μέθοδος αυτή δοκιμάστηκε σε πραγματικά ανθρώπινα κύτταρα (Η9) με δεδομένα από το αποθετήριο FANTOM5 και η ακρίβειά τους συγκρίθηκε με άλλους αλγορίθμους όπως επίσης και την πραγματικότητα (Ground Truth). Όλα τα αποτελέσματα παρουσιάζονται στη παρούσα μελέτη.Genomic signal processing (GSP) can solve various biological problems in low computational cost. There are many mathematical algorithms mostly used for gene identification and comparison between sequences, making use of several DNA representations that did not evolve due to lack of efficiency. The knowledge of the exact position of the transcription start sites (TSS), which is the location where transcription starts at the 5'-end of a gene sequence in an RNA molecule, is critical for the identification of the regulatory regions that flank it. Many approaches have been mentioned in the literature about locating the TSS positions. This study presents a novel method for identifying transcription start sites (TSS) from CAGE (Cap Analysis of Gene Expression) data and applying features and techniques borrowed form GSP that also aim to identify TSSs. A fairly new representation method for nucleotides has been introduces able to extract and represent the information in a time series signal vector. Signals were transferred from time to frequency domain, which allows for filtering artifacts in an efficient robust way, and vice versa. Several filters have been used and their parameters were optimized to maximize the accuracy and performance in results. In the context of this work a fully modular computational tool has been designed and implemented using GSP techniques and mathematical algorithms able to detect TSSs with high accuracy. The method was tested in real human cells (H9 line) with data downloaded from FANTOM5 repository and the accuracy has been compared with other algorithms and the ground truth. All the results are presented in this study

The reproductive behaviour of pigs in a dynamic service system for gilts

Abstract The behaviour of 80 gilts and 14 boars was observed over a 54-day period in a dynamic service system with pens of 20 gilts and 4-5 boars. The female population of this system was Ž . changed on a regular basis four animals in four animals out per week while boars were resident. Ž . Altogether 933 mating attempts MAs were recorded and their quality was classified using quantitative behavioural criteria. Only 9% and 18% of the observed MAs were classified as ' very good' and 'good', while 14, 24 and 35% were 'fair', 'poor' and ' very poor', respectively. Ž Differences between and within boar teams in the mating quality parameters were significant all . Ž . p -0.05 . A significant correlation was found between time to first mount TTFM and MA Ž . duration r sq0.58, p -0.01 . MAs followed a diurnal pattern and had a peak at about 0900 h Ž . after feeding time . The number of MAs a gilt received per hour of oestrus decreased Ž . Ž . r sy0.55, p -0.001 , while mating quality score improved r sq0.38, p -0.005 . The overall pregnancy rate was 84%. Gilts with a positive PD result had received more total MAs and Ž . total 'good'q' very good' MAs T s 2.33, p -0.05 and T s 2.25, p -0.05, respectively , and Ž . were significantly heavier at the time of selection T s 2.80, p -0.01 . Mating quality grade Ž 2 . differed significantly with boar social status x s 35.8, df s 16, p -0.01 but this had no Ž . influence on mating frequency, time to first mount or mating duration all p ) 0.05 , indicating that subordinate boars were not deprived of sexual partners. Gilt lesion scores reached a maximum Ž . 3 days after entry then subsequently declined r sy0.75, p -0.05 . It was concluded that with a good knowledge of the factors influencing the activity of the sexual partners kept in such a system, the dynamic service system could be a valuable alternative in future pig production.

2D LES of breaking waves on seawalls with recurved parapets

The utilization of recurves on vertical seawalls reduces overtopping without drastic increases in the structures’ freeboard. As part of ISOPE22 blind test challenge, an in-house developed computational fluid dynamics code is used to simulate the breaking of waves on a vertical seawall and the interaction of the violent up-rushing flow with the recurve. The code combines recent advances which speed-up the solution of Poison’s equation, with an immersed boundary method and a Large Eddy Simulation model. The comparison of the numerical results with the experimental data provided by the organisers shows a satisfactory reproduction of the wave conditions in the flume and a non-negligible underestimation for the predicted peak pressures. This, with a computational cost of approximately 2 hours per wave period

2D LES of breaking waves on seawalls with recurved parapets

The utilization of recurves on vertical seawalls reduces overtopping without drastic increases in the structures’ freeboard. As part of ISOPE22 blind test challenge, an in-house developed computational fluid dynamics code is used to simulate the breaking of waves on a vertical seawall and the interaction of the violent up-rushing flow with the recurve. The code combines recent advances which speed-up the solution of Poison’s equation, with an immersed boundary method and a Large Eddy Simulation model. The comparison of the numerical results with the experimental data provided by the organisers shows a satisfactory reproduction of the wave conditions in the flume and a non-negligible underestimation for the predicted peak pressures. This, with a computational cost of approximately 2 hours per wave period