280 research outputs found

    psort

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    psort \ue8 stato il pi\uf9 veloce software di ordinamento per macchine di classe PC dal 2008 al 2011 (benchmark Pennysort, http://sortbenchmark.org) e un suo adattamento per cluster ha migliorato il record per il benchmark datamation di quasi un ordine di grandezza nel 2011. Il rapporto tecnico ufficiale si trova sul sito sortbenchmark.org (che cataloga i pi\uf9 efficienti software di ordinamento per varie categorie di task/hardware - originariamente mantenuto dal premio Turing Jim Gray) all'URL http://sortbenchmark.org/psort_2011.pdf -- Ulteriori dettagli si possono trovare nelle pubblicazioni: P. Bertasi, M. Bressan, E. Peserico. psort, yet another fast stable sorting software, ACM Journal of Experimental Algorithmics, vol. 16, 2011 -- P. Bertasi, M. Bonazza, M. Bressan, E. Peserico. Datamation: a quarter of a century and four orders of magnitude later. Proc. of IEEE CLUSTER 201

    Psort: automated code tuning

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    This thesis describes the design and implementation of an automated code tuner for psort, a fast sorting library for large datasets. Our work, motivated by the necessity of guaranteeing a high performance while keeping a low cost on the end user, provides a reusable and portable framework that can be easily extended to automatically tune virtually every portion of the source code, including code that has not yet been written. Experiments show that our system produces code which is significantly faster than original code, suggesting that psort should include it among its tools SOMMARIO Questa tesi descrive la progettazione e la realizzazione di un ottimizzatore di codice automatico per psort, una libreria di ordinamento veloce per grandi moli di dati. Il nostro lavoro, motivato dalla necessità di garantire alte prestazioni mantenendo un basso costo sull'utente finale, fornisce una infrastruttura rius- abile e portabile che può essere facilmente estesa per ottimizzare in maniera automatica virtualmente ogni porzione di codice sorgente, incluso codice che ancora non è stato scritto. Gli esperimenti mostrano che il nostro sistema pro- duce codice che è significativamente più veloce del codice originale, suggerendo che psort dovrebbe includerlo tra i suoi strument

    psort: automated estimation of hardware parameters

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    This thesis describes the design and implementation of an automated hardware-detection environment for psort, a fast library for stable sorting of large datasets on external memory. Our goal was to create a tool that provides a complete set of estimated hardware parameters which will be used to auto-tune psort both at compiling and at runtime. The entire detection system has been designed to be scalable and modular in order to simplify the addition of new tests, remaining as transparent as possible to the end user. Experiments prove that our code is high reliable and that there is a strict connection between hardware parameters and software performance, suggesting that psort should include our system among its tools // Questa tesi descrive il design e l’implementazione di un apparato automatico in grado di rilevare l’hardware per psort, una libreria ad alte prestazioni per l’ordinamento stabile di grandi moli di dati su memoria esterna. Il nostro obiettivo è stato quello di creare uno strumento che fornisca un insieme completo di parametri hardware stimati che saranno utilizzati per ottimizzare automaticamente psort, sia al momento della compilazione, che in quello dell’esecuzione. L’intero sistema di rilevazione è stato creato per essere scalabile e modulare in modo da semplificare l’aggiunta di nuovi test, pur rimanendo il più trasparente possibile per l’utente finale. Gli esperimenti provano che il nostro codice è affidabile e che c’è una stretta connessione tra parametri hardware e prestazione del software, suggerendo che psort dovrebbe includere il nostro sistema tra i suoi strument

    psort: sistema di documentazione

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    L'elaborato presenta alcune applicazioni pratiche della documentazione di un software (nello specifico nel progetto psort). In particolare fornisce delle guide rapide per l'utilizzo di Doxygen e la creazione di una man pageopenEmbarg

    Identification of novel functional domains of Rad52 in Saccharomyces cerevisiae

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    Electron Transfer Function versus Oxygen Delivery: A Comparative Study for Several Hexacoordinated Globins Across the Animal Kingdom

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    Caenorhabditis elegans globin GLB-26 (expressed from gene T22C1.2) has been studied in comparison with human neuroglobin (Ngb) and cytoglobin (Cygb) for its electron transfer properties. GLB-26 exhibits no reversible binding for O2 and a relatively low CO affinity compared to myoglobin-like globins. These differences arise from its mechanism of gaseous ligand binding since the heme iron of GLB-26 is strongly hexacoordinated in the absence of external ligands; the replacement of this internal ligand, probably the E7 distal histidine, is required before binding of CO or O2 as for Ngb and Cygb. Interestingly the ferrous bis-histidyl GLB-26 and Ngb, another strongly hexacoordinated globin, can transfer an electron to cytochrome c (Cyt-c) at a high bimolecular rate, comparable to those of inter-protein electron transfer in mitochondria. In addition, GLB-26 displays an unexpectedly rapid oxidation of the ferrous His-Fe-His complex without O2 actually binding to the iron atom, since the heme is oxidized by O2 faster than the time for distal histidine dissociation. These efficient mechanisms for electron transfer could indicate a family of hexacoordinated globin which are functionally different from that of pentacoordinated globins

    Structural Characterization of Acidic M17 Leucine Aminopeptidases from the TriTryps and Evaluation of Their Role in Nutrient Starvation in Trypanosoma brucei

