title: Anthropogenic Influences on the Sedimentary Evolution of the Coromandel Harbour

authors: Harpur, Alexander

subjects: Coromandel Harbour

abstract: The Coromandel Harbour is located on the eastern side of the Coromandel Peninsula, North Island, New Zealand. To date, sedimentological research conducted in the harbour has been confined to nearshore areas, with limited data existing for the subtidal regions of the harbour. The primary aim of this thesis is to identify whether and how various human activities in the catchment have altered harbour-wide, intertidal and subtidal, sedimentation rates and sediment geochemistry. A secondary aim is to identify the sedimentary evolution of the whole Coromandel Harbour over broad time scales (i.e. thousands of years).

Sedimentological data has been collected from 17 intertidal and subtidal sediment cores. Cores have been analysed for down-core changes in sediment texture, mineralogy, observational characteristics and geochemistry measured through portable X-ray fluorescence (pXRF). A facies model constructed from this data has been used to interpret the sedimentary development of the harbour. Pre-human and anthropogenic sediment accumulation rates (SARs) have been estimated using radiocarbon dating, qualitative pollen analysis and facies analysis. Anthropogenic heavy metals have been interpreted against pre-human baselines to identify influences on natural contaminant levels, with specific values compared with regional contaminant guidelines to assess ecological threats. 

Deeply weathered soils developed in a subaerial environment somewhere between the last interglacial at c.120 ka and the extended last glacial maximum (eLGM) at 29 ka. These soils were overtopped by streambank and floodplain deposits at the eLGM to the onset of the mid-Holocene sea level rise at c.7500 cal yr B.P. As sea level rose, inundated eLGM and early estuarine sediments were initially pyritised in a stratified, restricted marine setting. Over time, sea level rose and the stratification of the harbour was destroyed, ceasing pyritisation. Streams began to rapidly aggrade at the harbour with the positive change in base level, giving early estuarine (c.7500-5000 cal yr B.P) subtidal SARs of ~0.31-0.45 mm/yr. As streams reached stable profiles, SARs decreased to generally conformable rates of 0.25-0.47 mm/yr in the intertidal regions and ~0.1-0.25 mm/yr in the subtidal regions during the pre-Polynesian phase (c.7500-700 cal yr B.P). Polynesian SARs (700-130 cal yr B.P) decreased to ~0.05-0.13 mm/yr. Whole European (1820 A.D-present) SARs in the northern parts of the harbour are ~0.52-0.77 mm/yr and appear to be chiefly related to mining and deforestation. Recent European (1975 A.D-present) SARs are ~3.52-10.37 mm/yr in the southern parts of the harbour and are chiefly related to pine plantation erosion. A secondary depocentre for pine plantation sediments appears to be at the inlet where rates of ~4.98 mm/yr occur. 

Only arsenic and mercury exist over Australian and New Zealand Environment and Conservation Council (ANZECC) Interim Sediment Quality Guidelines (ISQG) Low concentrations in anthropogenic sediments analysed. Maximum harbour-wide arsenic concentrations of up to 33.5 mg/kg that exceed the ISQG-Low value of 20 mg/kg are associated with mining related sediments near the Whangarahi Stream mouth. Maximum arsenic concentrations in pine plantation sediments is 22.3 mg/kg. Mercury may also exceed ISQG-Low/High values throughout all harbour sediments, though it is unclear whether mercury has been incorrectly measured by pXRF.

text: Anthropogenic Influences on the Sedimentary Evolution of the Coromandel Harbour The Coromandel Harbour is located on the eastern side of the Coromandel Peninsula, North Island, New Zealand. To date, sedimentological research conducted in the harbour has been confined to nearshore areas, with limited data existing for the subtidal regions of the harbour. The primary aim of this thesis is to identify whether and how various human activities in the catchment have altered harbour-wide, intertidal and subtidal, sedimentation rates and sediment geochemistry. A secondary aim is to identify the sedimentary evolution of the whole Coromandel Harbour over broad time scales (i.e. thousands of years).

Sedimentological data has been collected from 17 intertidal and subtidal sediment cores. Cores have been analysed for down-core changes in sediment texture, mineralogy, observational characteristics and geochemistry measured through portable X-ray fluorescence (pXRF). A facies model constructed from this data has been used to interpret the sedimentary development of the harbour. Pre-human and anthropogenic sediment accumulation rates (SARs) have been estimated using radiocarbon dating, qualitative pollen analysis and facies analysis. Anthropogenic heavy metals have been interpreted against pre-human baselines to identify influences on natural contaminant levels, with specific values compared with regional contaminant guidelines to assess ecological threats. 

Deeply weathered soils developed in a subaerial environment somewhere between the last interglacial at c.120 ka and the extended last glacial maximum (eLGM) at 29 ka. These soils were overtopped by streambank and floodplain deposits at the eLGM to the onset of the mid-Holocene sea level rise at c.7500 cal yr B.P. As sea level rose, inundated eLGM and early estuarine sediments were initially pyritised in a stratified, restricted marine setting. Over time, sea level rose and the stratification of the harbour was destroyed, ceasing pyritisation. Streams began to rapidly aggrade at the harbour with the positive change in base level, giving early estuarine (c.7500-5000 cal yr B.P) subtidal SARs of ~0.31-0.45 mm/yr. As streams reached stable profiles, SARs decreased to generally conformable rates of 0.25-0.47 mm/yr in the intertidal regions and ~0.1-0.25 mm/yr in the subtidal regions during the pre-Polynesian phase (c.7500-700 cal yr B.P). Polynesian SARs (700-130 cal yr B.P) decreased to ~0.05-0.13 mm/yr. Whole European (1820 A.D-present) SARs in the northern parts of the harbour are ~0.52-0.77 mm/yr and appear to be chiefly related to mining and deforestation. Recent European (1975 A.D-present) SARs are ~3.52-10.37 mm/yr in the southern parts of the harbour and are chiefly related to pine plantation erosion. A secondary depocentre for pine plantation sediments appears to be at the inlet where rates of ~4.98 mm/yr occur. 

Only arsenic and mercury exist over Australian and New Zealand Environment and Conservation Council (ANZECC) Interim Sediment Quality Guidelines (ISQG) Low concentrations in anthropogenic sediments analysed. Maximum harbour-wide arsenic concentrations of up to 33.5 mg/kg that exceed the ISQG-Low value of 20 mg/kg are associated with mining related sediments near the Whangarahi Stream mouth. Maximum arsenic concentrations in pine plantation sediments is 22.3 mg/kg. Mercury may also exceed ISQG-Low/High values throughout all harbour sediments, though it is unclear whether mercury has been incorrectly measured by pXRF.

year: 2016

title: Mutations of p53 gene and SV40 sequences in asbestos associated and non- asbestos-associated mesotheliomas

authors: Mayall, Frederick G.

subjects: mesothelioma

abstract: AIM: To examine mesotheliomas for a possible relation between p53 immunostaining, p53 gene mutation, simian virus 40 (SV40), and asbestos exposure. METHODS: Paraffin sections from 11 mesotheliomas were used for p53 immunostaining and also to extract DNA. This was analysed for the presence of mutations in exons 5 to 8 of the p53 gene using a "cold" single strand conformational polymorphism method, together with sequencing. The DNA from the paraffin sections was also used to search for SV40 sequences. A 105 base pair segment at the 3' of the SV40 large T antigen (Tag) was targeted and any PCR amplification products were sequenced to confirm that they were of SV40 origin. EDAX electron microscopic differential mineral fibre counts were performed on dried lung tissue at a specialist referral centre. RESULTS: The fibre counts showed that seven of the mesotheliomas were associated with abnormally high asbestos exposure. Of these, two showed p53 immunostaining, none showed p53 gene mutation, and five showed SV40. Of the four other mesotheliomas, three showed p53 immunostaining, one showed a (silent) p53 mutation, and none showed SV40. The difference in frequency of SV40 detection was significant at the p < 0.05 level. CONCLUSIONS: Immunostaining for the p53 gene was relatively common but p53 mutations were rare in this series. SV40 virus sequence was detected in five of seven asbestos associated mesotheliomas but in none of the non-asbestos-associated mesotheliomas. This suggests there may be a synergistic interaction between asbestos and SV40 in human mesotheliomas. A study with a larger number of cases is needed to investigate these observations further.

