Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01

<p>Abstract</p> <p>Background</p> <p>Many strains of <it>Thermus </it>have been isolated from hot environments around the world. <it>Thermus scotoductus </it>SA-01 was isolated from fissure water collected 3.2 km below surface in a South African gold mine. The isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. The genomes from two different <it>Thermus thermophilus </it>strains have been completed. This paper represents the completed genome from a second <it>Thermus </it>species - <it>T. scotoductus</it>.</p> <p>Results</p> <p>The genome of <it>Thermus scotoductus </it>SA-01 consists of a chromosome of 2,346,803 bp and a small plasmid which, together are about 11% larger than the <it>Thermus thermophilus </it>genomes. The <it>T. thermophilus </it>megaplasmid genes are part of the <it>T. scotoductus </it>chromosome and extensive rearrangement, deletion of nonessential genes and acquisition of gene islands have occurred, leading to a loss of synteny between the chromosomes of <it>T. scotoductus and T. thermophilus</it>. At least nine large inserts of which seven were identified as alien, were found, the most remarkable being a denitrification cluster and two operons relating to the metabolism of phenolics which appear to have been acquired from <it>Meiothermus ruber</it>. The majority of acquired genes are from closely related species of the Deinococcus-Thermus group, and many of the remaining genes are from microorganisms with a thermophilic or hyperthermophilic lifestyle. The natural competence of <it>Thermus scotoductus </it>was confirmed experimentally as expected as most of the proteins of the natural transformation system of <it>Thermus thermophilus </it>are present. Analysis of the metabolic capabilities revealed an extensive energy metabolism with many aerobic and anaerobic respiratory options. An abundance of sensor histidine kinases, response regulators and transporters for a wide variety of compounds are indicative of an oligotrophic lifestyle.</p> <p>Conclusions</p> <p>The genome of <it>Thermus scotoductus </it>SA-01 shows remarkable plasticity with the loss, acquisition and rearrangement of large portions of its genome compared to <it>Thermus thermophilus</it>. Its ability to naturally take up foreign DNA has helped it adapt rapidly to a subsurface lifestyle in the presence of a dense and diverse population which acted as source of nutrients. The genome of <it>Thermus scotoductus </it>illustrates how rapid adaptation can be achieved by a highly dynamic and plastic genome.</p

Estimating the number of children exposed to parental psychiatric disorders through a national health survey

<p>Abstract</p> <p>Objective</p> <p>Children whose parents have psychiatric disorders experience an increased risk of developing psychiatric disorders, and have higher rates of developmental problems and mortality. Assessing the size of this population is important for planning of preventive strategies which target these children.</p> <p>Methods</p> <p>National survey data (CCHS 1.2) was used to estimate the number of children exposed to parental psychiatric disorders. Disorders were diagnosed using the World Psychiatric Health Composite International Diagnostic Interview (WMH-CIDI) (12 month prevalence). Data on the number of children below 12 years of age in the home, and the relationship of the respondents with the children, was used to estimate exposure. Parent-child relations were identified, as was single parenthood. Using a design-based analysis, the number of children exposed to parental psychiatric disorders was calculated.</p> <p>Results</p> <p>Almost 570,000 children under 12 live in households where the survey respondent met criteria for one or more mood, anxiety or substance use disorders in the previous 12 months, corresponding to 12.1% of Canadian children under the age of 12. Almost 3/4 of these children have parents that report receiving no mental health care in the 12 months preceding the survey. For 17% of all Canadian children under age 12, the individual experiencing a psychiatric disorder is the only parent in the household.</p> <p>Conclusion</p> <p>The high number of children exposed causes major concern and has important implications. Although these children will not necessarily experience adversities, they possess an elevated risk of accidents, mortality, and of developing psychiatric disorders. We expect these estimates will promote further research and stimulate discussion at both health policy and planning tables.</p

Changing environments during the Middle-Upper Palaeolithic transition in the eastern Cantabrian Region (Spain): direct evidence from stable isotope studies on ungulate bones

Environmental change has been proposed as a factor that contributed to the extinction of the Neanderthals in Europe during MIS3. Currently, the different local environmental conditions experienced at the time when Anatomically Modern Humans (AMH) met Neanderthals are not well known. In the Western Pyrenees, particularly, in the eastern end of the Cantabrian coast of the Iberian Peninsula, extensive evidence of Neanderthal and subsequent AMH activity exists, making it an ideal area in which to explore the palaeoenvironments experienced and resources exploited by both human species during the Middle to Upper Palaeolithic transition. Red deer and horse were analysed using bone collagen stable isotope analysis to reconstruct environmental conditions across the transition. A shift in the ecological niche of horses after the Mousterian demonstrates a change in environment, towards more open vegetation, linked to wider climatic change. In the Mousterian, Aurignacian and Gravettian, high inter-individual nitrogen ranges were observed in both herbivores. This could indicate that these individuals were procured from areas isotopically different in nitrogen. Differences in sulphur values between sites suggest some variability in the hunting locations exploited, reflecting the human use of different parts of the landscape. An alternative and complementary explanation proposed is that there were climatic fluctuations within the time of formation of these archaeological levels, as observed in pollen, marine and ice cores.This research was funded by the European Commission through a Marie Curie Career Integration Grant (FP7- PEOPLE-2012-CIG-322112), by the Spanish Ministry of Economy and Competitiveness (HAR2012-33956 and Ramon y Cajal-2011-00695), the University of Cantabria and Campus International to ABMA. Radiocarbon dating at ORAU was funded by MINECO-HAR2012-33956 project. J.J was supported initially by the FP7- PEOPLE-2012-CIG-322112 and later by a Marie Curie Individual Fellowship (H2020-MSCA-IF-2014-656122). Laboratory work, associated research expenses and isotopic analysis were kindly funded by the Max Planck Society to M.R

Planck intermediate results: LVII. Joint Planck LFI and HFI data processing

We present the NPIPE processing pipeline, which produces calibrated frequency maps in temperature and polarization from data from the Planck Low Frequency Instrument (LFI) and High Frequency Instrument (HFI) using high-performance computers. NPIPE represents a natural evolution of previous Planck analysis efforts, and combines some of the most powerful features of the separate LFI and HFI analysis pipelines. For example, following the LFI 2018 processing procedure, NPIPE uses foreground polarization priors during the calibration stage in order to break scanninginduced degeneracies. Similarly, NPIPE employs the HFI 2018 time-domain processing methodology to correct for bandpass mismatch at all frequencies. In addition, NPIPE introduces several improvements, including, but not limited to: inclusion of the 8% of data collected during repointing manoeuvres; smoothing of the LFI reference load data streams; in-flight estimation of detector polarization parameters; and construction of maximally independent detector-set split maps. For component-separation purposes, important improvements include: maps that retain the CMB Solar dipole, allowing for high-precision relative calibration in higher-level analyses; well-defined single-detector maps, allowing for robust CO extraction; and HFI temperature maps between 217 and 857 GHz that are binned into 0.09 pixels (Nside = 4096), ensuring that the full angular information in the data is represented in the maps even at the highest Planck resolutions. The net effect of these improvements is lower levels of noise and systematics in both frequency and component maps at essentially all angular scales, as well as notably improved internal consistency between the various frequency channels. Based on the NPIPE maps, we present the first estimate of the Solar dipole determined through component separation across all nine Planck frequencies. The amplitude is (3366.6 ± 2.7) µK, consistent with, albeit slightly higher than, earlier estimates. From the large-scale polarization data, we derive an updated estimate of the optical depth of reionization of τ = 0.051 ± 0.006, which appears robust with respect to data and sky cuts. There are 600 complete signal, noise and systematics simulations of the full-frequency and detector-set maps. As a Planck first, these simulations include full time-domain processing of the beam-convolved CMB anisotropies. The release of NPIPE maps and simulations is accompanied with a complete suite of raw and processed time-ordered data and the software, scripts, auxiliary data, and parameter files needed to improve further on the analysis and to run matching simulations

Planck 2018 results. VII. Isotropy and statistics of the CMB

Analysis of the Planck 2018 data set indicates that the statistical properties of the cosmic microwave background (CMB) temperature anisotropies are in excellent agreement with previous studies using the 2013 and 2015 data releases. In particular, they are consistent with the Gaussian predictions of the $\Lambda$CDM cosmological model, yet also confirm the presence of several so-called "anomalies" on large angular scales. The novelty of the current study, however, lies in being a first attempt at a comprehensive analysis of the statistics of the polarization signal over all angular scales, using either maps of the Stokes parameters, $Q$ and $U$, or the $E$-mode signal derived from these using a new methodology (which we describe in an appendix). Although remarkable progress has been made in reducing the systematic effects that contaminated the 2015 polarization maps on large angular scales, it is still the case that residual systematics (and our ability to simulate them) can limit some tests of non-Gaussianity and isotropy. However, a detailed set of null tests applied to the maps indicates that these issues do not dominate the analysis on intermediate and large angular scales (i.e., $\ell \lesssim 400$). In this regime, no unambiguous detections of cosmological non-Gaussianity, or of anomalies corresponding to those seen in temperature, are claimed. Notably, the stacking of CMB polarization signals centred on the positions of temperature hot and cold spots exhibits excellent agreement with the $\Lambda$CDM cosmological model, and also gives a clear indication of how Planck provides state-of-the-art measurements of CMB temperature and polarization on degree scales

