cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4225/03/58b8da0cd901d
title: Chaotic advection in a three-dimensional volume-preserving potential flow

description: While mixing and particle transport in 2D incompressible flows are well-understood, much less is known about 3D incompressible flows. This is because the addition of a third dimension adds to the topological complexity, and more importantly, the link between 2D incompressible flows and Hamiltonian systems that proved so fruitful breaks down for 3D flows. Therefore, there is a need for fundamental studies on 3D fluid transport and mixing, with applications in groundwater flows, micro-fluidics, industrial mixers and biological flows.

Here fluid transport and mixing is studied using a model fluid flow, the 3D Reoriented Potential Mixing (3DRPM) flow, as a case study to reveal novel transport mechanisms and associated coherent structures that are generic to 3D volume-preserving flows. The 3DRPM flow consists of a periodically reoriented dipole flow, and is a 3D analogue of the 2D RPM flow that has been studied in the past. 

In the 3DRPM flow it is found that there are a number of competing transport mechanisms, that together drive a transition from 1D to 3D particle transport. Periodic points and lines play an important role for all volume-preserving flows, revealing regions of chaos and impenetrable barriers to transport. Here it is shown that degenerate/parabolic periodic points are particularly important, as they represent bifurcations in flow stability. Conversely, discontinuous deformations are an unexpected consequence of dipole reorientation, akin to slip deformations seen in shear-banding materials, and occur even though the steady dipole flow is smooth. This has a significant impact on the transport behaviour of particles, and can either enhance or impede the rate of mixing. The combination of smooth and discontinuous deformations is generic to a wide range of systems, including flows with extraction and reinjection of fluid, granular flows, and deformations of shear-banding materials. Here it is shown that discontinuous deformations can destroy impenetrable barriers to transport, allowing greater freedom for particle transport. In 3D systems they can create a novel mechanism for fully 3D transport that is similar in effect to Resonance Induced Dispersion.
DOI: 10.4225/03/58b8da75060ac
title: A genome-wide gene overexpression screen for mitophagy mutants in the yeast Saccharomyces cerevisiae

description: Autophagy is a fundamental pathway conserved amongst all eukaryotic cells that is necessary for the degradation of intracellular structures, including organelles, to maintain cellular homeostasis. Being a fundamental process, autophagy is linked with many other intracellular pathways, and its dysfunction is associated with many human diseases.
Mitochondria can be degraded by autophagy after delivery to the vacuole (in yeast) or lysosome (in mammalian cells) in a selective process termed mitophagy. Significant contribution to the understanding of mitophagy has come from research on the model organism Saccharomyces cerevisiae. Two non-essential gene deletion screens have identified two genes, ATG32 and ATG33, encoding components of the mitophagy pathway both localised at the outer mitochondrial membrane (OMM). Atg32p acts as the essential receptor activated by phosphorylation allowing interaction with core autophagy proteins resulting in mitophagy. However, our knowledge of mitophagy and its regulation in yeast is incomplete requiring further investigation.
To this end, I developed a high-throughput imaging assay based on the use of a mitochondrially targeted fluorescent protein biosensor called mt-Rosella. The assay is performed using a 96-well format in a semi-automated fashion and allows the screening of different strain libraries under a range of different conditions.
Using this assay I investigated the effects of gene overexpression on mitophagy using a library comprised of 1588 high-copy number plasmids that cover more than 95% of the yeast genome including essential genes (previously excluded from the deletion library). Each plasmid contains on average 5 contiguous genes each under the expression control of their endogenous promoter.
The screen revealed that increased expression of a number of genes can affect mitophagy. Among such genes, I found that OM14 encoding the OMM protein Om14p confers a strong decrease in mitophagy when overexpressed in cells. Subsequently a similar phenotype was observed in cells in which the OM14 gene was deleted. Om14p is required for co-translational import of proteins into mitochondria and also forms a complex with the OMM proteins Por1p and Om45p. Preliminary results indicate that lack of Om14p leads to a significant reduction in amounts of Atg32p in cells suggesting the involvement of Om14p in the co-translational import of Atg32p in mitochondria. Another line of evidence indicates that the absence of Om14p causes a perturbation in the ultrastructure of mitochondria suggesting a role for Om14p in mitochondrial architecture, the alteration of which could indirectly affect proteins essential for mitophagy, including Atg32p. Further investigation is required to fully understand the role of Om14p in mitophagy.
DOI: 10.4225/03/58b8daf063970
title: Intelligent audit code generation from free text in the context of neurosurgery

