Technical note: The effects of five different defaunation methods on biogeochemical properties of intertidal sediment

Various methods have been used to remove organisms from sediments to investigate structure and function of faunal assemblages in intertidal habitats. Nevertheless, little is known about how these treatments affect properties of the sediments themselves, although changing these properties may cause changes in the assemblages, independently of other hypotheses being tested. This study assesses the efficacy of defaunation and effect on selected biogeochemical properties of five different methods of defaunating soft muddy sediments in an estuary. The methods were removal and freezing of sediment, removal and oven-heating, freezing in situ with liquid N2, spraying with formalin and spraying with hydrogen peroxide. The first four of these methods have been used in previous studies, whilst the fifth was considered to be a potentially useful defaunator because it does not leave toxic residues. The first two methods required sediment to be brought back to the lab, disrupting the natural structure of the sediment; the last three were done in situ, with much less disturbance.  Variables measured to assess effects of the treatments on the sediment were amount of water, grain size, total carbohydrate, suspension index (relative erosion rate), erosion threshold, chlorophyll a and b, colloidal carbohydrate, Fo (minimal fluorescence) and Fv/ Fm (photosynthetic yield). There were no significant effects of any treatment on the first four variables. For the others, effects of defaunation varied from treatment to treatment and with time after treatment. Generally, the greatest disturbance was to the microphytobenthos (MPB, measured by chlorophyll and fluorescence) and related variables. For most treatments, recovery was rapid, but the effects of formalin and H2O2 persisted for a few days. Effects on physical properties of the sediment were mostly minor and insignificant. Removal and freezing or heating, however, caused major changes to the sediments because of the disturbances involved. Choosing the appropriate method of defaunation is very important if interpretations are not to be confounded between the effects of defaunation per se and any effects of changes to other biota (such as microphytobenthos) and/or the properties of sediments caused by the method used to defaunate experimental areas

Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques

Cre is widely used for DNA tailoring and, in combination with recombineering techniques, to modify BAC/PAC sequences for generating transgenic animals. However, mammalian genomes contain recombinase recognition sites (cryptic loxP sites) that can promote illegitimate DNA recombination and damage when cells express the Cre recombinase gene. We have created a new bioinformatic tool, FuzznucComparator, which searches for cryptic loxP sites and we have applied it to the analysis of the whole mouse genome. We found that cryptic loxP sites occur frequently and are homogeneously distributed in the genome. Given the mammalian nature of BAC/PAC genomic inserts, we hypothesised that the presence of cryptic loxP sites may affect the ability to grow and modify BAC and PAC clones in E. coli expressing Cre recombinase. We have observed a defect in bacterial growth when some BACs and PACs were transformed into EL350, a DH10B-derived bacterial strain that expresses Cre recombinase under the control of an arabinose-inducible promoter. In this study, we have demonstrated that Cre recombinase expression is leaky in un-induced EL350 cells and that some BAC/PAC sequences contain cryptic loxP sites, which are active and mediate the introduction of single-strand nicks in BAC/PAC genomic inserts

A scoping review of use of wearable devices to evaluate outcomes in survivors of critical illness

Objective: Wearable devices using new technology may be a cost-effective method to assess functional outcomes in survivors of critical illness. Our primary objective was to review the extent to which wearable devices such as smartphones, pedometers, accelerometers and global positioning systems have been used to evaluate outcomes in survivors of an intensive care unit admission. Design: We included studies of patients surviving an ICU admission and which measured outcomes using wearable devices. We performed a scoping review of studies found by searching the CINAHL, Embase, MEDLINE and PubMed databases. Results: The seven studies we identifi ed were published in or after 2012 and were predominantly descriptive (n = 6) with one randomised controlled trial. All studies described outcomes in cohorts of relatively few participants (range, 11–51 participants). Duration to follow-up was mostly short, at a median time of 3 months after ICU discharge (range, in-hospital to 27 years). All studies used accelerometers to monitor patient movement: physical activity (n = 5), sleep quality (n = 1), and infant movement (n = 1). The accelerometers were bi-axial (n = 3), uni-axial (n = 2) combined uni-axial (n = 1) and tri-axial (n = 1). Common outcomes evaluated were the number of participants walking for < 30 min/day, mean daily step count and walking speed. Conclusions: Wearable devices have infrequently been used to measure physical activity in survivors of critical illness and all identifi ed studies were published recently, which suggests that the use of wearable devices for research may be increasing. To date, only accelerometry has been reported, and the wide variation in methodologies used and the outcomes measured limits synthesis of these data.Samuel Gluck, Lee-anne S Chapple, Marianne J Chapman, Theodore J Iwashyna and Adam M Dean

The Uncertainty in Newton's Constant and Precision Predictions of the Primordial Helium Abundance

The current uncertainty in Newton's constant, G_N, is of the order of 0.15%. For values of the baryon to photon ratio consistent with both cosmic microwave background observations and the primordial deuterium abundance, this uncertainty in G_N corresponds to an uncertainty in the primordial 4He mass fraction, Y_P, of +-1.3 x 10^{-4}. This uncertainty in Y_P is comparable to the effect from the current uncertainty in the neutron lifetime, which is often treated as the dominant uncertainty in calculations of Y_P. Recent measurements of G_N seem to be converging within a smaller range; a reduction in the estimated error on G_N by a factor of 10 would essentially eliminate it as a source of uncertainty in the calculation of the primordial 4He abundance.Comment: 3 pages, no figures, fixed typos, to appear in Phys. Rev.

