title: (The Futility of) Trying to Predict Carcinogenicity of Chemical Compounds

authors: Pfahringer, Bernhard

subjects: computer science

abstract: This paper describes my submission to one of the sub-problems formulated for the Predictive Toxicology Challenge 2001. The challenge is to predict the carcinogenicity of chemicals based on structural information only. I have only tackled such predictions for bioassays involving male rats. As we currently do not know the true predictions for the test-set, all we can say is that one of the models supplied by us seems to be optimal over some subrange of the ROC spectrum. The successful model uses a voting approach based on most of the sets of structural features made available by various other contestants as well as the organizers in an earlier phase of the Challenge. The WEKA Machine Learning workbench served as the core learning utility. Based on a preliminary examination of our submission we conclude that reliable prediction of carcinogenicity is still a far away goal.

text: (The Futility of) Trying to Predict Carcinogenicity of Chemical Compounds This paper describes my submission to one of the sub-problems formulated for the Predictive Toxicology Challenge 2001. The challenge is to predict the carcinogenicity of chemicals based on structural information only. I have only tackled such predictions for bioassays involving male rats. As we currently do not know the true predictions for the test-set, all we can say is that one of the models supplied by us seems to be optimal over some subrange of the ROC spectrum. The successful model uses a voting approach based on most of the sets of structural features made available by various other contestants as well as the organizers in an earlier phase of the Challenge. The WEKA Machine Learning workbench served as the core learning utility. Based on a preliminary examination of our submission we conclude that reliable prediction of carcinogenicity is still a far away goal.

year: 2001

title: Provenance and geochemistry of exotic clasts in conglomerates of the Oligocene Torehina Formation, Coromandel Peninsula, New Zealand

authors: Nelson, Campbell S.

subjects: Coromandel Peninsula

abstract: Non-marine pebble to cobble conglomerates of the lower Torehina Formation (Oligocene) crop out along western Coromandel Peninsula and overlie, with strong angular discordance, continental-margin metasedimentary rocks (Manaia Hill Group) of Mesozoic (Late Jurassic to ?Early Cretaceous) age. The conglomerates contain provenance information that identifies a pre-Oligocene depositional history obscured by the unconformable juxtaposition of these Tertiary and Mesozoic strata. Most clasts in the lower Torehina Formation are visually similar to local bedrock lithologies, including metamorphosed sandstones and argillites, but are kaolinitic and contain more detrital and authigenic chert, quartz, and potash feldspar. Local derivation of these clasts seems unlikely. By comparing geochemical ratios with those defined for continental margin sandstones, and well characterised New Zealand tectonic terranes, we interpret the majority of clasts in the lower Torehina Formation to have been derived from a dissected orogen, with mixtures of felsic and volcanogenic-derived sediment. The most likely sources are the Waipapa and Torlesse Terranes. The remaining 20–30% of the clasts in the lower Torehina Formation were originally friable, are coarse grained, and appear to be lithologically exotic relative to known metamorphosed sandstones in basement terrane sources on North Island. Some clasts contain coal laminae and particles, and all contain detrital kaolinite as lithic fragments and matrix. Such characteristics imply a non-marine to marginal-marine source containing sediment derived from strongly weathered granite or granodiorite. Mechanical fragility implies a likely proximal, easily erodible source. We propose that this group of clasts was derived from an Upper Cretaceous sedimentary cover, either part of a locally developed basin fill or part of a once regionally extensive cover on North Island. Either case defines a more widely distributed Cretaceous source than found today.

text: Provenance and geochemistry of exotic clasts in conglomerates of the Oligocene Torehina Formation, Coromandel Peninsula, New Zealand Non-marine pebble to cobble conglomerates of the lower Torehina Formation (Oligocene) crop out along western Coromandel Peninsula and overlie, with strong angular discordance, continental-margin metasedimentary rocks (Manaia Hill Group) of Mesozoic (Late Jurassic to ?Early Cretaceous) age. The conglomerates contain provenance information that identifies a pre-Oligocene depositional history obscured by the unconformable juxtaposition of these Tertiary and Mesozoic strata. Most clasts in the lower Torehina Formation are visually similar to local bedrock lithologies, including metamorphosed sandstones and argillites, but are kaolinitic and contain more detrital and authigenic chert, quartz, and potash feldspar. Local derivation of these clasts seems unlikely. By comparing geochemical ratios with those defined for continental margin sandstones, and well characterised New Zealand tectonic terranes, we interpret the majority of clasts in the lower Torehina Formation to have been derived from a dissected orogen, with mixtures of felsic and volcanogenic-derived sediment. The most likely sources are the Waipapa and Torlesse Terranes. The remaining 20–30% of the clasts in the lower Torehina Formation were originally friable, are coarse grained, and appear to be lithologically exotic relative to known metamorphosed sandstones in basement terrane sources on North Island. Some clasts contain coal laminae and particles, and all contain detrital kaolinite as lithic fragments and matrix. Such characteristics imply a non-marine to marginal-marine source containing sediment derived from strongly weathered granite or granodiorite. Mechanical fragility implies a likely proximal, easily erodible source. We propose that this group of clasts was derived from an Upper Cretaceous sedimentary cover, either part of a locally developed basin fill or part of a once regionally extensive cover on North Island. Either case defines a more widely distributed Cretaceous source than found today.

