A Bayesian hierarchical approach for multiple outcomes in routinely collected healthcare data

Clinical trials are the standard approach for evaluating new treatments, but may lack the power to assess rare outcomes. Trial results are also necessarily restricted to the population considered in the study. The availability of routinely collected healthcare data provides a source of information on the performance of treatments beyond that offered by clinical trials, but the analysis of this type of data presents a number of challenges. Hierarchical methods, which take advantage of known relationships between clinical outcomes, while accounting for bias, may be a suitable statistical approach for the analysis of this data. A study of direct oral anticoagulants in Scotland is discussed and used to motivate a modeling approach. A Bayesian hierarchical model, which allows a stratification of the population into clusters with similar characteristics, is proposed and applied to the direct oral anticoagulant study data. A simulation study is used to assess its performance in terms of outcome detection and error rates

Ablative therapy for people with localised prostate cancer: a systematic review and economic evaluation

© Queen’s Printer and Controller of HMSO 2015.Background People diagnosed with cancer of the prostate, a sex gland in the pelvis, have a choice of treatment options depending on the severity of disease. For people whose cancer is at medium and low risk of spread, the main options are surgical removal of the prostate, radical prostatectomy (RP), use of external beam radiotherapy (EBRT) to destroy the cancer or delaying treatment until there are signs that the cancer is getting worse [active surveillance (AS)]. RP and radiotherapy are effective at curing the cancer but may also cause long-term urinary incontinence and sexual problems. AS, on the other hand, may be quite difficult for people to cope with as they know that the cancer is still present. Newer treatments aim to target the disease more precisely so that surrounding normal tissues can be preserved, reducing the risk of side effects but still effectively destroying the cancer. These more targeted ablative therapies include cryotherapy, high-intensity focused ultrasound (HIFU), brachytherapy, photodynamic therapy (PDT), radiofrequency interstitial tumour ablation (RITA) and laser therapy, among others. Aims This study aimed to develop clinical care pathways relevant to a UK NHS context review systematically the evidence of the clinical effectiveness and safety of each newer ablative therapy concerning primary and salvage treatment of localised prostate cancer• determine which therapies are most likely to be cost-effective for implementation in the UK NHS identify and prioritise future research needs. Methods Clinical effectiveness review We conducted two discrete systematic reviews: (a) primary ablative treatment of localised prostate cancer compared with AS, RP or EBRT (b) salvage ablative treatment for local prostate cancer relapse after primary EBRT compared with salvage RP. MEDLINE, MEDLINE In-Process & Other Non-Indexed Citations, EMBASE, Bioscience Information Service (BIOSIS), Science Citation Index, Cochrane Central Register of Controlled Trials (CENTRAL), Cochrane Database of Systematic Reviews (CDSR), Database of Abstracts of Reviews of Effects (DARE) and the Health Technology Assessment (HTA) databases were searched to the end of March 2013. Reference lists of all included studies were scanned and experts on our advisory panel were contacted for details of additional reports. Evidence came from randomised controlled trials (RCTs), non-randomised comparative studies (NRCSs) (if no RCT evidence was identified) and single-arm cohort studies (case series) with greater than 10 participants for the ablative procedures only. Conference abstracts or non-English-language reports were excluded. For the primary therapy systematic review, the ablative therapies considered were cryotherapy, HIFU, PDT, RITA, laser ablation and brachytherapy. The comparators were AS, RP and EBRT. For the salvage therapy systematic review, the ablative therapies considered were cryotherapy and HIFU. The comparator was RP. Outcomes were cancer related, adverse effects (functional and procedural) and quality of life. Two reviewers extracted data and carried out quality assessment. For meta-analysis, a Bayesian indirect mixed-treatment comparison was used. Cost-effectiveness The cost-effectiveness of the different treatments and their subsequent care pathways was assessed using a modified Markov individual simulation model, applied to a UK NHS setting. The perspective for the model was a health services perspective. Parameter estimates were derived from the systematic review of clinical effectiveness, a micro-costing exercise, other literature, the expert advisory group and other UK sources. The outputs of the model were costs and quality-adjusted life-years (QALYs) for each procedure, incremental costs and QALYs and incremental cost per QALY over the remaining lifetime. Both costs and QALYs were discounted at 3.5%. An elasticity analysis, together with probabilistic and deterministic sensitivity analyses, were performed to explore the uncertainty surrounding parameter estimates. Results Clinical effectiveness Cryotherapy Data from 3995 patients