The orientation-preserving diffeomorphism group of S^2 deforms to SO(3) smoothly

Smale proved that the orientation-preserving diffeomorphism group of S^2 has a continuous strong deformation retraction to SO(3). In this paper, we construct such a strong deformation retraction which is diffeologically smooth.Comment: 16 page

Time-varying covariates and semi-parametric regression in capture-recapture: an adaptive spline approach

Advances in capture–recapture methodology have allowed the inclusion of continuous, time-dependent individual-covariates as predictors of survival and capture probabilities. The problem posed by these covariates is that they are only observed for an individual when that individual is captured. One solution is to assume a model of the covariate which defines the distribution of unobserved values, conditional on the observed values, and apply Bayesian methods to compute parameter estimates and to test the covariate’s effect. Previous applications of this approach have modeled the survival probability as a linear function of the covariate on some scale (e.g. identity or logistic). In some applications a linear function may not adequately describe the true relationship. Here we incorporate semi-parametric regression to allow for more flexibility in the relationship between the covariate and the survival probabilities of the Cormack– Jolly–Seber model. A fully Bayesian, adaptive algorithm is used to model the relationship with splines, in which the complexity of the relationship is governed by the number and location of the knots in the spline. A reversible jump Markov chain Monte Carlo algorithm is implemented to explore splines with different knot configurations, and model averaging is used to compute the final estimates of the survival probabilities. The method is applied to a simulated data set and to data collected through the Dutch Constant Effort Sites ringing project to study the survival of reed warblers (Acrocephalus scirpaceus) as a function of condition.postprin

The Bloom Clock for Causality Testing

Testing for causality between events in distributed executions is a fundamental problem. Vector clocks solve this problem but do not scale well. The probabilistic Bloom clock can determine causality between events with lower space, time, and message-space overhead than vector clock; however, predictions suffer from false positives. We give the protocol for the Bloom clock based on Counting Bloom filters and study its properties including the probabilities of a positive outcome and a false positive. We show the results of extensive experiments to determine how these above probabilities vary as a function of the Bloom timestamps of the two events being tested, and to determine the accuracy, precision, and false positive rate of a slice of the execution containing events in the temporal proximity of each other. Based on these experiments, we make recommendations for the setting of the Bloom clock parameters. We postulate the causality spread hypothesis from the application's perspective to indicate whether Bloom clocks will be suitable for correct predictions with high confidence. The Bloom clock design can serve as a viable space-, time-, and message-space-efficient alternative to vector clocks if false positives can be tolerated by an application

Incorporating ‘recruitment’ in matrix projection models : estimation, parameters, and the influence of model structure

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Journal of Ornithology 152, Suppl.2 (2012):585-595, doi:10.1007/s10336-010-0573-1.Advances in the estimation of population parameters using encounter data from marked individuals have made it possible to include estimates of the probability of recruitment in population projection models. However, the projected growth rate of the population, and the sensitivity of projected growth to changes in recruitment, can vary significantly depending upon both the structural form of the model and how recruitment is parameterized. We show that the common practices of (1) collapsing some age classes into a single, terminal ‘aggregated’ age-class, and (2) parameterizing recruitment using the proportion of recruited individuals (breeders) in a given age-class may confound analysis of age-based (Leslie) matrix projection models in some instances, relative to state-based projection models where recruited and pre-recruited individuals are treated as separate states. Failing to account for these differences can lead to misinterpretation of the relative role of recruitment in the dynamics of an age-structured population.We show that such problems can be avoided, either by structural changes to the terminal aggregated age-class in age-based models, or by using using a state-based model instead. Since all the metrics of general interest from a classical age-based matrix models are readily derived from a state-based model equivalent, this suggests there may be little reason to use the classical age-based approach in situations where recruitment is a parameter of interest

Protocol: does sodium nitrite administration reduce ischaemia-reperfusion injury in patients presenting with acute ST segment elevation myocardial infarction? Nitrites in acute myocardial infarction (NIAMI)

BACKGROUND: Whilst advances in reperfusion therapies have reduced early mortality from acute myocardial infarction, heart failure remains a common complication, and may develop very early or long after the acute event. Reperfusion itself leads to further tissue damage, a process described as ischaemia-reperfusion-injury (IRI), which contributes up to 50% of the final infarct size. In experimental models nitrite administration potently protects against IRI in several organs, including the heart. In the current study we investigate whether intravenous sodium nitrite administration immediately prior to percutaneous coronary intervention (PCI) in patients with acute ST segment elevation myocardial infarction will reduce myocardial infarct size. This is a phase II, randomised, placebo-controlled, double-blinded and multicentre trial. METHODS AND OUTCOMES: The aim of this trial is to determine whether a 5 minute systemic injection of sodium nitrite, administered immediately before opening of the infarct related artery, results in significant reduction of IRI in patients with first acute ST elevation myocardial infarction (MI). The primary clinical end point is the difference in infarct size between sodium nitrite and placebo groups measured using cardiovascular magnetic resonance imaging (CMR) performed at 6-8 days following the AMI and corrected for area at risk (AAR) using the endocardial surface area technique. Secondary end points include (i) plasma creatine kinase and Troponin I measured in blood samples taken pre-injection of the study medication and over the following 72 hours; (ii) infarct size at six months; (iii) Infarct size corrected for AAR measured at 6-8 days using T2 weighted triple inversion recovery (T2-W SPAIR or STIR) CMR imaging; (iv) Left ventricular (LV) ejection fraction measured by CMR at 6-8 days and six months following injection of the study medication; and (v) LV end systolic volume index at 6-8 days and six months. FUNDING,ETHICS AND REGULATORY APPROVALS: This study is funded by a grant from the UK Medical Research Council. This protocol is approved by the Scotland A Research Ethics Committee and has also received clinical trial authorisation from the Medicines and Healthcare products Regulatory Agency (MHRA) (EudraCT number: 2010-023571-26)

Simple Metals at High Pressure

In this lecture we review high-pressure phase transition sequences exhibited by simple elements, looking at the examples of the main group I, II, IV, V, and VI elements. General trends are established by analyzing the changes in coordination number on compression. Experimentally found phase transitions and crystal structures are discussed with a brief description of the present theoretical picture.Comment: 22 pages, 4 figures, lecture notes for the lecture given at the Erice course on High-Pressure Crystallography in June 2009, Sicily, Ital

Dietary soy and meat proteins induce distinct physiological and gene expression changes in rats

This study reports on a comprehensive comparison of the effects of soy and meat proteins given at the recommended level on physiological markers of metabolic syndrome and the hepatic transcriptome. Male rats were fed semi-synthetic diets for 1 wk that differed only regarding protein source, with casein serving as reference. Body weight gain and adipose tissue mass were significantly reduced by soy but not meat proteins. The insulin resistance index was improved by soy, and to a lesser extent by meat proteins. Liver triacylglycerol contents were reduced by both protein sources, which coincided with increased plasma triacylglycerol concentrations. Both soy and meat proteins changed plasma amino acid patterns. The expression of 1571 and 1369 genes were altered by soy and meat proteins respectively. Functional classification revealed that lipid, energy and amino acid metabolic pathways, as well as insulin signaling pathways were regulated differently by soy and meat proteins. Several transcriptional regulators, including NFE2L2, ATF4, Srebf1 and Rictor were identified as potential key upstream regulators. These results suggest that soy and meat proteins induce distinct physiological and gene expression responses in rats and provide novel evidence and suggestions for the health effects of different protein sources in human diets

A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58.

Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle