Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight and crown birds

Branch lengths—measured in character changes—are an essential requirement of clock-based divergence estimation, regardless of whether the fossil calibrations used represent nodes or tips. However, a separate set of divergence time approaches are typically used to date palaeontological trees, which may lack such branch lengths. Among these methods, sophisticated probabilistic approaches have recently emerged, in contrast with simpler algorithms relying on minimum node ages. Here, using a novel phylogenetic hypothesis for Mesozoic dinosaurs, we apply two such approaches to estimate divergence times for: (i) Dinosauria, (ii) Avialae (the earliest birds) and (iii) Neornithes (crown birds). We find: (i) the plausibility of a Permian origin for dinosaurs to be dependent on whether Nyasasaurus is the oldest dinosaur, (ii) a Middle to Late Jurassic origin of avian flight regardless of whether Archaeopteryx or Aurornis is considered the first bird and (iii) a Late Cretaceous origin for Neornithes that is broadly congruent with other node- and tip-dating estimates. Demonstrating the feasibility of probabilistic time-scaling further opens up divergence estimation to the rich histories of extinct biodiversity in the fossil record, even in the absence of detailed character data

Undetected Blooms in Prince William Sound: Using Multiple Techniques to Elucidate the Base of the Summer Food Web

© 2015, Coastal and Estuarine Research Federation. Prince William Sound supports many commercially and culturally important species. The phytoplankton community dynamics which support and sustain the high biomass and diversity of this ecosystem are largely unknown. The aim of this study was to describe the phytoplankton community composition during the summer, the time at which this system supports many additional migrants and commercially important fisheries. Phytoplankton community composition (pigments), dissolved nutrients, Secchi depth, total and particulate organic carbon and nitrogen, and export to deep water were measured during the summers of 2008–2010. In addition, natural abundance stable isotopes (δ13C and δ15N) of particulate organic matter (POM) and faunal samples were measured in 2010. The analysis of the phytoplankton community composition using multivariate statistics showed that changes over the summer were driven by changes in the proportion of the dominant groups: diatoms, dinoflagellates, cyanobacteria, cryptophytes, chlorophytes, and prasinophytes. These changes were driven by changes in nutrients including an organic nitrogen source, phosphate, and silica and correspond to shifts in particulate concentrations. A consistent pattern was observed each year: a large Noctiluca sp. bloom in June concurrent with low nutrients, low diversity, and high particulate organic carbon (POC) concentrations was followed by a shift in the phytoplankton community to a more diverse smaller size class community in July and equilibrating in August. This annual summer bloom could be an important contributor to the energy and nutrient inputs at the base of the regional marine food web

Holographic Metamagnetism, Quantum Criticality, and Crossover Behavior

Using high-precision numerical analysis, we show that 3+1 dimensional gauge theories holographically dual to 4+1 dimensional Einstein-Maxwell-Chern-Simons theory undergo a quantum phase transition in the presence of a finite charge density and magnetic field. The quantum critical theory has dynamical scaling exponent z=3, and is reached by tuning a relevant operator of scaling dimension 2. For magnetic field B above the critical value B_c, the system behaves as a Fermi liquid. As the magnetic field approaches B_c from the high field side, the specific heat coefficient diverges as 1/(B-B_c), and non-Fermi liquid behavior sets in. For B<B_c the entropy density s becomes non-vanishing at zero temperature, and scales according to s \sim \sqrt{B_c - B}. At B=B_c, and for small non-zero temperature T, a new scaling law sets in for which s\sim T^{1/3}. Throughout a small region surrounding the quantum critical point, the ratio s/T^{1/3} is given by a universal scaling function which depends only on the ratio (B-B_c)/T^{2/3}. The quantum phase transition involves non-analytic behavior of the specific heat and magnetization but no change of symmetry. Above the critical field, our numerical results are consistent with those predicted by the Hertz/Millis theory applied to metamagnetic quantum phase transitions, which also describe non-analytic changes in magnetization without change of symmetry. Such transitions have been the subject of much experimental investigation recently, especially in the compound Sr_3 Ru_2 O_7, and we comment on the connections.Comment: 23 pages, 8 figures v2: added ref

Treatment delays in paediatric dento-alveolar trauma at a tertiary referral hospital

Background: Paediatric dento-alveolar trauma is a common event. Delays in treatment can have adverse effects on long term outcomes and the aim of this study was to quantify the treatment delays in paediatric dento-alveolar trauma in a tertiary referral hospital. Methods: All cases of paediatric dento-alveolar trauma over a two-year period from July 2000 to June 2002 were identified and the charts were reviewed retrospectively. All children presenting the emergency department with dento-alveolar trauma within 48 hours of injury during the time period were included. Results: Forty-three patients were identified. The average age was 5.51 years, though there was a bias towards one and two year olds. Males were injured 1.5 times more frequently than females. There was an average delay of 9.6 hours between injury and treatment for all patients. Transit time from outside practitioners to hospital and waiting times in hospital made up the greatest delays. Children injured an average of 2.37 teeth and only 14 per cent were uncomplicated crown fractures. Conclusions: Children who present to children's hospitals for treatment of dento-alveolar trauma have more severe injuries than those treated elsewhere. They have large but potentially reducible delays between injury and treatment

