Population genetic analyses reveal distinct geographical blooms of the jellyfish Rhizostoma octopus (Scyhpozoa)

Understanding the spatial integrity and connectivity of jellyfish blooms is important for ecologists and coastal stakeholders alike. Previous studies have shown that the distribution of jellyfish blooms can display a marked consistency in space and time, suggesting that such patterns cannot be attributed to passive processes alone. In the present study, we used a combination of microsatellite markers and mitochondrial cytochrome oxidase I sequences to investigate genetic structuring of the scyphozoan jellyfish Rhizostoma octopus in the Irish and Celtic Seas. The mitochondrial data indicated far higher levels of population differentiation than the microsatellites: ΦST[MT] = 0.300 vs. ΦST[NUC] = 0.013. Simulation studies indicated that the low levels of nuclear differentiation were not the result of limited power because of low levels of polymorphism. These findings, supported by palaeodistribution modelling and mismatch distribution analysis, are consistent with expansion of R. octopus from a single, limited refugium after the Last Glacial Maximum, followed by subsequent isolation, and that the discrepancy between the mitochondrial and nuclear markers is a result of the nuclear loci taking longer to reach mutation–drift equilibrium following the expansion as a result of their four-fold larger effective population size. The populations studied are probably not well connected via gene flow, and thus genetically as well as geographically distinct, although our findings also highlight the need to use a combination of organellar and nuclear markers to enable a more complete understanding of population demography and structure, particularly for species with large effective population sizes.

Phylogeographical analyses of shellfish viruses: inferring a geographical origin for ostreid herpesviruses OsHV-1 (Malacoherpesviridae)

Mortality episodes have regularly been affecting the shellfish industry throughout its history. Some of these mortalities, especially in the oyster industry, have been attributed to herpesviruses. Purification of viral particles and molecular characterization have led to the development of routine monitoring, as well as improved taxonomic classification. Ostreid herpesviruses (Malacoherpesviridae), mostly affecting Pacific oysters Crassostrea gigas, have been sporadically recorded in the French oyster industry since the early 1990s (OsHV-1 'reference'). From 2008, a new variant of ostreid herpesvirus (OsHV-1 mu Var) has emerged and seriously impacted oyster production in France and other European countries. Consequently, the presence of ostreid herpesviruses has been monitored in different oyster producing areas around the world. The present study compiles molecular data that are available from survey efforts and takes a biogeographical approach, in order to infer an origin for ostreid herpesviruses. The highest genotype diversity was found in East Asia, despite a lower survey effort in that area than in Europe. Genotype network analyses show that both populations of ostreid herpesviruses present in Europe (OsHV-1 'reference' and OsHV-1 mu Var) are closely related to genotypes recorded in Asia. Moreover, ostreid herpesviruses have been detected in wild and symptom-free populations of various Asian native Crassostrea species. In the rest of the world, ostreid herpesvirus genotypes were recorded from cultivated C. gigas, and mostly associated with mortality episodes. Results of this study are therefore highly suggestive of an Asian origin for these viruses, which can be pathogenic under farming conditions. It also highlights the risks of European stock improvements, by means of overseas shellfish imports.

Bdellovibrio predation in the presence of decoys:Three-way bacterial interactions revealed by mathematical and experimental analyses

Bdellovibrio bacteriovorus is a small, gram-negative, motile bacterium that preys upon other gram-negative bacteria, including several known human pathogens. Its predation efficiency is usually studied in pure cultures containing solely B. bacteriovorus and a suitable prey. However, in natural environments, as well as in any possible biomedical uses as an antimicrobial, Bdellovibrio is predatory in the presence of diverse decoys, including live nonsusceptible bacteria, eukaryotic cells, and cell debris. Here we gathered and mathematically modeled data from three-member cultures containing predator, prey, and nonsusceptible bacterial decoys. Specifically, we studied the rate of predation of planktonic late-log-phase Escherichia coli S17-1 prey by B. bacteriovorus HD100, both in the presence and in the absence of Bacillus subtilis nonsporulating strain 671, which acted as a live bacterial decoy. Interestingly, we found that although addition of the live Bacillus decoy did decrease the rate of Bdellovibrio predation in liquid cultures, this addition also resulted in a partially compensatory enhancement of the availability of prey for predation. This effect resulted in a higher final yield of Bdellovibrio than would be predicted for a simple inert decoy. Our mathematical model accounts for both negative and positive effects of predator-prey-decoy interactions in the closed batch environment. In addition, it informs considerations for predator dosing in any future therapeutic applications and sheds some light on considerations for modeling the massively complex interactions of real mixed bacterial populations in nature.

Simulating reinforced concrete members. Part 2: displacement-based analyses

A companion paper described the partial-interaction localised properties that require the development of pseudo properties. If the quantification through experimental testing of these pseudo properties could be removed by the use of mechanics-based models, which is the subject of this paper, then this would: (a) substantially reduce the cost of developing new reinforced concrete products by reducing the amount of testing; (b) increase the accuracy of designing existing and novel reinforced concrete members and structures, bearing in mind that experimentally derived pseudo properties are only applicable within the range of the testing from which they were derived; and (c) reduce the cost and increase the accuracy of developing reinforced concrete design rules. This paper deals with the development of pseudo properties and behaviours directly through mechanics, as opposed to experimental testing, and their incorporation into member global simulations. It also addresses the need for a fundamental shift to displacement-based analyses as opposed to strain-based analyses.

Adjuvant bisphosphonate treatment in early breast cancer: meta-analyses of individual patient data from randomised trials

BACKGROUND: Bisphosphonates have profound effects on bone physiology, and could modify the process of metastasis. We undertook collaborative meta-analyses to clarify the risks and benefits of adjuvant bisphosphonate treatment in breast cancer.

METHODS: We sought individual patient data from all unconfounded trials in early breast cancer that randomised between bisphosphonate and control. Primary outcomes were recurrence, distant recurrence, and breast cancer mortality. Primary subgroup investigations were site of first distant recurrence (bone or other), menopausal status (postmenopausal [combining natural and artificial] or not), and bisphosphonate class (aminobisphosphonate [eg, zoledronic acid, ibandronate, pamidronate] or other [ie, clodronate]). Intention-to-treat log-rank methods yielded bisphosphonate versus control first-event rate ratios (RRs).

FINDINGS: We received data on 18 766 women (18 206 [97%] in trials of 2-5 years of bisphosphonate) with median follow-up 5·6 woman-years, 3453 first recurrences, and 2106 subsequent deaths. Overall, the reductions in recurrence (RR 0·94, 95% CI 0·87-1·01; 2p=0·08), distant recurrence (0·92, 0·85-0·99; 2p=0·03), and breast cancer mortality (0·91, 0·83-0·99; 2p=0·04) were of only borderline significance, but the reduction in bone recurrence was more definite (0·83, 0·73-0·94; 2p=0·004). Among premenopausal women, treatment had no apparent effect on any outcome, but among 11 767 postmenopausal women it produced highly significant reductions in recurrence (RR 0·86, 95% CI 0·78-0·94; 2p=0·002), distant recurrence (0·82, 0·74-0·92; 2p=0·0003), bone recurrence (0·72, 0·60-0·86; 2p=0·0002), and breast cancer mortality (0·82, 0·73-0·93; 2p=0·002). Even for bone recurrence, however, the heterogeneity of benefit was barely significant by menopausal status (2p=0·06 for trend with menopausal status) or age (2p=0·03), and it was non-significant by bisphosphonate class, treatment schedule, oestrogen receptor status, nodes, tumour grade, or concomitant chemotherapy. No differences were seen in non-breast cancer mortality. Bone fractures were reduced (RR 0·85, 95% CI 0·75-0·97; 2p=0·02).

INTERPRETATION: Adjuvant bisphosphonates reduce the rate of breast cancer recurrence in the bone and improve breast cancer survival, but there is definite benefit only in women who were postmenopausal when treatment began.

FUNDING: Cancer Research UK, Medical Research Council.

Individual Participant Data (IPD) Meta-analyses of Randomised Controlled Trials: Guidance on Their Use

Jayne Tierney and colleagues offer guidance on how to spot a well-designed and well-conducted individual participant data meta-analysis.

Summary Points 

• Systematic reviews are most commonly based on aggregate data extracted from publications or obtained from trial investigators. 

• Systematic reviews involving the central collection and analysis of individual participant data (IPD) usually are larger-scale, international, collaborative projects that can bring about substantial improvements to the quantity and quality of data, give greater scope in the analyses, and provide more detailed and robust results. 

• The process of collecting, checking, and analysing IPD is more complex than for aggregate data, and not all IPD meta-analyses are done to the same standard, making it difficult for researchers, clinicians, patients, policy makers, funders, and publishers to judge their quality. 

