A Cenozoic-style scenario for the end-Ordovician glaciation

The end-Ordovician was an enigmatic interval in the Phanerozoic, known for massive glaciation potentially at elevated CO2 levels, biogeochemical cycle disruptions recorded as large isotope anomalies and a devastating extinction event. Ice-sheet volumes claimed to be twice those of the Last Glacial Maximum paradoxically coincided with oceans as warm as today. Here we argue that some of these remarkable claims arise from undersampling of incomplete geological sections that led to apparent temporal correlations within the relatively coarse resolution capability of Palaeozoic biochronostratigraphy. We examine exceptionally complete sedimentary records from two, low and high, palaeolatitude settings. Their correlation framework reveals a Cenozoic-style scenario including three main glacial cycles and higher-order phenomena. This necessitates revision of mechanisms for the end-Ordovician events, as the first extinction is tied to an early phase of melting, not to initial cooling, and the largest δ13C excursion occurs during final deglaciation, not at the glacial apex

Missing data and multiple imputation in clinical epidemiological research

Missing data are ubiquitous in clinical epidemiological research. Individuals with missing data may differ from those with no missing data in terms of the outcome of interest and prognosis in general. Missing data are often categorized into the following three types: missing completely at random (MCAR), missing at random (MAR), and missing not at random (MNAR). In clinical epidemiological research, missing data are seldom MCAR. Missing data can constitute considerable challenges in the analyses and interpretation of results and can potentially weaken the validity of results and conclusions. A number of methods have been developed for dealing with missing data. These include complete-case analyses, missing indicator method, single value imputation, and sensitivity analyses incorporating worst-case and best-case scenarios. If applied under the MCAR assumption, some of these methods can provide unbiased but often less precise estimates. Multiple imputation is an alternative method to deal with missing data, which accounts for the uncertainty associated with missing data. Multiple imputation is implemented in most statistical software under the MAR assumption and provides unbiased and valid estimates of associations based on information from the available data. The method affects not only the coefficient estimates for variables with missing data but also the estimates for other variables with no missing data

Identification of possible virulence marker from Campylobacter jejuni isolates

This is the final version of the article. Available from the publisher via the DOI in this record.A novel protein translocation system, the type-6 secretion system (T6SS), may play a role in virulence of Campylobacter jejuni. We investigated 181 C. jejuni isolates from humans, chickens, and environmental sources in Vietnam, Thailand, Pakistan, and the United Kingdom for T6SS. The marker was most prevalent in human and chicken isolates from Vietnam.The work was partly supported by the UK Biotechnology and Biological Sciences Research Council, award BB/1024631/1 to R.T., D.S., and O.C.; by a Wellcome Trust Institutional Strategic Support Award (WT097835MF); and by a studentship awarded to J.H. Mr Harrison is a PhD student at the University of Exeter under the supervision of D.S. His research focuses on using bioinformatic methods to investigate the comparative genomics of emerging diseases and plant-associated microbes

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

Marine sponges are well known for their associations with highly diverse, yet very specific and often highly similar microbiota. The aim of this study was to identify potential bacterial sub-populations in relation to sponge phylogeny and sampling sites and to define the core bacterial community. 16S ribosomal RNA gene amplicon pyrosequencing was applied to 32 sponge species from eight locations around the world's oceans, thereby generating 2567 operational taxonomic units (OTUs at the 97% sequence similarity level) in total and up to 364 different OTUs per sponge species. The taxonomic richness detected in this study comprised 25 bacterial phyla with Proteobacteria, Chloroflexi and Poribacteria being most diverse in sponges. Among these phyla were nine candidate phyla, six of them found for the first time in sponges. Similarity comparison of bacterial communities revealed no correlation with host phylogeny but a tropical sub-population in that tropical sponges have more similar bacterial communities to each other than to subtropical sponges. A minimal core bacterial community consisting of very few OTUs (97%, 95% and 90%) was found. These microbes have a global distribution and are probably acquired via environmental transmission. In contrast, a large species-specific bacterial community was detected, which is represented by OTUs present in only a single sponge species. The species-specific bacterial community is probably mainly vertically transmitted. It is proposed that different sponges contain different bacterial species, however, these bacteria are still closely related to each other explaining the observed similarity of bacterial communities in sponges in this and previous studies. This global analysis represents the most comprehensive study of bacterial symbionts in sponges to date and provides novel insights into the complex structure of these unique associations

Penetrating cardiac trauma: 20-y experience from a university teaching hospital

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Background: Penetrating traumas, including gunshot and stab wounds, are the major causes of cardiac trauma. Our aim was to describe and compare the variables between patients with penetrating cardiac trauma in the past 20 y in a university hospital, identifying risk factors for morbidity and death. Methods: Review of trauma registry data followed by descriptive statistical analysis comparing the periods 1990-1999 (group 1, 54 cases) and 2000-2009 (group 2, 39 cases). Clinical data at hospital admission, Injury Severity Score (ISS), Glasgow Coma Scale (GCS), and Revised Trauma Score (RTS) were recorded. Results: The incidences of penetrating cardiac injuries were steady within the period of study in the chosen metropolitan area. The two groups were similar regarding age, mechanism of trauma (gunshot x stab), and ISS. Group 1 showed lower systolic blood pressure at admission (mean 87 versus 109 mm Hg), lower GCS (12.9 versus 14.1), lower RTS (6.4 versus 7.3), higher incidence of grade IV-V cardiac lesions (74% versus 48.7%), and were less likely to survive (0.83 versus 0.93). The major risk factor for death was gunshot wound (13 times higher than stab wound), systolic blood pressure < 90 mm Hg, GCS < 8, RTS < 7.84, associated injuries, grade IV-V injury, and ISS > 25. We observed a tendency in mortality reduction from 20.3% to 10.3% within the period of observation. Conclusions: Several associated factors for mortality and morbidity were identified. In the last decade, patients were admitted in better physiological condition, perhaps reflecting an improvement on prehospital treatment. We observed a trend toward a lower mortality rate. (c) 2013 Elsevier Inc. All rights reserved.1832792797Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAPESP [FAPESP - 09/52986-1