title: Biomarker Detection in Association Studies: Modeling SNPs Simultaneously via Logistic ANOVA

authors: Jung, Yoonsuh

subjects: BIC

abstract: In genome-wide association studies, the primary task is to detect biomarkers in the form of Single Nucleotide Polymorphisms (SNPs) that have nontrivial associations with a disease phenotype and some other important clinical/environmental factors. However, the extremely large number of SNPs comparing to the sample size inhibits application of classical methods such as the multiple logistic regression. Currently the most commonly used approach is still to analyze one SNP at a time. In this pa- per, we propose to consider the genotypes of the SNPs simultaneously via a logistic analysis of variance (ANOVA) model, which expresses the logit transformed mean of SNP genotypes as the summation of the SNP effects, effects of the disease phenotype and/or other clinical variables, and the interaction effects. We use a reduced-rank representation of the interaction-effect matrix for dimensionality reduction, and employ the L1-penalty in a penalized likelihood framework to filter out the SNPs that have no associations. We develop a Majorization-Minimization algorithm for computational implementation. In addition, we propose a modified BIC criterion to select the penalty parameters and determine the rank number. The proposed method is applied to a Multiple Sclerosis data set and simulated data sets and shows promise in biomarker detection.

text: Biomarker Detection in Association Studies: Modeling SNPs Simultaneously via Logistic ANOVA In genome-wide association studies, the primary task is to detect biomarkers in the form of Single Nucleotide Polymorphisms (SNPs) that have nontrivial associations with a disease phenotype and some other important clinical/environmental factors. However, the extremely large number of SNPs comparing to the sample size inhibits application of classical methods such as the multiple logistic regression. Currently the most commonly used approach is still to analyze one SNP at a time. In this pa- per, we propose to consider the genotypes of the SNPs simultaneously via a logistic analysis of variance (ANOVA) model, which expresses the logit transformed mean of SNP genotypes as the summation of the SNP effects, effects of the disease phenotype and/or other clinical variables, and the interaction effects. We use a reduced-rank representation of the interaction-effect matrix for dimensionality reduction, and employ the L1-penalty in a penalized likelihood framework to filter out the SNPs that have no associations. We develop a Majorization-Minimization algorithm for computational implementation. In addition, we propose a modified BIC criterion to select the penalty parameters and determine the rank number. The proposed method is applied to a Multiple Sclerosis data set and simulated data sets and shows promise in biomarker detection.

year: 2014-06-12

title: When salient science is not enough to advance climate change adaptation: Lessons from Brazil and Australia

authors: Serrao-Neumann, Silvia

subjects: Boundary organisation

abstract: Increased social and environmental vulnerability to extreme climatic events and inherent aggravation of environmental and social problems has placed climate change adaptation as an urgent challenge for decision-makers. Understanding and using climate change information to advance the implementation of climate-friendly policies further compounds this challenge. A rich scholarly literature focusing on climate change adaptation endorses that investing in mechanisms that narrow the gap between climate change information production and its use is crucial to increase adaptive capacity. Based on this assumption, this paper investigates the extent to which two collaborative projects that functioned as boundary organisations in Brazil (CiAdapta project) and Australia (Climate Change Adaptation for Natural Resource Management in East Coast Australia) increased access to information, and enabled the continual and continuous usefulness of produced knowledge for climate change adaptation. Considering the distinction between usable and useful information, we applied six criteria to guide the data analysis and extract key lessons from each project. Our findings confirm that face-to-face interactions are more likely to result in research having the societal impact that is being increasingly required by research and funding bodies. Our findings also indicate that two key systemic changes are critical for the long-term influence of boundary organisations for advancing climate change adaptation. These include changes to the science, knowledge production process; and shift in the political culture.

text: When salient science is not enough to advance climate change adaptation: Lessons from Brazil and Australia Increased social and environmental vulnerability to extreme climatic events and inherent aggravation of environmental and social problems has placed climate change adaptation as an urgent challenge for decision-makers. Understanding and using climate change information to advance the implementation of climate-friendly policies further compounds this challenge. A rich scholarly literature focusing on climate change adaptation endorses that investing in mechanisms that narrow the gap between climate change information production and its use is crucial to increase adaptive capacity. Based on this assumption, this paper investigates the extent to which two collaborative projects that functioned as boundary organisations in Brazil (CiAdapta project) and Australia (Climate Change Adaptation for Natural Resource Management in East Coast Australia) increased access to information, and enabled the continual and continuous usefulness of produced knowledge for climate change adaptation. Considering the distinction between usable and useful information, we applied six criteria to guide the data analysis and extract key lessons from each project. Our findings confirm that face-to-face interactions are more likely to result in research having the societal impact that is being increasingly required by research and funding bodies. Our findings also indicate that two key systemic changes are critical for the long-term influence of boundary organisations for advancing climate change adaptation. These include changes to the science, knowledge production process; and shift in the political culture.

year: 2020

title: Academic success amongst a cohort of gifted and talented Māori and Pasifika secondary school boys: Elements that have contributed to their achievement

authors: Miller, Graeme Oliver

subjects: Māori

abstract: In recent years Māori and Pasifika students have been the focus of much discussion and a significant amount of research relating to underachievement. Despite this, many Māori and Pasifika secondary school boys are achieving highly in the academic sphere within the context of mainstream boys’ state secondary schools in New Zealand. Achievement aside, evidence shows that Māori and Pasifika secondary school boys are seriously under-represented in programmes for the gifted and talented. This enquiry examines factors in relation to identifying gifted and talented students, and investigates how their abilities are forged and nurtured. The reasons for student success merit serious investigation because of how the multiple elements contributing to their achievement are likely to be applicable to others, and are a pressing concern for academic attainment in the New Zealand education system. 
 
