Stochastic Optimisation Methods Applied to PET Image Reconstruction

Positron Emission Tomography (PET) is a medical imaging technique that is used to pro- vide functional information regarding physiological processes. Statistical PET reconstruc- tion attempts to estimate the distribution of radiotracer in the body but this methodology is generally computationally demanding because of the use of iterative algorithms. These algorithms are often accelerated by the utilisation of data subsets, which may result in con- vergence to a limit set rather than the unique solution. Methods exist to relax the update step sizes of subset algorithms but they introduce additional heuristic parameters that may result in extended reconstruction times. This work investigates novel methods to modify subset algorithms to converge to the unique solution while maintaining the acceleration benefits of subset methods. This work begins with a study of an automatic method for increasing subset sizes, called AutoSubsets. This algorithm measures the divergence between two distinct data subset update directions and, if significant, the subset size is increased for future updates. The algorithm is evaluated using both projection and list mode data. The algorithm’s use of small initial subsets benefits early reconstruction but unfortunately, at later updates, the subsets size increases too early, which impedes convergence rates. The main part of this work investigates the application of stochastic variance reduction optimisation algorithms to PET image reconstruction. These algorithms reduce variance due to the use of subsets by incorporating previously computed subset gradients into the update direction. The algorithms are adapted for the application to PET reconstruction. This study evaluates the reconstruction performance of these algorithms when applied to various 3D non-TOF PET simulated, phantom and patient data sets. The impact of a number of algorithm parameters are explored, which includes: subset selection methodologies, the number of subsets, step size methodologies and preconditioners. The results indicate that these stochastic variance reduction algorithms demonstrate superior performance after only a few epochs when compared to a standard PET reconstruction algorithm

Tracking ancient beach-lines inland: 2600-year-old dentate-stamped ceramics at Hopo, Vailala River region, Papua New Guinea

The Lapita expansion took Austronesian seafaring peoples with distinctive pottery eastward from the Bismarck Archipelago to western Polynesia during the late second millennium BC, marking the first stage in the settlement of Oceania. Here it is shown that a parallel process also carried Lapita pottery and people many hundreds of kilometres westward along the southern shore of Papua New Guinea. The key site is Hopo, now 4.5km inland owing to the progradation of coastal sand dunes, but originally on the sea edge. Pottery and radiocarbon dates indicate Lapita settlement in this location c.600 BC, and suggest that the long-distance maritime networks linking the entire southern coast of Papua New Guinea in historical times may trace their origin to this period

Kumukumu 1, a hilltop site in the Aird Hills: Implications for occupational trends and dynamics in the Kikori River delta, south coast of Papua New Guinea

We report on archaeological excavations undertaken at Kumukumu 1 atop the dense rainforest-clad Aird Hills of the Kikori river delta islands, south coast of Papua New Guinea. Results indicate exploitation of the nearby environment, including the gathering of some 200 million shellfish from riverine habitats at the base of the hill some 600 years ago, and deposition of shell remains onto hilltop middens. We ask what the implications of such a site in a defensive location on the upper, steep hillslope of Kumukumu hill are for regional occupation and dynamics. We conclude that the hinterland-marine fringe islands of the river deltas that include the site of Kumukumu 1 were especially sensitive to heightened cross-cultural influences and inter-group raids and competition, leading to accelerated processes of centralisation and aggrandisement among some groups, and the subjugation, fragmentation and dispersal of less powerful neighbouring groups

Delay Discounting is Associated with Treatment Response among Cocaine-Dependent Outpatients

Rationale—Delay discounting (DD) describes the rate at which reinforcers lose value as the temporal delay to their receipt increases. Steeper discounting has been positively associated with vulnerability to substance use disorders, including cocaine use disorders. Objectives—In the present study, we examined whether DD of hypothetical monetary reinforcers is associated with the duration of cocaine abstinence achieved among cocainedependent outpatients. Methods—Participants were 36 adults who were participating in a randomized controlled trial examining the efficacy of voucher-based contingency management (CM) using low-magnitude (N = 18) or high-magnitude (N = 18) voucher monetary values. Results—DD was associated with the number of continuous weeks of cocaine abstinence achieved, even after adjusting for treatment condition during the initial 12-week (t(33) = 2.48, p = .045) and entire recommended 24-week of treatment (t(33) = 2.40, p = .022). Participants who exhibited steeper discounting functions achieved shorter periods of abstinence in the Lowmagnitude voucher condition (12-week: t(16) = 2.48, p = .025; 24-week: t(16) = 2.68, p = .017), but not in the High-magnitude voucher condition (12-week: t(16) = 0.51, p = .618; 24-week: t(16) = 1.08, p = .298), although the interaction between DD and treatment condition was not significant (12-week: t(32) = −1.12, p = .271; 24-week: t(32) = −0.37, p = .712). Conclusions—These results provide further evidence on associations between DD and treatment response and extend those observations to a new clinical population (i.e., cocainedependent outpatients), while also suggesting that a more intensive intervention like the Highmagnitude CM condition may diminish this negative relationship between DD and treatment response

Archaeological investigations at Waredaru and the origins of the Keipte Kuyumen clan estate, upper Kikori River, Papua New Guinea

In 2008-2009, the patriarch of the Keipte Kuyumen clan of the upper Kikori River near the Highlands foothills, Papua New Guinea, requested that archaeological excavations be undertaken at the site of Waredaru in a dense rainforest setting, an ancestral village only known from oral traditions. According to these oral traditions, Waredaru was a sago adze-head (‘sago-pounder’) manufacturing centre, and it is at this village that the Keipte Kuyumen underwent an important ceremony by which they obtained their clan lands. This paper reports on these archaeological excavations, enabling the rare dating of the origins of the Keipte Kuyumen as a landed social group

Recruitment and Retention Strategies for a Community-Based Weight Management Study for Multi-Ethnic Elementary School Children and Their Parents

This paper describes successful recruitment and retention strategies for a community-based weight management study in two school districts in North Carolina. Recruitment and retention on both district and school levels and child and parent levels are discussed

Epidemiological Interactions between Urogenital and Intestinal Human Schistosomiasis in the Context of Praziquantel Treatment across Three West African Countries

© 2015 Knowles et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN