Bayesian total evidence dating reveals the recent crown radiation of penguins

The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples. The fossilized birth-death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ~12.7 Ma and most splits leading to extant species occurring in the last 2 million years. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (v. 2.4) www.beast2.org with packages SA (v. at least 1.1.4) and morph-models (v. at least 1.0.4).Comment: 50 pages, 6 figure

Case mix, outcomes and comparison of risk prediction models for admissions to adult, general and specialist critical care units for head injury: a secondary analysis of the ICNARC Case Mix Programme Database

INTRODUCTION: This report describes the case mix and outcome (mortality, intensive care unit (ICU) and hospital length of stay) for admissions to ICU for head injury and evaluates the predictive ability of five risk adjustment models. METHODS: A secondary analysis was conducted of data from the Intensive Care National Audit and Research Centre (ICNARC) Case Mix Programme, a high quality clinical database, of 374,594 admissions to 171 adult critical care units across England, Wales and Northern Ireland from 1995 to 2005. The discrimination and calibration of five risk prediction models, SAPS II, MPM II, APACHE II and III and the ICNARC model plus raw Glasgow Coma Score (GCS) were compared. RESULTS: There were 11,021 admissions following traumatic brain injury identified (3% of all database admissions). Mortality in ICU was 23.5% and in-hospital was 33.5%. Median ICU and hospital lengths of stay were 3.2 and 24 days, respectively, for survivors and 1.6 and 3 days, respectively, for non-survivors. The ICNARC model, SAPS II and MPM II discriminated best between survivors and non-survivors and were better calibrated than raw GCS, APACHE II and III in 5,393 patients eligible for all models. CONCLUSION: Traumatic brain injury requiring intensive care has a high mortality rate. Non-survivors have a short length of ICU and hospital stay. APACHE II and III have poorer calibration and discrimination than SAPS II, MPM II and the ICNARC model in traumatic brain injury; however, no model had perfect calibration

The epidemiology of severe sepsis in England, Wales and Northern Ireland, 1996 to 2004: secondary analysis of a high quality clinical database, the ICNARC Case Mix Programme Database

INTRODUCTION: To evaluate the impact of recent evidence-based treatments for severe sepsis in routine clinical care requires an understanding of the underlying epidemiology, particularly with regard to trends over time. We interrogated a high quality clinical database to examine trends in the incidence and mortality of severe sepsis over a nine-year period. METHODS: Admissions with severe sepsis occurring at any time within 24 hours of admission to critical care were identified to an established methodology using raw physiological data from the Intensive Care National Audit & Research Centre (ICNARC) Case Mix Programme Database, containing data from 343,860 admissions to 172 adult, general critical care units in England, Wales and Northern Ireland between December 1995 and January 2005. Generalised linear models were used to assess changes in the incidence, case mix, outcomes and activity of these admissions. RESULTS: In total, 92,672 admissions (27.0%) were identified as having severe sepsis in the first 24 hours following admission. The percentage of admissions with severe sepsis during the first 24 hours rose from 23.5% in 1996 to 28.7% in 2004. This represents an increase from an estimated 18,500 to 31,000 admissions to all 240 adult, general critical care units in England, Wales and Northern Ireland. Hospital mortality for admissions with severe sepsis decreased from 48.3% in 1996 to 44.7% in 2004, but the total number of deaths increased from an estimated 9,000 to 14,000. The treated incidence of severe sepsis per 100,000 population rose from 46 in 1996 to 66 in 2003, with the associated number of hospital deaths per 100,000 population rising from 23 to 30. CONCLUSION: The population incidence of critical care admission with severe sepsis during the first 24 hours and associated hospital deaths are increasing. These baseline data provide essential information to those wishing to evaluate the introduction of the Surviving Sepsis Campaign care bundles in UK hospitals

Isomerisation of nido-[C₂B₁₀H₁₂]²⁻ dianions::Unprecedented rearrangements and new structural motifs in carborane cluster chemistry

