RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine

Phylogenetic tree reconstruction is one of the grand challenge problems in Bioinformatics. The search for a best-scoring tree with 50 organisms, under a reasonable optimality criterion, creates a topological search space which is as large as the number of atoms in the universe. Computational phylogeny is challenging even for the most powerful supercomputers. It is also an ideal candidate for benchmarking emerging multiprocessor architectures, because it exhibits various levels of fine and coarse-grain parallelism. In this paper, we present the porting, optimization, and evaluation of RAxML on the Cell Broadband Engine. RAxML is a provably efficient, hill climbing algorithm for computing phylogenetic trees based on the Maximum Likelihood (ML) method. The algorithm uses an embarrassingly parallel search method, which also exhibits data-level parallelism and control parallelism in the computation of the likelihood functions. We present the optimization of one of the currently fastest tree search algorithms, on a real Cell blade prototype. We also investigate problems and present solutions pertaining to the optimization of floating point code, control flow, communication, scheduling, and multi-level parallelization on the Cell

Dynamic Multigrain Parallelization on the Cell Broadband Engine

This paper addresses the problem of orchestrating and scheduling parallelism at multiple levels of granularity on heterogeneous multicore processors. We present policies and mechanisms for adaptive exploitation and scheduling of multiple layers of parallelism on the Cell Broadband Engine. Our policies combine event-driven task scheduling with malleable loop-level parallelism, which is exposed from the runtime system whenever task-level parallelism leaves cores idle. We present a runtime system for scheduling applications with layered parallelism on Cell and investigate its potential with RAxML, a computational biology application which infers large phylogenetic trees, using the Maximum Likelihood (ML) method. Our experiments show that the Cell benefits significantly from dynamic parallelization methods, that selectively exploit the layers of parallelism in the system, in response to workload characteristics. Our runtime environment outperforms naive parallelization and scheduling based on MPI and Linux by up to a factor of 2.6. We are able to execute RAxML on one Cell four times faster than on a dual-processor system with Hyperthreaded Xeon processors, and 5--10\% faster than on a single-processor system with a dual-core, quad-thread IBM Power5 processor

Η διαπίστωση της αγιότητας αυτοκρατόρων και μελών αυτοκρατορικών οικογενειών στο Βυζάντιο από τον 4ο έως τον 10ο αιώνα.

Η διατριβή μου ασχολείται με τους αυτοκράτορες ή τα μέλη των αυτοκρατορικών οικογενειών μίας συγκεκριμένης βυζαντινής περιόδου (4ος - 10ος αι.) που αναφέρονται σε διάφορα αγιολόγια, συναξάρια, μηναία ή άλλα αγιολογικά κείμενα της βυζαντινής ή μεταγενέστερης περιόδου. Τα πρόσωπα είναι πολλά. Το Συναξάριο της Κωνσταντινούπολης (Ι΄ αι.) αναφέρει δεκάδες αυτοκρατορικά πρόσωπα. Άλλα συναξάρια ή μηναία της βυζαντινής περιόδου αναφέρονται σε περισσότερα ή λιγότερα πρόσωπα. Σε αυτά θα πρέπει να προστεθούν και τα πρόσωπα εκείνα που αναφέρονται μόνο σε νεότερα αγιολογικά κείμενα (π.χ. του 20ου αι.). Γιατί λοιπόν κάποια αγιολογικά κείμενα αναφέρουν αυτά τα πρόσωπα; Ποιοί ήταν οι λόγοι που προχώρησαν σε αυτήν την αναφορά; Μπορούμε να καταλήξουμε σε ένα μοτίβο;My PhD thesis deals with the emperors or members of the imperial families of a specific Byzantine period (4th - 10th century) mentioned in various hagiological texts of the Byzantine or later period. There are many faces. The Synaxarium of Constantinople (10th century) mentions dozens of imperial figures. Other synaxaria of the Byzantine period refer to more or fewer persons. To these should be added those persons mentioned only in newer hagiological texts (e.g. of the 20th century). So why do some hagiological texts mention these persons? What were the reasons for this petition? Can we come up with a pattern

On the quenching behaviour of a semilinear wave equation modelling MEMS technology

This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Discrete and Continuous Dynamical Systems - Series A following peer review. The definitive publisher-authenticated version 2015, 35(3), pp. 1009-1037 is available online at: http://dx.doi.org/10.3934/dcds.2015.35.100

Automatic natural language generation applied to alternative and augmentative communication for online video content services using SimpleNLG for Spanish

We present our work to build the Spanish version of SimpleNLG by adapting it and creating new code to satisfy the Spanish linguistic requirements. Not only have we developed this version but also we have achieved a library that only needs the main words as input and it is able to conduct the generation process on its own. The adaptation of the library uses aLexiS, a complete and reliable lexicon with morphology that we created. On the other hand, our enhanced version uses Elsa created from the pictogram domain, which also contains syntactic and semantic information needed to conduct the generation process automatically. Both the adaptation and its enhanced version may be useful integrated in several applications as well as web applications, bringing them natural language generation functionalities. We provide a use case of the system focused on Augmentative and Alternative Communication and online video content services.Xunta de Galicia | Ref. GRC2014/046Xunta de Galicia | Ref. ED341D R2016/012Ministerio de Economía, Industria y Competitividad | Ref. TEC2016-76465-C2-2-

