A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.Comment: 30 pages, 1 table, 4 figures, 1 supplementary table, 3 supplementary figure

Scaling and singularities in the entrainment of globally-coupled oscillators

The onset of collective behavior in a population of globally coupled oscillators with randomly distributed frequencies is studied for phase dynamical models with arbitrary coupling. The population is described by a Fokker-Planck equation for the distribution of phases which includes the diffusive effect of noise in the oscillator frequencies. The bifurcation from the phase-incoherent state is analyzed using amplitude equations for the unstable modes with particular attention to the dependence of the nonlinearly saturated mode $|\alpha_\infty|$ on the linear growth rate $\gamma$. In general we find $|\alpha_\infty|\sim \sqrt{\gamma(\gamma+l^2D)}$ where $D$ is the diffusion coefficient and $l$ is the mode number of the unstable mode. The unusual $(\gamma+l^2D)$ factor arises from a singularity in the cubic term of the amplitude equation.Comment: 11 pages (Revtex); paper submitted to Phys. Rev. Let

Performance Characteristics and Validation of Next-Generation Sequencing for Human Leucocyte Antigen Typing

High-resolution human leukocyte antigen (HLA) matching reduces graft-versus-host disease and improves overall patient survival after hematopoietic stem cell transplant. Sanger sequencing has been the gold standard for HLA typing since 1996. However, given the increasing number of new HLA alleles identified and the complexity of the HLA genes, clinical HLA typing by Sanger sequencing requires several rounds of additional testing to provide allele-level resolution. Although next-generation sequencing (NGS) is routinely used in molecular genetics, few clinical HLA laboratories use the technology. The performance characteristics of NGS HLA typing using TruSight HLA were determined using Sanger sequencing as the reference method. In total, 211 samples were analyzed with an overall accuracy of 99.8% (2954/2961) and 46 samples were analyzed for precision with 100% (368/368) reproducibility. Most discordant alleles were because of technical error rather than assay performance. More important, the ambiguity rate was 3.5% (103/2961). Seventy-four percentage of the ambiguities were within the DRB1 and DRB4 loci. HLA typing by NGS saves approximately $6000 per run when compared to Sanger sequencing. Thus, TruSight HLA assay enables high-throughput HLA typing with an accuracy, precision, ambiguity rate, and cost savings that should facilitate adoption of NGS technology in clinical HLA laboratories

THE RELATIONSHIP BETWEEN MUSCULOSKELETAL STRENGTH, PHYSIOLOGICAL CHARACTERISTICS, AND KNEE KINESTHESIA FOLLOWING FATIGUING EXERCISE

Fatiguing exercise may result in impaired functional joint stability and increased risk of unintentional injury. While there are several musculoskeletal and physiological characteristics related to fatigue onset, their relationship with proprioceptive changes following fatigue has not been examined. The purpose of this study was to establish the relationship between musculoskeletal and physiological characteristics and changes in proprioception, measured by threshold to detect passive motion (TTDPM), following fatiguing exercise. Twenty, physically active females participated (age: 28.65 ± 5.6 years, height: 165.6 ± 4.3 cm, weight: 61.8 ± 8.0 kg, BMI: 22.5± 2.3 kg/m2, BF: 23.3 ± 5.4%). During Visit 1, subjects completed an exercise history and 24-hour dietary questionnaire, and body composition, TTDPM familiarization, isokinetic knee strength, and maximal oxygen uptake/lactate threshold assessments. During Visit 2, subjects completed TTDPM and isometric knee strength testing prior to and following a fatiguing exercise protocol. Wilcoxon signed rank tests determined TTDPM and isometric knee strength changes from pre- to post- fatigue. Spearman’s rho correlation coefficients determined the relationship between strength and physiological variables with pre- to post-fatigue changes in TTDPM and with pre-fatigue and post-fatigue TTDPM in extension and flexion (α=0.05). No significant differences were demonstrated from pre-fatigue to post-fatigue TTDPM despite a significant decrease in isometric knee flexion strength (P<0.01) and flexion/extension ratio (P<0.05) following fatigue. No significant correlations were observed between strength or physiological variables and changes in TTDPM from pre- to post-fatigue in extension or flexion. Flexion/extension ratio was significantly correlated with pre-fatigue TTDPM in extension (r=-0.231, P<0.05). Peak oxygen uptake was significantly correlated with pre-fatigue (r=-0.500, P<0.01) and post-fatigue (r=-0.520, P<0.05) TTDPM in extension. No significant relationships were demonstrated between musculoskeletal and physiological characteristics and changes in TTDPM following fatigue. The results suggest that highly trained individuals may have better proprioception, and that the high fitness level of subjects in this investigation may have contributed to absence of TTDPM deficits following fatigue despite reaching a high level of perceptual and physiological fatigue. Future studies should consider various subject populations, other musculoskeletal strength characteristics, and different modalities of proprioception to determine the most important contributions to proprioceptive changes following fatigue

