Investigation of the Effects of Image Signal-to-Noise Ratio on TSPO PET Quantification of Neuroinflammation

Neuroinflammation may be imaged using positron emission tomography (PET) and the tracer [11C]-PK11195. Accurate and precise quantification of 18 kilodalton Translocator Protein (TSPO) binding parameters in the brain has proven difficult with this tracer, due to an unfavourable combination of low target concentration in tissue, low brain uptake of the tracer and relatively high non-specific binding, all of which leads to higher levels of relative image noise. To address these limitations, research into new radioligands for the TSPO, with higher brain uptake and lower non-specific binding relative to [11C]-PK11195, is being conducted world-wide. However, factors other than radioligand properties are known to influence signal-to-noise ratio in quantitative PET studies, including the scanner sensitivity, image reconstruction algorithms and data analysis methodology. The aim of this thesis was to investigate and validate computational tools for predicting image noise in dynamic TSPO PET studies, and to employ those tools to investigate the factors that affect image SNR and reliability of TSPO quantification in the human brain. The feasibility of performing multiple (n≥40) independent Monte Carlo simulations for each dynamic [11C]-PK11195 frame- with realistic modelling of the radioactivity source, attenuation and PET tomograph geometries- was investigated. A Beowulf-type high performance computer cluster, constructed from commodity components, was found to be well suited to this task. Timing tests on a single desktop computer system indicated that a computer cluster capable of simulating an hour-long dynamic [11C]-PK11195 PET scan, with 40 independent repeats, and with a total simulation time of less than 6 weeks, could be constructed for less than 10,000 Australian dollars. A computer cluster containing 44 computing cores was therefore assembled, and a peak simulation rate of 2.84x105 photon pairs per second was achieved using the GEANT4 Application for Tomographic Emission (GATE) Monte Carlo simulation software. A simulated PET tomograph was developed in GATE that closely modelled the performance characteristics of several real-world clinical PET systems in terms of spatial resolution, sensitivity, scatter fraction and counting rate performance. The simulated PET system was validated using adaptations of the National Electrical Manufacturers Association (NEMA) quality assurance procedures within GATE. Image noise in dynamic TSPO PET scans was estimated by performing n=40 independent Monte Carlo simulations of an hour-long [11C]-PK11195 scan, and of an hour- long dynamic scan for a hypothetical TSPO ligand with double the brain activity concentration of [11C]-PK11195. From these data an analytical noise model was developed that allowed image noise to be predicted for any combination of brain tissue activity concentration and scan duration. The noise model was validated for the purpose of determining the precision of kinetic parameter estimates for TSPO PET. An investigation was made into the effects of activity concentration in tissue, radionuclide half-life, injected dose and compartmental model complexity on the reproducibility of kinetic parameters. Injecting 555 MBq of carbon-11 labelled TSPO tracer produced similar binding parameter precision to 185 MBq of fluorine-18, and a moderate (20%) reduction in precision was observed for the reduced carbon-11 dose of 370 MBq. Results indicated that a factor of 2 increase in frame count level (relative to [11C]-PK11195, and due for example to higher ligand uptake, injected dose or absolute scanner sensitivity) is required to obtain reliable binding parameter estimates for small regions of interest when fitting a two-tissue compartment, four-parameter compartmental model. However, compartmental model complexity had a similarly large effect, with the reduction of model complexity from the two-tissue compartment, four-parameter to a one-tissue compartment, two-parameter model producing a 78% reduction in coefficient of variation of the binding parameter estimates at each tissue activity level and region size studied. In summary, this thesis describes the development and validation of Monte Carlo methods for estimating image noise in dynamic TSPO PET scans, and analytical methods for predicting relative image noise for a wide range of tissue activity concentration and acquisition durations. The findings of this research suggest that a broader consideration of the kinetic properties of novel TSPO radioligands, with a view to selection of ligands that are potentially amenable to analysis with a simple one-tissue compartment model, is at least as important as efforts directed towards reducing image noise, such as higher brain uptake, in the search for the next generation of TSPO PET tracers

Spectral Line Removal in the LIGO Data Analysis System (LDAS)

High power in narrow frequency bands, spectral lines, are a feature of an interferometric gravitational wave detector's output. Some lines are coherent between interferometers, in particular, the 2 km and 4 km LIGO Hanford instruments. This is of concern to data analysis techniques, such as the stochastic background search, that use correlations between instruments to detect gravitational radiation. Several techniques of `line removal' have been proposed. Where a line is attributable to a measurable environmental disturbance, a simple linear model may be fitted to predict, and subsequently subtract away, that line. This technique has been implemented (as the command oelslr) in the LIGO Data Analysis System (LDAS). We demonstrate its application to LIGO S1 data.Comment: 11 pages, 5 figures, to be published in CQG GWDAW02 proceeding

