Fossil trees, tree moulds and tree casts in the Palaeocene Mull Lava Field, NW Scotland: context, formation and implications for lava emplacement

Megafossils and macrofossils of terrestrial plants (trees, leaves, fruiting bodies, etc.) are found in sedimentary and pyroclastic units interbedded with lavas in many ancient lava fields worldwide, attesting to subaerial environments of eruption and the establishment of viable plant communities during periods of volcanic quiescence. Preservation within lava is relatively rare and generally confined to the more robust woody tissues of trees, which are then revealed in the form of charcoal, mineralised tissue or as trace fossil moulds (tree moulds) and casts of igneous rock (tree casts, s.s.). In this contribution, we document several such fossil trees (s.l.), and the lavas with which they are associated, from the Palaeocene Mull Lava Field (MLF) on the Isle of Mull, NW Scotland. We present the first detailed geological account of a unique site within the Mull Plateau Lava Formation (MPLF) at Quinish in the north of the island and provide an appraisal of the famous upright fossil tree – MacCulloch's Tree – remotely located on the Ardmeanach Peninsula on the west coast of the island, and another large upright tree (the Carsaig Tree) near Malcolm's Point in the district of Brolass, SW Mull; both occurring within the earlier Staffa Lava Formation (SLF). The taphonomy of these megafossils, along with palynological and lithofacies assessments of associated strata, allows speculation of likely taxonomic affinity and the duration of hiatuses supporting the establishment of forest/woodland communities. The Ardmeanach and Carsaig specimens, because of their size and preservation as upright (? in situ) casts enveloped by spectacularly columnar-jointed basaltic lava, appear to be unique. The aspect of these trees, the thickness of the enveloping lavas and the arrangement of cooling joints adjacent to the trees, implies rapid emplacement, ponding and slow, static cooling of voluminous and highly fluid basaltic magma. The specimens from Quinish include two prostrate casts and several prostrate moulds that collectively have a preferred orientation, aligning approximately perpendicular to that of the regional Mull Dyke Swarm, the putative fissure source of the lavas, suggesting local palaeo-flow was directed towards the WSW. The Quinish Lava is an excellent example of a classic pāhoehoe (compound-braided) type, preserving some of the best examples of surface and internal features so far noted from the Hebridean Igneous Province (HIP) lava fields. These Mull megafossils are some of the oldest recorded examples, remarkably well preserved, and form a significant feature of the island's geotourism industry

Investigations on the Mannans of Ivory Nut (Phytelephas macrocarpa)

Mannan A:1. Mannan A was extracted from delignified ivory nut shavings with 7;., potassium hydroxide solution, and the polysaccharide precipitated by acidification of the extract and addition of methylated spirits.2. The mannan, purified by means of the copper complex, gave on hydrolysis 97.6% mannose, 1.8% galactose, and o.8% glucose.3. The reducing power of the mannan determined by oxidation with alkaline hypoiodite gave a degree of polymerisation of 100, and by treatment with 3 :5- dinitrosalicylic acid, 28. The values of the chain length of mannan A obtained by these two methods were different and disagreed with the value obtained by other methods. Values of the chain length of the polysaccharide which are derived from measurement of the reducing power are, therefore, of doubtful validity.4. A triacetate was prepared which was found by Barger's method to have a degree of polymerisation of 10 -13.5. The mannan was methylated and the methylated polysaccharide hydrolysed. The hydrolysate was separated on a cellulose column and the following sugars were obtained: 2:3:4:6- tetramethyl Dmannose, 2:3:4 :6- tetramethyl D- galactose, 2:3:6 -trimethyl Dmannose, 2 :3 :4- trimethyl D- mannose, and 2:3- dimethyl D- mannose in the molar ratios of, respectively, 1.0: 0.2: 11.6: 1.0: 0.2. All the galactose present in the purified mannan was accounted for as 2:3:4 :6- tetramethyl galactose.6. The 2:3 :4- trimethyl mannose fraction crystallised as a disaccharide, which was shown to be 1 -[ 2:3:4 -trimethyl D-mannopyranosido] - 2:3:4 -trimethyl D-mannopyranoside.7. The degree of polymerisation of the methylated mannan was determined by Barger's method and found to be 9 -11.8. Periodate oxidation experiments on the mannan showed that 1.6 moles of periodate were consumed per anhydrohexose unit, and one mole of formic acid was liberated per 4 anhydrohexose units.9. On the basis of these results possible structures for the mannan are proposed.Mannan B:1. Mannan B was extracted from the residue left after removal of mannan A from ivory nuts. The residue was extracted with cuprammonium hydroxide and the solution treated with sodium hydroxide. Several fractions were obtained and one which was considered to be mannan B was purified by dissolution in anhydrous formic acid and precipitation with ethanol.2. Purified mannan B gave on hydrolysis 98.3% mannose, 1.1% galactose, and 0.8% glucose.3 The reducing power of the mannan was determined by hypoiodite oxidation and colorimetrically by means of 3:5- dinitrosalicylic acid. The first method gave an apparent degree of polymerisation of 12, the second, 130. The values of the Chain length of mannan B obtained by these two methods were different and disagreed with the value obtained by other methods. Values of the chain length of the polysaccharide which are derived from measurement of the reducing power are, therefore, of doubtful validity.4. Mannan B was meth lated and the methylated polysaccharide hydrolysed. Separation of the mixture of sugars on a cellulose column gave 2:3:4:6 -tetramethyl D- mannose, 2:3 :4 :6- tetramethyl D- galactose, 2:3:6 -trimethyl D- mannose, 2:3:4 -trimethyl D- mannose, and 2:3- dimethyl D-mannose in the molar ratios of, respectively, 1 :1:63 :11 :1. All the galactose present in purified mannan B was accounted for as 2:3:4:6 -tetramethyl galactose.5. The 2 :3 :4- trimethyl mannose fraction crystallised as a disaccharide, which was shown to be 1 -[2 :3 :4- trimethyl D- mannopyranosido ] - 2:3:4- trimethyl D- mannopyranoside.6. The degree of polymerisation of methylated mannan B was determined by Barger's method and found to be 35-43.7. Periodate oxidation experiments on the mannan showed that 0.98 moles of periodate were consumed per anhydrohexose unit, and one mole of formic acid was liberated per 2.4 anhydrohexose units.8. On the basis of these results possible structures for the mannan are proposed

