Seabed biotope characterisation based on acoustic sensing

The background to this thesis is Australia’s Oceans Policy, which aims to develop an integrated and ecosystem-based approach to planning and management. An important part of this approach is the identification of natural regions in regional marine planning, for example by establishing marine protected areas for biodiversity conservation. These natural regions will need to be identified on a range of scales for different planning and management actions. The scale of the investigation reported in this thesis is applicable to spatial management at 1 km to 10 km scale and monitoring impacts at the 10s of m to 1 km biotope scale. Seabed biotopes represent a combination of seabed physical attributes and related organisms. To map seabed biotopes in deep water, remote sensing using a combination of acoustic, optical and physical sensors is investigated. The hypothesis tested in this thesis is that acoustic bathymetry and backscatter data from a Simrad EM1002 multi-beam sonar (MBS) can be used to infer (act as a surrogate of) seabed biotopes. To establish a link between the acoustic data and seabed biotopes the acoustic metrics are compared to the physical attributes of the seabed in terms of its substrate and geomorphology at the 10s m to 1 km scale using optical and physical sensors. At this scale the relationship between the dominant faunal functional groups and both the physical attributes of the seabed and the acoustic data is also tested. These tests use data collected from 14 regions and 2 biomes to the south of Australia during a voyage in 2000. Based on 62 reference sites of acoustic, video and physical samples, a significant relationship between ecological seabed terrain types and acoustic backscatter and bathymetry was observed.These ecological terrain types of soft-smooth, soft-rough, hard-smooth and hard-rough were chosen as they were the most relevant to the biota in their ability to attach on or burrow into the seabed. A seabed scattering model supported this empirical relationship and the overall shape of backscatter to incidence angle relationship for soft and hard seabed types. The correlation between acoustic data (backscatter mean and standard deviation) and the visual and physical samples was most consistent between soft-smooth and hard-rough terrain types for a large range of incidence angles (16o to 70o). Using phenomenological backscatter features segmented into 10 common incidence angle bins from -70o to 70o the length resolution of the data decreased to 0.55 times depth. The decreased resolution was offset by improved near normal incidence (0o to 30o) seabed type discrimination with cross validation error reducing from 32% to 4%. A significant relationship was also established between the acoustic data and the dominant functional groups of fauna. Faunal functional groups were based on the ecological function, feeding mode and substrate preference, with 8 out of the 10 groups predicted with 70% correctness by the four acoustically derived ecological terrain types. Restricting the terrain classification to simple soft and hard using the acoustic backscatter data improved the prediction of three faunal functional groups to greater than 80%. Combining the acoustic bathymetry and backscatter data an example region, Everard Canyon, was interpreted at a range of spatial scales and the ability to predict the preferred habitat of a stalked crinoid demonstrated.Seabed terrain of soft and hard was predicted from the acoustic backscatter data referenced to a common seabed incidence angle of 40o. This method of analysis was selected due to its combined properties of high spatial resolution, consistent between terrain discrimination at the widest range of incidence angles and consistent data quality checking at varying ranges. Based in part on the research reported in this thesis a mid-depth Simrad EM300 multibeam sonar was purchased for use in Australian waters. A sampling strategy is outlined to map all offshore waters with priority within the 100 m to 1500 m depths

Faith and STEM Education: A Path to Mutual Elevation in Catholic Schools

Amidst increasing religious disaffiliation, often due to a perceived tension between faith and the STEM disciplines, Catholic schools provide critical opportunities for young people to recognize how these domains can be mutually elevating. The field, however, lacks guidance as to how this integration should occur in practice. This conceptual paper first provides an overarching framework for how aspects of the Catholic tradition, like Scripture and the Catholic social tradition, can shape traditional educational domains of STEM teaching and learning. Secondly, we provide a heuristic of three criteria for deeply engaging students at the interface of the Catholic faith and the STEM disciplines. Finally, we narrow in on K-12 science standards and provide six examples of how the three criteria can be applied to authentically and deeply advance understanding at the intersection of science and the Catholic faith

Human Papillomavirus Typing in HIV-Positive Women

Objective: Human papillomavirus (HPV) is the major cause of cervical carcinoma and cervical intraepithelial neoplasia worldwide. Certain HPV types have a strong association with and probably a causative role in the pathogenesis of premalignant cervical lesions. Epidemiologic studies in women infected by the human immunodeficiency virus (HIV) have shown an increased incidence of squamous intraepithelial lesions (SILs), whichwere predominantly high-grade. Six to 30 per cent of women diagnosed with atypical squamous cells of undetermined significance (ASCUS) on a Papanicolaou (Pap) smear harbor SIL in normal screening populations. This study was undertaken to determine the presence of low- and high-risk HPV types in women infected by HIV and to correlate the results to those of the Pap smear. Study design: HPV DNA typing (low- and high-risk) by Digene™ (Digene Corporation, Gathesburg, MD) hybrid capture methodology was performed on cervical swabs from 209 HIV-positive women. The results of HPV typing were correlated with those of the Pap smear in a retrospective analysis. Results: One hundred and one women (48%) tested positive for HPV subtypes by DNA typing by the hybrid capture method. Of these, 64 patients (63%) had Pap smears whichwere read as being normal, having benign cellular changes, or having ASCUS (favor reactive process). Of these, 19 patients tested positive for both high-risk and low-risk subtypes, 32 patients tested positive only for high-risk subtypes, and 13 patients tested positive only for low-risk subtypes. Conclusion: HPV subtyping identifies a significant group of HIV-positive women who are at risk for developing cervical intraepithelial neoplasia, although they may not show significant abnormalities on their Pap smears

Automatic active acoustic target detection in turbulent aquatic environments

This work is funded by the Environment and Food Security theme Ph.D. studentship from the University of Aberdeen, the Natural Environment Research Council (NERC) and Department for Environment, Food, and Rural Affairs (Defra grant NE/J004308/1), and the Marine Collaboration Research Forum (MarCRF). We would like to gratefully acknowledge the support from colleagues at Marine Scotland Science.Peer reviewedPublisher PD

From siphonophores to deep scattering layers : uncertainty ranges for the estimation of global mesopelagic fish biomass

Funding: Horizon 2020 Framework Programme, (Grant/Award Number: “692173”).The mesopelagic community is important for downward oceanic carbon transportation and is a potential food source for humans. Estimates of global mesopelagic fish biomass vary substantially (between 1 and 20 Gt). Here, we develop a global mesopelagic fish biomass model using daytime 38 kHz acoustic backscatter from deep scattering layers. Model backscatter arises predominantly from fish and siphonophores but the relative proportions of siphonophores and fish, and several of the parameters in the model, are uncertain. We use simulations to estimate biomass and the variance of biomass determined across three different scenarios; S1, where all fish have gas-filled swimbladders, and S2 and S3, where a proportion of fish do not. Our estimates of biomass ranged from 1.8 to 16 Gt (25–75% quartile ranges), and median values of S1 to S3 were 3.8, 4.6, and 8.3 Gt, respectively. A sensitivity analysis shows that for any given quantity of fish backscatter, the fish swimbladder volume, its size distribution and its aspect ratio are the parameters that cause most variation (i.e. lead to greatest uncertainty) in the biomass estimate. Determination of these parameters should be prioritized in future studies, as should determining the proportion of backscatter due to siphonophores.Publisher PDFPeer reviewe

Opportunities and challenges for eCooking on mini-grids in Malawi : case study insight