Energy spectrum of turbulent fluctuations in boundary driven reduced magnetohydrodynamics

The nonlinear dynamics of a bundle of magnetic flux ropes driven by stationary fluid motions at their endpoints is studied, by performing numerical simulations of the magnetohydrodynamic (MHD) equations. The development of MHD turbulence is shown, where the system reaches a state that is characterized by the ratio between the Alfven time (the time for incompressible MHD waves to travel along the field lines) and the convective time scale of the driving motions. This ratio of time scales determines the energy spectra and the relaxation toward different regimes ranging from weak to strong turbulence. A connection is made with phenomenological theories for the energy spectra in MHD turbulence.Comment: Published in Physics of Plasma

Job scheduling considering best-effort and soft real-time applications on non-dedicated clusters

As Network Of Workstations (NOWs) emerge as a viable platform for a wide range of workloads, new scheduling approaches are needed to allocate the collection of resources from competing applications. New workload types introduce high uncertainty into the predictability of the system, hindering the applicability of the job scheduling strategies. A new kind of parallel applications has appeared in business or scientific domains, namely Soft Real-Time (SRT). They, together with new SRT desktop applications, turn prediction into a more difficult goal by adding inherent complexity to estimation procedures. In previous work, we introduced an estimation engine into our job scheduling system, termed CISNE. In this work, the estimation engine is extended, by adding two new kernels, both SRT aware. Experimental results confirm the better performance of simulated respect to the analytical kernels and show a maximum average prediction error deviation of 20%.Mientras las Redes de Estaciones de Trabajo (NOWs) emergen como una plataforma viable para un amplio espectro de aplicaciones, son necesarios nuevos enfoques para planificar los recursos disponibles entre las aplicaciones que compiten por ellos. Los nuevos tipos de cargas introducen una alta incertidumbre en la predictibilidad del sistema, afectando la aplicabilidad de las estrategias de planificación de tareas. Un nuevo tipo de aplicaciones paralelas, denominado tiempo real débil (SRT), ha aparecido tanto en los ámbitos comerciales como científicos. Las nuevas aplicaciones paralelas SRT, conjuntamente con los nuevos tipos de aplicaciones SRT de escritorio, convierten la predicción en una meta aún más difícil, al agregar complejidad a los procedimientos de estimación. En trabajos anteriores dotamos al sistema CISNE de un motor de estimación. En este trabajo añadimos al sistema de predicción fuera de línea dos nuevos núcleos de estimación con capacidad SRT. Los resultados experimentales muestran un mejor rendimiento del núcleo simulado con respecto a su homólogo analítico, mostrando un promedio de desviación máximo del 20%.VIII Workshop de Procesamiento Distribuido y ParaleloRed de Universidades con Carreras en Informática (RedUNCI

Enhancing reliability with Latin Square redundancy on desktop grids.

Computational grids are some of the largest computer systems in existence today. Unfortunately they are also, in many cases, the least reliable. This research examines the use of redundancy with permutation as a method of improving reliability in computational grid applications. Three primary avenues are explored - development of a new redundancy model, the Replication and Permutation Paradigm (RPP) for computational grids, development of grid simulation software for testing RPP against other redundancy methods and, finally, running a program on a live grid using RPP. An important part of RPP involves distributing data and tasks across the grid in Latin Square fashion. Two theorems and subsequent proofs regarding Latin Squares are developed. The theorems describe the changing position of symbols between the rows of a standard Latin Square. When a symbol is missing because a column is removed the theorems provide a basis for determining the next row and column where the missing symbol can be found. Interesting in their own right, the theorems have implications for redundancy. In terms of the redundancy model, the theorems allow one to state the maximum makespan in the face of missing computational hosts when using Latin Square redundancy. The simulator software was developed and used to compare different data and task distribution schemes on a simulated grid. The software clearly showed the advantage of running RPP, which resulted in faster completion times in the face of computational host failures. The Latin Square method also fails gracefully in that jobs complete with massive node failure while increasing makespan. Finally an Inductive Logic Program (ILP) for pharmacophore search was executed, using a Latin Square redundancy methodology, on a Condor grid in the Dahlem Lab at the University of Louisville Speed School of Engineering. All jobs completed, even in the face of large numbers of randomly generated computational host failures

The doctoral research abstracts. Vol:7 2015 / Institute of Graduate Studies, UiTM

