Singing from the Grave: DNA from a 180 Year Old Type Specimen Confirms the Identity of Chrysoperla carnea (Stephens)

Copyright: © 2015 Price et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

B mu G@Sbase-a microbial gene expression and comparative genomic database

The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bioinformatics resources and tool development. The Bacterial Microarray Group at St George's (BμG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BμG@Sbase, a microbial gene expression and comparative genomic database. BμG@Sbase (http://bugs.sgul.ac.uk/bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehensive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation information for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to present complex experimental details clearly and concisely. Furthermore the modular design of the database will provide a robust platform for integrating other data types beyond microarrays into a more Systems analysis based future

Air-sea transfer of gas phase controlled compounds

Gases in the atmosphere/ocean have solubility that spans several orders of magnitude. Resistance in the molecular sublayer on the waterside limits the air-sea exchange of sparingly soluble gases such as SF6 and CO2. In contrast, both aerodynamic and molecular diffusive resistances on the airside limit the exchange of highly soluble gases (as well as heat). Here we present direct measurements of air-sea methanol and acetone transfer from two open cruises: the Atlantic Meridional Transect in 2012 and the High Wind Gas Exchange Study in 2013. The transfer of the highly soluble methanol is essentially completely airside controlled, while the less soluble acetone is subject to both airside and waterside resistances. Both compounds were measured concurrently using a proton-transfer-reaction mass spectrometer, with their fluxes quantified by the eddy covariance method. Up to a wind speed of 15 m s-1, observed air-sea transfer velocities of these two gases are largely consistent with the expected near linear wind speed dependence. Measured acetone transfer velocity is ~30% lower than that of methanol, which is primarily due to the lower solubility of acetone. From this difference we estimate the "zero bubble" waterside transfer velocity, which agrees fairly well with interfacial gas transfer velocities predicted by the COARE model. At wind speeds above 15 m s-1, the transfer velocities of both compounds are lower than expected in the mean. Air-sea transfer of sensible heat (also airside controlled) also appears to be reduced at wind speeds over 20 m s-1. During these conditions, large waves and abundant whitecaps generate large amounts of sea spray, which is predicted to alter heat transfer and could also affect the air-sea exchange of soluble trace gases. We make an order of magnitude estimate for the impacts of sea spray on air-sea methanol transfer

Effort estimation of FLOSS projects: A study of the Linux kernel

This is the post-print version of the Article. The official published version can be accessed from the link below - Copyright @ 2011 SpringerEmpirical research on Free/Libre/Open Source Software (FLOSS) has shown that developers tend to cluster around two main roles: “core” contributors differ from “peripheral” developers in terms of a larger number of responsibilities and a higher productivity pattern. A further, cross-cutting characterization of developers could be achieved by associating developers with “time slots”, and different patterns of activity and effort could be associated to such slots. Such analysis, if replicated, could be used not only to compare different FLOSS communities, and to evaluate their stability and maturity, but also to determine within projects, how the effort is distributed in a given period, and to estimate future needs with respect to key points in the software life-cycle (e.g., major releases). This study analyses the activity patterns within the Linux kernel project, at first focusing on the overall distribution of effort and activity within weeks and days; then, dividing each day into three 8-hour time slots, and focusing on effort and activity around major releases. Such analyses have the objective of evaluating effort, productivity and types of activity globally and around major releases. They enable a comparison of these releases and patterns of effort and activities with traditional software products and processes, and in turn, the identification of company-driven projects (i.e., working mainly during office hours) among FLOSS endeavors. The results of this research show that, overall, the effort within the Linux kernel community is constant (albeit at different levels) throughout the week, signalling the need of updated estimation models, different from those used in traditional 9am–5pm, Monday to Friday commercial companies. It also becomes evident that the activity before a release is vastly different from after a release, and that the changes show an increase in code complexity in specific time slots (notably in the late night hours), which will later require additional maintenance efforts

Whitecap coverage dependence on wind and wave statistics as observed during SO GasEx and HiWinGS

