On the roles of cell size and trophic strategy in North Atlantic diatom and dinoflagellate communities

We have examined the inter- and intra-group seasonal succession of 113 diatom and dinoflagellate taxa, as surveyed by the Continuous Plankton Recorder (CPR) in the North Atlantic, by grouping taxa according to two key functional traits: cell size (mg C cell21) and trophic strategy (photoautotrophy, mixotrophy, or heterotrophy). Mixotrophic dinoflagellates follow photoautotrophic diatoms but precede their obligate heterotrophic counterparts in the succession because of the relative advantages afforded by photosynthesizing when light and nutrients are available in spring. The mean cell size of the sampled diatoms is smallest in the summer, likely because of the higher specific nutrient affinity of smaller relative to larger cells. Contrastingly, we hypothesize that mixotrophy diminishes the size selection based on nutrient limitation and accounts for the lack of a seasonal size shift among surveyed dinoflagellates. Relatively small, heterotrophic dinoflagellates (mg C cell21 , 1023) peak after other, larger dinoflagellates, in part because of the increased abundance of their small prey during nutrientdeplete summer months. The largest surveyed diatoms (mg C cell21 . 1022) bloom later than others, and we hypothesize that this may be because of their relatively slow maximum potential growth rates and high internal nutrient storage, as well as to the slower predation of these larger cells. The new trait database and analysis presented here helps translate the taxonomic information of the CPR survey into metrics that can be directly compared with trait-based models

ATM and Artemis promote homologous recombination of radiation-induced DNA double-strand breaks in G2

Homologous recombination (HR) and non‐homologous end joining (NHEJ) represent distinct pathways for repairing DNA double‐strand breaks (DSBs). Previous work implicated Artemis and ATM in an NHEJ‐dependent process, which repairs a defined subset of radiation‐induced DSBs in G1‐phase. Here, we show that in G2, as in G1, NHEJ represents the major DSB‐repair pathway whereas HR is only essential for repair of ∼15% of X‐ or γ‐ray‐induced DSBs. In addition to requiring the known HR proteins, Brca2, Rad51 and Rad54, repair of radiation‐induced DSBs by HR in G2 also involves Artemis and ATM suggesting that they promote NHEJ during G1 but HR during G2. The dependency for ATM for repair is relieved by depleting KAP‐1, providing evidence that HR in G2 repairs heterochromatin‐associated DSBs. Although not core HR proteins, ATM and Artemis are required for efficient formation of single‐stranded DNA and Rad51 foci at radiation‐induced DSBs in G2 with Artemis function requiring its endonuclease activity. We suggest that Artemis endonuclease removes lesions or secondary structures, which inhibit end resection and preclude the completion of HR or NHEJ

Levonorgestrel-releasing intrauterine system vs. usual medical treatment for menorrhagia: An economic evaluation alongside a randomised controlled trial

Objective: To undertake an economic evaluation alongside the largest randomised controlled trial comparing Levonorgestrel-releasing intrauterine device ('LNG-IUS') and usual medical treatment for women with menorrhagia in primary care; and compare the cost-effectiveness findings using two alternative measures of quality of life. Methods: 571 women with menorrhagia from 63 UK centres were randomised between February 2005 and July 2009. Women were randomised to having a LNG-IUS fitted, or usual medical treatment, after discussing with their general practitioner their contraceptive needs or desire to avoid hormonal treatment. The treatment was specified prior to randomisation. For the economic evaluation we developed a state transition (Markov) model with a 24 month follow-up. The model structure was informed by the trial women's pathway and clinical experts. The economic evaluation adopted a UK National Health Service perspective and was based on an outcome of incremental cost per Quality Adjusted Life Year (QALY) estimated using both EQ-5D and SF-6D. Results: Using EQ-5D, LNG-IUS was the most cost-effective treatment for menorrhagia. LNG-IUS costs £100 more than usual medical treatment but generated 0.07 more QALYs. The incremental cost-effectiveness ratio for LNG-IUS compared to usual medical treatment was £1600 per additional QALY. Using SF-6D, usual medical treatment was the most cost-effective treatment. Usual medical treatment was both less costly (£100) and generated 0.002 more QALYs. Conclusion: Impact on quality of life is the primary indicator of treatment success in menorrhagia. However, the most costeffective treatment differs depending on the quality of life measure used to estimate the QALY. Under UK guidelines LNG-IUS would be the recommended treatment for menorrhagia. This study demonstrates that the appropriate valuation of outcomes in menorrhagia is crucial. Copyright: © 2014 Sanghera et al