Risk factors analysis concerning infections in general surgery

Σκοπός:Oι λοιμώξεις που ακολουθούν τις χειρουργικές επεμβάσεις αποτελούν σημαντική πηγή νοσηρότητας και θνητότητας στους ασθενείς. Με σειρά συχνότητας καταγράφονται η λοίμωξη του χειρουργικού πεδίου, η πνευμονία, η βακτηριαιμία που σχετίζεται με τον φλεβικό καθετήρα και οι ουρολοιμώξεις. Σε δύο τμήματα γενικής χειρουργικής τριτοβάθμιου νοσοκομείου διεξήχθη μελέτη ασθενών-μαρτύρων προκειμένου να εκτμηθούν οι παράγοντες κινδύνου για τις μετεγχειρητικές λοιμώξεις.Υλικά-Μέθοδοι: Ως παράγοντες κινδύνου καθορίσθηκαν: το γένος, η ηλικία, η συννοσηρότητα (σακχαρώδης διαβήτης, ηπατική ανεπάρκεια, καρδιακή ανεπάρκεια, αναπνευστική ανεπάρκεια, νόσος κολλαγόνου, νεοπλασία), η χρήση κορτικοστεροειδών, η χρήση αντινεοπλασματικών, η παχυσαρκία (>30 kg/m2), η υποθρεψία, ο χρόνος της επέμβασης (επείγουσα ή προγραμματισμένη), η ταξινόμηση της επέμβασης (καθαρή, καθαρή-μολυσμένη, μολυσμένη, ρυπαρή), η διάρκεια της επέμβασης, η φυσική κατάσταση του ασθενούς όπως καθορίζεται από το ASA score, το είδος της αναισθησίας (γενική, ραχιαία, επισκληρίδιος), η χρήση καπνού ή/και αλκοόλ.Αποτελέσματα:Η λοίμωξη του χειρουργικού πεδίου ήταν η συχνότερη μετεγχειρητική λοίμωξη στη μελέτη. Χρησιμοποιώντας μοντέλο μονοπαραγοντικής λογιστικής παλινδρόμησης οι ακόλουθοι παράγοντες βρέθηκαν στατιστικά σημαντικοί για την πρόκληση λοίμωξης (p3, και το άρρεν φύλο.Συμπεράσματα: Η λοίμωξη του χειρουργικού πεδίου είναι η συχνότερη μετεγχειρητική λοίμωξη. Παράγοντες κινδύνου στατιστικά σημαντικοί για λοίμωξη είναι ο σακχαρώδης διαβήτης, ο χρόνος της επέμβασης, ASA score >3, και το άρρεν φύλο.Background: Postoperative infectious complications are important source of morbidity and mortality in surgical patients. Surgical Site Infection (SSI), is the most common followed by pneumonia, Central Venous Catheter (CVC) bloodstream infection and Urinary Tract Infection (UTI).Methods: A case-control study was conducted in two general surgery departments trying to assess the risk factors for postsurgical infections. Gender, age, co-morbidities (diabetes mellitus, liver failure, heart failure, respiratory failure, connective tissue disease, neoplasia), use of corticosteroids, use of chemotherapeutic agents, obesity (>30 kg/m2), malnutrition, time of operation (elective or scheduled), wound classification (clean, clean-contaminated, contaminated, dirty), duration of surgical procedure, ASA score, type of anesthesia (general, epidural, spinal), smoke abuse and alcohol abuse were defined as risk factors.Results: SSI was the most common postsurgical infection in our study. The univariable logistic regression model revealed the following significant predictors (p3 and male sex, retained statistical significance (p3 and emergency procedure, are considered statistically significant

A study of a nonlocal problem with Robin boundary conditions arising from technology

From Wiley via Jisc Publications RouterHistory: received 2020-08-03, rev-recd 2021-02-18, accepted 2021-02-22, pub-electronic 2021-05-04Article version: VoRPublication status: PublishedIn the current work, we study a nonlocal parabolic problem with Robin boundary conditions. The problem arises from the study of an idealized electrically actuated MEMS (micro‐electro‐mechanical system) device, when the ends of the device are attached or pinned to a cantilever. Initially, the steady‐state problem is investigated estimates of the pull‐in voltage are derived. In particular, a Pohožaev's type identity is also obtained, which then facilitates the derivation of an estimate of the pull‐in voltage for radially symmetric N‐dimensional domains. Next a detailed study of the time‐dependent problem is delivered and global‐in‐time as well as quenching results are obtained for generic and radially symmetric domains. The current work closes with a numerical investigation of the presented nonlocal model via an adaptive numerical method. Various numerical experiments are presented, verifying the previously derived analytical results as well as providing new insights on the qualitative behavior of the studied nonlocal model

Retroactive Packet Sampling for Traffic Receipts

Is it possible to design a packet-sampling algorithm that prevents the network node that performs the sampling from treating the sampled packets preferentially? We study this problem in the context of designing a "network transparency" system. In this system, networks emit receipts for a small sample of the packets they observe, and a monitor collects these receipts to estimate each network's loss and delay performance. Sampling is a good building block for this system, because it enables a solution that is flexible and combines low resource cost with quantifiable accuracy. The challenge is cheating resistance: when a network's performance is assessed based on the conditions experienced by a small traffic sample, the network has a strong incentive to treat the sampled packets better than the rest. We contribute a sampling algorithm that is provably robust to such prioritization attacks, enables network performance estimation with quantifiable accuracy, and requires minimal resources. We confirm our analysis using real traffic traces