year: 2003

title: An investigation into the commercial feasibility of Jasus edwardsii aquaculture in New Zealand

authors: Ruru, Ian Hector

subjects: New Zealand

abstract: In 1996 New Zealand introduced legislation to allow Jasus edwardsii pueruli to be collected as "seedstock" and ongrown in a commercial aquaculture trial. The aim of this thesis was to investigate the commercial feasibility of J. edwardsii aquaculture in New Zealand by working with an organisation involved in the trial.
The methodology involved a combination of experiments in the field, in laboratories, and within an ongrowing facility. This thesis examined five key areas and found the following:
1. Data obtained in the research indicates that New Zealand will continue to rely on harvesting pueruli from the wild since significant technical obstacles remain in the development of commercial scale pueruli hatcheries. Forecast data, obtained using the delphi technique and information about current research on larval rearing, indicates that commercial scale supply of pueruli from hatcheries may occur between 2017 and 2021.
2. Harvesting trials collected a low number of pueruli with the lowest unit cost for collection being $1.80. A greater collection rate could be achieved with a better understanding of seasonal and local settlement patterns.
3. Survival rates in pueruli transporting experiments were significantly affected by stocking density, time and temperature. The safest transit conditions were achieved with 15 pueruli per litre for less than 6 hours at 14°C.
4. A range of stocking densities, from 3 lobsters per tank to 12 per tank, were tested for their effect on growth of six-month old lobsters. The lobsters were reared in a total recirculation seawater system at a constant 16°C, and fed fresh mussels (Perna canaliculus). For the 121 day trial, no statistically significant effect was detected. However, there was a trend for growth rates to be highest at 3 and 6 lobsters per tank and for growth rates at stocking densities of 9 and 12 lobsters per tank to decrease after Day 50. Lobsters showed increased mortality at the highest stocking rate.
5. A bioeconomic model of a hypothetical farm was developed to assess economic benefits and risks and to determine overall profitability. The model showed an annual net cash position of $287,100 and cumulative cash position of $859,200 by the 10th year of operation based on annual sales of 10,837 kg at $65 per kg. The model indicates that the highest cost components in the first 10 years are processing and transport, and labour. Based on the model and the scenarios examined, profitability is very sensitive to factors such as the farm size, processing and transport costs, and sale price. Biological factors such as growth rates, survival, and feed requirements also influence overall profitability. Good returns will depend upon consistent exports of high quality lobsters.
The study concludes that commercial feasibility will be affected by these key areas. The potential of J. edwardsii aquaculture in New Zealand will continue to benefit from further research.

text: An investigation into the commercial feasibility of Jasus edwardsii aquaculture in New Zealand In 1996 New Zealand introduced legislation to allow Jasus edwardsii pueruli to be collected as "seedstock" and ongrown in a commercial aquaculture trial. The aim of this thesis was to investigate the commercial feasibility of J. edwardsii aquaculture in New Zealand by working with an organisation involved in the trial.
The methodology involved a combination of experiments in the field, in laboratories, and within an ongrowing facility. This thesis examined five key areas and found the following:
1. Data obtained in the research indicates that New Zealand will continue to rely on harvesting pueruli from the wild since significant technical obstacles remain in the development of commercial scale pueruli hatcheries. Forecast data, obtained using the delphi technique and information about current research on larval rearing, indicates that commercial scale supply of pueruli from hatcheries may occur between 2017 and 2021.
2. Harvesting trials collected a low number of pueruli with the lowest unit cost for collection being $1.80. A greater collection rate could be achieved with a better understanding of seasonal and local settlement patterns.
3. Survival rates in pueruli transporting experiments were significantly affected by stocking density, time and temperature. The safest transit conditions were achieved with 15 pueruli per litre for less than 6 hours at 14°C.
4. A range of stocking densities, from 3 lobsters per tank to 12 per tank, were tested for their effect on growth of six-month old lobsters. The lobsters were reared in a total recirculation seawater system at a constant 16°C, and fed fresh mussels (Perna canaliculus). For the 121 day trial, no statistically significant effect was detected. However, there was a trend for growth rates to be highest at 3 and 6 lobsters per tank and for growth rates at stocking densities of 9 and 12 lobsters per tank to decrease after Day 50. Lobsters showed increased mortality at the highest stocking rate.
5. A bioeconomic model of a hypothetical farm was developed to assess economic benefits and risks and to determine overall profitability. The model showed an annual net cash position of $287,100 and cumulative cash position of $859,200 by the 10th year of operation based on annual sales of 10,837 kg at $65 per kg. The model indicates that the highest cost components in the first 10 years are processing and transport, and labour. Based on the model and the scenarios examined, profitability is very sensitive to factors such as the farm size, processing and transport costs, and sale price. Biological factors such as growth rates, survival, and feed requirements also influence overall profitability. Good returns will depend upon consistent exports of high quality lobsters.
The study concludes that commercial feasibility will be affected by these key areas. The potential of J. edwardsii aquaculture in New Zealand will continue to benefit from further research.

year: 2000