title: Providing pin-point page-level precision to 1 trillion tokens of text for workset creation

authors: Bainbridge, David

subjects: computer science

abstract: We report on the work undertaken developing a web environment that allows users to search over 1 trillion tokens of text -- down to the page-level -- of the HathiTrust Part-of-Speech Extracted Features Dataset to help produce worksets for scholarly analysis. We present an extended example of the web environment in use, along with details about its implementation.

text: Providing pin-point page-level precision to 1 trillion tokens of text for workset creation We report on the work undertaken developing a web environment that allows users to search over 1 trillion tokens of text -- down to the page-level -- of the HathiTrust Part-of-Speech Extracted Features Dataset to help produce worksets for scholarly analysis. We present an extended example of the web environment in use, along with details about its implementation.

year: 2018

title: Verifying clustered mutation regions inside the newly-completed genome of a clinically-significant New Zealand Mycobacterium tuberculosis strain

authors: Steele, Mackenzie

subjects: Tuberculosis

abstract: In 2019, active infections of Mycobacterium tuberculosis (Mtb) affected 10 million people globally, with 1.4 million deaths, and an additional 1.7-1.9 billion people infected without symptomatic disease (latent Mtb). While Mtb is often associated with Asia and Africa, New Zealand had 360 Mtb infections and 21 deaths in 2019, and roughly 20% of cases were caused by three strains unique to New Zealand. One is CS1 (formerly Rangipo), which is known to be more transmissible than its relatives and has been causing outbreaks in the Waikato region for 30 years. As CS1 has genetic features linked to virulence in unrelated Mtb strains, having a complete and accurate record of genetic features is important, in particular those with the potential to change protein structure (Variable Regions Inside Proteins, VRIPs). Resolving VRIPs would simultaneously remove sequencing mistakes and increase knowledge about Mtb virulence. The aim of this project was to investigate the genetic cause of improved transmissibility in CS1 and produce a closed genome.
Sequencing data from Illumina and PacBio reads was processed, assembled, and checked for quality discrepancies which would require more sequencing to resolve. VRIPs were mapped alongside regions of low-quality data, low data-coverage, and repeat regions. Characteristics of the CS1 genome, such as repeat levels and size, were found by comparing with the reference strain H37Rv.
The read data and assembly were found to be good quality, and the genome is of high enough quality to be considered closed. As expected, some regions of low coverage and poor quality were discovered inside large repeat regions, and more work on these would be valuable. 13 of the 32 VRIPs were verified, all linked with virulence factors. 5 verified VRIPs caused genes to split into domains, accumulating mutations in the non-coding region. Further work resolving the remaining 19 VRIPs is recommended.

text: Verifying clustered mutation regions inside the newly-completed genome of a clinically-significant New Zealand Mycobacterium tuberculosis strain In 2019, active infections of Mycobacterium tuberculosis (Mtb) affected 10 million people globally, with 1.4 million deaths, and an additional 1.7-1.9 billion people infected without symptomatic disease (latent Mtb). While Mtb is often associated with Asia and Africa, New Zealand had 360 Mtb infections and 21 deaths in 2019, and roughly 20% of cases were caused by three strains unique to New Zealand. One is CS1 (formerly Rangipo), which is known to be more transmissible than its relatives and has been causing outbreaks in the Waikato region for 30 years. As CS1 has genetic features linked to virulence in unrelated Mtb strains, having a complete and accurate record of genetic features is important, in particular those with the potential to change protein structure (Variable Regions Inside Proteins, VRIPs). Resolving VRIPs would simultaneously remove sequencing mistakes and increase knowledge about Mtb virulence. The aim of this project was to investigate the genetic cause of improved transmissibility in CS1 and produce a closed genome.
Sequencing data from Illumina and PacBio reads was processed, assembled, and checked for quality discrepancies which would require more sequencing to resolve. VRIPs were mapped alongside regions of low-quality data, low data-coverage, and repeat regions. Characteristics of the CS1 genome, such as repeat levels and size, were found by comparing with the reference strain H37Rv.
The read data and assembly were found to be good quality, and the genome is of high enough quality to be considered closed. As expected, some regions of low coverage and poor quality were discovered inside large repeat regions, and more work on these would be valuable. 13 of the 32 VRIPs were verified, all linked with virulence factors. 5 verified VRIPs caused genes to split into domains, accumulating mutations in the non-coding region. Further work resolving the remaining 19 VRIPs is recommended.

year: 2021

title: Indigenous knowledge, methodology and mayhem: What is the role of methodology in producing indigenous insights? A discussion from Mātauranga Māori

authors: Smith, Linda Tuhiwai

abstract: The emergence of an academic discourse called Indigenous knowledge internationally, and mātauranga Māori in Aotearoa New Zealand, presents some substantive challenges to concepts of knowing and being, of knowledge creation, knowledge work and the making of meaning. These challenges engage us across philosophical, disciplinary, institutional, inter-generational, territorial and community boundaries, presenting an opportunity to imagine this field anew, and the theories and methodologies that inform contemporary Māori or Indigenous Studies. This article raises some discussion about ‘research methodologies’ being used when discussing mātauranga Māori and Indigenous knowledge (hereafter referred to as IK mātauranga). Research methodologies are often associated with specific disciplines of knowledge and viewed as the primary if not singular way in which knowledge is generated. Arguably, IK mātauranga occupies a different knowledge space from traditional academic disciplines, including their transdisciplinary interstices. This article speaks to a gnawing sense that mayhem is at play, as the academic work around IK mātauranga begins to consolidate and become institutionalised away from its indigenous communities and contexts, where it began and where it still informs identities, ways of living and being.

text: Indigenous knowledge, methodology and mayhem: What is the role of methodology in producing indigenous insights? A discussion from Mātauranga Māori The emergence of an academic discourse called Indigenous knowledge internationally, and mātauranga Māori in Aotearoa New Zealand, presents some substantive challenges to concepts of knowing and being, of knowledge creation, knowledge work and the making of meaning. These challenges engage us across philosophical, disciplinary, institutional, inter-generational, territorial and community boundaries, presenting an opportunity to imagine this field anew, and the theories and methodologies that inform contemporary Māori or Indigenous Studies. This article raises some discussion about ‘research methodologies’ being used when discussing mātauranga Māori and Indigenous knowledge (hereafter referred to as IK mātauranga). Research methodologies are often associated with specific disciplines of knowledge and viewed as the primary if not singular way in which knowledge is generated. Arguably, IK mātauranga occupies a different knowledge space from traditional academic disciplines, including their transdisciplinary interstices. This article speaks to a gnawing sense that mayhem is at play, as the academic work around IK mātauranga begins to consolidate and become institutionalised away from its indigenous communities and contexts, where it began and where it still informs identities, ways of living and being.

year: 2016