title: Visualisation of semantic enrichment

authors: Schlegel, Alexa

subjects: computer science

abstract: Automatically creating semantic enrichments for text may lead to annotations that allow for excellent recall but poor precision. Manual enrichment is potentially more targeted, leading to greater precision. We aim to support nonexperts in manually enriching texts with semantic annotations. Neither the visualisation of semantic enrichment nor the process of manually enriching texts has been evaluated before. This paper presents the results of our user study on visualisation of text enrichment during the annotation process. We performed extensive analysis of work related to the visualisation of semantic annotations. In a prototype implementation, we then explored two layout alternatives for visualising semantic annotations and their linkage to the text atoms. Here we summarise and discuss our results and their design implications for tools creating semantic annotations.

text: Visualisation of semantic enrichment Automatically creating semantic enrichments for text may lead to annotations that allow for excellent recall but poor precision. Manual enrichment is potentially more targeted, leading to greater precision. We aim to support nonexperts in manually enriching texts with semantic annotations. Neither the visualisation of semantic enrichment nor the process of manually enriching texts has been evaluated before. This paper presents the results of our user study on visualisation of text enrichment during the annotation process. We performed extensive analysis of work related to the visualisation of semantic annotations. In a prototype implementation, we then explored two layout alternatives for visualising semantic annotations and their linkage to the text atoms. Here we summarise and discuss our results and their design implications for tools creating semantic annotations.

year: 2012

title: Microbial contaminant removal and alternative nitrogen removal pathways in denitrifying bioreactors

authors: Rambags, Femke

subjects: wastewater treatment

abstract: Denitrifying bioreactors, simple treatment systems consisting of a container filled with a particulate organic carbon source, are an effective and low-cost technology for the effective removal of nitrogen (N) from water by enhancing denitrification (i.e. the bacterial conversion of nitrate [NO3-] to N gas). To date, studies on denitrifying bioreactors have mainly focused on the ability of, and factors influencing, the removal of NO3- within these systems. In the research presented in this thesis, a more holistic view of denitrifying bioreactors was taken in which N removal was assessed in conjunction with the removal of faecal microbial contaminants. The objectives of this research were: (1) to assess how well denitrifying bioreactors can remove microbial contaminant loads from wastewater and (2) to assess the potential role of alternative N removal pathways, namely anaerobic ammonium oxidation (anammox) and codenitrification for N removal in denitrifying bioreactors.

The first part of this thesis focused on the removal of microbial contaminants in denitrifying bioreactors. Removal of microbial contaminants from wastewater is a key factor in wastewater treatment, since the contamination of receiving waters with inadequately treated wastewater can contribute to the transmission of infectious disease caused by waterborne pathogenic microorganisms. First, the removal of bacterial and viral indicators (Escherichia coli [E. coli] and F-specific RNA bacteriophage [FRNA bacteriophage]) was assessed along the longitudinal transect of a full-scale operating woodchip bioreactor (~114 m3 in size with 9 sampling wells along the length of the bioreactors) loaded with nitrified septic tank effluent. In addition to significant reduction in NO3- loads, the bioreactor demonstrated consistent and substantial reduction of E. coli (2.9 log10 reduction) and FRNA bacteriophage (3.9 log10 reduction) despite receiving highly fluctuating inflow concentrations (up to 3.5 × 105 MPN/100mL and 1.1 × 105 PFU/100 mL,respectively). In a follow-up experiment, removal of E. coli, total coliforms (TC) and FRNA bacteriophage was analysed in fifteen mesocosm scale bioreactors (~700 L each) filled with two different carbon sources: woodchip or coconut husk. The effect of media age on attenuation of microbial contaminants was assessed by comparing the performance of 8-year old systems with equivalent newly constructed woodchip and coconut husk bioreactors. Additionally, removal performance of these carbon substrates was compared to that of gravel, a non-carbon substrate commonly used in subsurface flow constructed wetlands. Substantial reduction of E. coli, TC and FRNA bacteriophage from primary treated municipal wastewater was achieved in all bioreactors. Mean annual log10 removal efficiencies were similar between microbial indicators ranging from 1.4 to 1.9 for TC, 1.3 to 1.8 for E. coli and 1.3 to 2.0 for FRNA bacteriophage. All denitrifying bioreactors showed consistent year-round performance and long-term performance that was not greatly dependent on age of carbon material. The results from both studies suggested that denitrifying bioreactors, as well as reducing N loads, can effectively reduce microbial contaminants in wastewater, providing a complimentary disinfection role.