Foreword: The Seventh Issue of The Doctoral Research Abstracts captures the novelty of 65 doctorates receiving their scrolls in UiTM’s 82nd Convocation in the field of Science and Technology, Business and Administration, and Social Science and Humanities. To the recipients I would like to say that you have most certainly done UiTM proud by journeying through the scholastic path with its endless challenges and impediments, and persevering right till the very end. This convocation should not be regarded as the end of your highest scholarly achievement and contribution to the body of knowledge but rather as the beginning of embarking into high impact innovative research for the community and country from knowledge gained during this academic journey. As alumni of UiTM, we will always hold you dear to our hearts. A new ‘handshake’ is about to take place between you and UiTM as joint collaborators in future research undertakings. I envisioned a strong research pact between you as our alumni and UiTM in breaking the frontier of knowledge through research. I wish you all the best in your endeavour and may I offer my congratulations to all the graduands. ‘UiTM sentiasa dihati ku’ / Tan Sri Dato’ Sri Prof Ir Dr Sahol Hamid Abu Bakar , FASc, PEng Vice Chancellor Universiti Teknologi MAR

Performance modelling, analysis and prediction of Spark jobs in Hadoop cluster : a thesis by publications presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Computer Science, School of Mathematical & Computational Sciences, Massey University, Auckland, New Zealand

Big Data frameworks have received tremendous attention from the industry and from academic research over the past decade. The advent of distributed computing frameworks such as Hadoop MapReduce and Spark are powerful frameworks that offer an efficient solution for analysing large-scale datasets running under the Hadoop cluster. Spark has been established as one of the most popular large-scale data processing engines because of its speed, low latency in-memory computation, and advanced analytics. Spark computational performance heavily depends on the selection of suitable parameters, and the configuration of these parameters is a challenging task. Although Spark has default parameters and can deploy applications without much effort, a significant drawback of default parameter selection is that it is not always the best for cluster performance. A major limitation for Spark performance prediction using existing models is that it requires either large input data or system configuration that is time-consuming. Therefore, an analytical model could be a better solution for performance prediction and for establishing appropriate job configurations. This thesis proposes two distinct parallelisation models for performance prediction: the 2D-Plate model and the Fully-Connected Node model. Both models were constructed based on serial boundaries for a certain arrangement of executors and size of the data. In order to evaluate the cluster performance, various HiBench workloads were used, and workload’s empirical data were fitted with the models for performance prediction analysis. The developed models were benchmarked with the existing models such as Amdahl’s, Gustafson, ERNEST, and machine learning. Our experimental results show that the two proposed models can quickly and accurately predict performance in terms of runtime, and they can outperform the accuracy of machine learning models when extrapolating predictions

Dynamically adaptive partition-based interest management in distributed simulation

Performance and scalability of distributed simulations depends primarily on the effectiveness of the employed interest management (IM) schema that aims at reducing the overall computational and messaging effort on the shared data to a necessary minimum. Existing IM approaches, which are based on variations or combinations of two principle data distribution techniques, namely region-based and grid-based techniques, perform poorly if the simulation develops an overloaded host. In order to facilitate distributing the processing load from overloaded areas of the shared data to less loaded hosts, the partition-based technique is introduced that allows for variable-size partitioning the shared data. Based on this data distribution technique, an IM approach is sketched that is dynamically adaptive to access latencies of simulation objects on the shared data as well as to the physical location of the objects. Since this re-distribution is decided depending on the messaging effort of the simulation objects for updating data partitions, any load balanced constellation has the additional advantage to be of minimal overall messaging effort. Hence, the IM schema dynamically resolves messaging overloading as well as overloading of hosts with simulation objects and therefore facilitates dynamic system scalability

DF 2.0: An Automated, Privacy Preserving, and Efficient Digital Forensic Framework That Leverages Machine Learning for Evidence Prediction and Privacy Evaluation

The current state of digital forensic investigation is continuously challenged by the rapid technological changes, the increase in the use of digital devices (both the heterogeneity and the count), and the sheer volume of data that these devices could contain. Although data privacy protection is not a performance measure, however, preventing privacy violations during the digital forensic investigation, is also a big challenge. With a perception that the completeness of investigation and the data privacy preservation are incompatible with each other, the researchers have provided solutions to address the above-stated challenges that either focus on the effectiveness of the investigation process or the data privacy preservation. However, a comprehensive approach that preserves data privacy without affecting the capabilities of the investigator or the overall efficiency of the investigation process is still an open problem. In the current work, the authors have proposed a digital forensic framework that uses case information, case profile data and expert knowledge for automation of the digital forensic analysis process; utilizes machine learning for finding most relevant pieces of evidence; and maintains data privacy of non-evidential private files. All these operations are coordinated in a way that the overall efficiency of the digital forensic investigation process increases while the integrity and admissibility of the evidence remain intact. The framework improves validation which boosts transparency in the investigation process. The framework also achieves a higher level of accountability by securely logging the investigation steps. As the proposed solution introduces notable enhancements to the current investigative practices more like the next version of Digital Forensics, the authors have named the framework `Digital Forensics 2.0\u27, or `DF 2.0\u27 in short