The structure of gravel-bed flow with intermediate submergence: a laboratory study

The paper reports an experimental study of the flow structure over an immobile gravel bed in open channel at intermediate submergence, with particular focus on the near-bed region. The experiments consisted of velocity measurements using three-component (stereoscopic) Particle Image Velocimetry (PIV) in near-bed horizontal plane and two-component PIV in three vertical planes that covered three distinctly different hydraulic scenarios where the ratio of flow depth to roughness height (i.e., relative submergence) changes from 7.5 to 10.8. Detailed velocity measurements were supplemented with fine-scale bed elevation data obtained with a laser scanner. The data revealed longitudinal low-momentum and high-momentum "strips'' in the time-averaged velocity field, likely induced by secondary currents. This depth-scale pattern was superimposed with particle-scale patches of flow heterogeneity induced by gravel particle protrusions. A similar picture emerged when considering second-order velocity moments. The interaction between the flow field and gravel-bed protrusions is assessed using cross correlations of velocity components and bed elevations in a horizontal plane just above gravel particle crests. The cross correlations suggest that upward and downward fluid motions are mainly associated with upstream-facing and lee sides of particles, respectively. Results also show that the relative submergence affects the turbulence intensity profiles for vertical velocity over the whole flow depth, while only a weak effect, limited to the near-bed region, is noticed for streamwise velocity component. The approximation of mean velocity profiles with a logarithmic formula reveals that log-profile parameters depend on relative submergence, highlighting inapplicability of a conventional "universal'' logarithmic law for gravel-bed flows with intermediate submergence

ISPIDER Central: an integrated database web-server for proteomics

Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics

Investigating the distribution and regional occurrence of anthropogenic litter in English Marine Protected Areas using 25 years of citizen-science beach clean data

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordMarine Protected Areas (MPAs) are designated to enable the management of damaging activities within a discrete spatial area, and can be effective at reducing the associated impacts, including habitat loss and over-exploitation. Such sites, however, may be exposed to the potential impacts from broader scale pressures, such as anthropogenic litter, due to its diffuse nature and lack of constraint by legislative and/or political boundaries. Plastic, a large component of litter, is of particular concern, due to increasing evidence of its potential to cause ecological and socio-economic damage. The presence of sensitive marine features may mean that some MPAs are at greater potential risk from the impacts of plastic pollution than some non-protected sites. Understanding the abundance, distribution and composition of litter along coastlines is important for designing and implementing effective management strategies. Gathering such data, however, can be expensive and time37 consuming but litter survey programmes that enlist citizen scientists are often able to resolve many of the logistical or financial constraints. Here, we examine data collected over 25-years (1994 – 2018), by Marine Conservation Society volunteers, for spatial patterns in relation to the English MPA network, with the aim of highlighting key sources of litter and identifying management priority areas. We found that MPAs in southeast (Kent) and southwest (Cornwall and Devon) England have the highest densities of shore-based litter. Plastic is the main material constituent and public littering the most common identifiable source. Items attributed to fishing activities were most prevalent in southwest MPAs and sewage related debris was highest in MPAs near large rivers and estuaries, indicating localised accumulation. When comparing inside and outside of MPAs, we found no difference in litter density, demonstrating the need for wider policy intervention at local, national and international scales to reduce the amount of plastic pollution.Natural EnglandNatural Environment Research Council (NERC)Engineering and Physical Sciences Research Council (EPSRC

Pest and disease management system for supporting winter oilseed rape decisions (PASSWORD) - vaildation phase (HGCA Project Report No. 390)

Pests and particularly diseases cause serious loss of yield and quality in winter oilseed rape estimated to exceed £80 million/annum in some years. These losses have occurred despite an annual expenditure of about £3.5 million for insecticides and £12 million on fungicides. Decision-making is difficult because there is complex spatial and temporal variation in pest and disease problems and improved guidance is required. The main objective of this project was to test new disease models developed in the first phase of this project and deliver a decision support system for both pest and disease control in oilseed rape. The regional light leaf spot forecast is well-established and reliable and indicates an increased risk of this disease in spring 2006. A new regional forecast for stem canker incidence preharvest has been developed and made available on the Internet. It was successful in 2004/05 and offers strategic guidance on risk provided weather factors are within the range used to develop the model. A four-stage crop-specific stem canker risk assessment method was developed that predicts the onset of phoma leaf spotting using post-harvest weather data and thermal time relationships for canker development and canker severity. Yield loss can then be calculated from canker severity and the economic impact of stem canker predicted. There is some flexibility in the timing of fungicide sprays to control stem canker. Delays of 2 to 3 weeks beyond a 10-20% plants affected threshold did not adversely affect yield. Stem canker severity and yield of different cultivars showed large variation between years and sites and smaller, but significant, variation in responses to fungicide. When phoma leaf spot appears in late autumn, it is only when plants are small that stem canker is likely to cause yield loss. In commercial crops, there were consistent trends for higher yields to be associated with higher fungicide inputs. Light leaf spot was very difficult to control with fungicides in the Aberdeen area where use of resistant cultivars is essential. The most effective disease control was obtained using a combination of resistant cultivars and fungicides. In some years, responses to fungicides were not cost-effective and targeting their use to high-risk situations is necessary to give the best margins over input costs. Close contact was maintained with potential users during the project and they influenced priorities and design features. The components of PASSWORD decision support system were tested and provide guidance for the management of invertebrate pests, phoma stem canker and light leaf spot. The system will be available to ArableDS for use in autumn 2006