Denitrification has generally been considered the major pathway converting NO3- to dinitrogen gas (N2) in denitrifying bioreactors. In the second part of the thesis, the importance of anaerobic ammonium oxidation and codenitrification (jointly referred to as An/coD), was assessed by monitoring the removal of N species from partially nitrified municipal wastewater passing through the mesocosm scale bioreactors described above. Lab experiments using a 15N isotope-pairing technique were also performed to partition production of N2 to these different microbial processes. Results obtained from this study altered our understanding of the potential mechanisms responsible for N loss in these systems. The effective removal of both NO3- and ammonium (NH4+) and the formation of hybrid N2 (i.e. 29N2) observed in bioreactors demonstrated that the An/coD pathway was an effective pathway for N removal when both NO3- and NH4+ were present. An/coD removal rates ranged from 0.6 to 3.8 g N per m3 reactor volume per day while denitrification rates ranged from 0.7 to 2.6 g N per m3. The contributions of An/coD to N removal was dependent on media, with An/coD becoming more dominant in bioreactors where denitrification was carbon limited.

The research presented in this thesis has important implications for the use of denitrifying bioreactors for domestic wastewater treatment, since it demonstrates that in addition to removing NO3-, denitrifying bioreactors can also remove microbial contaminants and NH4+, both commonly present in domestic wastewater. A greater understanding of factors controlling microbial contaminant removal, denitrification and An/coD activity in these systems would allow improved design of bioreactors with the capacity to treat a broader range of wastewater contaminants. The thesis opens a discussion on the potential of denitrifying bioreactors to evolve into a reliable treatment technology for different types of wastewater contaminants.

text: Microbial contaminant removal and alternative nitrogen removal pathways in denitrifying bioreactors Denitrifying bioreactors, simple treatment systems consisting of a container filled with a particulate organic carbon source, are an effective and low-cost technology for the effective removal of nitrogen (N) from water by enhancing denitrification (i.e. the bacterial conversion of nitrate [NO3-] to N gas). To date, studies on denitrifying bioreactors have mainly focused on the ability of, and factors influencing, the removal of NO3- within these systems. In the research presented in this thesis, a more holistic view of denitrifying bioreactors was taken in which N removal was assessed in conjunction with the removal of faecal microbial contaminants. The objectives of this research were: (1) to assess how well denitrifying bioreactors can remove microbial contaminant loads from wastewater and (2) to assess the potential role of alternative N removal pathways, namely anaerobic ammonium oxidation (anammox) and codenitrification for N removal in denitrifying bioreactors.

The first part of this thesis focused on the removal of microbial contaminants in denitrifying bioreactors. Removal of microbial contaminants from wastewater is a key factor in wastewater treatment, since the contamination of receiving waters with inadequately treated wastewater can contribute to the transmission of infectious disease caused by waterborne pathogenic microorganisms. First, the removal of bacterial and viral indicators (Escherichia coli [E. coli] and F-specific RNA bacteriophage [FRNA bacteriophage]) was assessed along the longitudinal transect of a full-scale operating woodchip bioreactor (~114 m3 in size with 9 sampling wells along the length of the bioreactors) loaded with nitrified septic tank effluent. In addition to significant reduction in NO3- loads, the bioreactor demonstrated consistent and substantial reduction of E. coli (2.9 log10 reduction) and FRNA bacteriophage (3.9 log10 reduction) despite receiving highly fluctuating inflow concentrations (up to 3.5 × 105 MPN/100mL and 1.1 × 105 PFU/100 mL,respectively). In a follow-up experiment, removal of E. coli, total coliforms (TC) and FRNA bacteriophage was analysed in fifteen mesocosm scale bioreactors (~700 L each) filled with two different carbon sources: woodchip or coconut husk. The effect of media age on attenuation of microbial contaminants was assessed by comparing the performance of 8-year old systems with equivalent newly constructed woodchip and coconut husk bioreactors. Additionally, removal performance of these carbon substrates was compared to that of gravel, a non-carbon substrate commonly used in subsurface flow constructed wetlands. Substantial reduction of E. coli, TC and FRNA bacteriophage from primary treated municipal wastewater was achieved in all bioreactors. Mean annual log10 removal efficiencies were similar between microbial indicators ranging from 1.4 to 1.9 for TC, 1.3 to 1.8 for E. coli and 1.3 to 2.0 for FRNA bacteriophage. All denitrifying bioreactors showed consistent year-round performance and long-term performance that was not greatly dependent on age of carbon material. The results from both studies suggested that denitrifying bioreactors, as well as reducing N loads, can effectively reduce microbial contaminants in wastewater, providing a complimentary disinfection role.