who received cryotherapy across 19 studies (1 RCT, 4 NRCSs and 14 case series) were included, with most studies considered to be at high risk of bias. In the short term, there was conflicting evidence relating to cancer-specific outcomes when cryotherapy was compared with either EBRT or surgery. The only finding that reached statistical significance was 1-year disease-free survival, which was worse for cryotherapy than for either EBRT or RP. However, none of the other cancer-specific outcomes, such as biochemical failure or overall survival, showed any significant differences between them. The findings in relation to cancer-specific outcomes are best regarded as inconclusive. There was evidence that the rate of urinary incontinence at 1 year was lower for people undergoing cryotherapy than for those undergoing RP [3% vs. 66%; odds ratio (OR) 0.02, 95% credible interval (CrI) < 0.01 to 0.34], but the size of the difference decreased with longer follow-up. There was a general trend for cryotherapy to have fewer procedural complications, apart from urinary retention. The only difference that reached statistical significance was for urethral stricture, which was less frequent after cryotherapy than after RP (1% vs. 8%; OR 0.24, 95% CrI 0.09 to 0.54). High-intensity focused ultrasound Data from 4000 patients who received HIFU across 21 studies (1 NRCS and 20 case series) were included, with all studies considered to be at high risk of bias. There was some evidence that biochemical failure rates were higher at 1 year when using HIFU than when using EBRT, and this was statistically significant. However, the difference was no longer statistically significant at 5 years. Similar findings were observed with regard to disease-free survival at 1 year, with worse outcomes for HIFU than for EBRT, which were statistically significant. The differences were no longer significant at 3 years. The biochemical result was in contrast to overall survival at 4 years, which was higher when using HIFU. There were insufficient data on any urinary incontinence, erectile dysfunction or bowel problems to draw any robust conclusions, although at 1 year HIFU had lower incontinence rates than RP (10% vs. 66%; OR 0.06, 95% CrI 0.01 to 0.48). The safety profile for HIFU was generally good, apart from a potential numerical increase in rates of urinary retention and dysuria. However, HIFU appeared to have a slightly higher incidence of urethral stricture than EBRT, and the difference was statistically significant (8% vs. 1%; OR 5.8, 95% CrI 1.2 to 24.5). Brachytherapy This review considered data from 26,129 patients who received brachytherapy across 40 studies (2 RCTs and 38 NRCSs), with most studies considered to be at high risk of bias. The data for brachytherapy were generally more robust than for other ablative therapies. In the short term, there was some evidence at 5-year follow-up that the rate of biochemical failure was lower for brachytherapy (7%) than for EBRT (13%; OR 0.46, 95% CrI 0.32 to 0.67) or RP (11%; OR 0.35, 95% CrI 0.21 to 0.56). There was also some evidence that disease-free survival was better for brachytherapy at 3-year follow-up. There was evidence that the rate of urinary incontinence up to 5 years after treatment was lower for people undergoing brachytherapy than for RP, but the size of the difference decreased with longer follow-up. There was also a trend towards lower erectile dysfunction rates for brachytherapy than for EBRT or RP and this reached statistical significance at 3 years after treatment (60% vs. 81% for EBRT and 88% for RP). There were insufficient data to draw any conclusions on bowel problems. The findings regarding procedural complications were mixed. Dysuria rates were higher for brachytherapy and this reached statistical significance when compared with RP. Urinary retention was also statistically significantly higher for brachytherapy than for EBRT. Stricture rates for brachytherapy were higher than those for EBRT, but lower than those for RP. The differences for stricture reached statistical significance when compared with RP. For rectal pain, there was evidence that rates were significantly lower for brachytherapy than for EBRT. Acute genitourinary toxicity, though rare, had statistically higher rates for brachytherapy than for EBRT, but acute gastrointestinal toxicity was lower for brachytherapy. Other ablative therapies Only two other ablative therapies were identified in the review: focal laser ablative therapy and PDT. Data were too scarce (a total of 35 participants for these two procedures) for any conclusions. Salvage therapy Data from 400 participants who were treated with salvage therapy following primary EBRT across nine case series were included. Six studies involved salvage RP, two involved salvage cryotherapy and one involved salvage HIFU. In six studies, data were not collected prospectively, and only short-term outcomes were reported. As such, all of the studies were considered as having a high risk of bias. There was no robust evidence that mortality or other cancer-specific outcomes differed between salvage cryotherapy and salvage RP in the short term. There were no data on cancer-specific outcomes for salvage HIFU. In regard to functional and quality of life outcomes, lack of data prevented any conclusions. In terms of adverse event outcomes, salvage