Extreme Energy Cosmic Rays: Bottom-up vs. Top-down scenarii

We present an overview on extreme energy cosmic rays (EECR) and the fundamental physics connected with them. The top-down and bottom-up scenarii are contrasted. We summarize the essential features underlying the top-down scenarii for EECR, namely, the lifetime and the mass {\bf imposed} to the heavy relics whatever they be: topological and non-topological solitons, X-particles, cosmic defects, microscopic black-holes, fundamental strings. An unified formula for the quantum decay rate of all these objects was provided in hep-ph/0202249. The key point in the top-down scenarii is the necessity to {\bf adjust} the lifetime of the heavy object to the age of the universe. The natural lifetimes of such heavy objects are, however, microscopic times associated to the GUT energy scale (sim 10^{-28} sec. or shorter); such heavy objects could have been abundantly formed by the end of inflation and it seems natural they decayed shortly after being formed. The arguments produced to {\bf fine tune} the relics lifetime to the age of the universe are critically analyzed. The annihilation scenario (`Wimpzillas') is analyzed too. Top-down scenarii based on networks of topological defects are strongly disfavored at the light of the recent CMB anisotropy observations. We discuss the acceleration mechanisms of cosmic rays,their possible astrophysical sources and the main open physical problems and difficulties in the context of bottom-up scenarii, and we conclude by outlining the expectations from future observatories like EUSO and where the theoretical effort should be placed.Comment: LaTex, 16 pages, 2 .eps figures. The annihilation scenario (Wimpzillas) is included and the discussion on gamma ray bursts improved. Based on lectures at the Fourth International Workshop on `New Worlds in Astroparticle Physics' in Faro, Portugal, September 2002, at the 9th Course on Astrofundamental Physics of the Chalonge School, Palermo, Italia, September 2002 and at the SOWG EUSO meeting, Roma, Italia, November 200

A holographic model for the fractional quantum Hall effect

Experimental data for fractional quantum Hall systems can to a large extent be explained by assuming the existence of a modular symmetry group commuting with the renormalization group flow and hence mapping different phases of two-dimensional electron gases into each other. Based on this insight, we construct a phenomenological holographic model which captures many features of the fractional quantum Hall effect. Using an SL(2,Z)-invariant Einstein-Maxwell-axio-dilaton theory capturing the important modular transformation properties of quantum Hall physics, we find dyonic diatonic black hole solutions which are gapped and have a Hall conductivity equal to the filling fraction, as expected for quantum Hall states. We also provide several technical results on the general behavior of the gauge field fluctuations around these dyonic dilatonic black hole solutions: We specify a sufficient criterion for IR normalizability of the fluctuations, demonstrate the preservation of the gap under the SL(2,Z) action, and prove that the singularity of the fluctuation problem in the presence of a magnetic field is an accessory singularity. We finish with a preliminary investigation of the possible IR scaling solutions of our model and some speculations on how they could be important for the observed universality of quantum Hall transitions.Comment: 86 pages, 16 figures; v.2 references added, typos fixed, improved discussion of ref. [39]; v.3 more references added and typos fixed, several statements clarified, v.4 version accepted for publication in JHE

The Supertree Tool Kit

<p>Abstract</p> <p>Background</p> <p>Large phylogenies are crucial for many areas of biological research. One method of creating such large phylogenies is the supertree method, but creating supertrees containing thousands of taxa, and hence providing a comprehensive phylogeny, requires hundred or even thousands of source input trees. Managing and processing these data in a systematic and error-free manner is challenging and will become even more so as supertrees contain ever increasing numbers of taxa. Protocols for processing input source phylogenies have been proposed to ensure data quality, but no robust software implementations of these protocols as yet exist.</p> <p>Findings</p> <p>The aim of the Supertree Tool Kit (STK) is to aid in the collection, storage and processing of input source trees for use in supertree analysis. It is therefore invaluable when creating supertrees containing thousands of taxa and hundreds of source trees. The STK is a Perl module with executable scripts to carry out various steps in the processing protocols. In order to aid processing we have added meta-data, via XML, to each tree which contains information such as the bibliographic source information for the tree and how the data were derived, for instance the character data used to carry out the original analysis. These data are essential parts of previously proposed protocols.</p> <p>Conclusions</p> <p>The STK is a bioinformatics tool designed to make it easier to process source phylogenies for inclusion in supertree analysis from hundreds or thousands of input source trees, whilst reducing potential errors and enabling easy sharing of such datasets. It has been successfully used to create the largest known supertree to date containing over 5000 taxa from over 700 source phylogenies.</p

