Total-evidence framework reveals complex morphological evolution in nightbirds (Strisores)

Strisores is a clade of neoavian birds that include diurnal aerial specialists such as swifts and hummingbirds, as well as several predominantly nocturnal lineages such as nightjars and potoos. Despite the use of genome-scale molecular datasets, the phylogenetic interrelationships among major strisorean groups remain controversial. Given the availability of next-generation sequence data for Strisores and the clade’s rich fossil record, we reassessed the phylogeny of Strisores by incorporating a large-scale sequence dataset with anatomical data from living and fossil strisoreans within a Bayesian total-evidence framework. Combined analyses of molecular and morphological data resulted in a phylogenetic topology for Strisores that is congruent with the findings of two recent molecular phylogenomic studies, supporting nightjars (Caprimulgidae) as the extant sister group of the remainder of Strisores. This total-evidence framework allowed us to identify morphological synapomorphies for strisorean clades previously recovered using molecular-only datasets. However, a combined analysis of molecular and morphological data highlighted strong signal conflict between sequence and anatomical data in Strisores. Furthermore, simultaneous analysis of molecular and morphological data recovered differing placements for some fossil taxa compared with analyses of morphological data under a molecular scaffold, highlighting the importance of analytical decisions when conducting morphological phylogenetic analyses of taxa with molecular phylogenetic data. We suggest that multiple strisorean lineages have experienced convergent evolution across the skeleton, obfuscating the phylogenetic position of certain fossils, and that many distinctive specializations of strisorean subclades were acquired early in their evolutionary history. Despite this apparent complexity in the evolutionary history of Strisores, our results provide fossil support for aerial foraging as the ancestral ecological strategy of Strisores, as implied by recent phylogenetic topologies derived from molecular data.Parts of this project were supported by Systematics Research Fund awards to A.C. and D.J.F. by the Linnean Society of London and the Systematics Association. D.J.F. also acknowledges support from the Isaac Newton Trust early career support scheme. Parts of this project were also funded by the European Union’s Horizon 2020 research and innovation program 2014–2018 under grant agreement 677774 (European Research Council [ERC] Starting Grant: TEMPO) to R.B.J.B. N.D.W. and M.J.B. received Smithsonian Institution support through the Predoctoral Fellowship Program (N.D.W.), the Frontiers in Phylogenetics Program, the Scholarly Studies Program, and the Consortium for Understanding and Sustaining a Biodiverse Planet

Cigarette smoking and risk of acoustic neuromas and pituitary tumours in the Million Women Study

BACKGROUND: The relationship between cigarette smoking and incidence of acoustic neuromas and pituitary tumours is uncertain. METHODS: We examined the relation between smoking and risk of acoustic neuromas and pituitary tumours in a prospective study of 1.2 million middle-aged women in the United Kingdom. RESULTS: Over 10.2 million person years of follow-up, 177 women were diagnosed with acoustic neuromas and 174 with pituitary tumours. Current smokers at recruitment were at significantly reduced risk of incident acoustic neuroma compared with never smokers (adjusted relative risk (RR)=0.41, 95% confidence interval (CI)=0.24-0.70, P=0.001). Past smokers did not have significantly different risk of acoustic neuroma than never smokers (RR=0.87, 95% CI=0.62-1.22, P=0.4). Smoking was not associated with incidence of pituitary tumours (RR in current vs never smokers=0.91, 95% CI=0.60-1.40, P=0.7). CONCLUSION: Women who smoke are at a significantly reduced risk of acoustic neuromas, but not of pituitary tumours, compared with never smokers. Acoustic neuromas are much rarer than the cancers that are increased among smokers

A systematic review of postgraduate training programmes directed at pharmacists entering primary care

This systematic review explores the international postgraduate education and training programmes designed to provide or develop knowledge or skills focused on enabling pharmacists to work in a general practice setting. Four thousand, eight hundred and seventy-one (4,871) articles were identified from database searches of SCOPUS, EMBASE, Medline, CINAHL, IPA, Web of Science and ERIC. After removal of duplicates and article screening, seven articles were included. Educational content, setting, contact time and methods of assessment varied across all studies. There is paucity of published literature relating to the development and evaluation of education programmes directed at pharmacists entering into general practice. A combination of work and classroom-based education provided by general practitioners and pharmacists already working in primary care is deemed most beneficial coupled with systematic debriefing sessions at the completion of training courses. The findings suggest future training should focus on specific disease states.</jats:p

Fracture and damage localization in volcanic edifice rocks from El Hierro, Stromboli and Tenerife

