Semi-automatic selection of summary statistics for ABC model choice

A central statistical goal is to choose between alternative explanatory models of data. In many modern applications, such as population genetics, it is not possible to apply standard methods based on evaluating the likelihood functions of the models, as these are numerically intractable. Approximate Bayesian computation (ABC) is a commonly used alternative for such situations. ABC simulates data x for many parameter values under each model, which is compared to the observed data xobs. More weight is placed on models under which S(x) is close to S(xobs), where S maps data to a vector of summary statistics. Previous work has shown the choice of S is crucial to the efficiency and accuracy of ABC. This paper provides a method to select good summary statistics for model choice. It uses a preliminary step, simulating many x values from all models and fitting regressions to this with the model as response. The resulting model weight estimators are used as S in an ABC analysis. Theoretical results are given to justify this as approximating low dimensional sufficient statistics. A substantive application is presented: choosing between competing coalescent models of demographic growth for Campylobacter jejuni in New Zealand using multi-locus sequence typing data

Primary Circulating Prostate Cells Are Not Detected in Men with Low Grade Small Volume Prostate Cancer

Objective. To determine if primary circulating prostate cells (CPCs) are found in all men with prostate cancer. Methods and Patients. A prospective study, to analyze all men with an elevated PSA between 4.0 and 10.0 ng/mL undergoing initial biopsy. Primary CPCs were obtained by differential gel centrifugation and detected using standard immunocytochemistry using anti-PSA; positive samples underwent a second process with anti-P504S. A malignant primary CPC was defined as PSA (+) P504S (+) and a test positive if 1 cell/4 mL was detected. Biopsy results were registered as cancer/no-cancer, number of cores positive, and percent infiltration of the cores. Results. 328/1123 (29.2%) of the study population had prostate cancer diagnosed on initial biopsy, and 42/328 (12.8%) were negative for primary CPCs. CPC negative men were significantly older, and had lower PSA levels, lower Gleason scores, and fewer positive cores and with infiltration by the cancer. 38/42 (91%) of CPC negative men complied with the criteria for active surveillance in comparison with 34/286 (12%) of CPC positive men. Conclusions. Using primary CPC detection as a sequential test to select men with an elevated PSA for biopsy, the risk of missing clinically significant prostate cancer is minimal when the patient is primary CPC negative; less than 0.5% of all primary CPC negative men had a clinically significant prostate cancer

Research priorities in children and adults with congenital heart disease: a James Lind Alliance Priority Setting Partnership

Objective To bring together patients, parents, charities and clinicians in a Priority Setting Partnership to establish national clinical priorities for research in children and adults with congenital heart disease. Methods The established James Lind Alliance methodology was used to identify and prioritise research on the management of congenital heart disease, focusing on diagnosis, treatment and outcomes. An initial open survey was used to gather potential uncertainties which were filtered, categorised, converted into summary questions and checked against current evidence. In a second survey, respondents identified the unanswered questions most important to them. At two final workshops, patients, parents, charities and healthcare professionals agreed the top 10 lists of priorities for child/antenatal and adult congenital heart disease research. Results 524 respondents submitted 1373 individual questions, from which 313 out of scope or duplicate questions were removed. The remaining 1060 questions were distilled into summary questions and checked against existing literature, with only three questions deemed entirely answered and removed. 250 respondents completed the child/antenatal survey (56 uncertainties) and 252 completed the adult survey (47 uncertainties). The questions ranked the highest by clinicians and non-clinicians were taken forward to consensus workshops, where two sets of top 10 research priorities were agreed. Conclusions Through an established and equitable process, we determined national clinical priorities for congenital heart disease research. These will be taken forward by specific working groups, a national patient and public involvement group, and through the establishment of a UK and Ireland network for collaborative, multicentre clinical trials in congenital heart disease

Selective small molecule inhibitors of glycogen synthase kinase-3 modulate glycogen metabolism and gene transcription

AbstractBackground: Glycogen synthase kinase-3 (GSK-3) is a serine/threonine protein kinase, the activity of which is inhibited by a variety of extracellular stimuli including insulin, growth factors, cell specification factors and cell adhesion. Consequently, inhibition of GSK-3 activity has been proposed to play a role in the regulation of numerous signalling pathways that elicit pleiotropic cellular responses. This report describes the identification and characterisation of potent and selective small molecule inhibitors of GSK-3.Results: SB-216763 and SB-415286 are structurally distinct maleimides that inhibit GSK-3α in vitro, with Kis of 9 nM and 31 nM respectively, in an ATP competitive manner. These compounds inhibited GSK-3β with similar potency. However, neither compound significantly inhibited any member of a panel of 24 other protein kinases. Furthermore, treatment of cells with either compound stimulated responses characteristic of extracellular stimuli that are known to inhibit GSK-3 activity. Thus, SB-216763 and SB-415286 stimulated glycogen synthesis in human liver cells and induced expression of a β-catenin-LEF/TCF regulated reporter gene in HEK293 cells. In both cases, compound treatment was demonstrated to inhibit cellular GSK-3 activity as assessed by activation of glycogen synthase, which is a direct target of this kinase.Conclusions: SB-216763 and SB-415286 are novel, potent and selective cell permeable inhibitors of GSK-3. Therefore, these compounds represent valuable pharmacological tools with which the role of GSK-3 in cellular signalling can be further elucidated. Furthermore, development of similar compounds may be of use therapeutically in disease states associated with elevated GSK-3 activity such as non-insulin dependent diabetes mellitus and neurodegenerative disease