Nonadherence to treatment protocol in published randomised controlled trials: a review.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.This review aimed to ascertain the extent to which nonadherence to treatment protocol is reported and addressed in a cohort of published analyses of randomised controlled trials (RCTs). One hundred publications of RCTs, randomly selected from those published in BMJ, New England Journal of Medicine, the Journal of the American Medical Association and The Lancet during 2008, were reviewed to determine the extent and nature of reported nonadherence to treatment protocol, and whether statistical methods were used to examine the effect of such nonadherence on both benefit and harms analyses. We also assessed the quality of trial reporting of treatment protocol nonadherence and the quality of reporting of the statistical analysis methods used to investigate such nonadherence. Nonadherence to treatment protocol was reported in 98 of the 100 trials, but reporting on such nonadherence was often vague or incomplete. Forty-two publications did not state how many participants started their randomised treatment. Reporting of treatment initiation and completeness was judged to be inadequate in 64% of trials with short-term interventions and 89% of trials with long-term interventions. More than half (51) of the 98 trials with treatment protocol nonadherence implemented some statistical method to address this issue, most commonly based on per protocol analysis (46) but often labelled as intention to treat (ITT) or modified ITT (23 analyses in 22 trials). The composition of analysis sets for their benefit outcomes were not explained in 57% of trials, and 62% of trials that presented harms analyses did not define harms analysis populations. The majority of defined harms analysis populations (18 out of 26 trials, 69%) were based on actual treatment received, while the majority of trials with undefined harms analysis populations (31 out of 43 trials, 72%) appeared to analyse harms using the ITT approach. Adherence to randomised intervention is poorly considered in the reporting and analysis of published RCTs. The majority of trials are subject to various forms of nonadherence to treatment protocol, and though trialists deal with this nonadherence using a variety of statistical methods and analysis populations, they rarely consider the potential for bias introduced. There is a need for increased awareness of more appropriate causal methods to adjust for departures from treatment protocol, as well as guidance on the appropriate analysis population to use for harms outcomes in the presence of such nonadherence

A framework for the design, conduct and interpretation of randomised controlled trials in the presence of treatment changes.

BACKGROUND: When a randomised trial is subject to deviations from randomised treatment, analysis according to intention-to-treat does not estimate two important quantities: relative treatment efficacy and effectiveness in a setting different from that in the trial. Even in trials of a predominantly pragmatic nature, there may be numerous reasons to consider the extent, and impact on analysis, of such deviations from protocol. Simple methods such as per-protocol or as-treated analyses, which exclude or censor patients on the basis of their adherence, usually introduce selection and confounding biases. However, there exist appropriate causal estimation methods which seek to overcome these inherent biases, but these methods remain relatively unfamiliar and are rarely implemented in trials. METHODS: This paper demonstrates when it may be of interest to look beyond intention-to-treat analysis for answers to alternative causal research questions through illustrative case studies. We seek to guide trialists on how to handle treatment changes in the design, conduct and planning the analysis of a trial; these changes may be planned or unplanned, and may or may not be permitted in the protocol. We highlight issues that must be considered at the trial planning stage relating to: the definition of nonadherence and the causal research question of interest, trial design, data collection, monitoring, statistical analysis and sample size. RESULTS AND CONCLUSIONS: During trial planning, trialists should define their causal research questions of interest, anticipate the likely extent of treatment changes and use these to inform trial design, including the extent of data collection and data monitoring. A series of concise recommendations is presented to guide trialists when considering undertaking causal analyses

Variance reduction in randomised trials by inverse probability weighting using the propensity score.