Denitrification has generally been considered the major pathway converting NO3- to dinitrogen gas (N2) in denitrifying bioreactors. In the second part of the thesis, the importance of anaerobic ammonium oxidation and codenitrification (jointly referred to as An/coD), was assessed by monitoring the removal of N species from partially nitrified municipal wastewater passing through the mesocosm scale bioreactors described above. Lab experiments using a 15N isotope-pairing technique were also performed to partition production of N2 to these different microbial processes. Results obtained from this study altered our understanding of the potential mechanisms responsible for N loss in these systems. The effective removal of both NO3- and ammonium (NH4+) and the formation of hybrid N2 (i.e. 29N2) observed in bioreactors demonstrated that the An/coD pathway was an effective pathway for N removal when both NO3- and NH4+ were present. An/coD removal rates ranged from 0.6 to 3.8 g N per m3 reactor volume per day while denitrification rates ranged from 0.7 to 2.6 g N per m3. The contributions of An/coD to N removal was dependent on media, with An/coD becoming more dominant in bioreactors where denitrification was carbon limited.

The research presented in this thesis has important implications for the use of denitrifying bioreactors for domestic wastewater treatment, since it demonstrates that in addition to removing NO3-, denitrifying bioreactors can also remove microbial contaminants and NH4+, both commonly present in domestic wastewater. A greater understanding of factors controlling microbial contaminant removal, denitrification and An/coD activity in these systems would allow improved design of bioreactors with the capacity to treat a broader range of wastewater contaminants. The thesis opens a discussion on the potential of denitrifying bioreactors to evolve into a reliable treatment technology for different types of wastewater contaminants.

year: 2019

title: Mai uta ki tai: Cyclone-driven suspended sediment effects on early benthic juvenile kōura (Jasus edwardsii), Te Ākau o Tokomaru, Aotearoa

authors: Karaha-Paki, Vijuan

abstract: Kōura (Jasus edwardsii) are ecologically, culturally, and economically significant taonga species central to mahinga kai systems throughout Aotearoa New Zealand. In Te Tairāwhiti, particularly Te Ākau o Tokomaru, Cyclone Gabrielle (February 2023) resulted in unprecedented sediment loads being delivered to coastal waters, smothering inshore rocky reefs that serve as critical nursery habitats for settling puerulus and juvenile kōura. This research investigated how repeated suspended sediment exposure affects the body condition, survival, and physiological condition of early benthic juvenile kōura, integrating Western scientific methods with mātauranga Māori perspectives to support kaitiakitanga and ecosystem recovery. 

A 52-day pulse-based laboratory experiment exposed 81 early benthic juvenile kōura to three treatment levels: Control (0 mg/L), Tobserved (1,000 mg/L), and Tmaximised (5,000 mg/L) suspended sediment concentrations, alternating between exposure phases and recovery periods to simulate natural post-storm sedimentation dynamics. Sediment was sourced from the Mangahauini River mouth to reflect local conditions. Kōura were initially housed communally (Days 1-19), and then separated into individual tāruke following observed cannibalism. Across the experiment, body weight to carapace length (BW:CL) ratios, survival, blood refractive index, gill condition, and moult stage were assessed. 

All treatment groups began with statistically equivalent body condition (p = 0.135), but cumulative effects emerged over time. During communal housing, mortality was highest in the Tobserved treatment (51.9%) compared with Control and Tmaximised treatments (both 18.5%). After separation, Tmaximised individuals showed the greatest losses (45.5%), mostly during the recovery rather than exposure phases. Overall mortality reached 45.7%, with sediment-exposed treatments experiencing 55% (Tmaximised) to 59% (Tobserved) losses compared with 22.2% in the Controls (p = 0.001). 

By Day 52, sediment exposure significantly reduced body condition (p = 0.016), with the Controls maintaining higher BW:CL ratios than Tmaximised (p = 0.013). Gill assessments indicated universal and severe damage in sediment-exposed kōura (100%) but none in the Controls (0%). Quantitative image analysis confirmed strong sediment concentration- dependent effects across all damage metrics – particle lodgement, filament integrity, surface discolouration, and composite scores (all p < 0.001) – with structural deformities in 66.7% of Tobserved and 100% of Tmaximised individuals. Blood refractive index showed no treatment differences, and 84.1% of kōura remained in intermoult stage at Day 52, with no significant difference in moult stage distribution between treatments (p = 0.328). However, moult frequency during the individual phase was lower in sediment-exposed groups compared to the Controls (Control: n = 11, Tobserved: n = 4, Tmaximised: n = 5). 