cryotherapy had numerically fewer periprocedural complications (especially for bladder neck stenosis) than salvage HIFU or salvage RP, but there was a high level of uncertainty with this observation. Focal ablation Descriptive subgroup assessment within studies reporting the use of focal ablation was limited, but suggested that cancer-specific outcomes were at least comparable with those seen in full-gland therapy studies. Urinary incontinence rates may be lower following focal ablation, but the evidence is weak in light of the poor quality and quantity of the data. Active surveillance Lack of outcome data prevented comparison of the efficacy of ablative therapies with a programme of AS, apart from the rate of erectile dysfunction at 12 months, where there was no statistically significant difference. Cost-effectiveness Assuming equal recurrence in line with the lack of statistical differences from the effectiveness review, EBRT was the least costly (£19,363 per patient) and least effective (3.63 QALYs), whereas HIFU was more costly (£19,860 per patient) and more effective (3.86 QALYs). HIFU was more effective and less costly than the other newer ablative interventions. The lifetime incremental cost per QALY for HIFU compared with EBRT was £2915. There was a 75% chance that HIFU would be considered cost-effective at a £30,000-per-QALY threshold. In a plausible best-and-worst-case analysis, the probability that HIFU would be considered cost-effective varied between 60% and 70%. Strengths and limitations The main strength of the study was the systematic approach taken to review the literature and the inclusion of a relatively large quantity of studies, giving a high total number of participants. The main limitations were the low quantity and poor quality of the data available on cancer-related outcomes and long-term adverse events of urinary incontinence, sexual and bowel dysfunction, and the changing technology over the review period. Many published studies were poorly reported or lacked sufficient detail. Inconsistency in outcome definition, measurement and reporting was also a significant problem, and much of the information available was unsuitable for meta-analysis. Another major limitation resulted from the majority of comparisons being made using case series, with few head-to-head comparisons of ablative therapies against current practice. The estimates were therefore generated using indirect comparisons. Like all analyses, they require assumptions to be made that may or may not be reasonable. Accordingly, the results should be interpreted with a large degree of caution. Despite the considerable efforts to construct a model and seek the best data available, the lack of effectiveness data had implications for the economic evaluation. The limited data meant that there was insufficient evidence to assume that there was any difference between interventions for a number of parameters, a particular issue for biochemical recurrence, which was a key parameter in the evaluation. The impact of these assumptions was explored in sensitivity analyses. Conclusions Implications for health care For primary ablative therapy, neither cryotherapy nor HIFU had sufficiently robust data to enable any definitive conclusions to be made. The effectiveness data on brachytherapy were more robust and there was some evidence that cancer-specific outcomes in the short term were either better or equivalent to either EBRT or RP, with comparable adverse effect profiles apart from a possible increased risk of dysuria and urinary retention. The findings on focal ablative therapy were mostly derived from data on focal cryotherapy, which suggested that cancer-specific outcomes were at least comparable with those of full-gland cryotherapy, and there was a suggestion that the urinary incontinence outcome may be better following focal cryotherapy than whole-gland cryotherapy. The cost-effectiveness analysis confirmed the uncertainty from the clinical review and that there is no technology which appears superior, on the basis of current evidence, in terms of average cost-effectiveness. The probabilistic sensitivity analyses suggest that a number of ablative techniques are worthy of further research. For salvage ablative therapy following primary EBRT, a lack of reliable and robust data prevented any meaningful conclusions from being made, in comparison with salvage RP. The findings from the review indicate that there is insufficient evidence to help inform recommendations on the use of ablative therapies in the UK NHS. Need for further research The main gaps in the evidence base are the lack of direct comparative studies of ablative therapies; the consequent lack of robust data to inform calculations of cost-effectiveness and the role of focal ablative therapies; and the lack of longer-term data on cancer control, such as overall and cancer-specific mortality. The key research recommendations, in order of importance, are as follows: 1. HIFU and brachytherapy seem the most promising newer interventions but they lack high-quality evaluation. Such evaluation should ideally be by multicentre RCT with long-term follow-up, and would include predefined assessment of cancer-specific, dysfunction and health-related quality-of-life measures. Such studies should incorporate economic evaluations and also inform economic modelling