Twenty-eighth annual report of the Power Affiliates Program.

Includes bibliographical references

Short Gamma Ray Bursts as possible electromagnetic counterpart of coalescing binary systems

Coalescing binary systems, consisting of two collapsed objects, are among the most promising sources of high frequency gravitational waves signals detectable, in principle, by ground-based interferometers. Binary systems of Neutron Star or Black Hole/Neutron Star mergers should also give rise to short Gamma Ray Bursts, a subclass of Gamma Ray Bursts. Short-hard-Gamma Ray Bursts might thus provide a powerful way to infer the merger rate of two-collapsed object binaries. Under the hypothesis that most short Gamma Ray Bursts originate from binaries of Neutron Star or Black Hole/Neutron Star mergers, we outline here the possibility to associate short Gamma Ray Bursts as electromagnetic counterpart of coalescing binary systems.Comment: 4 pages, 1 figur

Peatland afforestation in the UK and consequences for carbon storage

Peatlands are a globally significant store of carbon. During the second half of the 20th century new planting techniques combined with tax incentives encouraged commercial forestry across large areas of peat bog in the UK, particularly in the Flow Country of northern Scotland. Such planting was controversial and was ultimately halted by removal of the tax incentives, and policies to prevent new planting. Here we review the literature on UK peatland afforestation in relation to carbon and climate implications, and identify key issues for future research. The effects of conifer planting on peat bog carbon storage in the UK are poorly understood. A large body of research on peatland forestry exists, particularly from naturally forested fen peatlands in Fennoscandia and Russia, but the different conditions in the UK mean that results are not directly transferable. Data on the responses of UK peat bogs to afforestation are required to address this shortfall. Studies are required that quantify the loss of carbon from the peat and evaluate it against the accumulation of carbon above and below ground in trees, considering the likely residence time of carbon in wood products

Peatland afforestation in the UK and consequences for carbon storage

Peatlands are a globally significant store of carbon. During the second half of the 20th century new planting techniques combined with tax incentives encouraged commercial forestry across large areas of peat bog in the UK, particularly in the Flow Country of northern Scotland. Such planting was controversial and was ultimately halted by removal of the tax incentives, and policies to prevent new planting. Here we review the literature on UK peatland afforestation in relation to carbon and climate implications, and identify key issues for future research. The effects of conifer planting on peat bog carbon storage in the UK are poorly understood. A large body of research on peatland forestry exists, particularly from naturally forested fen peatlands in Fennoscandia and Russia, but the different conditions in the UK mean that results are not directly transferable. Data on the responses of UK peat bogs to afforestation are required to address this shortfall. Studies are required that quantify the loss of carbon from the peat and evaluate it against the accumulation of carbon above and below ground in trees, considering the likely residence time of carbon in wood products

Multimessenger astronomy with the Einstein Telescope

Gravitational waves (GWs) are expected to play a crucial role in the development of multimessenger astrophysics. The combination of GW observations with other astrophysical triggers, such as from gamma-ray and X-ray satellites, optical/radio telescopes, and neutrino detectors allows us to decipher science that would otherwise be inaccessible. In this paper, we provide a broad review from the multimessenger perspective of the science reach offered by the third generation interferometric GW detectors and by the Einstein Telescope (ET) in particular. We focus on cosmic transients, and base our estimates on the results obtained by ET's predecessors GEO, LIGO, and Virgo.Comment: 26 pages. 3 figures. Special issue of GRG on the Einstein Telescope. Minor corrections include

Gastroesophageal reflux and antacid therapy in IPF: analysis from the Australia IPF Registry

BACKGROUND AND OBJECTIVE:Gastroesophageal reflux disease (GORD) is highly prevalent in idiopathic pulmonary fibrosis (IPF) and may play a role in its pathogenesis. Recent IPF treatment guidelines suggest that all patients with IPF be considered for antacid therapy. However, emerging evidence suggests that antacid therapy does not improve IPF patient outcomes and may increase the risk of pulmonary infection. METHODS:Using prospectively collected data from the Australian IPF Registry including use of antacid therapy, GORD diagnosis and GORD symptoms, the relationship of these GORD variables to survival and disease progression was assessed. The severity of GORD symptoms using the frequency scale for symptoms of GORD (FSSG) and its relationships to outcomes was also assessed for the first time in an IPF cohort. RESULTS:Five hundred eighty-seven (86%) of the 684 patients in the Australian IPF Registry were eligible for inclusion. Patients were mostly male (69%), aged 71.0 ± 8.5 years with moderate disease (FVC 81.7 ± 21.5%; DLco 48.5 ± 16.4%). Most patients were taking antacids (n = 384; 65%), though fewer had a diagnosis of GORD (n = 243, 41.4%) and typical GORD symptoms were even less common (n = 171, 29.1%). The mean FSSG score was 8.39 ± 7.45 with 43% (n = 251) having a score > 8. Overall, there was no difference in survival or disease progression, regardless of antacid treatment, GORD diagnosis or GORD symptoms. CONCLUSIONS:Neither the use of antacid therapy nor the presence of GORD symptoms affects longer term outcomes in IPF patients. This contributes to the increasing evidence that antacid therapy may not be beneficial in IPF patients and that GORD directed therapy should be considered on an individual basis to treat the symptoms of reflux.Helen E. Jo, Tamera J. Corte, Ian Glaspole, Christopher Grainge, Peter M. A. Hopkins ... Peter A. Bampton ... et al