description: Clinical auditing requires structured data for aggregation and analysis of patterns. Clinicians however, need to record clinical encounters in written or spoken language, not only for its work-flow naturalness but also for its expressivity, precision, and capacity to convey all required information, which codified structured data is incapable of. Therefore, structured data must be obtained from clinical text as a later step, a task known as information extraction. Specialised areas of medicine use their own clinical language and clinical coding systems, resulting in unique challenges for the extraction process. 

This research is devoted to creating a novel semi-automated method for generating codified auditing data from clinical notes recorded in a neurosurgical department in an Australian teaching hospital. The department has its own audit coding system, and language used in its clinical notes is highly specific to the neurological and neurosurgical domains, which necessitated a customised approach.

The principles of Design Science Research were followed to design a method that combines Natural Language Information Extraction and Machine Learning techniques. The method was tested by developing a computer programme that incorporates text extraction algorithms trained and tested on data supplied by the neurosurgical department. The software implements rules initially provided by a domain expert and extended during the development of the software; combined with a custom built machine learning-based prediction system. The software architecture was informed by the requirement for it to be an instantiation of the method, therefore that it should be capable of evaluation within the department’s computer systems. 

To the author’s knowledge there has been no previous published research addressing the challenges of codifying neurosurgical-specific audit categories from free text. By combining highly specific rules-based information extraction with the weighted word counts of a machine learning component in a unique way, the method demonstrates a unique approach to creating applications that solve this codification problem.
DOI: 10.4225/03/58b8db5c55739
title: Console modification in the video game industry
an empirical study of the technological protection measure reforms of the
Australian Copyright Act 1968 (Cth)

description: The Australian-United States Free Trade Agreement expanded the access rights provisions, including the technological protection measures (TPM) and anti-circumvention prohibitions in the Copyright Act 1968 (Cth), to address the unauthorised distribution of copyrighted content, colloquially referred to as piracy.  Copyright users object to these "paracopyright" principles being implemented as criminal penalties and restrictive Digital Rights Management (DRM).  Evidence that piracy has persisted despite the implementation of TPMs raises the question of the effectiveness of copyright as a control of piracy.  The thesis examines through empirical methodologies the effectiveness of the access rights provisions of the Act that are required in light of persistent circumvention and piracy.  

To address this, a case study using video game console modification was undertaken as its functions highlight the issue of access restriction and cultural acceptance of DRM circumvention to access content illegally.  More significantly, while console modification is defined by the video game industry as a gateway into piracy, video-gamers argue that it allows interoperable software and privately copied games to be accessed without restriction.  A series of interviews and focus groups, comprising video game industry professionals and gamers, were conducted to highlight these opposing perspectives.  

The thesis found copyright as law is powerless in light of the cultural norms developed by internet users which accept console modification and piracy as a convention.  The economic factors such as the high price of video games in Australia and technological advances in console modification and DRM mean a multifaceted approach to the re-adjustment is required.  The thesis makes recommendations to achieve an acceptable re-adjustment through the recognition of cultural norms, and the introduction of business models that provide user-friendly solutions in accessing content.
DOI: 10.4225/03/58b8db6d0bd2c
title: Script choice and indexicality in Japanese manga

description: This study investigates the use of script as an index within written Japanese. More specifically, it attempts to identify and explain how script is used to index meaning throughout three series of Japanese manga comprising 22 total volumes. Building on a large body of research into how script contributes to the meaning of Japanese writing, the study analyzes script selection in a context-sensitive manner to explore its potential as a socially meaningful act. 