The Caenorhabditis chemoreceptor gene families

Background: Chemoreceptor proteins mediate the first step in the transduction of environmental chemical stimuli, defining the breadth of detection and conferring stimulus specificity. Animal genomes contain families of genes encoding chemoreceptors that mediate taste, olfaction, and pheromone responses. The size and diversity of these families reflect the biology of chemoperception in specific species. Results: Based on manual curation and sequence comparisons among putative G-protein-coupled chemoreceptor genes in the nematode Caenorhabditis elegans, we identified approximately 1300 genes and 400 pseudogenes in the 19 largest gene families, most of which fall into larger superfamilies. In the related species C. briggsae and C. remanei, we identified most or all genes in each of the 19 families. For most families, C. elegans has the largest number of genes and C. briggsae the smallest number, suggesting changes in the importance of chemoperception among the species. Protein trees reveal family-specific and species-specific patterns of gene duplication and gene loss. The frequency of strict orthologs varies among the families, from just over 50% in two families to less than 5% in three families. Several families include large species-specific expansions, mostly in C. elegans and C. remanei. Conclusion: Chemoreceptor gene families in Caenorhabditis species are large and evolutionarily dynamic as a result of gene duplication and gene loss. These dynamics shape the chemoreceptor gene complements in Caenorhabditis species and define the receptor space available for chemosensory responses. To explain these patterns, we propose the gray pawn hypothesis: individual genes are of little significance, but the aggregate of a large number of diverse genes is required to cover a large phenotype space.JHT was supported by NIH grant RO1GM48700 and HMR by R01AI56081

'So wide and varied': The origins and character of British information science

This paper examines some characteristics of the ‘British School’ of information science. Three main forces driving the development of the new subject in Britain are identified: the documentation movement; special libraries; and the need for better treatment of scientific and technical information. Five characteristics which, taken together, distinguish the early British approach to information science from those adopted elsewhere are identified: its subject-based nature; its broad approach to information and information science; its status as an academic subject with a strong professional remit; its involvement with, but distinction from, information technology; and its involvement with memory institutions. Lessons are drawn for the future development of the information sciences

Environmental and Genetic Determinants of Colony Morphology in Yeast

Nutrient stresses trigger a variety of developmental switches in the budding yeast Saccharomyces cerevisiae. One of the least understood of such responses is the development of complex colony morphology, characterized by intricate, organized, and strain-specific patterns of colony growth and architecture. The genetic bases of this phenotype and the key environmental signals involved in its induction have heretofore remained poorly understood. By surveying multiple strain backgrounds and a large number of growth conditions, we show that limitation for fermentable carbon sources coupled with a rich nitrogen source is the primary trigger for the colony morphology response in budding yeast. Using knockout mutants and transposon-mediated mutagenesis, we demonstrate that two key signaling networks regulating this response are the filamentous growth MAP kinase cascade and the Ras-cAMP-PKA pathway. We further show synergistic epistasis between Rim15, a kinase involved in integration of nutrient signals, and other genes in these pathways. Ploidy, mating-type, and genotype-by-environment interactions also appear to play a role in the controlling colony morphology. Our study highlights the high degree of network reuse in this model eukaryote; yeast use the same core signaling pathways in multiple contexts to integrate information about environmental and physiological states and generate diverse developmental outputs

Measurement of the branching fraction and CP content for the decay B(0) -> D(*+)D(*-)

This is the pre-print version of the Article. The official published version can be accessed from the links below. Copyright @ 2002 APS.We report a measurement of the branching fraction of the decay B0→D*+D*- and of the CP-odd component of its final state using the BABAR detector. With data corresponding to an integrated luminosity of 20.4  fb-1 collected at the Υ(4S) resonance during 1999–2000, we have reconstructed 38 candidate signal events in the mode B0→D*+D*- with an estimated background of 6.2±0.5 events. From these events, we determine the branching fraction to be B(B0→D*+D*-)=[8.3±1.6(stat)±1.2(syst)]×10-4. The measured CP-odd fraction of the final state is 0.22±0.18(stat)±0.03(syst).This work is supported by DOE and NSF (USA), NSERC (Canada), IHEP (China), CEA and CNRS-IN2P3 (France), BMBF (Germany), INFN (Italy), NFR (Norway), MIST (Russia), and PPARC (United Kingdom). Individuals have received support from the A.P. Sloan Foundation, Research Corporation, and Alexander von Humboldt Foundation

Pregnancy Does Not Affect HIV Incidence Test Results Obtained Using the BED Capture Enzyme Immunoassay or an Antibody Avidity Assay

Accurate incidence estimates are needed for surveillance of the HIV epidemic. HIV surveillance occurs at maternal-child health clinics, but it is not known if pregnancy affects HIV incidence testing.We used the BED capture immunoassay (BED) and an antibody avidity assay to test longitudinal samples from 51 HIV-infected Ugandan women infected with subtype A, C, D and intersubtype recombinant HIV who were enrolled in the HIVNET 012 trial (37 baseline samples collected near the time of delivery and 135 follow-up samples collected 3, 4 or 5 years later). Nineteen of 51 women were also pregnant at the time of one or more of the follow-up visits. The BED assay was performed according to the manufacturer's instructions. The avidity assay was performed using a Genetic Systems HIV-1/HIV-2 + O EIA using 0.1M diethylamine as the chaotropic agent.During the HIVNET 012 follow-up study, there was no difference in normalized optical density values (OD-n) obtained with the BED assay or in the avidity test results (%) when women were pregnant (n = 20 results) compared to those obtained when women were not pregnant (n = 115; for BED: p = 0.9, generalized estimating equations model; for avidity: p = 0.7, Wilcoxon rank sum). In addition, BED and avidity results were almost exactly the same in longitudinal samples from the 18 women who were pregnant at only one study visit during the follow-up study (p = 0.6, paired t-test).These results from 51 Ugandan women suggest that any changes in the antibody response to HIV infection that occur during pregnancy are not sufficient to alter results obtained with the BED and avidity assays. Confirmation with larger studies and with other HIV subtypes is needed

Measurement of D-s(+) and D-s(*+) production in B meson decays and from continuum e(+)e(-) annihilation at √s=10.6 GeV

This is the pre-print version of the Article. The official published version can be accessed from the links below. Copyright @ 2002 APSNew measurements of Ds+ and Ds*+ meson production rates from B decays and from qq̅ continuum events near the Υ(4S) resonance are presented. Using 20.8 fb-1 of data on the Υ(4S) resonance and 2.6 fb-1 off-resonance, we find the inclusive branching fractions B(B⃗Ds+X)=(10.93±0.19±0.58±2.73)% and B(B⃗Ds*+X)=(7.9±0.8±0.7±2.0)%, where the first error is statistical, the second is systematic, and the third is due to the Ds+→φπ+ branching fraction uncertainty. The production cross sections σ(e+e-→Ds+X)×B(Ds+→φπ+)=7.55±0.20±0.34pb and σ(e+e-→Ds*±X)×B(Ds+→φπ+)=5.8±0.7±0.5pb are measured at center-of-mass energies about 40 MeV below the Υ(4S) mass. The branching fractions ΣB(B⃗Ds(*)+D(*))=(5.07±0.14±0.30±1.27)% and ΣB(B⃗Ds*+D(*))=(4.1±0.2±0.4±1.0)% are determined from the Ds(*)+ momentum spectra. The mass difference m(Ds+)-m(D+)=98.4±0.1±0.3MeV/c2 is also measured.This work was supported by DOE and NSF (USA), NSERC (Canada), IHEP (China), CEA and CNRS-IN2P3 (France), BMBF (Germany), INFN (Italy), NFR (Norway), MIST (Russia), and PPARC (United Kingdom). Individuals have received support from the Swiss NSF, A. P. Sloan Foundation, Research Corporation, and Alexander von Humboldt Foundation