text: Mutations of p53 gene and SV40 sequences in asbestos associated and non- asbestos-associated mesotheliomas AIM: To examine mesotheliomas for a possible relation between p53 immunostaining, p53 gene mutation, simian virus 40 (SV40), and asbestos exposure. METHODS: Paraffin sections from 11 mesotheliomas were used for p53 immunostaining and also to extract DNA. This was analysed for the presence of mutations in exons 5 to 8 of the p53 gene using a "cold" single strand conformational polymorphism method, together with sequencing. The DNA from the paraffin sections was also used to search for SV40 sequences. A 105 base pair segment at the 3' of the SV40 large T antigen (Tag) was targeted and any PCR amplification products were sequenced to confirm that they were of SV40 origin. EDAX electron microscopic differential mineral fibre counts were performed on dried lung tissue at a specialist referral centre. RESULTS: The fibre counts showed that seven of the mesotheliomas were associated with abnormally high asbestos exposure. Of these, two showed p53 immunostaining, none showed p53 gene mutation, and five showed SV40. Of the four other mesotheliomas, three showed p53 immunostaining, one showed a (silent) p53 mutation, and none showed SV40. The difference in frequency of SV40 detection was significant at the p < 0.05 level. CONCLUSIONS: Immunostaining for the p53 gene was relatively common but p53 mutations were rare in this series. SV40 virus sequence was detected in five of seven asbestos associated mesotheliomas but in none of the non-asbestos-associated mesotheliomas. This suggests there may be a synergistic interaction between asbestos and SV40 in human mesotheliomas. A study with a larger number of cases is needed to investigate these observations further.

year: 2013

title: Diacritic Restoration and the Development of a Part-of-Speech Tagset for the Māori Language

authors: Cocks, John

subjects: Māori

abstract: This thesis investigates two fundamental problems in natural language processing: diacritic restoration and part-of-speech tagging. Over the past three decades, statistical approaches to diacritic restoration and part-of-speech tagging have grown in interest as a consequence of the increasing availability of manually annotated training data in major languages such as English and French. However, these approaches are not practical for most minority languages, where appropriate training data is either non-existent or not publically available. Furthermore, before developing a part-of-speech tagging system, a suitable tagset is required for that language. In this thesis, we make the following contributions to bridge this gap:

Firstly, we propose a method for diacritic restoration based on naive Bayes classifiers that act at word-level. Classifications are based on a rich set of features, extracted automatically from training data in the form of diacritically marked text. This method requires no additional resources, which makes it language independent. The algorithm was evaluated on one language, namely Māori, and an accuracy exceeding 99% was observed.

Secondly, we present our work on creating one of the necessary resources for the development of a part-of-speech tagging system in Māori, that of a suitable tagset. The tagset described was developed in accordance with the EAGLES guidelines for morphosyntactic annotation of corpora, and was the result of in-depth analysis of the Māori grammar.

text: Diacritic Restoration and the Development of a Part-of-Speech Tagset for the Māori Language This thesis investigates two fundamental problems in natural language processing: diacritic restoration and part-of-speech tagging. Over the past three decades, statistical approaches to diacritic restoration and part-of-speech tagging have grown in interest as a consequence of the increasing availability of manually annotated training data in major languages such as English and French. However, these approaches are not practical for most minority languages, where appropriate training data is either non-existent or not publically available. Furthermore, before developing a part-of-speech tagging system, a suitable tagset is required for that language. In this thesis, we make the following contributions to bridge this gap:

Firstly, we propose a method for diacritic restoration based on naive Bayes classifiers that act at word-level. Classifications are based on a rich set of features, extracted automatically from training data in the form of diacritically marked text. This method requires no additional resources, which makes it language independent. The algorithm was evaluated on one language, namely Māori, and an accuracy exceeding 99% was observed.

Secondly, we present our work on creating one of the necessary resources for the development of a part-of-speech tagging system in Māori, that of a suitable tagset. The tagset described was developed in accordance with the EAGLES guidelines for morphosyntactic annotation of corpora, and was the result of in-depth analysis of the Māori grammar.

year: 2012