The dialogue in the three manga make up the primary data source of this study. Each lexeme was coded based on whether it was written in the kanji, hiragana, or katakana script, and the resultant corpora were used to establish each author’s individual preferences for script use in their manga. The study then examined the contexts where locally nonstandard selections of script occurred, and contrasted them with the contexts where other variants were selected, or the manga’s standards were maintained. Repeated use of a variant within a particular context was examined as a possible use of script to index something about a character or their self-presentation in a particular scene. For two of the three manga series, analysis of the orthographic variation was complemented by a stimulated-recall interview with the manga’s author regarding uses of script within their works.

The study found that the use of script as an index in Japanese writing is a far more complicated and intricate process than has been described to date. The creation of meaning through script often went beyond any single marked selection, and relied heavily on patterns of script use that ran throughout each manga. The effects intended by any script’s use were more targeted and interactive than has been previously recognized, as authors indexed specific differences between characters or character types through using contrasting conventions for script use to represent different social voices. Furthermore, the study uncovered multiple techniques that the authors used to adjust the meaning created by the marked use of a particular script, such as varying the extent of the script’s use, or combining lexical and orthographic variants to create effects that draw upon elements of each item’s indexical field. 

Ultimately, the results of this study found that script selection is an intricate and ever-present part of the creation of meaning in the analyzed texts. Rather than just a method of adding color to an individual word or sentence, script selection is shown to be a versatile channel through which authors are able to create multiple distinct effects, and index a number of defined social voices and registers. The findings have important implications for how we understand orthography as an avenue for indexing meaning within writing, and how we engage with and attempt to explain the indexical use of kanji, hiragana, and katakana in contemporary Japanese.
DOI: 10.4225/03/58b8db8d2aa36
title: Phase transitions of some discrete models in statistical mechanics

description: We studied in this thesis the critical behaviours of percolation and directed percolation models using Monte Carlo simulations, including estimating percolation thresholds, critical exponents, and various universal amplitudes. In addition, we examined the geometric structure of percolation clusters, and verified the critical behaviours of a leaf-excluded percolation model belong to the standard percolation universality class. Finally, we rigorously studied an n-component face-cubic model on the complete graph, by a large deviations analysis. We proved limit theorems for the standard face-cubic model, and studied phase diagrams for the general face-cubic model.
DOI: 10.4225/03/58b8dbe4874d5
title: The social context of Lamaholots' fertility desires

description: This thesis explores the social context of the relatively high fertility desires among the Lamaholots, a people in Eastern Indonesia. Over half of the married couples participating in this study desired at least four living children in 2013 (Table 8.5). Also, about the same proportion of those who had come to this desired number wanted no more children (Table 8.6). These desired figures are higher than the national (2.6) and even regional (Nusa Tenggara Timur Province: 3.3) total fertility rate in 2012. This study also discusses their prioritized values of children (VOC), a mediating concept between one’s social contexts and fertility desire. Primary data for analysis was first collected through 12 Focus Group Discussions, through which people’s 15 VOC were generated. The VOC were later regrouped into six categories: continuity, cohesion, self-enrichment, emotion, economic, and religious. A face to face survey of the VOC prioritization and intent for another child was then carried out with 1,040 respondents. In-depth interviews with 19 individuals, to discuss issues surfacing in the previous stages, ended the data collection. This study confirms that the Lamaholots still value the roles of children to carry on the family/clan name and to secure their old age, leading to their preference for a relatively large family. Living according to the clan system, poor economic conditions, and cultural norms such as respect for elderly parents are conducive to the VOC prioritization. With such findings, the study helps raise issues that need to be addressed in the strategic effort for lowering fertility. Its major theoretical contribution is its emphasis on the importance of ethnicity and the use of the VOC concept in fertility studies.
DOI: 10.4225/03/58b8dbf499f79
title: Dynamics of transcription factor targeting and chromatin states during reprogramming

