A working guide to the assessment, implementation and post project monitoring of fisheries habitat improvement schemes in South Cumbria

Due to changes in land use over the last century, the physical nature of many streams and rivers in the British Isles has probably changed. In some cases this change may be large for example as a result of flood defence schemes and is easily observed, whilst in other cases altered land use, farming, forestry or urbanization may have resulted in more subtle changes to river features. This working guide draws together a way of assessing habitat in any stream or river and determine sites or reaches on the assessed watercourse that may benefit from habitat improvement schemes. It will determine a method of measuring existing habitat in a broad sense, whilst referring to R and D studies currently being undertaken in this area. A method of prioritising any proposed habitat restoration work will be suggested. The limitations of fisheries improvement schemes in terms of cross functional acceptance (flood defence and conservation) will be examined along with suggested proposals for some example watercourses. The need for pre and post enhancement monitoring will be discussed as will the requirement for maintenance programs on schemes. Finally methods for determining the cost benefits of small schemes will be examined, compared to other currently used enhancement strategies. This will allow small scale revenue schemes to be used to back up pre project cost benefit analysis as required in future capital submissions

Imaging of high-Z material for nuclear contraband detection with a minimal prototype of a Muon Tomography station based on GEM detectors

Muon Tomography based on the measurement of multiple scattering of atmospheric cosmic ray muons in matter is a promising technique for detecting heavily shielded high-Z radioactive materials (U, Pu) in cargo or vehicles. The technique uses the deflection of cosmic ray muons in matter to perform tomographic imaging of high-Z material inside a probed volume. A Muon Tomography Station (MTS) requires position-sensitive detectors with high spatial resolution for optimal tracking of incoming and outgoing cosmic ray muons. Micro Pattern Gaseous Detector (MPGD) technologies such as Gas Electron Multiplier (GEM) detectors are excellent candidates for this application. We have built and operated a minimal MTS prototype based on 30cm \times 30cm GEM detectors for probing targets with various Z values inside the MTS volume. We report the first successful detection and imaging of medium-Z and high-Z targets of small volumes (~0.03 liters) using GEM-based Muon Tomography

SN 2016iet: The Pulsational or Pair Instability Explosion of a Low Metallicity Massive CO Core Embedded in a Dense Hydrogen-Poor Circumstellar Medium

We present optical photometry and spectroscopy of SN 2016iet, an unprecedented Type I supernova (SN) at $z=0.0676$ with no obvious analog in the existing literature. The peculiar light curve has two roughly equal brightness peaks ($\approx -19$ mag) separated by 100 days, and a subsequent slow decline by 5 mag in 650 rest-frame days. The spectra are dominated by emission lines of calcium and oxygen, with a width of only $3400$ km s$^{-1}$, superposed on a strong blue continuum in the first year, and with a large ratio of $L_{\rm [Ca\,II]}/L_{\rm [O\,I]}\approx 4$ at late times. There is no clear evidence for hydrogen or helium associated with the SN at any phase. We model the light curves with several potential energy sources: radioactive decay, central engine, and circumstellar medium (CSM) interaction. Regardless of the model, the inferred progenitor mass near the end of its life (i.e., CO core mass) is $\gtrsim 55$ M$_\odot$ and up to $120$ M$_\odot$, placing the event in the regime of pulsational pair instability supernovae (PPISNe) or pair instability supernovae (PISNe). The models of CSM interaction provide the most consistent explanation for the light curves and spectra, and require a CSM mass of $\approx 35$ M$_\odot$ ejected in the final decade before explosion. We further find that SN 2016iet is located at an unusually large offset ($16.5$ kpc) from its low metallicity dwarf host galaxy ($Z\approx 0.1$ Z$_\odot$, $M\approx 10^{8.5}$ M$_\odot$), supporting the PPISN/PISN interpretation. In the final spectrum, we detect narrow H$\alpha$ emission at the SN location, likely due to a dim underlying galaxy host or an H II region. Despite the overall consistency of the SN and its unusual environment with PPISNe and PISNe, we find that the inferred properties of SN\,2016iet challenge existing models of such events.Comment: 26 Pages, 17 Figures, Submitted to Ap

The development of a new measure of quality of life in the management of gastro-oesophageal reflux disease: the Reflux Questionnaire.

