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: The utility of the psychopathy checklist- screening version for predicting serious violent recidivism in a New Zealand offender sample

authors: Wilson, Nicol John

abstract: This study set out to evaluate the ability of the Psychopathy Checklist: Screening Version (PCL: SV) to predict criminal reoffending by New Zealand offenders convicted of previous serious violent offences. Psychopathy has been identified in a large number of overseas studies as a significant risk factor for general reoffending and in particular for violent reoffending. Using a retrospective-prospective design, a representative sample (N = 199; 48% of Māori descent) was selected from a database of male offenders serving sentences of seven years or more, the majority for violent crimes, who had been released into the community for a minimum of five years. 

Inmate institutional file information up to the time of their release was used to score the PCL: SV. Current offender criminal records were then accessed to establish if recidivism had occurred since release, and if so, the type of sentence imposed and the seriousness of the reoffending. In addition, PCL: SV scores were compared to two static actuarial measures of recidivism in use by the New Zealand Department of Corrections. The PCL: SV total, Factor 1, and Factor 2 scores correlated .50, .37, and .53, respectively with reconviction, and .49, .40, and .47 respectively with reimprisonment. Both discriminant function analysis (Wilkes Lambda = .79) and Receiver Operator Curve analysis (AUC = .80) confirmed the overall predictive accuracy of the PCL: SV for serious violent reoffending and its ability to add support to actuarial instruments based solely on static risk predictors. 

The unique nature of this contribution was supported by regression analysis identifying that PCL: SV Factor 1 scores, regarded as measuring core psychopathic traits, had a high negative correlation (r = -.41) with time to reimprisonment for violent offences. The final part of the study involved an investigation into the ‘false positive’ group (N = 32). Men with PCL: SV scores of 16 or greater but no further offending resulting in reimprisonment within five years of release. The study of this group was carried out to establish if indeed they were low risk, and to explore the strategies they used to reduce their risk. A number were found to have died or to have committed serious offending that was not originally detected (n = 5) reducing the false positive rate to 24% (sensitivity 76% and specificity of 24%). 

A structured interview was administered focused on post-release problems and strategies that also included a psychometric battery measuring static and dynamic risk variables, anger, personality pathology, and interpersonal and affective deficits. The results from those agreeing to be interviewed (n = 14) found the majority continued to experience regular thoughts about potential criminal acts and were still assessed at high recidivism risk, but the majority used strategies such as increased control over substance abuse, avoidance of criminal friends and family, and geographic isolation to reduce engaging in serious crime. In addition, ill health and the debilitating effects from their high-risk criminal lifestyle (accidents, substance abuse, and long sentences of imprisonment) had reduced their ability to engage in violent criminal activity. 

It was concluded that the PCL: SV has a high level of predictive validity in predicting serious reoffending for a New Zealand male offender population. The research has been successful in adding to the growing body of knowledge on the ability of the PCL: SV and the concept of psychopathy to predict serious recidivism by criminal populations. Evidence was found of a strong relation between PCL: SV Factor 1 scores and speed of violent reoffending supporting the special ability of the psychopathic personality construct to predict violent behaviour. The follow-up of the false positive group helped to account for part of the false positive decision error rate and has provided further support for the predictive accuracy of the PCL: SV and its inclusion in comprehensive risk assessment. In addition, insights into the beliefs and lifestyles of this parole group were gained that will assist in the development of effective correctional re-integrative initiatives and accurate parole decision-making.

text: The utility of the psychopathy checklist- screening version for predicting serious violent recidivism in a New Zealand offender sample This study set out to evaluate the ability of the Psychopathy Checklist: Screening Version (PCL: SV) to predict criminal reoffending by New Zealand offenders convicted of previous serious violent offences. Psychopathy has been identified in a large number of overseas studies as a significant risk factor for general reoffending and in particular for violent reoffending. Using a retrospective-prospective design, a representative sample (N = 199; 48% of Māori descent) was selected from a database of male offenders serving sentences of seven years or more, the majority for violent crimes, who had been released into the community for a minimum of five years. 