This qualitative study examines why 30 academically successful Māori and Pasifika secondary school boys achieved highly in the mainstream education system. The boys ranged from 13 to 19 years, the youngest being in his first year at high school as a Year 9 student, and the oldest being in his second year at university. The thesis argues their academic success was due to the complex interplay of home and school environmental elements, and the boys’ intrapersonal characteristics. The study explored the boys’ and parents’ narratives to explain why students had achieved highly, and examined both the parents’ and boys’ perceptions of how well the schools had provided for their intellectual, emotional and cultural needs. Sociocultural learning theory is the main theoretical lens through which the findings are viewed. The methodology is primarily built upon narrative inquiry. The main method of data collection was by semi-structured interview, both individually and in focus groups. Supplementary methods utilised were questionnaires and observation.  
  
An issue in the research was the disparity between the cultural and ethnic background of the participants and myself as the researcher. However, an endeavour was made to mitigate this by consulting with Māori and Pasifika educators, a kaumatua (elder) and iwi (tribal) representative prior to the research commencing. In addition, models developed through this study were submitted to Māori and Pasifika educators for their comment and approval prior to being included. 
 
With its focus specifically on highly-achieving Māori and Pasifika secondary school boys, this thesis makes an original contribution to the national and international discussion about raising student achievement. It provides a platform for further research to 	address the particular concerns around the underachievement of Māori and Pasifika secondary school boys. 
 
While there are several implications arising from the research, all are linked to the need for policy makers and educators to address the issue of the underrepresentation of Māori and Pasifika students in programmes for the gifted and talented. Policies, practices and relationships need to be examined to evaluate how effectively they contribute to gifted and talented Māori and Pasifika students receiving the academic opportunities they deserve. A key part of this examination will need to include consultation with students and their whānau.

text: Academic success amongst a cohort of gifted and talented Māori and Pasifika secondary school boys: Elements that have contributed to their achievement In recent years Māori and Pasifika students have been the focus of much discussion and a significant amount of research relating to underachievement. Despite this, many Māori and Pasifika secondary school boys are achieving highly in the academic sphere within the context of mainstream boys’ state secondary schools in New Zealand. Achievement aside, evidence shows that Māori and Pasifika secondary school boys are seriously under-represented in programmes for the gifted and talented. This enquiry examines factors in relation to identifying gifted and talented students, and investigates how their abilities are forged and nurtured. The reasons for student success merit serious investigation because of how the multiple elements contributing to their achievement are likely to be applicable to others, and are a pressing concern for academic attainment in the New Zealand education system. 
 
This qualitative study examines why 30 academically successful Māori and Pasifika secondary school boys achieved highly in the mainstream education system. The boys ranged from 13 to 19 years, the youngest being in his first year at high school as a Year 9 student, and the oldest being in his second year at university. The thesis argues their academic success was due to the complex interplay of home and school environmental elements, and the boys’ intrapersonal characteristics. The study explored the boys’ and parents’ narratives to explain why students had achieved highly, and examined both the parents’ and boys’ perceptions of how well the schools had provided for their intellectual, emotional and cultural needs. Sociocultural learning theory is the main theoretical lens through which the findings are viewed. The methodology is primarily built upon narrative inquiry. The main method of data collection was by semi-structured interview, both individually and in focus groups. Supplementary methods utilised were questionnaires and observation.  
  
An issue in the research was the disparity between the cultural and ethnic background of the participants and myself as the researcher. However, an endeavour was made to mitigate this by consulting with Māori and Pasifika educators, a kaumatua (elder) and iwi (tribal) representative prior to the research commencing. In addition, models developed through this study were submitted to Māori and Pasifika educators for their comment and approval prior to being included. 
 
With its focus specifically on highly-achieving Māori and Pasifika secondary school boys, this thesis makes an original contribution to the national and international discussion about raising student achievement. It provides a platform for further research to 	address the particular concerns around the underachievement of Māori and Pasifika secondary school boys. 
 
While there are several implications arising from the research, all are linked to the need for policy makers and educators to address the issue of the underrepresentation of Māori and Pasifika students in programmes for the gifted and talented. Policies, practices and relationships need to be examined to evaluate how effectively they contribute to gifted and talented Māori and Pasifika students receiving the academic opportunities they deserve. A key part of this examination will need to include consultation with students and their whānau.

year: 2015