INTRODUCTION This paper reports on the development of a new measure of health-related quality of life for use among patients with gastro-oesophageal reflux disease (GORD), funded as part of the REFLUX trial. This is a large UK multi centre trial that aims to compare the clinical and cost effectiveness of minimal access surgery with best medical treatment for patients with GORD within the NHS. Method Potential items were identified via a series of interviews and focus groups carried out with patients who were receiving/had received medical or surgical treatment for GORD. The final measure consisted of 31 items covering 7 categories (Heartburn; Acid reflux; Wind; Eating and swallowing; Bowel movements; Sleep; Work, physical and social activities). The measure produced two outputs: a quality of life score (RQLS) and five Reflux symptom scores. Reliability (internal consistency), criterion validity with the SF-36 and, sensitivity to change in terms of relationship with reported change in prescribed medication were assessed amongst a sample of 794 patients recruited into the trial. RESULTS The measure was shown to be internally consistent, to show criterion validity with the SF-36 and sensitive to changes in patients use of prescribed medication at baseline and 3 month follow-up. DISCUSSION The Reflux questionnaire is a new self-administered questionnaire for use amongst patients with GORD. Initial findings suggest that the new measure is valid, reliable, acceptable to respondents and simple to administer in both a clinical and research context

A report on the strategic stock assessment survey of the Colton Beck catchment 1994 with particular reference to salmonids

This is the report on the strategic stock assessment survey of the Colton Beck catchment in 1994 with particular reference to salmonids in Colton Beck, River Ea, River Gilpin and Rusland Pool. This report forms one part of the third year of a triennial survey programme for the South West Cumbria and South Cumbria catchments. It was produced by the National Rivers Authority in 1994. Colton Beck had excellent densities of sea trout (Salmo trutta) and a small population of salmon (Salmo salar) in its lowest reaches. The total productivity was very good throughout the catchment. Stocking of sea trout fry in 1993 has enhanced the population with survivors through to parr probably adding to the scoring of double class A at two sites in the survey in 1994. Stocking was not undertaken in 1994, but the population appears to be maintaining itself at a very high level

High-throughput sequencing reveals a simple model of nucleosome energetics

We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of finite-size particles in an arbitrary external potential and arrays of DNA-bound histone octamers. We derive an analytical solution to infer free energies of nucleosome formation directly from nucleosome occupancies measured in high-throughput experiments. The sequence-specific part of free energies is then captured by fitting them to a sum of energies assigned to individual nucleotide motifs. We have developed hierarchical models of increasing complexity and spatial resolution, establishing that nucleosome occupancies can be explained by systematic differences in mono- and dinucleotide content between nucleosomal and linker DNA sequences, with periodic dinucleotide distributions and longer sequence motifs playing a secondary role. Furthermore, similar sequence signatures are exhibited by control experiments in which genomic DNA is either sonicated or digested with micrococcal nuclease in the absence of nucleosomes, making it possible that current predictions based on high-throughput nucleosome positioning maps are biased by experimental artifacts.Comment: 36 pages, 13 figure

Understanding and informing decisions on Sustainable Agricultural Intensification in Sub-Saharan Africa

Sustainable Agricultural Intensification (SAI) was initially defined as increasing agricultural production without adverse environmental impacts and without increasing the area under agriculture. Overtime the concept has been broadened to integrate social, economic, and environmental components of sustainability, each of which covers multiple facets or indicators of performance. It is recognized however that it may not be possible to optimise all these aspects of sustainability simultaneously and that trade-offs between them are likely to occur, although synergies are also possible. There has been disagreement over how to achieve SAI, with some proposing that only an “agroecological” intensification pathway delivers sustainability. Others take a broader perspective arguing that all aspects of ecological, genetic, and socio-economic intensification need to be considered, but then assessed in terms of the sustainability of the outcomes. A major concern is that intensification that focuses on agricultural technology can lead to inequitable outcomes for women and poorer households, while agroecological intensification building upon local capitals is generally considered more equitable. Understanding the potential outcomes and inherent trade-offs of different approaches requires interdisciplinary research, evidence and decision-making tools, some examples of which are presented in this Special Issue

Screening for HIV-Associated Neurocognitive Impairment

Neurocognitive impairment (NCI) is common in people aging with HIV and can adversely affect health-related quality of life. However, early NCI may be largely asymptomatic and neurocognitive function is rarely assessed in the context of routine clinical care. In this study, we considered the utility of two assessment tools as screens for NCI in patients attending a community-based clinic (N=58; mean age=57 years): the Montreal Cognitive Assessment (MoCA) and a 3-item cognitive concerns questionnaire derived from the HIV Dementia Scale. Health-related quality of life and depression/anxiety were also measured. Indication of NCI using the MoCA was more prevalent compared to the 3-item questionnaire and was associated with the patients’ initial antiretroviral therapy commencing between the years of 1997 and 2001, independently of age. Findings of the MoCA were not confounded by existing mood disorders, unlike the 3-item questionnaire. Therefore, we suggest implementing the MoCA as an initial screen for NCI