In individually randomised controlled trials, adjustment for baseline characteristics is often undertaken to increase precision of the treatment effect estimate. This is usually performed using covariate adjustment in outcome regression models. An alternative method of adjustment is to use inverse probability-of-treatment weighting (IPTW), on the basis of estimated propensity scores. We calculate the large-sample marginal variance of IPTW estimators of the mean difference for continuous outcomes, and risk difference, risk ratio or odds ratio for binary outcomes. We show that IPTW adjustment always increases the precision of the treatment effect estimate. For continuous outcomes, we demonstrate that the IPTW estimator has the same large-sample marginal variance as the standard analysis of covariance estimator. However, ignoring the estimation of the propensity score in the calculation of the variance leads to the erroneous conclusion that the IPTW treatment effect estimator has the same variance as an unadjusted estimator; thus, it is important to use a variance estimator that correctly takes into account the estimation of the propensity score. The IPTW approach has particular advantages when estimating risk differences or risk ratios. In this case, non-convergence of covariate-adjusted outcome regression models frequently occurs. Such problems can be circumvented by using the IPTW adjustment approach

Using the Delphi Technique to Determine Which Outcomes to Measure in Clinical Trials: Recommendations for the Future Based on a Systematic Review of Existing Studies

Ian Sinha and colleagues advise that when using the Delphi process to develop core outcome sets for clinical trials, patients and clinicians be involved, researchers and facilitators avoid imposing their views on participants, and attrition of participants be minimized

Planning a method for covariate adjustment in individually randomised trials: a practical guide

Background: It has long been advised to account for baseline covariates in the analysis of confirmatory randomised trials, with the main statistical justifications being that this increases power and, when a randomisation scheme balanced covariates, permits a valid estimate of experimental error. There are various methods available to account for covariates but it is not clear how to choose among them. // Methods: Taking the perspective of writing a statistical analysis plan, we consider how to choose between the three most promising broad approaches: direct adjustment, standardisation and inverse-probability-of-treatment weighting. // Results: The three approaches are similar in being asymptotically efficient, in losing efficiency with mis-specified covariate functions and in handling designed balance. If a marginal estimand is targeted (for example, a risk difference or survival difference), then direct adjustment should be avoided because it involves fitting non-standard models that are subject to convergence issues. Convergence is most likely with IPTW. Robust standard errors used by IPTW are anti-conservative at small sample sizes. All approaches can use similar methods to handle missing covariate data. With missing outcome data, each method has its own way to estimate a treatment effect in the all-randomised population. We illustrate some issues in a reanalysis of GetTested, a randomised trial designed to assess the effectiveness of an electonic sexually transmitted infection testing and results service. // Conclusions: No single approach is always best: the choice will depend on the trial context. We encourage trialists to consider all three methods more routinely

Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure

The DetectDeviatingCells algorithm was a useful addition to the toolkit for cellwise error detection in observational data

OBJECTIVE: We evaluated the error detection performance of the DetectDeviatingCells (DDC) algorithm, which flags data anomalies at observation (casewise) and variable (cellwise) level in continuous variables. We compared its performance to other approaches in a simulated dataset. STUDY DESIGN AND SETTING: We simulated height and weight data for hypothetical individuals aged 2-20 years. We changed a proportion of height values according to pre-determined error patterns. We applied the DDC algorithm and other error-detection approaches (descriptive statistics, plots, fixed-threshold rules, classic and robust Mahalanobis distance) and we compared error detection performance with sensitivity, specificity, likelihood ratios, predictive values and ROC curves. RESULTS: At our chosen thresholds, error detection specificity was excellent across all scenarios for all methods and sensitivity was higher for multivariable and robust methods. The DDC algorithm performance was similar to other robust multivariable methods. Analysis of ROC curves suggested that all methods had comparable performance for gross errors (e.g. wrong measurement unit), but the DDC algorithm outperformed the others for more complex error patterns (e.g. transcription errors that are still plausible, although extreme). CONCLUSIONS: The DDC algorithm has the potential to improve error detection processes for observational data

An evolutionarily-unique heterodimeric voltage-gated cation channel found in aphids

We describe the identification in aphids of a unique heterodimeric voltage-gated sodium channel which has an atypical ion selectivity filter and, unusually for insect channels, is highly insensitive to tetrodotoxin. We demonstrate that this channel has most likely arisen by adaptation (gene fission or duplication) of an invertebrate ancestral mono(hetero)meric channel. This is the only identifiable voltage-gated sodium channel homologue in the aphid genome(s), and the channel's novel selectivity filter motif (DENS instead of the usual DEKA found in other eukaryotes) may result in a loss of sodium selectivity, as indicated experimentally in mutagenised Drosophila channels