Concurrent wavefield and turbulent flux measurements acquired during the Southern Ocean (SO) Gas Exchange (GasEx) and the High Wind Speed Gas Exchange Study (HiWinGS) projects permit evaluation of the dependence of the whitecap coverage W on wind speed, wave age, wave steepness, mean square slope, and wind-wave and breaking Reynolds numbers. The W was determined from over 600 high-frequency visible imagery recordings of 20 min each. Wave statistics were computed from in situ and remotely sensed data as well as from a WAVEWATCH III hindcast. The first shipborne estimates of W under sustained 10-m neutral wind speeds U10N of 25 m s−1 were obtained during HiWinGS. These measurements suggest that W levels off at high wind speed, not exceeding 10% when averaged over 20 min. Combining wind speed and wave height in the form of the wind-wave Reynolds number resulted in closely agreeing models for both datasets, individually and combined. These are also in good agreement with two previous studies. When expressing W in terms of wavefield statistics only or wave age, larger scatter is observed and/or there is little agreement between SO GasEx, HiWinGS, and previously published data. The wind speed–only parameterizations deduced from the SO GasEx and HiWinGS datasets agree closely and capture more of the observed W variability than Reynolds number parameterizations. However, these wind speed–only models do not agree as well with previous studies than the wind-wave Reynolds numbers

Wave‐Related Reynolds Number Parameterizations of CO₂ and DMS Transfer Velocities

Predicting future climate hinges on our understanding of and ability to quantify air‐sea gas transfer. The latter relies on parameterizations of the gas transfer velocity k, which represents physical mass transfer mechanisms and is usually parameterized as a nonlinear function of wind forcing. In an attempt to reduce uncertainties in k, this study explores empirical parameterizations that incorporate both wind speed and sea state dependence via wave‐wind and breaking Reynolds numbers, RH and RB. Analysis of concurrent eddy covariance gas transfer and measured wavefield statistics supplemented by wave model hindcasts shows for the first time that wave‐related Reynolds numbers collapse four open ocean data sets that have a wind speed dependence of CO₂ transfer velocity ranging from lower than quadratic to cubic. Wave‐related Reynolds number and wind speed show comparable performance for parametrizing dimethyl sulfide (DMS) which, because of its higher solubility, is less affected by bubble‐mediated exchange associated with wave breaking

Which older people decline participation in a primary care trial of physical activity and why: insights from a mixed methods approach

This article is available through the Brunel Open Access Publishing Fund. Copyright 2014 Rogers et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Background: Physical activity is of vital importance to older peoples’ health. Physical activity intervention studies with older people often have low recruitment, yet little is known about non-participants. Methods: Patients aged 60–74 years from three UK general practices were invited to participate in a nurse-supported pedometer-based walking intervention. Demographic characteristics of 298 participants and 690 non-participants were compared. Health status and physical activity of 298 participants and 183 non-participants who completed a survey were compared using age, sex adjusted odds ratios (OR) (95% confidence intervals). 15 non-participants were interviewed to explore perceived barriers to participation. Results: Recruitment was 30% (298/988). Participants were more likely than non-participants to be female (54% v 47%; p = 0.04) and to live in affluent postcodes (73% v 62% in top quintile; p < 0.001). Participants were more likely than non-participants who completed the survey to have an occupational pension OR 2.06 (1.35-3.13), a limiting longstanding illness OR 1.72 (1.05-2.79) and less likely to report being active OR 0.55 (0.33-0.93) or walking fast OR 0.56 (0.37-0.84). Interviewees supported general practice-based physical activity studies, particularly walking, but barriers to participation included: already sufficiently active, reluctance to walk alone or at night, physical symptoms, depression, time constraints, trial equipment and duration. Conclusion: Gender and deprivation differences suggest some selection bias. However, trial participants reported more health problems and lower activity than non-participants who completed the survey, suggesting appropriate trial selection in a general practice population. Non-participant interviewees indicated that shorter interventions, addressing physical symptoms and promoting confidence in pursuing physical activity, might increase trial recruitment and uptake of practice-based physical activity endeavours.The National Institute for Health Research (NIHR) under its Research for Patient Benefit Programme (Grant Reference Number PB-PG-0909-20055)

Burden of anemia in patients with osteoarthritis and rheumatoid arthritis in French secondary care