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    Leucine aminopeptidase (LAP) is found in all kingdoms of life and catalyzes the metal-dependent hydrolysis of the N-terminal amino acid residue of peptide or amino acyl substrates. LAPs have been shown to participate in the N-terminal processing of certain proteins in mammalian cells and in homologous recombination and transcription regulation in bacteria, while in parasites, they are involved in host cell invasion and provision of essential amino acids for growth. The enzyme is essential for survival in Plasmodium falciparum, where its drug target potential has been suggested. We report here the X-ray structures of three kinetoplastid acidic LAPs (LAP-As from Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major) which were solved in the metal-free and unliganded forms, as well as in a number of ligand complexes, providing insight into ligand binding, metal ion requirements, and oligomeric state. In addition, we analyzed mutant cells defective in LAP-A in Trypanosoma brucei, strongly suggesting that the enzyme is not required for the growth of this parasite either in vitro or in vivo. In procyclic cells, LAP-A was equally distributed throughout the cytoplasm, yet upon starvation, it relocalizes in particles that concentrate in the perinuclear region. Overexpression of the enzyme conferred a growth advantage when parasites were grown in leucine-deficient medium. Overall, the results suggest that in T. brucei, LAP-A may participate in protein degradation associated with nutrient depletion. IMPORTANCE Leucine aminopeptidases (LAPs) catalyze the hydrolysis of the N-terminal amino acid of peptides and are considered potential drug targets. They are involved in multiple functions ranging from host cell invasion and provision of essential amino acids to site-specific homologous recombination and transcription regulation. In kinetoplastid parasites, there are at least three distinct LAPs. The availability of the crystal structures provides important information for drug design. Here we report the structure of the acidic LAPs from three kinetoplastids in complex with different inhibitors and explore their role in Trypanosoma brucei survival under various nutrient conditions. Importantly, the acidic LAP is dispensable for growth both in vitro and in vivo, an observation that questions its use as a specific drug target. While LAP-A is not essential, leucine depletion and subcellular localization studies performed under starvation conditions suggest a possible function of LAP-A in the response to nutrient restriction

    Human protein function prediction: application of machine learning for integration of heterogeneous data sources

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    Experimental characterisation of protein cellular function can be prohibitively expensive and take years to complete. To address this problem, this thesis focuses on the development of computational approaches to predict function from sequence. For sequences with well characterised close relatives, annotation is trivial, orphans or distant homologues present a greater challenge. The use of a feature based method employing ensemble support vector machines to predict individual Gene Ontology classes is investigated. It is found that different combinations of feature inputs are required to recognise different functions. Although the approach is applicable to any human protein sequence, it is restricted to broadly descriptive functions. The method is well suited to prioritisation of candidate functions for novel proteins rather than to make highly accurate class assignments. Signatures of common function can be derived from different biological characteristics; interactions and binding events as well as expression behaviour. To investigate the hypothesis that common function can be derived from expression information, public domain human microarray datasets are assembled. The questions of how best to integrate these datasets and derive features that are useful in function prediction are addressed. Both co-expression and abundance information is represented between and within experiments and investigated for correlation with function. It is found that features derived from expression data serve as a weak but significant signal for recognising functions. This signal is stronger for biological processes than molecular function categories and independent of homology information. The protein domain has historically been coined as a modular evolutionary unit of protein function. The occurrence of domains that can be linked by ancestral fusion events serves as a signal for domain-domain interactions. To exploit this information for function prediction, novel domain architecture and fused architecture scores are developed. Architecture scores rather than single domain scores correlate more strongly with function, and both architecture and fusion scores correlate more strongly with molecular functions than biological processes. The final study details the development of a novel heterogeneous function prediction approach designed to target the annotation of both homologous and non-homologous proteins. Support vector regression is used to combine pair-wise sequence features with expression scores and domain architecture scores to rank protein pairs in terms of their functional similarities. The target of the regression models represents the continuum of protein function space empirically derived from the Gene Ontology molecular function and biological process graphs. The merit and performance of the approach is demonstrated using homologous and non-homologous test datasets and significantly improves upon classical nearest neighbour annotation transfer by sequence methods. The final model represents a method that achieves a compromise between high specificity and sensitivity for all human proteins regardless of their homology status. It is expected that this strategy will allow for more comprehensive and accurate annotations of the human proteome

    Efficient algorithms for the realistic simulation of fluids

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    Nowadays there is great demand for realistic simulations in the computer graphics field. Physically-based animations are commonly used, and one of the more complex problems in this field is fluid simulation, more so if real-time applications are the goal. Videogames, in particular, resort to different techniques that, in order to represent fluids, just simulate the consequence and not the cause, using procedural or parametric methods and often discriminating the physical solution. This need motivates the present thesis, the interactive simulation of free-surface flows, usually liquids, which are the feature of interest in most common applications. Due to the complexity of fluid simulation, in order to achieve real-time framerates, we have resorted to use the high parallelism provided by actual consumer-level GPUs. The simulation algorithm, the Lattice Boltzmann Method, has been chosen accordingly due to its efficiency and the direct mapping to the hardware architecture because of its local operations. We have created two free-surface simulations in the GPU: one fully in 3D and another restricted only to the upper surface of a big bulk of fluid, limiting the simulation domain to 2D. We have extended the latter to track dry regions and is also coupled with obstacles in a geometry-independent fashion. As it is restricted to 2D, the simulation loses some features due to the impossibility of simulating vertical separation of the fluid. To account for this we have coupled the surface simulation to a generic particle system with breaking wave conditions; the simulations are totally independent and only the coupling binds the LBM with the chosen particle system. Furthermore, the visualization of both systems is also done in a realistic way within the interactive framerates; raycasting techniques are used to provide the expected light-related effects as refractions, reflections and caustics. Other techniques that improve the overall detail are also applied as low-level detail ripples and surface foam
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