© 2018 The Author(s). We present elastic wave velocity and strength data from a suite of three volcanic rocks taken from the volcanic edifices of El Hierro and Tenerife (Canary Islands, Spain), and Stromboli (Aeolian Islands, Italy). These rocks span a range of porosity and are taken from volcanoes that suffer from edifice instability. We measure elastic wave velocities at known incident angles to the generated through-going fault as a function of imposed strain, and examine the effect of the damage zone on P-wave velocity. Such data are important as field measurements of elastic wave tomography are key tools for understanding volcanic regions, yet hidden fractures are likely to have a significant effect on elastic wave velocity. We then use elastic wave velocity evolution to calculate concomitant crack density evolution which ranges from 0 to 0.17: highest values were correlated to the damage zone in rocks with the highest initial porosity

Psoriasin, one of several new proteins identified in nasal lavage fluid from allergic and non-allergic individuals using 2-dimensional gel electrophoresis and mass spectrometry

BACKGROUND: Extravasation and luminal entry of plasma occurs continuously in the nose. This process is markedly facilitated in patients with symptomatic allergic rhinitis, resulting in an increased secretion of proteins. Identification of these proteins is an important step in the understanding of the pathological mechanisms in allergic diseases. DNA microarrays have recently made it possible to compare mRNA profiles of lavage fluids from healthy and diseased patients, whereas information on the protein level is still lacking. METHODS: Nasal lavage fluid was collected from 11 patients with symptomatic allergic rhinitis and 11 healthy volunteers. 2-dimensional gel electrophoresis was used to separate proteins in the lavage fluids. Protein spots were picked from the gels and identified using mass spectrometry and database search. Selected proteins were confirmed with western blot. RESULTS: 61 spots were identified, of which 21 were separate proteins. 6 of these proteins (psoriasin, galectin-3, alpha enolase, intersectin-2, Wnt-2B and hypothetical protein MGC33648) had not previously been described in nasal lavage fluids. The levels of psoriasin were markedly down-regulated in allergic individuals. Prolactin-inducible protein was also found to be down-regulated, whereas different fragments of albumin together with Ig gamma 2 chain c region, transthyretin and splice isoform 1 of Wnt-2B were up-regulated among the allergic patients. CONCLUSION: The identification of proteins in nasal lavage fluid with 2-dimensional gelelectrophoresis in combination with mass spectrometry is a novel tool to profile protein expression in allergic rhinitis and it might prove useful in the hunt for new therapeutic targets or diagnostic markers for allergic diseases. Psoriasin is a potent chemotactic factor and its down-regulation during inflammation might be of importance for the outcome of the disease

RepSeq-A database of amino acid repeats present in lower eukaryotic pathogens

BACKGROUND Amino acid repeat-containing proteins have a broad range of functions and their identification is of relevance to many experimental biologists. In human-infective protozoan parasites (such as the Kinetoplastid and Plasmodium species), they are implicated in immune evasion and have been shown to influence virulence and pathogenicity. RepSeq http://repseq.gugbe.com is a new database of amino acid repeat-containing proteins found in lower eukaryotic pathogens. The RepSeq database is accessed via a web-based application which also provides links to related online tools and databases for further analyses. RESULTS The RepSeq algorithm typically identifies more than 98% of repeat-containing proteins and is capable of identifying both perfect and mismatch repeats. The proportion of proteins that contain repeat elements varies greatly between different families and even species (3 - 35% of the total protein content). The most common motif type is the Sequence Repeat Region (SRR) - a repeated motif containing multiple different amino acid types. Proteins containing Single Amino Acid Repeats (SAARs) and Di-Peptide Repeats (DPRs) typically account for 0.5 - 1.0% of the total protein number. Notable exceptions are P. falciparum and D. discoideum, in which 33.67% and 34.28% respectively of the predicted proteomes consist of repeat-containing proteins. These numbers are due to large insertions of low complexity single and multi-codon repeat regions. CONCLUSION The RepSeq database provides a repository for repeat-containing proteins found in parasitic protozoa. The database allows for both individual and cross-species proteome analyses and also allows users to upload sequences of interest for analysis by the RepSeq algorithm. Identification of repeat-containing proteins provides researchers with a defined subset of proteins which can be analysed by expression profiling and functional characterisation, thereby facilitating study of pathogenicity and virulence factors in the parasitic protozoa. While primarily designed for kinetoplastid work, the RepSeq algorithm and database retain full functionality when used to analyse other species

