title: Cylindrical spikes

authors: Moughal, Muhammad Zubair Ali

subjects: Science & Technology

abstract: The Geroch/Stephani transformation is a solution-generating transformation, and may generate spiky solutions. The spikes in solutions generated so far are either early-time permanent spikes or transient spikes. We want to generate a solution with a late-time permanent spike. We achieve this by applying Stephani's transformation with the rotational Killing vector field (KVF) of the locally rotationally symmetric Jacobs solution. The late-time permanent spike occurs along the cylindrical axis. Using a mixed KVF, the generated solution also features a rich variety of transient structures. We introduce a new technique to analyse these structures. Our findings lead us to discover a transient behaviour, which we call the overshoot transition. These discoveries compel us to revise the description of transient spikes.

text: Cylindrical spikes The Geroch/Stephani transformation is a solution-generating transformation, and may generate spiky solutions. The spikes in solutions generated so far are either early-time permanent spikes or transient spikes. We want to generate a solution with a late-time permanent spike. We achieve this by applying Stephani's transformation with the rotational Killing vector field (KVF) of the locally rotationally symmetric Jacobs solution. The late-time permanent spike occurs along the cylindrical axis. Using a mixed KVF, the generated solution also features a rich variety of transient structures. We introduce a new technique to analyse these structures. Our findings lead us to discover a transient behaviour, which we call the overshoot transition. These discoveries compel us to revise the description of transient spikes.

year: 2021

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: Manaaki whenua. Manaaki tangata: Care for the land, care for the people: Leading critical school reform with mana whenua and whānau Māori

authors: Ford, Therese

subjects: Critical school reform

abstract: Education disparities between Māori and Pākehā students in Aotearoa, have their origins in colonial education policies and practices which considerably advantaged Pākehā students and compromised the ability of Māori students to engage with learning and succeed.  Despite the promises of equality inherent in the Treaty of Waitangi,  this historical foundation has, for over 150 years, perpetuated intergenerational cycles of education failure for Māori resulting in high levels of endemic social and economic disadvantage in many Māori communities.
This thesis examines the leadership praxis of two Pākehā principals, to understand how, with more respectful connections with Māori communities, they were able to address education disparities and facilitate success for Māori students as Māori. Culturally responsive research methodologies guided two, in-depth case studies which employed mixed methods.
Two collaborative stories, with the voices of mana whenua and whānau Māori, identified the importance of school leaders developing critical levels of consciousness, through authentic, bidirectional relationships with Māori communities.  These relationships enabled the principals to understand the authentic local, pre-colonial iwi histories of the land. This in turn fostered connections between the schools and local Māori communities that enabled them to collaboratively respond to the implications of colonisation.  
The thesis challenges the monocultural, monolingual, unidirectional policies and practices that characterise the current model of colonial education.  It presents instead a decolonising model of critical school reform and a framework for implementation and evaluation.  It contends that honouring the Treaty of Waitangi requires an equity focused response with power sharing relationships, critically led by principals alongside Māori communities.

text: Manaaki whenua. Manaaki tangata: Care for the land, care for the people: Leading critical school reform with mana whenua and whānau Māori Education disparities between Māori and Pākehā students in Aotearoa, have their origins in colonial education policies and practices which considerably advantaged Pākehā students and compromised the ability of Māori students to engage with learning and succeed.  Despite the promises of equality inherent in the Treaty of Waitangi,  this historical foundation has, for over 150 years, perpetuated intergenerational cycles of education failure for Māori resulting in high levels of endemic social and economic disadvantage in many Māori communities.
This thesis examines the leadership praxis of two Pākehā principals, to understand how, with more respectful connections with Māori communities, they were able to address education disparities and facilitate success for Māori students as Māori. Culturally responsive research methodologies guided two, in-depth case studies which employed mixed methods.
Two collaborative stories, with the voices of mana whenua and whānau Māori, identified the importance of school leaders developing critical levels of consciousness, through authentic, bidirectional relationships with Māori communities.  These relationships enabled the principals to understand the authentic local, pre-colonial iwi histories of the land. This in turn fostered connections between the schools and local Māori communities that enabled them to collaboratively respond to the implications of colonisation.  
The thesis challenges the monocultural, monolingual, unidirectional policies and practices that characterise the current model of colonial education.  It presents instead a decolonising model of critical school reform and a framework for implementation and evaluation.  It contends that honouring the Treaty of Waitangi requires an equity focused response with power sharing relationships, critically led by principals alongside Māori communities.

year: 2020