Inmate institutional file information up to the time of their release was used to score the PCL: SV. Current offender criminal records were then accessed to establish if recidivism had occurred since release, and if so, the type of sentence imposed and the seriousness of the reoffending. In addition, PCL: SV scores were compared to two static actuarial measures of recidivism in use by the New Zealand Department of Corrections. The PCL: SV total, Factor 1, and Factor 2 scores correlated .50, .37, and .53, respectively with reconviction, and .49, .40, and .47 respectively with reimprisonment. Both discriminant function analysis (Wilkes Lambda = .79) and Receiver Operator Curve analysis (AUC = .80) confirmed the overall predictive accuracy of the PCL: SV for serious violent reoffending and its ability to add support to actuarial instruments based solely on static risk predictors. 

The unique nature of this contribution was supported by regression analysis identifying that PCL: SV Factor 1 scores, regarded as measuring core psychopathic traits, had a high negative correlation (r = -.41) with time to reimprisonment for violent offences. The final part of the study involved an investigation into the ‘false positive’ group (N = 32). Men with PCL: SV scores of 16 or greater but no further offending resulting in reimprisonment within five years of release. The study of this group was carried out to establish if indeed they were low risk, and to explore the strategies they used to reduce their risk. A number were found to have died or to have committed serious offending that was not originally detected (n = 5) reducing the false positive rate to 24% (sensitivity 76% and specificity of 24%). 

A structured interview was administered focused on post-release problems and strategies that also included a psychometric battery measuring static and dynamic risk variables, anger, personality pathology, and interpersonal and affective deficits. The results from those agreeing to be interviewed (n = 14) found the majority continued to experience regular thoughts about potential criminal acts and were still assessed at high recidivism risk, but the majority used strategies such as increased control over substance abuse, avoidance of criminal friends and family, and geographic isolation to reduce engaging in serious crime. In addition, ill health and the debilitating effects from their high-risk criminal lifestyle (accidents, substance abuse, and long sentences of imprisonment) had reduced their ability to engage in violent criminal activity. 

It was concluded that the PCL: SV has a high level of predictive validity in predicting serious reoffending for a New Zealand male offender population. The research has been successful in adding to the growing body of knowledge on the ability of the PCL: SV and the concept of psychopathy to predict serious recidivism by criminal populations. Evidence was found of a strong relation between PCL: SV Factor 1 scores and speed of violent reoffending supporting the special ability of the psychopathic personality construct to predict violent behaviour. The follow-up of the false positive group helped to account for part of the false positive decision error rate and has provided further support for the predictive accuracy of the PCL: SV and its inclusion in comprehensive risk assessment. In addition, insights into the beliefs and lifestyles of this parole group were gained that will assist in the development of effective correctional re-integrative initiatives and accurate parole decision-making.

year: 2003

title: Ngā tai e rere nei i waho o Mauao

authors: Ngahuia, Dixon

subjects: Waiata Māori

abstract: "I te ao o ngā tūpuna he maha ngā kaupapa o taua wā i mau ki rō waiata, e whakaata mai ana i ngā kōrero-ā-iwi, ngā taukumekume i waenganui Māori, Pākehā, i waenganui hoki i ngā Māori anō. Nā wai hoki ka puta mai ngā herenga ki waenganui i tēnā iwi, i tēnā hapū, ka whakahoahoa tēnā iwi ki tēnā, te mutunga mai ka whānau ake ngā rōpū hou hei wānanga i ngā kaupapa i manawapātia. I pērā anō hoki ngā iwi o Tauranga Moana, ka huri atu ki tēnei iwi, ki tēnā hei huarahi tautoko āwhina mai i aua kaupapa nei. Ko ngā pupurihanga o ēnei taonga tuku iho e whakaahua mai ana i ngā kaupapa i waenganui i te ao Māori i aua wā, mō te iwi, mō te tangata kotahi rānei. Mā ēnei hoki kitea atu ai tā rātou titiro ki te ao i aua wā. 

He whiringa kōrero tēnei pepa mō tētehi waiata a Ngāi-TeRangi e whakamōhio ake ana i tētehi taukumekume i waenganui i a rāua ko Ngāti Kahungunu. Ka kitea i roto i ngā kōrero ka puta ngā huarahi whakapā atu ai ki tēnā iwi, hapū i waenganui, i waho atu rānei o Ngāi-TeRangi hei āwhina mai i te pupuri mana. Arā anō hoki te whakanui i ēnei momo waiata, ōna mana me te mātauranga Māori e pupū ake ana i konei. 

