A parallel neuroscale implementation using C++ and MPI

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Holocene experiment with coupled atmosphere-ocean-model ECHAM5/MPI-OM

Changes in the Earth's orbit lead to changes in the seasonal and meridional distribution of insolation. We quantify the influence of orbitally induced changes on the seasonal temperature cycle in a transient simulation of the last 6000 years - from the mid-Holocene to today - using a coupled atmosphere-ocean general circulation model (ECHAM5/MPI-OM) including a land surface model (JSBACH). The seasonal temperature cycle responds directly to the insolation changes almost everywhere. In the Northern Hemisphere, its amplitude decreases according to an increase in winter insolation and a decrease in summer insolation. In the Southern Hemisphere, the opposite is true. Over the Arctic Ocean, decreasing summer insolation leads to an increase in sea-ice cover. The insulating effect of sea ice between the ocean and the atmosphere leads to decreasing heat flux and favors more "continental" conditions over the Arctic Ocean in winter, resulting in strongly decreasing temperatures. Consequently, there are two competing effects: the direct response to insolation changes and a sea-ice insulation effect. The sea-ice insulation effect is stronger, and thus an increase in the amplitude of the seasonal temperature cycle over the Arctic Ocean occurs. This increase is strongest over the Barents Shelf and influences the temperature response over northern Europe. We compare our modeled seasonal temperatures over Europe to paleo reconstructions. We find better agreements in winter temperatures than in summer temperatures and better agreements in northern Europe than in southern Europe, since the model does not reproduce the southern European Holocene summer cooling inferred from the paleo reconstructions. The temperature reconstructions for northern Europe support the notion of the influence of the sea-ice insulation effect on the evolution of the seasonal temperature cycle.

Quantifying subclinical central nervous lesions in primary antiphospholipid syndrome: The role of magnetization transfer imaging

Purpose: To define the role of magnetization transfer imaging (MTI) in detecting subclinical central nervous system (CNS) lesions in primary antiphospholipid syndrome (PAPS). Materials and Methods: Ten non-CNS PAPS patients were compared to 10 CNS PAPS patients and 10 age- and sex-matched controls. All PAPS patients met Sapporo criteria. All Subjects underwent conventional MRI and complementary MTI analysis to compose histograms. CNS viability was determined according to the magnetization transfer ratio (MTR) by mean pixel intensity (MPI) and the mean peak height (MPH). Volumetric cerebral measurements were assessed by brain parenchyma factor (BPF) and total/cerebral volume. Results: MTR histograms analysis revealed that MPI was significantly different among groups (P < 0.0001). Non-CNS PAPS had a higher MPI than CNS PAPS, (30.5 +/- 1.01 vs. 25.1 +/- 3.17 percent unit (pu); P < 0.05) although lower than controls (30.5 +/- 1.01 vs. 31.20 < 0.50 pu; P < 0.05). MPH in non-CNS PAPS (5.57 +/- 0.20% (1/pu)} was similar to controls (5.63 +/- 0.20% (1/pu), P > 0.05) and higher than CNS PAPS (4.71 +/- 0.30% (1/pu), P < 0.05). A higher peak location (PL) was also observed in the CNS PAPS group in comparison with the other groups (P < 0.0001). In addition, a lower BPF was found in non-CNS PAPS compared to controls (0.80 +/- 0.03 vs. 0.84 +/- 0.02 units; P < 0.05) but similar to CNS PAPS (0.80 +/- 0.03 vs. 0.79 +/- 0.05 units; P > 0.05). Conclusion: Our findings suggest that non-CNS PAPS patients have subclinical cerebral damage. The long-term-clinical relevance of MTI analysis in these patients needs to be defined by prospective studies.