The detection of the imprint of filaments on cosmic microwave background lensing

Galaxy redshift surveys, such as 2dF, SDSS, 6df, GAMA and VIPERS, have shown that the spatial distribution of matter forms a rich web, known as the cosmic web. The majority of galaxy survey analyses measure the amplitude of galaxy clustering as a function of scale, ignoring information beyond a small number of summary statistics. Since the matter density field becomes highly non-Gaussian as structure evolves under gravity, we expect other statistical descriptions of the field to provide us with additional information. One way to study the non-Gaussianity is to study filaments, which evolve non-linearly from the initial density fluctuations produced in the primordial Universe. In our study, we report the first detection of CMB (Cosmic Microwave Background) lensing by filaments and we apply a null test to confirm our detection. Furthermore, we propose a phenomenological model to interpret the detected signal and we measure how filaments trace the matter distribution on large scales through filament bias, which we measure to be around 1.5. Our study provides a new scope to understand the environmental dependence of galaxy formation. In the future, the joint analysis of lensing and Sunyaev-Zel'dovich observations might reveal the properties of `missing baryons', the vast majority of the gas which resides in the intergalactic medium and has so far evaded most observations

Geographic range did not confer resilience to extinction in terrestrial vertebrates at the end-Triassic crisis

Rates of extinction vary greatly through geological time, with losses particularly concentrated in mass extinctions. Species duration at other times varies greatly, but the reasons for this are unclear. Geographical range correlates with lineage duration amongst marine invertebrates, but it is less clear how far this generality extends to other groups in other habitats. It is also unclear whether a wide geographical distribution makes groups more likely to survive mass extinctions. Here we test for extinction selectivity amongst terrestrial vertebrates across the end-Triassic event. We demonstrate that terrestrial vertebrate clades with larger geographical ranges were more resilient to extinction than those with smaller ranges throughout the Triassic and Jurassic. However, this relationship weakened with increasing proximity to the end-Triassic mass extinction, breaking down altogether across the event itself. We demonstrate that these findings are not a function of sampling biases; a perennial issue in studies of this kind

An inexact dual logarithmic barrier method for solving sparse semidefinite programs

A dual logarithmic barrier method for solving large, sparse semidefinite programs is proposed in this paper. The method avoids any explicit use of the primal variable X and therefore is well-suited to problems with a sparse dual matrix S. It relies on inexact Newton steps in dual space which are computed by the conjugate gradient method applied to the Schur complement of the reduced KKT system. The method may take advantage of low-rank representations of matrices Ai to perform implicit matrix-vector products with the Schur complement matrix and to compute only specific parts of this matrix. This allows the construction of the partial Cholesky factorization of the Schur complement matrix which serves as a good preconditioner for it and permits the method to be run in a matrix-free scheme. Convergence properties of the method are studied and a polynomial complexity result is extended to the case when inexact Newton steps are employed. A Matlab-based implementation is developed and preliminary computational results of applying the method to maximum cut and matrix completion problems are reported

Stability of cluster solutions in a cooperative consumer chain model

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ Springer-Verlag Berlin Heidelberg 2012.We study a cooperative consumer chain model which consists of one producer and two consumers. It is an extension of the Schnakenberg model suggested in Gierer and Meinhardt [Kybernetik (Berlin), 12:30-39, 1972] and Schnakenberg (J Theor Biol, 81:389-400, 1979) for which there is only one producer and one consumer. In this consumer chain model there is a middle component which plays a hybrid role: it acts both as consumer and as producer. It is assumed that the producer diffuses much faster than the first consumer and the first consumer much faster than the second consumer. The system also serves as a model for a sequence of irreversible autocatalytic reactions in a container which is in contact with a well-stirred reservoir. In the small diffusion limit we construct cluster solutions in an interval which have the following properties: The spatial profile of the third component is a spike. The profile for the middle component is that of two partial spikes connected by a thin transition layer. The first component in leading order is given by a Green's function. In this profile multiple scales are involved: The spikes for the middle component are on the small scale, the spike for the third on the very small scale, the width of the transition layer for the middle component is between the small and the very small scale. The first component acts on the large scale. To the best of our knowledge, this type of spiky pattern has never before been studied rigorously. It is shown that, if the feedrates are small enough, there exist two such patterns which differ by their amplitudes.We also study the stability properties of these cluster solutions. We use a rigorous analysis to investigate the linearized operator around cluster solutions which is based on nonlocal eigenvalue problems and rigorous asymptotic analysis. The following result is established: If the time-relaxation constants are small enough, one cluster solution is stable and the other one is unstable. The instability arises through large eigenvalues of order O(1). Further, there are small eigenvalues of order o(1) which do not cause any instabilities. Our approach requires some new ideas: (i) The analysis of the large eigenvalues of order O(1) leads to a novel system of nonlocal eigenvalue problems with inhomogeneous Robin boundary conditions whose stability properties have been investigated rigorously. (ii) The analysis of the small eigenvalues of order o(1) needs a careful study of the interaction of two small length scales and is based on a suitable inner/outer expansion with rigorous error analysis. It is found that the order of these small eigenvalues is given by the smallest diffusion constant ε22.RGC of Hong Kon