Using interpretative phenomenological analysis to inform physiotherapy practice: An introduction with reference to the lived experience of cerebellar ataxia

The attached file is a pre-published version of the full and final paper which can be found at the link below.This article has been made available through the Brunel Open Access Publishing Fund.Qualitative research methods that focus on the lived experience of people with health conditions are relatively underutilised in physiotherapy research. This article aims to introduce interpretative phenomenological analysis (IPA), a research methodology oriented toward exploring and understanding the experience of a particular phenomenon (e.g., living with spinal cord injury or chronic pain, or being the carer of someone with a particular health condition). Researchers using IPA try to find out how people make sense of their experiences and the meanings they attach to them. The findings from IPA research are highly nuanced and offer a fine grained understanding that can be used to contextualise existing quantitative research, to inform understanding of novel or underresearched topics or, in their own right, to provoke a reappraisal of what is considered known about a specified phenomenon. We advocate IPA as a useful and accessible approach to qualitative research that can be used in the clinical setting to inform physiotherapy practice and the development of services from the perspective of individuals with particular health conditions.This article is available through the Brunel Open Access Publishing Fund

Variation in Estimated Medicare Prescription Drug Plan Costs and Affordability for Beneficiaries Living in Different States

BACKGROUND: Medicare Part D prescription drug plans (PDPs) implemented in January 2006 are designed to improve beneficiaries’ access to pharmaceuticals and use market competition to yield affordable drug costs. Variations in estimated PDP costs for beneficiaries living in different states have not previously been characterized. OBJECTIVE: To describe variations in the estimated costs of PDPs (plan premium, copays, and coinsurance) within and across states. DESIGN: To estimate PDP costs based on 4 actual patient cases that exemplify common conditions and prescription drug combinations for Medicare beneficiaries, we used the online tool provided by the Centers for Medicare and Medicaid Services. MEASUREMENTS: Principal study outcomes included (a) variation across states in the estimated annual cost of the lowest-cost PDP for each case and (b) variation in the estimated affordability of the lowest-cost PDPs across states, based on cost-of-living-adjusted median income for zero-earner households. RESULTS: For all 4 patient cases, we found substantive within-state and between-state differences in the estimated costs of Medicare PDPs incurred by beneficiaries. The estimated annual costs to beneficiaries of the lowest-cost PDPs varied across states by as much as $320 for medications in the least expensive scenario, and by as much as$13,000 for the most expensive scenario. On average across states, a beneficiary with cost-of-living-adjusted median income would expect to spend 3%–28% of annual income to pay for medications in the lowest-cost PDPs in the 4 patient cases. The affordability of the lowest-cost plans varied across states, and for 2 of the 4 cases the lowest-cost PDP estimates were negatively correlated with cost-of-living-adjusted median income. CONCLUSIONS: Substantive differences in estimated PDP costs are evident across states for patients with common Medicare conditions. Importantly, the lowest-cost plans were not proportionally affordable with respect to state-specific cost-of-living-adjusted median income. Refinement of the Medicare drug program may be needed to improve national balance in PDP affordability for beneficiaries living in different states. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available for this article at http://dx.doi.org/10.1007/s11606-006-0018-y and is accessible for authorized users

Genetic Interactions between Chromosomes 11 and 18 Contribute to Airway Hyperresponsiveness in Mice

We used two-dimensional quantitative trait locus analysis to identify interacting genetic loci that contribute to the native airway constrictor hyperresponsiveness to methacholine that characterizes A/J mice, relative to C57BL/6J mice. We quantified airway responsiveness to intravenous methacholine boluses in eighty-eight (C57BL/6J X A/J) F2 and twenty-seven (A/J X C57BL/6J) F2 mice as well as ten A/J mice and six C57BL/6J mice; all studies were performed in male mice. Mice were genotyped at 384 SNP markers, and from these data two-QTL analyses disclosed one pair of interacting loci on chromosomes 11 and 18; the homozygous A/J genotype at each locus constituted the genetic interaction linked to the hyperresponsive A/J phenotype. Bioinformatic network analysis of potential interactions among proteins encoded by genes in the linked regions disclosed two high priority subnetworks - Myl7, Rock1, Limk2; and Npc1, Npc1l1. Evidence in the literature supports the possibility that either or both networks could contribute to the regulation of airway constrictor responsiveness. Together, these results should stimulate evaluation of the genetic contribution of these networks in the regulation of airway responsiveness in humans