Myocardial Perfusion Imaging Is a Strong Predictor of Death in Women

OBJECTIVES We sought to assess the prognostic value and risk classification improvement using contemporary single-photon emission computed tomography myocardial perfusion imaging (SPECT-MPI) to predict all-cause mortality. BACKGROUND Myocardial perfusion is a strong estimator of prognosis. Evidence published to date has not established the added prognostic value of SPECT-MPI nor defined an approach to detect improve classification of risk in women from a developing nation. METHODS A total of 2,225 women referred for SPECT-MPI were followed by a mean period of 3.7 +/- 1.4 years. SPECT-MPI results were classified as abnormal on the presence of any perfusion defect. Abnormal scans were further classified as with mild/moderate reversible, severe reversible, partial reversible, or fixed perfusion defects. Risk estimates for incident mortality were categorized as <1%/year, 1% to 2%/year, and >2%/year using Cox proportional hazard models. Risk-adjusted models incorporated clinical risk factors, left ventricular ejection fraction (LVEF), and perfusion variables. RESULTS All-cause death occurred in 139 patients. SPECT-MPI significantly risk stratified the population; patients with abnormal scans had significantly higher death rates compared with patients with normal scans, 13.1% versus 4.0%, respectively (p < 0.001). Cox analysis demonstrated that after adjusting for clinical risk factors and LVEF, SPECT-MPI improved the model discrimination (integrated discrimination index = 0.009; p = 0.02), added significant incremental prognostic information (global chi-square increased from 87.7 to 127.1; p < 0.0001), and improved risk prediction (net reclassification improvement = 0.12; p = 0.005). CONCLUSIONS SPECT-MPI added significant incremental prognostic information to clinical and left ventricular functional variables while enhancing the ability to classify this Brazilian female population into low-and high-risk categories of all-cause mortality. (J Am Coll Cardiol Img 2011;4:880-8) (C) 2011 by the American College of Cardiology Foundation

Clinical, Histological, and Microbiological Findings in Peri-Implant Disease: A Pilot Study

Objectives: This study is intended to verify the correlation among clinical indices of the peri-implant soft tissues, the histological condition and the presence of 3 pathogens commonly associated with peri-implant diseases (Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and Tannerella forsythia). Materials: Four clinical indices, Gingival Index (GI), Sulcus Bleeding Index, GI modified by Mombelli, and Plaque Index modified by Mombelli (mPI) were evaluated around I dental implant of each subject (n = 10). Subgingival plaque was collected for bacterial analysis (polymerase chain reaction) and a biopsy of peri-implant soft tissues for histological analysis was harvested. The clinical indices and detected pathogens correlated with a developed histological index (HI). Results: There was no statistically significant relationship between the clinical indices (GI, Sulcus Bleeding Index, and GI modified by Mombelli) and the HI, except for the mPI on the central area of lingual aspects (r = 0.85, P = 0.0029). There was a tendency for a positive correlation between the mPI on the central area of buccal aspects and the HI (r = 0.63, P = 0.0544). The counting of lymphocytes and plasmocytes correlated positively with 111, thus suggesting the index reliability. The prevalence of A. actinomycetemcomitans, P. gingivalis, and T. forsythia did not present a significant relationship with the HI. Conclusion: Despite the small number of samples and the poor statistical significance, the mPI seems to be useful for evaluation of inflammatory severity on soft tissue around dental implants as demonstrated by its relationship with the HI. Further studies are necessary to elucidate this subject. (Implant Dent 2009;18:334-344)