Testing for HFE-related haemochromatosis

HFE-haemochromatosis is a genetic disorder resulting from mutations of the HFE gene. It primarily affects people of Northern European descent. Clinical manifestations result from the progressive deposition of iron into various organs including the liver. An elevated serum ferritin concentration greater than 300 microgram/L and a transferrin saturation of greater than 45% will identify almost all patients with HFE-haemochromatosis. HFE genotyping confirms the diagnosis. In some patients, liver biopsy may still be necessary as the degree of hepatic fibrosis has prognostic implications

Towards a Strategy for Improving Agricultural Inputs Markets in Africa

Agribusiness, Downloads July 2008-July 2009: 19,

Antiretroviral Therapy-Associated Acute Motor and Sensory Axonal Neuropathy

Guillain-Barré syndrome (GBS) has been reported in HIV-infected patients in association with the immune reconstitution syndrome whose symptoms can be mimicked by highly active antiretroviral therapy (HAART)-mediated mitochondrial toxicity. We report a case of a 17-year-old, HIV-infected patient on HAART with a normal CD4 count and undetectable viral load, presenting with acute lower extremity weakness associated with lactatemia. Electromyography/nerve conduction studies revealed absent sensory potentials and decreased compound muscle action potentials, consistent with a diagnosis of acute motor and sensory axonal neuropathy. Lactatemia resolved following cessation of HAART; however, neurological deficits minimally improved over several months in spite of immune modulatory therapy. This case highlights the potential association between HAART, mitochondrial toxicity and acute axonal neuropathies in HIV-infected patients, distinct from the immune reconstitution syndrome

BRIGHTHELMSTONE (Reino Unido) (Inglaterra). Planos de población (1788). 1:1950

Escala gráfica de un esadio o diez "chains" [= 9,9 cm]. Orientado con lis en rosa de ocho vientosOrografía a trazosRelación de los edificios más significativos de la ciudad indicados por clave alfabéticaToponimia de las calles y plazas principales de BrigthonTítulo enmarcado en cartela ovaladaImpreso en varios coloresForma parte de la Colección Mendoz

Nonlinear saturation of electrostatic waves: mobile ions modify trapping scaling

The amplitude equation for an unstable electrostatic wave in a multi-species Vlasov plasma has been derived. The dynamics of the mode amplitude $\rho(t)$ is studied using an expansion in $\rho$; in particular, in the limit $\gamma\rightarrow0^+$, the singularities in the expansion coefficients are analyzed to predict the asymptotic dependence of the electric field on the linear growth rate $\gamma$. Generically $|E_k|\sim \gamma^{5/2}$, as $\gamma\rightarrow0^+$, but in the limit of infinite ion mass or for instabilities in reflection-symmetric systems due to real eigenvalues the more familiar trapping scaling $|E_k|\sim \gamma^{2}$ is predicted.Comment: 13 pages (Latex/RevTex), 4 postscript encapsulated figures which are included using the utility "uufiles". They should be automatically included with the text when it is downloaded. Figures also available in hard copy from the authors ([email protected]

The Properties of Poor Groups of Galaxies: II. X-ray and Optical Comparisons

We use ROSAT PSPC data to study the X-ray properties of a sample of twelve poor groups that have extensive membership information (Zabludoff and Mulchaey 1997; Paper I). Diffuse X-ray emission is detected in nine of these groups. In all but one of the X-ray detected groups, the X-ray emission is centered on a luminous elliptical galaxy. Fits to the surface brightness profiles of the X-ray emission suggest the presence of two X-ray components in these groups. The first component is centered on the central elliptical galaxy. The location and extent of this component, combined with its X-ray temperature and luminosity, favor an origin in the interstellar medium of the central galaxy. Alternatively, the central component may be the result of a large-scale cooling flow. The second X-ray component is detected out to a radius of at least 100-300 kpc. This component follows the same relationships found among the X-ray temperature, X-ray luminosity and optical velocity dispersion of rich clusters. This result suggests that the X-ray detected groups are low-mass versions of clusters and that the extended gas component can properly be called the intragroup medium, in analogy to the intracluster medium in clusters. We also find a trend for the position angle of the optical light in the central elliptical galaxy to align with the position angle of the large-scale X-ray emission. (Abridged)Comment: 38 pages, AASLaTeX with 16 PS figures. Figure 1a-1l available in gzipped postscript format at ftp://corvus.ociw.edu/pub/mulchae