Planck 2018 results. VII. Isotropy and Statistics of the CMB

Analysis of the Planck 2018 data set indicates that the statistical properties of the cosmic microwave background (CMB) temperature anisotropies are in excellent agreement with previous studies using the 2013 and 2015 data releases. In particular, they are consistent with the Gaussian predictions of the $\Lambda$CDM cosmological model, yet also confirm the presence of several so-called "anomalies" on large angular scales. The novelty of the current study, however, lies in being a first attempt at a comprehensive analysis of the statistics of the polarization signal over all angular scales, using either maps of the Stokes parameters, $Q$ and $U$, or the $E$-mode signal derived from these using a new methodology (which we describe in an appendix). Although remarkable progress has been made in reducing the systematic effects that contaminated the 2015 polarization maps on large angular scales, it is still the case that residual systematics (and our ability to simulate them) can limit some tests of non-Gaussianity and isotropy. However, a detailed set of null tests applied to the maps indicates that these issues do not dominate the analysis on intermediate and large angular scales (i.e., $\ell \lesssim 400$). In this regime, no unambiguous detections of cosmological non-Gaussianity, or of anomalies corresponding to those seen in temperature, are claimed. Notably, the stacking of CMB polarization signals centred on the positions of temperature hot and cold spots exhibits excellent agreement with the $\Lambda$CDM cosmological model, and also gives a clear indication of how Planck provides state-of-the-art measurements of CMB temperature and polarization on degree scales

Completeness of reporting and risks of overstating impact in cluster randomised trials : a systematic review

Acknowledgments We received no funding specifically for this systematic review. ELT is funded in part by awards R01-AI141444 from the National Institute of Allergy and Infectious Diseases and R01-MH120649 from the US National Institute of Mental Health; both Institutes are part of the National Institutes of Health (NIH). JAG and ACP's support of this project was made possible (in part) by grant number UL1TR002553 from the National Center for Advancing Translational Sciences of the NIH, and the NIH Roadmap for Medical Research. JEM is supported by an Australian National Health and Medical Research Council Career Development Fellowship (APP1143429). SN was supported by an award that is jointly funded by the UK Medical Research Council (MRC) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement, and part of the EDCTP2 programme supported by the European Union (grant reference MR/R010161/1). ABF acknowledges funding support from the National Health and Medical Research Council of Australia (grant ID 1183303). KH is funded by a National Institute for Health Research Senior Research Fellowship SRF-2017-10-002. The contents of the research included in this manuscript are solely the responsibility of the authors and do not necessarily represent the official views of any of the funders. The research contributed by all authors of this manuscript are independent of their funders. Specifically, the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We wish to thank the three reviewers for their insightful comments and constructive feedback.Peer reviewedPublisher PD

The V471A polymorphism in autophagy-related gene ATG7 modifies age at onset specifically in Italian Huntington disease patients

The cause of Huntington disease (HD) is a polyglutamine repeat expansion of more than 36 units in the huntingtin protein, which is inversely correlated with the age at onset of the disease. However, additional genetic factors are believed to modify the course and the age at onset of HD. Recently, we identified the V471A polymorphism in the autophagy-related gene ATG7, a key component of the autophagy pathway that plays an important role in HD pathogenesis, to be associated with the age at onset in a large group of European Huntington disease patients. To confirm this association in a second independent patient cohort, we analysed the ATG7 V471A polymorphism in additional 1,464 European HD patients of the “REGISTRY” cohort from the European Huntington Disease Network (EHDN). In the entire REGISTRY cohort we could not confirm a modifying effect of the ATG7 V471A polymorphism. However, analysing a modifying effect of ATG7 in these REGISTRY patients and in patients of our previous HD cohort according to their ethnic origin, we identified a significant effect of the ATG7 V471A polymorphism on the HD age at onset only in the Italian population (327 patients). In these Italian patients, the polymorphism is associated with a 6-years earlier disease onset and thus seems to have an aggravating effect. We could specify the role of ATG7 as a genetic modifier for HD particularly in the Italian population. This result affirms the modifying influence of the autophagic pathway on the course of HD, but also suggests population-specific modifying mechanisms in HD pathogenesis