title: Bundle-driven move analysis: Sentence initial lexical bundles in PhD abstracts

authors: Li, Liang

abstract: Rhetorical moves are discoursal units that perform communicative functions in a given genre. They have been manually identified in many previous studies taking a corpus-based approach, and these studies have provided important contributions to discourse structure theories. However, manual analysis has restricted the scale and quantity of texts under investigation and the identification of moves is likely to be influenced by researchers' prior knowledge. In contrast, a corpus-driven approach, by applying automatic computational technology to process a large number of texts, possibly results in a better representation of the moves in a genre and minimises researcher bias in move identification. This study applies one typical corpus-driven approach, a bundle-driven approach, to analyse rhetorical moves of PhD abstracts, a move-intensive genre. The study focused on 5-word sentence initial bundles. Almost all the generated bundles could be identified as move indicators. The majority of the indicated moves aligned with the moves proposed for research article abstracts in previous studies, and one new move, Structure, was identified. This study indicates the potential of a bundle-driven approach in exploring rhetorical moves and in examining the linguistic features of moves by means of lexical bundles. Pedagogical implications for EAP writing are also suggested.

text: Bundle-driven move analysis: Sentence initial lexical bundles in PhD abstracts Rhetorical moves are discoursal units that perform communicative functions in a given genre. They have been manually identified in many previous studies taking a corpus-based approach, and these studies have provided important contributions to discourse structure theories. However, manual analysis has restricted the scale and quantity of texts under investigation and the identification of moves is likely to be influenced by researchers' prior knowledge. In contrast, a corpus-driven approach, by applying automatic computational technology to process a large number of texts, possibly results in a better representation of the moves in a genre and minimises researcher bias in move identification. This study applies one typical corpus-driven approach, a bundle-driven approach, to analyse rhetorical moves of PhD abstracts, a move-intensive genre. The study focused on 5-word sentence initial bundles. Almost all the generated bundles could be identified as move indicators. The majority of the indicated moves aligned with the moves proposed for research article abstracts in previous studies, and one new move, Structure, was identified. This study indicates the potential of a bundle-driven approach in exploring rhetorical moves and in examining the linguistic features of moves by means of lexical bundles. Pedagogical implications for EAP writing are also suggested.

year: 2020

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: Boat electrofishing survey of fish populations in the Ohau Channel in December 2010

authors: Hicks, Brendan J.

abstract: The original purpose of this series of surveys was to apply an independent method to estimate the densities of common smelt and bullies in the Ohau Channel at fixed points along the bank which coincided with trap netting sites used by the National Institute of Water and Atmospheric Research (NIWA). Since the low number of smelt captured by a single day’s boat electrofishing became apparent compared to the numbers captured by seasonal trapping, the aim of the survey has been modified to provide on-going monitoring of the fish communities and abundance in the Ohau Channel, especially fish species that are taonga to Maori (eels, goldfish, and koura).

text: Boat electrofishing survey of fish populations in the Ohau Channel in December 2010 The original purpose of this series of surveys was to apply an independent method to estimate the densities of common smelt and bullies in the Ohau Channel at fixed points along the bank which coincided with trap netting sites used by the National Institute of Water and Atmospheric Research (NIWA). Since the low number of smelt captured by a single day’s boat electrofishing became apparent compared to the numbers captured by seasonal trapping, the aim of the survey has been modified to provide on-going monitoring of the fish communities and abundance in the Ohau Channel, especially fish species that are taonga to Maori (eels, goldfish, and koura).

year: 2011-11-15