Extending density surface models to include multiple and double-observer survey data

David L. Miller was funded by OPNAV N45 and the SURTASS LFA Settlement Agreement, being managed by the U.S. Navy’s Living Marine Resources program under Contract No. N39430-17-C-1982, collaboration between Douglas B. Sigourney and David L. Miller was also facilitated by the DenMod working group (https://synergy.st-andrews.ac.uk/denmod/) funded under the same agreement. The survey that the fin whale data originate from was funded through two inter-agency agreements with the National Marine Fisheries Service: inter-agency agreement number M14PG00005 with the US Department of the Interior, Bureau of Ocean Energy Management, Environmental Studies Program, Washington, DC and inter-agency agreement number NEC-16-011-01-FY18 with the US Navy. The survey that the fulmar data originate from was funded by the UK Natural Environmental Research Council (NERC) grant NE/M017990/1.Spatial models of density and abundance are widely used in both ecological research (e.g., to study habitat use) and wildlife management (e.g., for population monitoring and environmental impact assessment). Increasingly, modellers are tasked with integrating data from multiple sources, collected via different observation processes. Distance sampling is an efficient and widely used survey and analysis technique. Within this framework, observation processes are modelled via detection functions. We seek to take multiple data sources and fit them in a single spatial model. Density surface models (DSMs) are a two-stage approach: first accounting for detectability via distance sampling methods, then modelling distribution via a generalized additive model. However, current software and theory does not address the issue of multiple data sources. We extend the DSM approach to accommodate data from multiple surveys, collected via conventional distance sampling, double-observer distance sampling (used to account for incomplete detection at zero distance) and strip transects. Variance propagation ensures that uncertainty is correctly accounted for in final estimates of abundance. Methods described here are implemented in the dsm R package. We briefly analyse two datasets to illustrate these new developments. Our new methodology enables data from multiple distance sampling surveys of different types to be treated in a single spatial model, enabling more robust abundance estimation, potentially over wider geographical or temporal domains.Publisher PDFPeer reviewe

Tracking a northern fulmar from a Scottish nesting site to the Charlie-Gibbs Fracture Zone : Evidence of linkage between coastal breeding seabirds and Mid-Atlantic Ridge feeding sites

Peer reviewedPublisher PD

Biodiversity characterisation and hydrodynamic consequences of marine fouling communities on submerged marine structures in the Orkney Islands Archipelago, Scotland, UK.

As part of ongoing commitments to produce electricity from renewable energy sources in Scotland, Orkney waters have been targeted for potential large-scale deployment of wave and tidal energy converting devices. Orkney has a well-developed infrastructure supporting the marine energy industry; recently enhanced by the construction of additional piers. A major concern to marine industries is biofouling on submerged structures, including energy converters and measurement instrumentation. In this study, the marine energy infrastructure and instrumentation were surveyed to characterise the biofouling. Fouling communities varied between deployment habitats; key species were identified allowing recommendations for scheduling device maintenance and preventing spread of invasive organisms. A method to measure the impact of biofouling on hydrodynamic response is described and applied to data from a wave-monitoring buoy deployed at a test site in Orkney. The results are discussed in relation to the accuracy of the measurement resources for power generation. Further applications are suggested for future testing in other scenarios, including tidal energy

Biodiversity characterisation and hydrodynamic consequences of marine fouling communities on submerged marine structures in the Orkney Islands Archipelago, Scotland, UK.

<p>As part of ongoing commitments to produce electricity from renewable energy sources in Scotland, Orkney waters have been targeted for potential large-scale deployment of wave and tidal energy converting devices. Orkney has a well-developed infrastructure supporting the marine energy industry; recently enhanced by the construction of additional piers. A major concern to marine industries is biofouling on submerged structures, including energy converters and measurement instrumentation. In this study, the marine energy infrastructure and instrumentation were surveyed to characterise the biofouling. Fouling communities varied between deployment habitats; key species were identified allowing recommendations for scheduling device maintenance and preventing spread of invasive organisms. A method to measure the impact of biofouling on hydrodynamic response is described and applied to data from a wave-monitoring buoy deployed at a test site in Orkney. The results are discussed in relation to the accuracy of the measurement resources for power generation. Further applications are suggested for future testing in other scenarios, including tidal energy.</p

A Comparison Between Denaturing Gradient Gel Electrophoresis and Denaturing High Performance Liquid Chromatography in Detecting Mutations in Genes Associated with Hereditary Non-Polyposis Colorectal Cancer (HNPCC) and the Identification of 9 New Mutations Previously Unidentified by DGGE

Denaturing high performance liquid chromatography is a relatively new method by which heteroduplex structures formed during the PCR amplification of heterozygote samples can be rapidly identified. The use of this technology for mutation detection in hereditary non-polyposis colorectal cancer (HNPCC) has the potential to appreciably shorten the time it takes to analyze genes associated with this disorder. Prior to acceptance of this method for screening genes associated with HNPCC, assessment of the reliability of this method should be performed. In this report we have compared mutation and polymorphism detection by denaturing gradient gel electrophoresis (DGGE) with denaturing high performance liquid chromatography (DHPLC) in a set of 130 families. All mutations/polymorphisms representing base substitutions, deletions, insertions and a 23 base pair inversion were detected by DHPLC whereas DGGE failed to identify four single base substitutions and a single base pair deletion. In addition, we show that DHPLC has been used for the identification of 5 different mutations in exon 7 of hMSH2 that could not be detected by DGGE