Excess cases of prostate cancer and estimated overdiagnosis associated with PSA testing in East Anglia

This study aimed to estimate the extent of 'overdiagnosis' of prostate cancer attributable to prostate-specific antigen (PSA) testing in the Cambridge area between 1996 and 2002. Overdiagnosis was defined conceptually as detection of prostate cancer through PSA testing that otherwise would not have been diagnosed within the patient's lifetime. Records of PSA tests in Addenbrookes Hospital were linked to prostate cancer registrations by NHS number. Differences in prostate cancer registration rates between those receiving and not receiving prediagnosis PSA tests were calculated. The proportion of men aged 40 years or over with a prediagnosis PSA test increased from 1.4 to 5.2% from 1996 to 2002. The rate of diagnosis of prostate cancer was 45% higher (rate ratios (RR) = 1.45, 95% confidence intervals (CI) 1.02-2.07) in men with a history of prediagnosis PSA testing. Assuming average lead times of 5 to 10 years, 40-64% of the PSA-detected cases were estimated to be overdiagnosed. In East Anglia, from 1996 to 2000, a 1.6% excess of cases was associated with PSA testing (around a quarter of the 5.3% excess incidence cases observed in East Anglia from 1996 to 2000). Further quantification of the overdiagnosis will result from continued surveillance and from linkage of incidence to testing in other hospitals

Economic impact analysis of natural gas development and the policy implications

In the US, the shale gas revolution ensured that the development costs of unconventional natural gas plummeted to the levels of $2–3/Mcf. This success has motivated the development of shale gas in other regions, including Australia and Europe. This study, focussing primarily on aspects of economic impact analysis, estimates the development costs of shale gas extraction in both Australia and Europe, based on both direct and fiscal costs, and also suggests policy initiatives. The increasing liquefied natural gas (LNG) developments in Australia are already straining domestic gas supplies. Hence, the development of more natural gas resources has been given a high priority. However, a majority of the Australian shale resources is non-marine in origin and significantly different to the marine-type shales in the US. In addition, the challenges of high development costs and the lack of infrastructure, service capacity and effective government policy are inhibiting shale gas development. Increasing the attractiveness of low risk investment by new, local, developers is critical for Australian shale gas success, which will simultaneously increase domestic gas security. In the European context, unconventional gas development will be challenged by direct, rather than fiscal costs. High direct costs will translate into average overall gas development costs over$13/Mcf, which is well over the existing market price

Serum methylarginines and spirometry-measured lung function in older adults

Rationale: Methylarginines are endogenous nitric oxide synthase inhibitors that have been implicated in animal models of lung disease but have not previously been examined for their association with spirometric measures of lung function in humans. Objectives: This study measured serum concentrations of asymmetric and symmetric dimethylarginine in a representative sample of older community-dwelling adults and determined their association with spirometric lung function measures. Methods: Data on clinical, lifestyle, and demographic characteristics, methylated arginines, and L-arginine (measured using LC-MS/MS) were collected from a population-based sample of older Australian adults from the Hunter Community Study. The five key lung function measures included as outcomes were Forced Expiratory Volume in 1 second, Forced Vital Capacity, Forced Expiratory Volume in 1 second to Forced Vital Capacity ratio, Percent Predicted Forced Expiratory Volume in 1 second, and Percent Predicted Forced Vital Capacity. Measurements and Main Results: In adjusted analyses there were statistically significant independent associations between a) higher asymmetric dimethylarginine, lower Forced Expiratory Volume in 1 second and lower Forced Vital Capacity; and b) lower L-arginine/asymmetric dimethylarginine ratio, lower Forced Expiratory Volume in 1 second, lower Percent Predicted Forced Expiratory Volume in 1 second and lower Percent Predicted Forced Vital Capacity. By contrast, no significant associations were observed between symmetric dimethylarginine and lung function. Conclusions: After adjusting for clinical, demographic, biochemical, and pharmacological confounders, higher serum asymmetric dimethylarginine was independently associated with a reduction in key measures of lung function. Further research is needed to determine if methylarginines predict the decline in lung function

N-Oleoyl-glycine reduces nicotine reward and withdrawal in mice.

Cigarette smokers with brain damage involving the insular cortex display cessation of tobacco smoking, suggesting that this region may contribute to nicotine addiction. In the present study, we speculated that molecules in the insular cortex that are sensitive to experimental traumatic brain injury (TBI) in mice might provide leads to ameliorate nicotine addiction. Using targeted lipidomics, we found that TBI elicited substantial increases of a largely uncharacterized lipid, N-acyl-glycine, N-oleoyl-glycine (OlGly), in the insular cortex of mice. We then evaluated whether intraperitoneal administration of OlGly would alter withdrawal responses in nicotine-dependent mice as well as the rewarding effects of nicotine, as assessed in the conditioned place preference paradigm (CPP). Systemic administration of OlGly reduced mecamylamine-precipitated withdrawal responses in nicotine-dependent mice and prevented nicotine CPP. However, OlGly did not affect morphine CPP, demonstrating a degree of selectivity. Our respective in vitro and in vivo observations that OlGly activated peroxisome proliferator-activated receptor alpha (PPAR-α) and the PPAR-α antagonist GW6471 prevented the OlGly-induced reduction of nicotine CPP in mice suggests that this lipid acts as a functional PPAR-α agonist to attenuate nicotine reward. These findings raise the possibility that the long chain fatty acid amide OlGly may possess efficacy in treating nicotine addiction