title: Investigating bioinformatic pipelines for De novo variant identification in New Zealand dairy cattle

authors: Erika, Duerre

subjects: Bioinformatic pipelines

abstract: New Zealand is the biggest single entity for milk and milk product export in the world and being the country’s main industry, keeping track of bovine mutations allows influence of the national herd’s health and the ability to breed cattle better suited to the current farming and climate needs. With advances in next-generation sequencing of whole genomes, research understanding and tracking germline de novo mutations (DNMs) is attainable. However, current techniques being used to identify and study candidate DNMs are unvetted and experimental. Some of these techniques include bioinformatic software packages such as DenovoCNN, DenovoGear, PedFilter, and RUFUS.
This thesis aimed to investigate and test two of these identification pipelines, DenovoGear and PedFilter using next-generation sequencing data from bovine trios. Output data was generated by writing scripts and extracting data from six trios into Excel workbooks or manual IGV validation of selected candidate DNMs. Of the total 714,393 candidates identified across PedFilter and DenovoGear, only 161 of them were identified by both programs. After Integrative Genomic Viewer validation, 50% of these candidates were deemed to be true positives while only 12% were deemed false positives. Data analysis shows neither technique is 100% accurate and they both should be used with secondary filtering and confirmation of the identified DNM candidates. It was also apparent that the different techniques would be better suited to different study situations. For example, (1) For smaller studies (e.g., 3–15 trios), with limited data available to them, using DenovoGear with a secondary software program for filtering would be best (2) If sufficient samples are available to provide a simulated population data set, PedFilter has higher accuracy than DenovoGear on its own (3) For fast analysis without requiring heavy filtering of the output data use a combination of both PedFilter and DenovoGear. 
Lastly, it is clear that further developments and more testing is required in this area of research before a set standard of practice or guidelines can be recommended and implemented. It is suggested to testing DenovoCNN and Rufus or branching out to other packages to trial like SynthDNM, DNMFilter_INDELs or HAPDeNovo.

text: Investigating bioinformatic pipelines for De novo variant identification in New Zealand dairy cattle New Zealand is the biggest single entity for milk and milk product export in the world and being the country’s main industry, keeping track of bovine mutations allows influence of the national herd’s health and the ability to breed cattle better suited to the current farming and climate needs. With advances in next-generation sequencing of whole genomes, research understanding and tracking germline de novo mutations (DNMs) is attainable. However, current techniques being used to identify and study candidate DNMs are unvetted and experimental. Some of these techniques include bioinformatic software packages such as DenovoCNN, DenovoGear, PedFilter, and RUFUS.
This thesis aimed to investigate and test two of these identification pipelines, DenovoGear and PedFilter using next-generation sequencing data from bovine trios. Output data was generated by writing scripts and extracting data from six trios into Excel workbooks or manual IGV validation of selected candidate DNMs. Of the total 714,393 candidates identified across PedFilter and DenovoGear, only 161 of them were identified by both programs. After Integrative Genomic Viewer validation, 50% of these candidates were deemed to be true positives while only 12% were deemed false positives. Data analysis shows neither technique is 100% accurate and they both should be used with secondary filtering and confirmation of the identified DNM candidates. It was also apparent that the different techniques would be better suited to different study situations. For example, (1) For smaller studies (e.g., 3–15 trios), with limited data available to them, using DenovoGear with a secondary software program for filtering would be best (2) If sufficient samples are available to provide a simulated population data set, PedFilter has higher accuracy than DenovoGear on its own (3) For fast analysis without requiring heavy filtering of the output data use a combination of both PedFilter and DenovoGear. 
Lastly, it is clear that further developments and more testing is required in this area of research before a set standard of practice or guidelines can be recommended and implemented. It is suggested to testing DenovoCNN and Rufus or branching out to other packages to trial like SynthDNM, DNMFilter_INDELs or HAPDeNovo.

year: 2023

title: Measuring inter-indexer consistency using a thesaurus

authors: Medelyan, Olena

subjects: computer science

abstract: When professional indexers independently assign terms to a given document, the term sets generally differ between indexers. Studies of inter-indexer consistency measure the percentage of matching index terms, but none of them consider the semantic relationships that exist amongst these terms. We propose to represent multiple-indexers data in a vector space and use the cosine metric as a new consistency measure that can be extended by semantic relations between index terms. We believe that this new measure is more accurate and realistic than existing ones and therefore more suitable for evaluation of automatically extracted index terms.