• Following our step-by-step guide will help reviewers and users of IPD meta-analyses to understand them better and recognise those that are well designed and conducted and so help ensure that policy, practice, and research are informed by robust evidence about the effects of interventions.

How individual participant data meta-analyses have influenced trial design, conduct, and analysis

OBJECTIVES: To demonstrate how individual participant data (IPD) meta-analyses have impacted directly on the design and conduct of trials and highlight other advantages IPD might offer.

STUDY DESIGN AND SETTING: Potential examples of the impact of IPD meta-analyses on trials were identified at an international workshop, attended by individuals with experience in the conduct of IPD meta-analyses and knowledge of trials in their respective clinical areas. Experts in the field who did not attend were asked to provide any further examples. We then examined relevant trial protocols, publications, and Web sites to verify the impacts of the IPD meta-analyses. A subgroup of workshop attendees sought further examples and identified other aspects of trial design and conduct that may inform IPD meta-analyses.

RESULTS: We identified 52 examples of IPD meta-analyses thought to have had a direct impact on the design or conduct of trials. After screening relevant trial protocols and publications, we identified 28 instances where IPD meta-analyses had clearly impacted on trials. They have influenced the selection of comparators and participants, sample size calculations, analysis and interpretation of subsequent trials, and the conduct and analysis of ongoing trials, sometimes in ways that would not possible with systematic reviews of aggregate data. We identified additional potential ways that IPD meta-analyses could be used to influence trials.

CONCLUSIONS: IPD meta-analysis could be better used to inform the design, conduct, analysis, and interpretation of trials.

Quality of reporting of dental survival analyses

To explore the quality of reporting (writing and graphics) of articles that used time-to-event analyses to report dental treatment outcomes. A systematic search of the top 50 dental journals in 2008 produced the sample of articles for this analysis. Articles reporting treatment outcomes with (n = 95) and without (n = 91) time-to-event statistics were reviewed. Survival descriptive words used in the two groups were analysed (Pearson's chi-square). The quality of life tables, survival curves and time-to-event statistics were assessed (Kappa analysed agreement) and explored. Words describing dental outcomes 'over time' were more common in time-to-event compared with control articles (77%, 3%, P < 0.001). Non-specific use of 'rate' was common across both groups. Life tables and survival curves were used by 39% and 48% of the time-to-event articles, with at least one used by 82%. Construction quality was poor: 21% of life tables and 28% of survival curves achieved an acceptable standard. Time-to-event statistical reporting was poor: 3% achieved a high and 59% achieved an acceptable standard. The survival statistic, summary figure and standard error were reported in 76%, 95% and 20% of time-to-event articles. Individual statistical terms and graphic aids were common within and unique to time-to-event articles. Unfortunately, important details were regularly omitted from statistical descriptions and survival figures making the overall quality poor. It is likely this will mean such articles will be incorrectly indexed in databases, missed by searchers and unable to be understood completely if identified.

Accuracy of medical subject heading indexing of dental survival analyses

PURPOSE: To assess the Medical Subject Headings (MeSH) indexing of articles that employed time-to-event analyses to report outcomes of dental treatment in patients.

MATERIALS AND METHODS: Articles published in 2008 in 50 dental journals with the highest impact factors were hand searched to identify articles reporting dental treatment outcomes over time in human subjects with time-to-event statistics (included, n = 95), without time-to-event statistics (active controls, n = 91), and all other articles (passive controls, n = 6,769). The search was systematic (kappa 0.92 for screening, 0.86 for eligibility). Outcome-, statistic- and time-related MeSH were identified, and differences in allocation between groups were analyzed with chi-square and Fischer exact statistics.

RESULTS: The most frequently allocated MeSH for included and active control articles were "dental restoration failure" (77% and 52%, respectively) and "treatment outcome" (54% and 48%, respectively). Outcome MeSH was similar between these groups (86% and 77%, respectively) and significantly greater than passive controls (10%, P < .001). Significantly more statistical MeSH were allocated to the included articles than to the active or passive controls (67%, 15%, and 1%, respectively, P < .001). Sixty-nine included articles specifically used Kaplan-Meier or life table analyses, but only 42% (n = 29) were indexed as such. Significantly more time-related MeSH were allocated to the included than the active controls (92% and 79%, respectively, P = .02), or to the passive controls (22%, P < .001).

CONCLUSIONS: MeSH allocation within MEDLINE to time-to-event dental articles was inaccurate and inconsistent. Statistical MeSH were omitted from 30% of the included articles and incorrectly allocated to 15% of active controls. Such errors adversely impact search accuracy.