Mini-grids are the least cost electrification option for over 30% of Malawi's population, however mini-grid financial sustainability is often compromised due to underutilised generation. Electric cooking is increasing in prominence globally and offers a low carbon alternative to biomass. Powering eCook devices on mini-grids in Malawi has the potential to improve mini-grid profitability while offering environmental and social benefits. This study explores this opportunity drawing on pilot case study data from mini-grid powered eCook devices gathered through smart meters and social impact surveys. Technical analysis presents statistical load profiles compared to modelled profiles, indicating lower eCook demand from measured profiles and likelihood of fuel stacking. Analysis is utilised to investigate opportunities and challenges for mini-grid eCooking in Malawi through technical and economic lenses, including potential impact of carbon credits on financial models. Recommendations given to accelerate mini-grid eCooking in Malawi include demand side management, smart cooking subsidies, and further data analysis

Monitoring fish weight using pulse-echo waveform metrics

[EN] Fish anatomical vertical dimensions are extracted from a time-of-flight analysis of fish echo shape using narrow bandwidth echosounding of swimming individuals. These vertical dimensions fit a Gumbel distribution model and are successfully correlated with fish weight. The proposed method can be used to estimate the mean weight of fish in aquaculture cages as an alternative to target strength measurements. Full-waveform acquisition and signal correlation techniques permitted to increase the signal-to-noise ratio and to improve the performance against traditional envelope-based echosounding.This work was developed with the financial support of project ARM/1790/010 of the Tecnological Develoment Program of MAGRAMA, Spanish Government. E. Soliveres acknowledges support of Spanish Government grant AP2009-4459 FPU Subprogram.Soliveres, E.; Poveda Martinez, P.; Estruch, VD.; Pérez Arjona, I.; Puig Pons, V.; Ordoñez-Cebrian, P.; Ramis Soriano, J.... (2017). Monitoring fish weight using pulse-echo waveform metrics. Aquacultural Engineering. 77:125-131. doi:10.1016/j.aquaeng.2017.04.002S1251317

Optimising fisheries management in relation to tuna catches in the western central Pacific Ocean: A review of research priorities and opportunities

Some of the most important development goals for the countries and territories of the Western and Central Pacific Ocean (WCPO) involve the sustainable management of their fisheries in light of environmental, economic and social uncertainties. The responses of fish populations to variability in the marine environment have implications for decision making processes associated with resource management. There is still considerable uncertainty in estimating the responses of tuna populations to short-to-medium-term variability and longer-term change in the oceanic environment. A workshop was organised to examine how advances in oceanography, fisheries science and fisheries economics could be applied to the tuna fisheries of the WCPO and in doing so identify research priorities to improve understanding relevant to progressing management. Research priorities identified included: (i) improved parameterisation of end to end ecosystem model components, processes and feedbacks through expanded biological observations and incorporation of higher resolution climate models; (ii) development of seasonal and inter-annual forecasting tools enabling management responses to short-term variability in tuna distributions and abundances; (iii) improved understanding of the population dynamics of and the energy transfer efficiencies between food web components; (iv) assessment of the optimal value of access rights and overall fishery value under multiple scenarios of tuna distribution and abundance and influences on decision making by fisheries managers and fleets and (v) development of management strategy evaluation frameworks for utilisation in the implementing and testing of fishery management procedures and to help prioritise research directions and investment. Issues discussed and research priorities identified during the workshop have synergies with other internationally managed fisheries and therefore are applicable to many other fisheries

Experience in implementing harvest strategies in Australia's south-eastern fisheries

The Southern and Eastern Scalefish and Shark Fishery (SESSF) is a complex multi-species fishery, with 34 stock units under quota management, for which a harvest strategy framework was developed in 2005. The framework involves the application of a set of tier-based harvest control rules (HCR) designed to provide a precautionary approach to management. The harvest strategy framework has been applied from 2005 to 2007, resulting in substantial reductions in quotas across the fishery. The experience in implementing the framework, both positive and negative, is described, and general lessons are drawn. Key lessons include the importance of formally testing such strategies using management strategy evaluation, the impact of external management drivers on implementation of the approach, the need to define strategies for setting "bycatch quotas" in multi-species fisheries, and the need for flexibility and pragmatism in the early stages of implementing such an approach