Modelo de especificação e controlo de execuções paralelas e distribuídas

O desenvolvimento actual de aplicações paralelas com processamento intensivo (HPC - High Performance Computing) para alojamento em computadores organizados em Cluster baseia-se muito no modelo de passagem de mensagens, do qual é de realçar os esforços de definição de standards, por exemplo, MPI - Message - Passing Interface. Por outro lado, com a generalização do paradigma de programação orientado aos objectos para ambientes distribuídos (Java RMI, .NET Remoting), existe a possibilidade de considerar que a execução de uma aplicação, de processamento paralelo e intensivo, pode ser decomposta em vários fluxos de execução paralela, em que cada fluxo é constituído por uma ou mais tarefas executadas no contexto de objectos distribuídos. Normalmente, em ambientes baseados em objectos distribuídos, a especificação, controlo e sincronização dos vários fluxos de execução paralela, é realizada de forma explicita e codificada num programa principal (hard-coded), dificultando possíveis e necessárias modificações posteriores. No entanto, existem, neste contexto, trabalhos que propõem uma abordagem de decomposição, seguindo o paradigma de workflow com interacções entre as tarefas por, entre outras, data-flow, control-flow, finite - state - machine. Este trabalho consistiu em propor e explorar um modelo de execução, sincronização e controlo de múltiplas tarefas, que permita de forma flexível desenhar aplicações de processamento intensivo, tirando partido da execução paralela de tarefas em diferentes máquinas. O modelo proposto e consequente implementação, num protótipo experimental, permite: especificar aplicações usando fluxos de execução; submeter fluxos para execução e controlar e monitorizar a execução desses fluxos. As tarefas envolvidas nos fluxos de execução podem executar-se num conjunto de recursos distribuídos. As principais características a realçar no modelo proposto, são a expansibilidade e o desacoplamento entre as diferentes componentes envolvidas na execução dos fluxos de execução. São ainda descritos casos de teste que permitiram validar o modelo e o protótipo implementado. Tendo consciência da necessidade de continuar no futuro esta linha de investigação, este trabalho é um contributo para demonstrar que o paradigma de workflow é adequado para expressar e executar, de forma paralela e distribuída, aplicações complexas de processamento intensivo.

Estudo da função sistólica do ventrículo direito por ecocardiografia transtorácica: relatório de projecto

Mestrado em Tecnologia de Diagnóstico e Intervenção Cardiovascular. Área de especialização - Ultrassonografia Cardiovascular

Influência de diferentes parâmetros na diminuição da atividade extra-miocárdica nos estudos Gated-SPECT

Introdução – A cintigrafia de perfusão do miocárdio (CPM) é um dos exames complementares de diagnóstico mais indicados na patologia cardiovascular. A atividade extramiocárdica é um problema recorrente na aquisição e avaliação da imagem. Parâmetros como o radiofármaco (RF) administrado, o tipo de esforço, a ingestão de alimentos, o posicionamento e o processamento de imagem influenciam a atividade extramiocárdica na CPM. O objetivo deste estudo é identificar o protocolo da CPM a nível nacional e avaliar a percentagem de repetições das aquisições provocadas por este problema. Metodologia – Para a realização deste estudo, a população selecionada foram os Serviços de Medicina Nuclear (SMN) em Portugal Continental. Foram analisados 15 questionários, respondidos pelos Técnicos Coordenadores dos vários SMN. Foi realizada a associação do comportamento das variáveis, através da estatística descritiva e do Coeficiente de Correlação de Spearman. Resultados – A percentagem de repetições é menor com o uso da 99mTecnécio(Tc)-Tetrofosmina, aquisição de imagens tardias, ingestão de diversos alimentos (água, leite, sumo, pão com manteiga) e com a correção de atenuação. Conclusão – Os resultados obtidos demonstram que a maioria das soluções aplicadas nos SMN resultam numa diminuição das repetições.

Analysing the usefulness of motion correction software in myocardial perfusion imaging

Introduction Myocardial Perfusion Imaging (MPI) is a very important tool in the assessment of Coronary Artery Disease ( CAD ) patient s and worldwide data demonstrate an increasingly wider use and clinical acceptance. Nevertheless, it is a complex process and it is quite vulnerable concerning the amount and type of possible artefacts, some of them affecting seriously the overall quality and the clinical utility of the obtained data. One of the most in convenient artefacts , but relatively frequent ( 20% of the cases ) , is relate d with patient motion during image acquisition . Mostly, in those situations, specific data is evaluated and a decisi on is made between A) accept the results as they are , consider ing that t he “noise” so introduced does not affect too seriously the final clinical information, or B) to repeat the acquisition process . Another possib ility could be to use the “ Motion Correcti on Software” provided within the software package included in any actual gamma camera. The aim of this study is to compare the quality of the final images , obtained after the application of motion correction software and after the repetition of image acqui sition. Material and Methods Thirty cases of MPI affected by Motion Artefacts and repeated , were used. A group of three, independent (blinded for the differences of origin) expert Nuclear Medicine Clinicians had been invited to evaluate the 30 sets of thre e images - one set for each patient - being ( A) original image , motion uncorrected , (B) original image, motion corrected, and (C) second acquisition image, without motion . The results so obtained were statistically analysed . Results and Conclusion Results obtained demonstrate that the use of the Motion Correction Software is useful essentiall y if the amplitude of movement is not too important (with this specific quantification found hard to define precisely , due to discrepancies between clinicians and other factors , namely between one to another brand); when that is not the case and the amplitude of movement is too important , the n the percentage of agreement between clinicians is much higher and the repetition of the examination is unanimously considered ind ispensable.