Increased diagnosis and treatment of hepatitis C in prison by universal offer of testing and use of telemedicine

With recent advances in anti‐viral therapy there is an opportunity to eliminate HCV from the UK population. HCV is common in incarcerated individuals, with previous estimates suggesting ~7% of the UK prison population is anti‐HCV antibody positive. Increasing diagnosis and treatment of HCV in prison is a priority in seeking to eliminate transmission in the general population. Thus the study aimed, to assess the impact implementation of: 1. A universal offer of blood borne virus testing (UOBBVT) using dry blood spot testing for prisoners at reception to increase diagnosis; 2. Telemedicine clinics (TC) within North East England (NEE) prisons to increase HCV treatment rates. UOBBVT was initially implemented at Her Majesty's Prison (HMP) Durham, commencing March 2016. From March 2016 to February 2017, 2,831 of 4,280 (66%) new receptions were offered BBV testing. Of these, 1,495 (53% of offered) accepted BBV testing, of whom 95 (6.4%) were HCV antibody positive, with 47 of those 95 (49.5%) HCV RNA positive, suggesting a prevalence of active infection in the tested population of 3.1% (95% CI 2.4% to 4.2%). Between August 2015 and October 2017, 80 individuals were seen in the TC and 57 (71%) commenced antiviral therapy. Of those with known outcome (n=29), 100% achieved sustained virological response. In the year prior to implementation, only 4 patients received HCV treatment. In conclusion, a universal offer of BBV testing to inmates presenting at HMP reception coupled with linkage into specialist care via TC can substantially increase rates of testing, diagnosis and treatment of HCV in this high prevalence population

Targeting the LOX/hypoxia axis reverses many of the features that make pancreatic cancer deadly: inhibition of LOX abrogates metastasis and enhances drug efficacy

Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer‐related mortality. Despite significant advances made in the treatment of other cancers, current chemotherapies offer little survival benefit in this disease. Pancreaticoduodenectomy offers patients the possibility of a cure, but most will die of recurrent or metastatic disease. Hence, preventing metastatic disease in these patients would be of significant benefit. Using principal component analysis (PCA), we identified a LOX/hypoxia signature associated with poor patient survival in resectable patients. We found that LOX expression is upregulated in metastatic tumors from Pdx1‐Cre KrasG12D/+ Trp53R172H/+ (KPC) mice and that inhibition of LOX in these mice suppressed metastasis. Mechanistically, LOX inhibition suppressed both migration and invasion of KPC cells. LOX inhibition also synergized with gemcitabine to kill tumors and significantly prolonged tumor‐free survival in KPC mice with early‐stage tumors. This was associated with stromal alterations, including increased vasculature and decreased fibrillar collagen, and increased infiltration of macrophages and neutrophils into tumors. Therefore, LOX inhibition is able to reverse many of the features that make PDAC inherently refractory to conventional therapies and targeting LOX could improve outcome in surgically resectable disease

Two 100 Mpc-scale structures in the 3-D distribution of radio galaxies and their implications

We present unequivocal evidence for a huge (~80 x 100 x 100 Mpc^3) super-structure at redshift z=0.27 in the 3-D distribution of radio galaxies from the TONS08 sample, confirming tentative evidence for such a structure from the 7C redshift survey (7CRS). A second, newly discovered super-structure is also less securely found at redshift 0.35 (of dimensions ~100 x 100 x 100 Mpc^3). We present full observational details on the TONS08 sample which was constructed to probe structures in the redshift range 0 < z < 0.5 by matching NVSS sources with objects in APM catalogues to obtain a sample of optically bright (E ~ R 3 mJy) radio galaxies in the same 25 deg^2 area as part-II of the 7CRS. Out of the total sample size of 84 radio galaxies, at least 25 are associated with the two ~100 Mpc-scale super-structures. We use quasi-linear structure formation theory to estimate the number of such structures expected in the TONS08 volume if the canonical value for radio galaxy bias is assumed. Under this assumption, the structures represent ~ 4-5 sigma peaks in the primordial density field and their expected number is low (~10^-2 - 10^-4). Fortunately, there are several plausible explanations (many of which are testable) for these low probabilities in the form of potential mechanisms for boosting the bias on large scales. These include: the association of radio galaxies with highly biased rich clusters in super-structures, enhanced triggering by group/group mergers, and enhanced triggering and/or redshift space distortion in collapsing systems as the growth of super-structures moves into the non-linear regime (abridged).Comment: Accepted for publication in MNRAS. 26 pages,16 figures. spectra can be found in: http://www-astro.physics.ox.ac.uk/~brand/08_paper.ps.g