Anthropogenic climate change impacts on copepod trait biogeography

Copepods are among the most abundant marine metazoans and form a key link between marine primary producers, higher trophic levels, and carbon sequestration pathways. Climate change is projected to change surface ocean temperature by up to 4°C in the North Atlantic with many associated changes including slowing of the overturning circulation, areas of regional freshening, and increased salinity and reductions in nutrients available in the euphotic zone over the next century. These changes will lead to a restructuring of phytoplankton and zooplankton communities with cascading effects throughout the food web. Here we employ observations of copepods, projected changes in ocean climate, and species distribution models to show how climate change may affect the distribution of copepod species in the North Atlantic. On average species move northeast at a rate of 14.1 km decade. Species turnover in copepod communities will range from 5% to 75% with the highest turnover rates concentrated in regions of pronounced temperature increase and decrease. The changes in species range vary according to copepod traits with the largest effects found to occur in the cooling, freshening area in the subpolar North Atlantic south of Greenland and in an area of significant warming along the Scotian shelf. Large diapausing copepods (>2.5 mm) which are higher in lipids and a crucial food source for whales, may have an advantage in the cooling waters due to their life-history strategy that facilitates their survival in the arctic environment. Carnivorous copepods show a basin wide increase in species richness and show significant habitat area increases when their distribution moves poleward while herbivores see significant habitat area losses. The trait-specific effects highlight the complex consequences of climate change for the marine food web

Can spacetime curvature induced corrections to Lamb shift be observable?

The Lamb shift results from the coupling of an atom to vacuum fluctuations of quantum fields, so corrections are expected to arise when the spacetime is curved since the vacuum fluctuations are modified by the presence of spacetime curvature. Here, we calculate the curvature-induced correction to the Lamb shift outside a spherically symmetric object and demonstrate that this correction can be remarkably significant outside a compact massive astrophysical body. For instance, for a neutron star or a stellar mass black hole, the correction is $\sim$ 25% at a radial distance of $4GM/c^2$, $\sim$ 16% at $10GM/c^2$ and as large as $\sim$ 1.6% even at $100GM/c^2$, where $M$ is the mass of the object, $G$ the Newtonian constant, and $c$ the speed of light. In principle, we can look at the spectra from a distant compact super-massive body to find such corrections. Therefore, our results suggest a possible way of detecting fundamental quantum effects in astronomical observations.Comment: 13 pages, 3 figures, slight title change, clarifications and more discussions added, version to be published in JHE

A pre–post intervention study of pulmonary rehabilitation for adults with post-tuberculosis lung disease in Uganda

Rupert Jones,1 Bruce J Kirenga,2 Wincelsas Katagira,2 Sally J Singh,3 Jill Pooler,4 Alphonse Okwera,2 Richard Kasiita,5 Doyo G Enki,6 Siobhan Creanor,6 Andy Barton4 1Population Studies and Clinical Trials, Peninsula Schools of Medicine and Dentistry, Plymouth University, Plymouth, UK; 2Population Studies and Clinical Trials, Makerere Lung Institute, Makerere University College of Health Sciences, Mulago Hospital, Kampala, Uganda; 3Cardio-Respiratory Directorate, University Hospitals of Leicester NHS Trust, Leicester, 4Population Studies and Clinical Trials, Peninsula Schools of Medicine and Dentistry, Plymouth University, Plymouth, UK; 5Department of Physiotherapy, Mulago Hospital, Kampala, Uganda; 6Medical Statistics, Peninsula Schools of Medicine and Dentistry, Plymouth University, Plymouth, UK Setting: The study was conducted at Mulago Hospital, Kampala, Uganda.Objective: As chronic respiratory disease (CRD) is a huge, growing burden in Africa, with few available treatments, we aimed to design and evaluate a culturally appropriate pulmonary rehabilitation (PR) program in Uganda for people with post-tuberculosis lung disorder (p-TBLD).Design: In a pre–post intervention study, a 6-week, twice-weekly PR program was designed for people with p-TBLD. Outcome measures included recruitment, retention, the Clinical COPD Questionnaire (CCQ), tests of exercise capacity, and biometrics. Given this was a developmental study, no formal statistical significance testing was undertaken.Results: In all, 34 participants started PR and 29 (85%) completed all data collection. The mean age of the 29 participants was 45 years, and 52% were female. The mean (95% confidence interval) CCQ score at baseline was 1.8 (1.5, 2.0), at the end of PR was 1.0 (0.8, 1.2), and at 6 weeks after the end of PR was 0.8 (0.7, 1.0). The Incremental Shuttle Walking Test (ISWT) was 299 m (268.5, 329.4) at baseline, 377 (339.6, 413.8) at the end of PR, and 374 (334.2, 413.5) at 6 weeks after the end of PR. Improvements were seen in measures of chest pain; 13/29 (45%) participants reported chest pain at baseline but only 7/29 (24%) at the end of PR, and in those with persistent pain, the mean pain scores decreased. Mild hemoptysis was reported in 4/29 (17%) participants at baseline and in 2/29 (7%) at the end of PR.Conclusion: PR for people with p-TBLD in Uganda was feasible and associated with clinically important improvements in quality of life, exercise capacity, and respiratory outcomes. PR uses local resources, requires little investment, and offers a new, sustainable therapy for p-TBLD in resource-limited settings. With the rising global burden of CRD, further studies are needed to assess the value of PR in p-TBLD and other prevalent forms of CRD. Keywords: tuberculosis, exercise training, self-management, nonpharmacological intervention&nbsp

MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts

<p>Abstract</p> <p>Background</p> <p>Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein function prediction, DNA motif recognition, and phylogenetic analysis. Therefore, improving the accuracy of multiple sequence alignment is important for advancing many bioinformatics fields.</p> <p>Results</p> <p>We designed and developed a new method, MSACompro, to synergistically incorporate predicted secondary structure, relative solvent accessibility, and residue-residue contact information into the currently most accurate posterior probability-based MSA methods to improve the accuracy of multiple sequence alignments. The method is different from the multiple sequence alignment methods (e.g. 3D-Coffee) that use the tertiary structure information of some sequences since the structural information of our method is fully predicted from sequences. To the best of our knowledge, applying predicted relative solvent accessibility and contact map to multiple sequence alignment is novel. The rigorous benchmarking of our method to the standard benchmarks (i.e. BAliBASE, SABmark and OXBENCH) clearly demonstrated that incorporating predicted protein structural information improves the multiple sequence alignment accuracy over the leading multiple protein sequence alignment tools without using this information, such as MSAProbs, ProbCons, Probalign, T-coffee, MAFFT and MUSCLE. And the performance of the method is comparable to the state-of-the-art method PROMALS of using structural features and additional homologous sequences by slightly lower scores.</p> <p>Conclusion</p> <p>MSACompro is an efficient and reliable multiple protein sequence alignment tool that can effectively incorporate predicted protein structural information into multiple sequence alignment. The software is available at <url>http://sysbio.rnet.missouri.edu/multicom_toolbox/</url>.</p

Modelling and analysis of time dependent processes in a chemically reactive mixture

In this paper, we study the propagation of sound waves and the dynamics of local wave disturbances induced by spontaneous internal fluctuations in a reactive mixture. We consider a non-diffusive, non-heat conducting and non-viscous mixture described by an Eulerian set of evolution equations. The model is derived from the kinetic theory in a hydrodynamic regime of a fast chemical reaction. The reactive source terms are explicitly computed from the kinetic theory and are built in themodel in a proper way. For both time-dependent problems, we first derive the appropriate dispersion relation, which retains the main effects of the chemical process, and then investigate the influence of the chemical reaction on the properties of interest in the problems studied here. We complete our study by developing a rather detailed analysis using the Hydrogen–Chlorine system as reference. Several numerical computations are included illustrating the behavior of the phase velocity and attenuation coefficient in a low-frequency regime and describing the spectrum of the eigenmodes in the small wavenumber limit.The paper is partially supported by the Research Centre of Mathematics of the University of Minho, with the Portuguese Funds from the Foundation for Science and Technology (FCT) through the Project UID/MAT/00013/2013. We wish to thank the anonymous Referees for their valuable comments and suggestions that helped us to improve the paper.info:eu-repo/semantics/publishedVersio

Blood parasites in endangered wildlife-trypanosomes discovered during a survey of haemoprotozoa from the Tasmanian devil

he impact of emerging infectious diseases is increasingly recognised as a major threat to wildlife. Wild populations of the endangered Tasmanian devil, Sarcophilus harrisii, are experiencing devastating losses from a novel transmissible cancer, devil facial tumour disease (DFTD); however, despite the rapid decline of this species, there is currently no information on the presence of haemoprotozoan parasites. In the present study, 95 Tasmanian devil blood samples were collected from four populations in Tasmania, Australia, which underwent molecular screening to detect four major groups of haemoprotozoa: (i) trypanosomes, (ii) piroplasms, (iii) Hepatozoon, and (iv) haemosporidia. Sequence results revealed Trypanosoma infections in 32/95 individuals. Trypanosoma copemani was identified in 10 Tasmanian devils from three sites and a second Trypanosoma sp. was identified in 22 individuals that were grouped within the poorly described T. cyclops clade. A single blood sample was positive for Babesia sp., which most closely matched Babesia lohae. No other blood protozoan parasite DNA was detected. This study provides the first insight into haemoprotozoa from the Tasmanian devil and the first identification of Trypanosoma and Babesia in this carnivorous marsupial

A toxicokinetic model for thiamethoxam in rats: implications for higher-tier risk assessment

Risk assessment for mammals is currently based on external exposure measurements, but effects of toxicants are better correlated with the systemically available dose than with the external administered dose. So for risk assessment of pesticides, toxicokinetics should be interpreted in the context of potential exposure in the field taking account of the timescale of exposure and individual patterns of feeding. Internal concentration is the net result of absorption, distribution, metabolism and excretion (ADME). We present a case study for thiamethoxam to show how data from ADME study on rats can be used to parameterize a body burden model which predicts body residue levels after exposures to LD50 dose either as a bolus or eaten at different feeding rates. Kinetic parameters were determined in male and female rats after an intravenous and oral administration of 14C labelled by fitting one-compartment models to measured pesticide concentrations in blood for each individual separately. The concentration of thiamethoxam in blood over time correlated closely with concentrations in other tissues and so was considered representative of pesticide concentration in the whole body. Body burden model simulations showed that maximum body weight-normalized doses of thiamethoxam were lower if the same external dose was ingested normally than if it was force fed in a single bolus dose. This indicates lower risk to rats through dietary exposure than would be estimated from the bolus LD50. The importance of key questions that should be answered before using the body burden approach in risk assessment, data requirements and assumptions made in this study are discussed in detail