These findings show that suspended sediment exposure poses population-level threats to kōura recruitment through irreversible gill damage and delayed mortality. Elevated cannibalism during communal holding, particularly observed in the Tobserved treatment, likely resulted from temporal clustering of moult events rather than sediment-induced behaviour. For Te Ākau o Tokomaru and the wider CRA 3 fishery, this highlights the need for integrated catchment-to- coast management addressing land-derived sediment inputs and protecting coastal nursery habitats. From a Te Ao Māori perspective, sedimentation represents a disruption to whakapapa relationships with Tangaroa and a weakening of mauri in coastal ecosystems. Restoring these connections requires co-governance frameworks that embed mātauranga Māori, empower kaitiaki-led monitoring and rāhui, and address the cumulative impacts of land-use intensification and repeated cyclone events on ecosystem resilience in Te Tairāwhiti.

text: Mai uta ki tai: Cyclone-driven suspended sediment effects on early benthic juvenile kōura (Jasus edwardsii), Te Ākau o Tokomaru, Aotearoa Kōura (Jasus edwardsii) are ecologically, culturally, and economically significant taonga species central to mahinga kai systems throughout Aotearoa New Zealand. In Te Tairāwhiti, particularly Te Ākau o Tokomaru, Cyclone Gabrielle (February 2023) resulted in unprecedented sediment loads being delivered to coastal waters, smothering inshore rocky reefs that serve as critical nursery habitats for settling puerulus and juvenile kōura. This research investigated how repeated suspended sediment exposure affects the body condition, survival, and physiological condition of early benthic juvenile kōura, integrating Western scientific methods with mātauranga Māori perspectives to support kaitiakitanga and ecosystem recovery. 

A 52-day pulse-based laboratory experiment exposed 81 early benthic juvenile kōura to three treatment levels: Control (0 mg/L), Tobserved (1,000 mg/L), and Tmaximised (5,000 mg/L) suspended sediment concentrations, alternating between exposure phases and recovery periods to simulate natural post-storm sedimentation dynamics. Sediment was sourced from the Mangahauini River mouth to reflect local conditions. Kōura were initially housed communally (Days 1-19), and then separated into individual tāruke following observed cannibalism. Across the experiment, body weight to carapace length (BW:CL) ratios, survival, blood refractive index, gill condition, and moult stage were assessed. 

All treatment groups began with statistically equivalent body condition (p = 0.135), but cumulative effects emerged over time. During communal housing, mortality was highest in the Tobserved treatment (51.9%) compared with Control and Tmaximised treatments (both 18.5%). After separation, Tmaximised individuals showed the greatest losses (45.5%), mostly during the recovery rather than exposure phases. Overall mortality reached 45.7%, with sediment-exposed treatments experiencing 55% (Tmaximised) to 59% (Tobserved) losses compared with 22.2% in the Controls (p = 0.001). 

By Day 52, sediment exposure significantly reduced body condition (p = 0.016), with the Controls maintaining higher BW:CL ratios than Tmaximised (p = 0.013). Gill assessments indicated universal and severe damage in sediment-exposed kōura (100%) but none in the Controls (0%). Quantitative image analysis confirmed strong sediment concentration- dependent effects across all damage metrics – particle lodgement, filament integrity, surface discolouration, and composite scores (all p < 0.001) – with structural deformities in 66.7% of Tobserved and 100% of Tmaximised individuals. Blood refractive index showed no treatment differences, and 84.1% of kōura remained in intermoult stage at Day 52, with no significant difference in moult stage distribution between treatments (p = 0.328). However, moult frequency during the individual phase was lower in sediment-exposed groups compared to the Controls (Control: n = 11, Tobserved: n = 4, Tmaximised: n = 5). 

These findings show that suspended sediment exposure poses population-level threats to kōura recruitment through irreversible gill damage and delayed mortality. Elevated cannibalism during communal holding, particularly observed in the Tobserved treatment, likely resulted from temporal clustering of moult events rather than sediment-induced behaviour. For Te Ākau o Tokomaru and the wider CRA 3 fishery, this highlights the need for integrated catchment-to- coast management addressing land-derived sediment inputs and protecting coastal nursery habitats. From a Te Ao Māori perspective, sedimentation represents a disruption to whakapapa relationships with Tangaroa and a weakening of mauri in coastal ecosystems. Restoring these connections requires co-governance frameworks that embed mātauranga Māori, empower kaitiaki-led monitoring and rāhui, and address the cumulative impacts of land-use intensification and repeated cyclone events on ecosystem resilience in Te Tairāwhiti.

year: 2025