title: Analysis of interval-censored data from circular migrant and non-migrant sexual partnerships using the EM algorithm

authors: Zuma, K.

subjects: statistics

abstract: In epidemiological studies where subjects are seen periodically on follow-up visits, interval-censored data occur naturally. The exact time the change of state (such as HIV seroconversion) occurs is not known exactly, only that it occurred sometime within a specific time interval. Methods of estimation for interval-censored data are readily available when data are independent. However, methods for correlated interval-censored data are not well developed. This paper considers an approach for estimating the parameters when data are interval-censored and correlated within sexual partnerships. We consider the exact event times for interval-censored observations as unobserved data, only known to be between two time points. Dependency induced by sexual partnerships is modelled as frailties assuming a gamma distribution for frailties and an exponential distribution on the time to infection. This formulation facilitates application of the expectation-maximization (EM) algorithm. Maximization process maximizes the standard survival frailty model. Results show high degree of heterogeneity between sexual partnerships. Intervention strategies aimed at combating the spread of HIV and other sexually transmitted infections (STI)s should treat sexual partnerships as social units and fully incorporate the effects of migration in their strategies. Copyright © 2006 John Wiley & Sons, Ltd.

text: Analysis of interval-censored data from circular migrant and non-migrant sexual partnerships using the EM algorithm In epidemiological studies where subjects are seen periodically on follow-up visits, interval-censored data occur naturally. The exact time the change of state (such as HIV seroconversion) occurs is not known exactly, only that it occurred sometime within a specific time interval. Methods of estimation for interval-censored data are readily available when data are independent. However, methods for correlated interval-censored data are not well developed. This paper considers an approach for estimating the parameters when data are interval-censored and correlated within sexual partnerships. We consider the exact event times for interval-censored observations as unobserved data, only known to be between two time points. Dependency induced by sexual partnerships is modelled as frailties assuming a gamma distribution for frailties and an exponential distribution on the time to infection. This formulation facilitates application of the expectation-maximization (EM) algorithm. Maximization process maximizes the standard survival frailty model. Results show high degree of heterogeneity between sexual partnerships. Intervention strategies aimed at combating the spread of HIV and other sexually transmitted infections (STI)s should treat sexual partnerships as social units and fully incorporate the effects of migration in their strategies. Copyright © 2006 John Wiley & Sons, Ltd.

year: 2006

title: Functional ecology of an Antarctic Dry Valley

authors: Chan, Yuki

abstract: The McMurdo Dry Valleys are the largest ice-free region in Antarctica and are critically at risk from climate change. The terrestrial landscape is dominated by oligotrophic mineral soils and extensive exposed rocky surfaces where biota are largely restricted to microbial communities, although their ability to perform the majority of geobiological processes has remained largely uncharacterized. Here, we identified functional traits that drive microbial survival and community assembly, using a metagenomic approach with GeoChip-based functional gene arrays to establish metabolic capabilities in communities inhabiting soil and rock surface niches in McKelvey Valley. Major pathways in primary metabolism were identified, indicating significant plasticity in autotrophic, heterotrophic, and diazotrophic strategies supporting microbial communities. This represents a major advance beyond biodiversity surveys in that we have now identified how putative functional ecology drives microbial community assembly. Significant differences were apparent between open soil, hypolithic, chasmoendolithic, and cryptoendolithic communities. A suite of previously unappreciated Antarctic microbial stress response pathways, thermal, osmotic, and nutrient limitation responses were identified and related to environmental stressors, offering tangible clues to the mechanisms behind the enduring success of microorganisms in this seemingly inhospitable terrain. Rocky substrates exposed to larger fluctuations in environmental stress supported greater functional diversity in stress-response pathways than soils. Soils comprised a unique reservoir of genes involved in transformation of organic hydrocarbons and lignin-like degradative pathways. This has major implications for the evolutionary origin of the organisms, turnover of recalcitrant substrates in Antarctic soils, and predicting future responses to anthropogenic pollution.

text: Functional ecology of an Antarctic Dry Valley The McMurdo Dry Valleys are the largest ice-free region in Antarctica and are critically at risk from climate change. The terrestrial landscape is dominated by oligotrophic mineral soils and extensive exposed rocky surfaces where biota are largely restricted to microbial communities, although their ability to perform the majority of geobiological processes has remained largely uncharacterized. Here, we identified functional traits that drive microbial survival and community assembly, using a metagenomic approach with GeoChip-based functional gene arrays to establish metabolic capabilities in communities inhabiting soil and rock surface niches in McKelvey Valley. Major pathways in primary metabolism were identified, indicating significant plasticity in autotrophic, heterotrophic, and diazotrophic strategies supporting microbial communities. This represents a major advance beyond biodiversity surveys in that we have now identified how putative functional ecology drives microbial community assembly. Significant differences were apparent between open soil, hypolithic, chasmoendolithic, and cryptoendolithic communities. A suite of previously unappreciated Antarctic microbial stress response pathways, thermal, osmotic, and nutrient limitation responses were identified and related to environmental stressors, offering tangible clues to the mechanisms behind the enduring success of microorganisms in this seemingly inhospitable terrain. Rocky substrates exposed to larger fluctuations in environmental stress supported greater functional diversity in stress-response pathways than soils. Soils comprised a unique reservoir of genes involved in transformation of organic hydrocarbons and lignin-like degradative pathways. This has major implications for the evolutionary origin of the organisms, turnover of recalcitrant substrates in Antarctic soils, and predicting future responses to anthropogenic pollution.

year: 2013

title: Māori language interfaces

authors: Keegan, Te Taka Adrian Gregory

abstract: This paper considers the usability of the interface and the ramifications for te reo Māori if the interface language, the messages displayed in those text boxes, is written in te reo Māori.

text: Māori language interfaces This paper considers the usability of the interface and the ramifications for te reo Māori if the interface language, the messages displayed in those text boxes, is written in te reo Māori.

year: 2017