We thank the EPSRC for support (DMcK funded by project EP/E02971X/1).Dianionic nido-[C2B10]2- species are key intermediates in the polyhedral expansion from 12- to 13-vertex carboranes and metallacarboranes, and the isomer adopted by these nido intermediates dictates the isomeric form of the 13-vertex product. Upon reduction and metallation of para-carborane up to five MC2B10 metallacarboranes can be produced (Angew. Chem., Int. Ed., 2007, 46, 6706), the structures of which imply the intermediacy of 1,7-, 3,7-, 4,7-, 7,9- and 7,10-isomers of the nido-[C2B10]2- species. In this paper we use density functional theory (DFT) calculations to characterise the reduction of closo-C2B10H12 carboranes and the subsequent isomerisations of the nido-[C2B10H12]2- dianions. Upon reduction para-carborane initially opens to [1,7-nido-C2B10H12]2- (abbreviated to 1,7) and [4,7-nido-C2B10H12]2- (4,7) and isomerisation pathways connecting 1,7 to 7,9, 4,7 to 7,10 and 1,7 to 3,7 have been characterised. For ortho- and meta-carborane the experimental reduction produces 7,9 in both cases and computed pathways for both processes are also defined; with ortho-carborane rearrangement occurs via 7,8, whereas with meta-carborane 7,9 is formed directly. The 7,9 isomer is the global minimum nido-structure. The characterisation of these isomerisation processes uncovers intermediates that adopt new structural motifs that we term basket and inverted nido. Basket intermediates feature a two-vertex basket handle bridging the remaining 10 vertices; inverted nido intermediates are related to known nido species, in that they have 5- and 6-membered belts, but where the latter, rather than the former, is capped, leaving a 5-membered open face. These new intermediates exhibit similar stability to the nido species, which is attributed to their relation to the 13-vertex docosahedron through the removal of 5-connected vertices. Isomerisation pathways starting from nido geometries are most often initiated by destabilisation of the cluster through a DSD process causing the 3-connected C7 vertex to move into a 4-connected site and a neighbouring B vertex to become 3-connected. The ensuing rearrangement of the cluster involves processes such as the pivoting of a 4-vertex diamond about its long diagonal, the pivoting of two 3-vertex triangles about a shared vertex and DSD processes. These processes are all ultimately driven by the preference for carbon to occupy low-connected vertices on the open 6-membered face of the resulting nido species.Publisher PDFPeer reviewe

Outcomes following oesophagectomy in patients with oesophageal cancer: a secondary analysis of the ICNARC Case Mix Programme Database

Introduction: This report describes the case mix and outcomes of patients with oesophageal cancer admitted to adult critical care units following elective oesophageal surgery in England, Wales and Northern Ireland. Methods: Admissions to critical care following elective oesophageal surgery for malignancy were identified using data from the Intensive Care National Audit and Research Centre (ICNARC) Case Mix Programme Database. Information on admissions between December 1995 and September 2007 were extracted and the association between in-hospital mortality and patient characteristics on admission to critical care was assessed using multiple logistic regression analysis. The performance of three prognostic models (Simplified Acute Physiology Score (SAPS) II, Acute Physiology and Chronic Health Evaluation (APACHE) II and the ICNARC physiology score) was also evaluated. Results: Between 1995 and 2007, there were 7227 admissions to 181 critical care units following oesophageal surgery for malignancy. Overall mortality in critical care was 4.4% and in-hospital mortality was 11%, although both declined steadily over time. Eight hundred and seventy-three (12.2%) patients were readmitted to critical care, most commonly for respiratory complications (49%) and surgical complications (25%). Readmitted patients had a critical care unit mortality of 24.7% and in-hospital mortality of 33.9%. Overall in-hospital mortality was associated with patient age, and various physiological measurements on admission to critical care (partial pressure of arterial oxygen (PaO2):fraction of inspired oxygen (FiO2) ratio, lowest arterial pH, mechanical ventilation, serum albumin, urea and creatinine). The three prognostic models evaluated performed poorly in measures of discrimination, calibration and goodness of fit. Conclusions: Surgery for oesophageal malignancy continues to be associated with significant morbidity and mortality. Age and organ dysfunction in the early postoperative period are associated with an increased risk of death. Postoperative serum albumin is confirmed as an additional prognostic factor. More work is required to determine how this knowledge may improve clinical management

Solid friction between soft filaments

Any macroscopic deformation of a filamentous bundle is necessarily accompanied by local sliding and/or stretching of the constituent filaments. Yet the nature of the sliding friction between two aligned filaments interacting through multiple contacts remains largely unexplored. Here, by directly measuring the sliding forces between two bundled F-actin filaments, we show that these frictional forces are unexpectedly large, scale logarithmically with sliding velocity as in solid-like friction, and exhibit complex dependence on the filaments' overlap length. We also show that a reduction of the frictional force by orders of magnitude, associated with a transition from solid-like friction to Stokes' drag, can be induced by coating F-actin with polymeric brushes. Furthermore, we observe similar transitions in filamentous microtubules and bacterial flagella. Our findings demonstrate how altering a filament's elasticity, structure and interactions can be used to engineer interfilament friction and thus tune the properties of fibrous composite materials

Contextualising ‘national security’

States quite naturally spend a great deal of time, energy, talent, and money on national security, prioritising protection against external armed attacks, for which traditional military forces are vital, and against internal threats such as espionage and subversion. In recent decades, this traditional security problématique has broadened to include defence against non-traditional security threats such as terrorism, cyber attacks, foreign meddling in domestic politics, and information warfare. Collectively, these challenges can be daunting, and the cost of failure can be high. But how do leaders know whether they are investing resources wisely? What would be an appropriate way of answering a question of this kind? In this paper, I suggest that calibrating resource allocations to security problems requires asking and attempting to answer a series of very basic questions that rarely attract the attention they warrant. These questions include the following. What does ‘security’ mean? How might one provide it? What things are worth securing, and why? How important are the various things the ‘security’ of which competes for resources? In most cases, I submit, if state leaders conducted a security audit using a rubric such as this, they would discover that they are spending their resources very unwisely indeed

Cybercrime in the Developing World

This paper attempts to discover the reasons behind the increase in cybercrime in developing nations over the past two decades. It discusses many examples and cases of projects to increase internet access in developing countries and how they enabled cybercrime. This paper examines how nations where many cybercrimes occurred, did not have the necessary resources or neglected to react appropriately. The other primary focus is how cybercrimes are not viewed the same as other crimes in many of these countries and how this perception allows cybercriminals to do as they please with no stigma from their neighbors. It concludes that laws and law enforcement, fund distribution, and ethics of these developing countries need to change to reduce the amount of cybercrime

Is the perception of time pressure a barrier to healthy eating and physical activity among women?

Objectives To describe the proportion of women reporting time is a barrier to healthy eating and physical activity, the characteristics of these women and the perceived causes of time pressure, and to examine associations between perceptions of time as a barrier and consumption of fruit, vegetables and fast food, and physical activity.Design A cross-sectional survey of food intake, physical activity and perceived causes of time pressure.Setting A randomly selected community sample.Subjects A sample of 1580 women self-reported their food intake and their perceptions of the causes of time pressure in relation to healthy eating. An additional 1521 women self-reported their leisure-time physical activity and their perceptions of the causes of time pressure in relation to physical activity.Results Time pressure was reported as a barrier to healthy eating by 41 % of the women and as a barrier to physical activity by 73 %. Those who reported time pressure as a barrier to healthy eating were significantly less likely to meet fruit, vegetable and physical activity recommendations, and more likely to eat fast food more frequently.Conclusions Women reporting time pressure as a barrier to healthy eating and physical activity are less likely to meet recommendations than are women who do not see time pressure as a barrier. Further research is required to understand the perception of time pressure issues among women and devise strategies to improve women’s food and physical activity behaviours