Machine Learning Algorithms at Myocardial Perfusion Imaging - a Preliminary Study

Introduction: A major focus of data mining process - especially machine learning researches - is to automatically learn to recognize complex patterns and help to take the adequate decisions strictly based on the acquired data. Since imaging techniques like MPI – Myocardial Perfusion Imaging on Nuclear Cardiology, can implicate a huge part of the daily workflow and generate gigabytes of data, there could be advantages on Computerized Analysis of data over Human Analysis: shorter time, homogeneity and consistency, automatic recording of analysis results, relatively inexpensive, etc.Objectives: The aim of this study relates with the evaluation of the efficacy of this methodology on the evaluation of MPI Stress studies and the process of decision taking concerning the continuation – or not – of the evaluation of each patient. It has been pursued has an objective to automatically classify a patient test in one of three groups: “Positive”, “Negative” and “Indeterminate”. “Positive” would directly follow to the Rest test part of the exam, the “Negative” would be directly exempted from continuation and only the “Indeterminate” group would deserve the clinician analysis, so allowing economy of clinician’s effort, increasing workflow fluidity at the technologist’s level and probably sparing time to patients. Methods: WEKA v3.6.2 open source software was used to make a comparative analysis of three WEKA algorithms (“OneR”, “J48” and “Naïve Bayes”) - on a retrospective study using the comparison with correspondent clinical results as reference, signed by nuclear cardiologist experts - on “SPECT Heart Dataset”, available on University of California – Irvine, at the Machine Learning Repository. For evaluation purposes, criteria as “Precision”, “Incorrectly Classified Instances” and “Receiver Operating Characteristics (ROC) Areas” were considered. Results: The interpretation of the data suggests that the Naïve Bayes algorithm has the best performance among the three previously selected algorithms. Conclusions: It is believed - and apparently supported by the findings - that machine learning algorithms could significantly assist, at an intermediary level, on the analysis of scintigraphic data obtained on MPI, namely after Stress acquisition, so eventually increasing efficiency of the entire system and potentially easing both roles of Technologists and Nuclear Cardiologists. In the actual continuation of this study, it is planned to use more patient information and significantly increase the population under study, in order to allow improving system accuracy.

Avaliação da influência dos estímulos alimentares na actividade extracardíaca

Mestrado em Medicina Nuclear - Ramo de especialização: Radiofarmácia

A framework for the development of parallel and distributed real-time embedded systems

Embedded real-time applications increasingly present high computation requirements, which need to be completed within specific deadlines, but that present highly variable patterns, depending on the set of data available in a determined instant. The current trend to provide parallel processing in the embedded domain allows providing higher processing power; however, it does not address the variability in the processing pattern. Dimensioning each device for its worst-case scenario implies lower average utilization, and increased available, but unusable, processing in the overall system. A solution for this problem is to extend the parallel execution of the applications, allowing networked nodes to distribute the workload, on peak situations, to neighbour nodes. In this context, this report proposes a framework to develop parallel and distributed real-time embedded applications, transparently using OpenMP and Message Passing Interface (MPI), within a programming model based on OpenMP. The technical report also devises an integrated timing model, which enables the structured reasoning on the timing behaviour of these hybrid architectures.