title: Efficient tuning parameter selection by cross-validated score in high dimensional models

authors: Jung, Yoonsuh

abstract: As DNA microarray data contain relatively small sample size compared to the number of genes, high dimensional models are often employed. In high dimensional models, the selection of tuning parameter (or, penalty parameter) is often one of the crucial parts of the modeling. Cross-validation is one of the most common methods for the tuning parameter selection, which selects a parameter value with the smallest cross-validated score. However, selecting a single value as an ‘optimal’ value for the parameter can be very unstable due to the sampling variation since the sample sizes of microarray data are often small. Our approach is to choose multiple candidates of tuning parameter first, then average the candidates with different weights depending on their performance. The additional step of estimating the weights and averaging the candidates rarely increase the computational cost, while it can considerably improve the traditional cross-validation. We show that the selected value from the suggested methods often lead to stable parameter selection as well as improved detection of significant genetic variables compared to the tradition cross-validation via real data and simulated data sets.

text: Efficient tuning parameter selection by cross-validated score in high dimensional models As DNA microarray data contain relatively small sample size compared to the number of genes, high dimensional models are often employed. In high dimensional models, the selection of tuning parameter (or, penalty parameter) is often one of the crucial parts of the modeling. Cross-validation is one of the most common methods for the tuning parameter selection, which selects a parameter value with the smallest cross-validated score. However, selecting a single value as an ‘optimal’ value for the parameter can be very unstable due to the sampling variation since the sample sizes of microarray data are often small. Our approach is to choose multiple candidates of tuning parameter first, then average the candidates with different weights depending on their performance. The additional step of estimating the weights and averaging the candidates rarely increase the computational cost, while it can considerably improve the traditional cross-validation. We show that the selected value from the suggested methods often lead to stable parameter selection as well as improved detection of significant genetic variables compared to the tradition cross-validation via real data and simulated data sets.

year: 2016-02-08

title: Within-mat variability in anatoxin-a and homoanatoxin-a production among benthic Phormidium (cyanobacteria) strains.

authors: Wood, Susanna A.

subjects: 16S rRNA gene sequence

abstract: Benthic Phormidium mats can contain high concentrations of the neurotoxins anatoxin-a and homoanatoxin-a. However, little is known about the co-occurrence of anatoxin-producing and non-anatoxin-producing strains within mats. There is also no data on variation in anatoxin content among toxic genotypes isolated from the same mat. In this study, 30 Phormidium strains were isolated from 1 cm(2) sections of Phormidium-dominated mats collected from three different sites. Strains were grown to stationary phase and their anatoxin-a, homoanatoxin-a, dihydroanatoxin-a and dihydrohomoanatoxin-a concentrations determined using liquid chromatography-mass spectrometry. Each strain was characterized using morphological and molecular (16S rRNA gene sequences) techniques. Eighteen strains produced anatoxin-a, dihydroanatoxin-a or homoanatoxin-a. Strains isolated from each mat either all produced toxins, or were a mixture of anatoxin and non-anatoxin-producing genotypes. Based on morphology these genotypes could not be separated. The 16S rRNA gene sequence comparisons showed a difference of at least 17 nucleotides among anatoxin and non-anatoxin-producing strains and these formed two separate sub-clades during phylogenetic analysis. The total anatoxin concentration among toxic strains varied from 2.21 to 211.88 mg kg(-1) (freeze dried weight), representing a 100 fold variation in toxin content. These data indicate that both the relative abundance of anatoxin and non-anatoxin-producing genotypes, and variations in anatoxin producing capability, can influence the overall toxin concentration of benthic Phormidium mat samples.

text: Within-mat variability in anatoxin-a and homoanatoxin-a production among benthic Phormidium (cyanobacteria) strains. Benthic Phormidium mats can contain high concentrations of the neurotoxins anatoxin-a and homoanatoxin-a. However, little is known about the co-occurrence of anatoxin-producing and non-anatoxin-producing strains within mats. There is also no data on variation in anatoxin content among toxic genotypes isolated from the same mat. In this study, 30 Phormidium strains were isolated from 1 cm(2) sections of Phormidium-dominated mats collected from three different sites. Strains were grown to stationary phase and their anatoxin-a, homoanatoxin-a, dihydroanatoxin-a and dihydrohomoanatoxin-a concentrations determined using liquid chromatography-mass spectrometry. Each strain was characterized using morphological and molecular (16S rRNA gene sequences) techniques. Eighteen strains produced anatoxin-a, dihydroanatoxin-a or homoanatoxin-a. Strains isolated from each mat either all produced toxins, or were a mixture of anatoxin and non-anatoxin-producing genotypes. Based on morphology these genotypes could not be separated. The 16S rRNA gene sequence comparisons showed a difference of at least 17 nucleotides among anatoxin and non-anatoxin-producing strains and these formed two separate sub-clades during phylogenetic analysis. The total anatoxin concentration among toxic strains varied from 2.21 to 211.88 mg kg(-1) (freeze dried weight), representing a 100 fold variation in toxin content. These data indicate that both the relative abundance of anatoxin and non-anatoxin-producing genotypes, and variations in anatoxin producing capability, can influence the overall toxin concentration of benthic Phormidium mat samples.

year: 2012-10

title: Experiences of Māori of Aotearoa New Zealand's public health system: a systematic review of two decades of published qualitative research

authors: Graham, Rebekah Sarah

subjects: Indigenous health

abstract: Objective: This paper aims to synthesise the broader perspectives of Māori patients and their whānau (extended family, family group) of their treatment within the public health system. Our research question was ‘What are the experiences of Māori in the public health and/or hospital system in Aotearoa New Zealand?’ Methods: A systematic search using PRISMA protocols and reflexive typology organised around the categories of Māori, public healthcare and qualitative research identified 14 papers that covered all three categories. We undertook a qualitative metasynthesis on these papers using a critical community psychology approach. Results: Māori patients and whānau from the included papers mention both barriers and facilitators to health. We categorised barriers as organisational structures, staff interactions and practical considerations. Facilitators were categorised as the provision of whānau support in the form of practical assistance, emotional care and health system navigation. Conclusions: For many Māori, the existing public health system is experienced as hostile and alienating. Whānau members provide support to mitigate this, but it comes as a cost to whānau. Implications for public health: Public health providers must find ways to ensure that Māori consistently experience positive, high-quality healthcare interactions that support Māori ways of being.

text: Experiences of Māori of Aotearoa New Zealand's public health system: a systematic review of two decades of published qualitative research Objective: This paper aims to synthesise the broader perspectives of Māori patients and their whānau (extended family, family group) of their treatment within the public health system. Our research question was ‘What are the experiences of Māori in the public health and/or hospital system in Aotearoa New Zealand?’ Methods: A systematic search using PRISMA protocols and reflexive typology organised around the categories of Māori, public healthcare and qualitative research identified 14 papers that covered all three categories. We undertook a qualitative metasynthesis on these papers using a critical community psychology approach. Results: Māori patients and whānau from the included papers mention both barriers and facilitators to health. We categorised barriers as organisational structures, staff interactions and practical considerations. Facilitators were categorised as the provision of whānau support in the form of practical assistance, emotional care and health system navigation. Conclusions: For many Māori, the existing public health system is experienced as hostile and alienating. Whānau members provide support to mitigate this, but it comes as a cost to whānau. Implications for public health: Public health providers must find ways to ensure that Māori consistently experience positive, high-quality healthcare interactions that support Māori ways of being.

year: 2020