The waiata of our tūpuna Māori (Māori ancestors) capture in verse many issues and topics that were of significance at the time they were composed. They provide us with snapshots of iwi histories, including accounts of battles between Māori and Pākehā and between Māori and Māori. They tell us of alliances formed and reformed between tribes and hapū and of the reasons for these alliances. We see how the alignment and realignment of kin loyalties related to the issues of the day. Tauranga Moana iwi were not immune to such activities: tribal loyalties were chameleon-like, many alliances being pursued in relation to common interests. The ‘oral mapping’ of these local narratives that we find in waiata provides an illustration of topics relevant to individuals and to iwi: personal and collective statements about the ‘order’ of their day. They provide us with an insight into our ancestors’ ‘ways of seeing the world’. Above all, they are fundamental to the illustration and preservation of Māori knowledge. 
 
This paper presents an analysis of a Ngāi-TeRangi waiata tangi (lament) which relates to activities linking the iwi in a political stance against Ngāti Kahungunu. What is demonstrated is the intricate network of iwi and hapū involvement, within and without Ngāi-TeRangi, in the quest for honour. What is also demonstrated is the importance of waiata as significant literary achievements, as oral treasures."

text: Ngā tai e rere nei i waho o Mauao "I te ao o ngā tūpuna he maha ngā kaupapa o taua wā i mau ki rō waiata, e whakaata mai ana i ngā kōrero-ā-iwi, ngā taukumekume i waenganui Māori, Pākehā, i waenganui hoki i ngā Māori anō. Nā wai hoki ka puta mai ngā herenga ki waenganui i tēnā iwi, i tēnā hapū, ka whakahoahoa tēnā iwi ki tēnā, te mutunga mai ka whānau ake ngā rōpū hou hei wānanga i ngā kaupapa i manawapātia. I pērā anō hoki ngā iwi o Tauranga Moana, ka huri atu ki tēnei iwi, ki tēnā hei huarahi tautoko āwhina mai i aua kaupapa nei. Ko ngā pupurihanga o ēnei taonga tuku iho e whakaahua mai ana i ngā kaupapa i waenganui i te ao Māori i aua wā, mō te iwi, mō te tangata kotahi rānei. Mā ēnei hoki kitea atu ai tā rātou titiro ki te ao i aua wā. 

He whiringa kōrero tēnei pepa mō tētehi waiata a Ngāi-TeRangi e whakamōhio ake ana i tētehi taukumekume i waenganui i a rāua ko Ngāti Kahungunu. Ka kitea i roto i ngā kōrero ka puta ngā huarahi whakapā atu ai ki tēnā iwi, hapū i waenganui, i waho atu rānei o Ngāi-TeRangi hei āwhina mai i te pupuri mana. Arā anō hoki te whakanui i ēnei momo waiata, ōna mana me te mātauranga Māori e pupū ake ana i konei. 

The waiata of our tūpuna Māori (Māori ancestors) capture in verse many issues and topics that were of significance at the time they were composed. They provide us with snapshots of iwi histories, including accounts of battles between Māori and Pākehā and between Māori and Māori. They tell us of alliances formed and reformed between tribes and hapū and of the reasons for these alliances. We see how the alignment and realignment of kin loyalties related to the issues of the day. Tauranga Moana iwi were not immune to such activities: tribal loyalties were chameleon-like, many alliances being pursued in relation to common interests. The ‘oral mapping’ of these local narratives that we find in waiata provides an illustration of topics relevant to individuals and to iwi: personal and collective statements about the ‘order’ of their day. They provide us with an insight into our ancestors’ ‘ways of seeing the world’. Above all, they are fundamental to the illustration and preservation of Māori knowledge. 
 
This paper presents an analysis of a Ngāi-TeRangi waiata tangi (lament) which relates to activities linking the iwi in a political stance against Ngāti Kahungunu. What is demonstrated is the intricate network of iwi and hapū involvement, within and without Ngāi-TeRangi, in the quest for honour. What is also demonstrated is the importance of waiata as significant literary achievements, as oral treasures."

year: 2002-09