text: Measuring inter-indexer consistency using a thesaurus When professional indexers independently assign terms to a given document, the term sets generally differ between indexers. Studies of inter-indexer consistency measure the percentage of matching index terms, but none of them consider the semantic relationships that exist amongst these terms. We propose to represent multiple-indexers data in a vector space and use the cosine metric as a new consistency measure that can be extended by semantic relations between index terms. We believe that this new measure is more accurate and realistic than existing ones and therefore more suitable for evaluation of automatically extracted index terms.

year: 2006

title: Ngā whakaaro o ngā ākonga: perspectives and experiences of Māori students in outdoor education in Aotearoa New Zealand

authors: Washbourn, Phil

subjects: Outdoor education

abstract: This study aims to develop an understanding of the perspectives and experiences of Māori students in a secondary school outdoor education programme in Aotearoa New Zealand. Lynch (2012) indicated that “there is a clear need, and wide scope, for research into: cultural elements of outdoor education programmes; cultural effects on participants; culturally appropriate research approaches and programme effects on, and experiences of, people who identify as Māori” (p.49). Outdoor education in Aotearoa New Zealand has been heavily influenced by ‘Eurocentric’ values and practices that contrast with those of Te Ao Māori. In line with a number of calls to re-envision the field, the perspectives and experiences of Māori and the incorporation of Te Ao Māori pedagogies are vital to the reconstruction of an integrated and inclusive Aotearoa New Zealand expression of Outdoor Education for the 21st century.
This study, guided by culturally responsive research methodology, used focus groups to investigate the opinions, thoughts and expectations of Māori students of outdoor education. Thematic analysis was used to analyse the focus group data, and four major themes were identified: the importance of shared experience and relationships to positive experiences of outdoor education; the distinctive practices of outdoor education make learning enjoyable and engaging; the importance to students of making connections with Te Ao Māori through experience, stories of places and history; and the complexity of engaging Māori in participation in outdoor education, including factors such as affordability, the influence of friends and whānau and prioritising educational pathways. A range of practices and approaches from Te Ao Māori are considered and presented, based on the contribution of the student participants, including pedagogical principles from Te Ao Māori such as wānanga, whanaungatanga and tauira. Suggestions for practice include developing connections within the community and experiencing Te Ao Māori learning contexts such as waka ama, noho marae and mahinga kai.

text: Ngā whakaaro o ngā ākonga: perspectives and experiences of Māori students in outdoor education in Aotearoa New Zealand This study aims to develop an understanding of the perspectives and experiences of Māori students in a secondary school outdoor education programme in Aotearoa New Zealand. Lynch (2012) indicated that “there is a clear need, and wide scope, for research into: cultural elements of outdoor education programmes; cultural effects on participants; culturally appropriate research approaches and programme effects on, and experiences of, people who identify as Māori” (p.49). Outdoor education in Aotearoa New Zealand has been heavily influenced by ‘Eurocentric’ values and practices that contrast with those of Te Ao Māori. In line with a number of calls to re-envision the field, the perspectives and experiences of Māori and the incorporation of Te Ao Māori pedagogies are vital to the reconstruction of an integrated and inclusive Aotearoa New Zealand expression of Outdoor Education for the 21st century.
This study, guided by culturally responsive research methodology, used focus groups to investigate the opinions, thoughts and expectations of Māori students of outdoor education. Thematic analysis was used to analyse the focus group data, and four major themes were identified: the importance of shared experience and relationships to positive experiences of outdoor education; the distinctive practices of outdoor education make learning enjoyable and engaging; the importance to students of making connections with Te Ao Māori through experience, stories of places and history; and the complexity of engaging Māori in participation in outdoor education, including factors such as affordability, the influence of friends and whānau and prioritising educational pathways. A range of practices and approaches from Te Ao Māori are considered and presented, based on the contribution of the student participants, including pedagogical principles from Te Ao Māori such as wānanga, whanaungatanga and tauira. Suggestions for practice include developing connections within the community and experiencing Te Ao Māori learning contexts such as waka ama, noho marae and mahinga kai.

year: 2018