<p>Abstract</p> <p>Background</p> <p>Arthritic disorders can be the cause of hospitalizations, especially among individuals 60 years and older. The objective of this study is to investigate associations between health care resource utilization in arthritis patients with and without concomitant anemia in a secondary care setting in France.</p> <p>Methods</p> <p>This retrospective cohort study utilized data on secondary care activity in 2001 from the Programme de Médicalisation des Systèmes d'Information database. Two cohorts were defined using ICD-10 codes: patients with an arthritis diagnosis with a concomitant diagnosis of anemia; and arthritis patients without anemia. Health care resource utilization for both populations was analyzed separately in public and private hospitals. Study outcomes were compared between the cohorts using standard bivariate and multivariable methods.</p> <p>Results</p> <p>There were 300,865 hospitalizations for patients with arthritis only, and 2,744 for those with concomitant anemia. Over 70% of patients with concomitant anemia were in public hospitals, compared with 53.5% of arthritis-only patients. Arthritis patients without anemia were younger than those with concomitant anemia (mean age 66.7 vs 74.6, public hospitals; 67.1 vs 72.2, private hospitals). Patients with concomitant anemia/arthritis only had a mean length of stay of 11.91 (SD 14.07)/8.04 (SD 9.93) days in public hospitals, and 10.68 (SD 10.16)/9.83 (SD 7.76) days in private hospitals. After adjusting for confounders, the mean (95% CI) additional length of stay for arthritis patients with concomitant anemia, compared with those with arthritis only, was 1.56 (1.14-1.98) days in public and 0.69 (0.22-1.16) days in private hospitals. Costs per hospitalization were €;480 (227-734) greater for arthritis patients with anemia in public hospitals, and €;30 (-113-52) less in private hospitals, than for arthritis-only patients.</p> <p>Conclusions</p> <p>Arthritis patients with concomitant anemia have a longer length of stay, undergo more procedures, and have higher hospitalization costs than nonanemic arthritis patients in public hospitals in France. In private hospitals, concomitant anemia was associated with modest increases in length of stay and number of procedures; however, this did not translate into higher costs. Such evidence of anemia-related health care utilization and costs can be considered as a proxy for the clinical significance of anemia.</p

Simultaneous Extraction of the Fermi constant and PMNS matrix elements in the presence of a fourth generation

Several recent studies performed on constraints of a fourth generation of quarks and leptons suffer from the ad-hoc assumption that 3 x 3 unitarity holds for the first three generations in the neutrino sector. Only under this assumption one is able to determine the Fermi constant G_F from the muon lifetime measurement with the claimed precision of G_F = 1.16637 (1) x 10^-5 GeV^-2. We study how well G_F can be extracted within the framework of four generations from leptonic and radiative mu and tau decays, as well as from K_l3 decays and leptonic decays of charged pions, and we discuss the role of lepton universality tests in this context. We emphasize that constraints on a fourth generation from quark and lepton flavour observables and from electroweak precision observables can only be obtained in a consistent way if these three sectors are considered simultaneously. In the combined fit to leptonic and radiative mu and tau decays, K_l3 decays and leptonic decays of charged pions we find a p-value of 2.6% for the fourth generation matrix element |U_{e 4}|=0 of the neutrino mixing matrix.Comment: 19 pages, 3 figures with 16 subfigures, references and text added refering to earlier related work, figures and text in discussion section added, results and conclusions unchange

Truncated and Helix-Constrained Peptides with High Affinity and Specificity for the cFos Coiled-Coil of AP-1

Protein-based therapeutics feature large interacting surfaces. Protein folding endows structural stability to localised surface epitopes, imparting high affinity and target specificity upon interactions with binding partners. However, short synthetic peptides with sequences corresponding to such protein epitopes are unstructured in water and promiscuously bind to proteins with low affinity and specificity. Here we combine structural stability and target specificity of proteins, with low cost and rapid synthesis of small molecules, towards meeting the significant challenge of binding coiled coil proteins in transcriptional regulation. By iteratively truncating a Jun-based peptide from 37 to 22 residues, strategically incorporating i-->i+4 helix-inducing constraints, and positioning unnatural amino acids, we have produced short, water-stable, alpha-helical peptides that bind cFos. A three-dimensional NMR-derived structure for one peptide (24) confirmed a highly stable alpha-helix which was resistant to proteolytic degradation in serum. These short structured peptides are entropically pre-organized for binding with high affinity and specificity to cFos, a key component of the oncogenic transcriptional regulator Activator Protein-1 (AP-1). They competitively antagonized the cJun–cFos coiled-coil interaction. Truncating a Jun-based peptide from 37 to 22 residues decreased the binding enthalpy for cJun by ~9 kcal/mol, but this was compensated by increased conformational entropy (TDS ≤ 7.5 kcal/mol). This study demonstrates that rational design of short peptides constrained by alpha-helical cyclic pentapeptide modules is able to retain parental high helicity, as well as high affinity and specificity for cFos. These are important steps towards small antagonists of the cJun-cFos interaction that mediates gene transcription in cancer and inflammatory diseases