title: An automated microaneurysm detector as a tool for identification of diabetic retinopathy in rural optometric practice

authors: Jelinek, Herbert J.

subjects: automated detection

abstract: Background: With the increase in the prevalence of diabetes, rural optometric clinics stand to increase their patient load and assessment of diabetic eye disease. This study aimed to assess whether automated identification of diabetic retinopathy based on the presence of microaneurysms is an effective tool in clinical practice.
Methods: We analysed 758 fundal images of 385 patients with diabetes attending the clinic obtained using a Canon CR5 with an EOS10 digital camera through a dilated pupil. Five optometrists employed in the clinic assessed the diabetic retinopathy using binocular indirect ophthalmoscopy. The sensitivity and specificity of the automated system used to analyse the retinal fundal images was determined by comparison with optometric and ophthalmologic assessment.
Results: The optometrists achieved 97 per cent sensitivity at 88 per cent specificity with respect to the ophthalmic classification for detecting retinopathy. The automated retinopathy detector achieved 85 per cent sensitivity at 90 per cent specificity at detecting retinopathy.
Conclusion: The automated microaneurysm detector has a lower sensitivity compared to the optometrists but meets NHMRC guidelines. It may impact on the efficiency of rural optometric practices by early identification of diabetic retinopathy. Automated assessment can save time and be cost-effective, and provide a history of changes in the retinal fundus and the opportunity for instant patient education using the digital images.

text: An automated microaneurysm detector as a tool for identification of diabetic retinopathy in rural optometric practice Background: With the increase in the prevalence of diabetes, rural optometric clinics stand to increase their patient load and assessment of diabetic eye disease. This study aimed to assess whether automated identification of diabetic retinopathy based on the presence of microaneurysms is an effective tool in clinical practice.
Methods: We analysed 758 fundal images of 385 patients with diabetes attending the clinic obtained using a Canon CR5 with an EOS10 digital camera through a dilated pupil. Five optometrists employed in the clinic assessed the diabetic retinopathy using binocular indirect ophthalmoscopy. The sensitivity and specificity of the automated system used to analyse the retinal fundal images was determined by comparison with optometric and ophthalmologic assessment.
Results: The optometrists achieved 97 per cent sensitivity at 88 per cent specificity with respect to the ophthalmic classification for detecting retinopathy. The automated retinopathy detector achieved 85 per cent sensitivity at 90 per cent specificity at detecting retinopathy.
Conclusion: The automated microaneurysm detector has a lower sensitivity compared to the optometrists but meets NHMRC guidelines. It may impact on the efficiency of rural optometric practices by early identification of diabetic retinopathy. Automated assessment can save time and be cost-effective, and provide a history of changes in the retinal fundus and the opportunity for instant patient education using the digital images.

year: 2006

title: Characterization of the bacterioplankton communities in the melt-water ponds of Bratina Island, Victoria Land, Antarctica

authors: Archer, Stephen David James

subjects: melt-water

abstract: Antarctic ecosystems (such as the ponds by Bratina Island, Antarctica) provide an excellent opportunity to examine organisms that can live in one of the most extreme and geochemically varied environments in the world. These ponds are of interest as each one can vary greatly in size, depth, and age as well as profiles of dissolved oxygen, metal concentrations, pH and salinity. Even within ponds geochemically distinct stratified layers can form which can greatly influence their microbial communities. There are a number of studies which indicate that microbial populations found in Antarctic ponds will be highly diverse and variable due to the uniqueness of the environment. This study aims to increase our knowledge of microbial biodiversity and the environmental factors which structure them, in particular the stratification transition zones within ponds water columns. A thorough set of biological samples were taken from five selected ponds during mid-summer in the 09-10 season to complement those taken during the winter freeze-up in the 07-08 extended season by Hawes and co-workers. Oxygen concentration, pH, conductivity and temperature of each pond water sample were measured in the field and water samples were taken back to the University of Waikato for further analysis. This research primarily used the DNA fingerprinting technique ARISA, matched with geochemistry to identify and characterise the resident and functional members of the microbial community and understand how the community is structured in relation to environmental conditions. We found that the planktonic populations of the Bratina Island ponds do vary between ponds, that each pond has its own chemical signature and that populations do change with depth. One of the studied ponds, Egg, was found to have an extreme chemical stratification leading to significantly different populations at each depth. Data analysis using BEST analysis determined that the changes in the bacterial populations in Egg are primarily in relation to the pH and conductivity at each depth which changes dramatically in the lower depths.

text: Characterization of the bacterioplankton communities in the melt-water ponds of Bratina Island, Victoria Land, Antarctica Antarctic ecosystems (such as the ponds by Bratina Island, Antarctica) provide an excellent opportunity to examine organisms that can live in one of the most extreme and geochemically varied environments in the world. These ponds are of interest as each one can vary greatly in size, depth, and age as well as profiles of dissolved oxygen, metal concentrations, pH and salinity. Even within ponds geochemically distinct stratified layers can form which can greatly influence their microbial communities. There are a number of studies which indicate that microbial populations found in Antarctic ponds will be highly diverse and variable due to the uniqueness of the environment. This study aims to increase our knowledge of microbial biodiversity and the environmental factors which structure them, in particular the stratification transition zones within ponds water columns. A thorough set of biological samples were taken from five selected ponds during mid-summer in the 09-10 season to complement those taken during the winter freeze-up in the 07-08 extended season by Hawes and co-workers. Oxygen concentration, pH, conductivity and temperature of each pond water sample were measured in the field and water samples were taken back to the University of Waikato for further analysis. This research primarily used the DNA fingerprinting technique ARISA, matched with geochemistry to identify and characterise the resident and functional members of the microbial community and understand how the community is structured in relation to environmental conditions. We found that the planktonic populations of the Bratina Island ponds do vary between ponds, that each pond has its own chemical signature and that populations do change with depth. One of the studied ponds, Egg, was found to have an extreme chemical stratification leading to significantly different populations at each depth. Data analysis using BEST analysis determined that the changes in the bacterial populations in Egg are primarily in relation to the pH and conductivity at each depth which changes dramatically in the lower depths.

year: 2011

title: Mātauranga Māori to inform understanding of population dynamics and health of pipi in Waihī Estuary, Bay of Plenty.

authors: Kettle, Tyla

abstract: Estuaries are among the most productive ecosystems on earth. They hold significant value to Māori as they connect the whenua (land), awa (river) and moana (ocean), and are an important source of kaimoana (seafood) including shellfish. However, due to increased anthropogenic pressures, many estuaries are degraded, affecting taonga (Māori treasure) species such as pipi (Paphies australis). My thesis uses kaupapa Māori methodology and is co-developed with Ngāti Whakahemo, tangata whenua (people of the land) of Waihī Estuary. This project fundamentally draws upon mātauranga Māori (traditional Māori knowledge), combined with western science to map the historic and current distribution, abundance and health of pipi in Waihī Estuary; as well as explore the perceptions of threats to pipi and estuary ecology from tangata whenua and the regional authority. 
Participatory mapping was used via kōrero/interviews with kaumātua to identify sites of significance for pipi, which were then sampled in November 2020. Mātauranga ā iwi from Ngāti Whakahemo informed the sampling locations. Previous pipi sampling methodology and protocols undertaken by the Ministry for Primary Industries (MPI) were used to facilitate temporal comparisons of pipi distribution and abundance. Environmental factors including sediment grain size, organic content, total nitrogen (TN) and total phosphorus (TP) were also measured to help understand what drives the population dynamics of pipi. Perceptions of tangata whenua and staff members of the Bay of Plenty Regional Council (BOPRC) were also explored following methods similar to Klain et al. (2018) and implementing a dread risk tool via participatory mapping.
Results show that culturally significant sites identified by kaumātua support high pipi abundances of large size (40mm+), with low abundances of pipi in the upper reaches of the estuary. The inclusion of sites identified by MPI allowed for more comprehensive survey on pipi population dynamics by utilising a stratified survey design. Pipi size and abundance was significantly correlated with environmental factors with high pipi densities associated with medium grain size fractions and low levels of TN, TP and organic content. Over harvesting was perceived by kaumātua and BOPRC staff members as the dominant threat to pipi abundance and Waihī Estuary. Nutrients related to sewage inputs and runoff were rated as the second highest perceived threat and diseased shellfish ranked third by kaumātua and BOPRC staff members. 
This study demonstrates that the sharing of mātauranga ā iwi can fundamentally inform western science methods and can be used as an approach to research in the marine science realm. The research space was shared by researchers and kaumātua, was honourable of the mātauranga, iwi voices were heard and a co-developed field survey plan/research plan was produced. Iwi concerns were made a priority throughout, and incorporated into the monitoring, mapping and management frameworks. Thus, I had a Māori-centred agenda which is important as Ngāti Whakahemo are looking to utilise the results from my research to inform their iwi environmental management plan. This approach will help to strengthen current marine management practices and in turn Aotearoa New Zealand’s ecosystems due to iwi environmental management plans being informed by such results.

text: Mātauranga Māori to inform understanding of population dynamics and health of pipi in Waihī Estuary, Bay of Plenty. Estuaries are among the most productive ecosystems on earth. They hold significant value to Māori as they connect the whenua (land), awa (river) and moana (ocean), and are an important source of kaimoana (seafood) including shellfish. However, due to increased anthropogenic pressures, many estuaries are degraded, affecting taonga (Māori treasure) species such as pipi (Paphies australis). My thesis uses kaupapa Māori methodology and is co-developed with Ngāti Whakahemo, tangata whenua (people of the land) of Waihī Estuary. This project fundamentally draws upon mātauranga Māori (traditional Māori knowledge), combined with western science to map the historic and current distribution, abundance and health of pipi in Waihī Estuary; as well as explore the perceptions of threats to pipi and estuary ecology from tangata whenua and the regional authority. 
Participatory mapping was used via kōrero/interviews with kaumātua to identify sites of significance for pipi, which were then sampled in November 2020. Mātauranga ā iwi from Ngāti Whakahemo informed the sampling locations. Previous pipi sampling methodology and protocols undertaken by the Ministry for Primary Industries (MPI) were used to facilitate temporal comparisons of pipi distribution and abundance. Environmental factors including sediment grain size, organic content, total nitrogen (TN) and total phosphorus (TP) were also measured to help understand what drives the population dynamics of pipi. Perceptions of tangata whenua and staff members of the Bay of Plenty Regional Council (BOPRC) were also explored following methods similar to Klain et al. (2018) and implementing a dread risk tool via participatory mapping.
Results show that culturally significant sites identified by kaumātua support high pipi abundances of large size (40mm+), with low abundances of pipi in the upper reaches of the estuary. The inclusion of sites identified by MPI allowed for more comprehensive survey on pipi population dynamics by utilising a stratified survey design. Pipi size and abundance was significantly correlated with environmental factors with high pipi densities associated with medium grain size fractions and low levels of TN, TP and organic content. Over harvesting was perceived by kaumātua and BOPRC staff members as the dominant threat to pipi abundance and Waihī Estuary. Nutrients related to sewage inputs and runoff were rated as the second highest perceived threat and diseased shellfish ranked third by kaumātua and BOPRC staff members. 
This study demonstrates that the sharing of mātauranga ā iwi can fundamentally inform western science methods and can be used as an approach to research in the marine science realm. The research space was shared by researchers and kaumātua, was honourable of the mātauranga, iwi voices were heard and a co-developed field survey plan/research plan was produced. Iwi concerns were made a priority throughout, and incorporated into the monitoring, mapping and management frameworks. Thus, I had a Māori-centred agenda which is important as Ngāti Whakahemo are looking to utilise the results from my research to inform their iwi environmental management plan. This approach will help to strengthen current marine management practices and in turn Aotearoa New Zealand’s ecosystems due to iwi environmental management plans being informed by such results.

year: 2021