description: Induced pluripotent stem cells (iPSCs) have been produced from a number of mouse and human somatic cell types, upon the enforced expression of the transcription factors (TFs) Oct4, Klf4, Sox2, and c-Myc (OKSM). Reprogramming leads to inactivation of the somatic cell program and activation of the embryonic stem (ES) cell-specific program for self-renewal and pluripotency. Cells undergoing reprogramming initially downregulate the fibroblast-associated marker Thy1, then activate the Ssea1 marker. However only Ssea1+ cells can form iPSCs and Thy1+ and Thy1- cells are refractory cells. I firstly find why some cells are refractory and how the refractory cells can be rescued. Next an efficient reprogramming mouse model generates. Then both the spatial and temporal binding properties of these transcription factors during reprogramming investigates using Chromatin Immunoprecipitation, followed by qPCR which showed different binding patterns during reprogramming. I also investigates the compaction and protection of chromatin by DNase-MLPA and ATAC- seq across the different cell populations. Finally we studied the correlation among the TF binding, chromatin changes, nucleosomes shifting and transcriptional activity. The results of this study will further our understanding of transcriptional regulation by OKSM and how gene regulatory networks transpire during cellular reprogramming
DOI: 10.14457/cmu.res.2003.392
title: คุณค่าทางโภชนาการของข้าวพันในอำเภอลับแล จังหวัดอุตรดิตถ์ /
DOI: 10.14457/cmu.res.2005.192
title: ค่าใช้จ่ายต่อหัวนักศึกษา ภาควิชาเคมีคลินิก คณะเทคนิคการแพทย์ มหาวิทยาลัยเชียงใหม่ ปีการศึกษา 2543-2545 /
DOI: 10.14457/cmu.res.2006.280
title: คุณค่าทางโภชนาการและใยอาหารของอาหารล้านนา /
DOI: 10.14457/cmu.res.2006.281
title: คุณภาพการนอนหลับและปัจจัยที่รบกวนการนอนหลับ ในผู้ป่วยมะเร็งตับและทางเดินน้ำดี ในโรงพยาบาลมหาราชนครเชียงใหม่ /
DOI: 10.14457/cmu.res.2007.232
title: คุณภาพการนอนหลับ และปัจจัยรบกวนการนอนหลับ ในผู้ป่วยกระดูกหัก ที่ได้รับการผ่าตัดในหอผู้ป่วยพิเศษ โรงพยาบาลเชียงใหม่ราม /
DOI: 10.14457/cmu.res.2007.233
title: คุณภาพการนอนหลับและปัจจัยที่รบกวนการนอนหลับ ของผู้ป่วยที่ได้รับบาดเจ็บจากอุบัติเหตุ ในหอผู้ป่วยศัลยกรรมอุบัติเหตุ โรงพยาบาลลำปาง /
DOI: 10.15468/0quezr
title: Redescription of Proformica nasuta (Nylander, 1856) (Hymenoptera, Formicidae) using an integrative approach

description: This dataset contains the digitized treatments in Plazi based on the original journal article Christophe Galkowski, Claude Lebas, Philippe Wegnez (2017): Redescription of Proformica nasuta (Nylander, 1856) (Hymenoptera, Formicidae) using an integrative approach. European Journal of Taxonomy 290: 1-40, DOI: 10.5852/ejt.2017.290
DOI: 10.4225/03/58b8dc0365576
title: Constructing free resolutions of cohomology algebras

description: The H(R)-algebra of a space is defined as the algebraic object consisting of the
graded cohomology groups of the space with coefficients in a general ring R, together
with all primary cohomology operations on these groups, subject to the
relations between the operations.This structure can be encoded as a functor from
the category H(R) containing products of Eilenberg-Mac Lane spaces over R to
the category of pointed sets.

The free H(R)-algebras are the H(R)-algebras of a product of Eilenberg-Mac Lane spaces.
In this thesis we show how to construct free simplicial resolutions of
H(R)-algebras using the free and underlying functors.

Given a space X, we also construct a cosimplicial space such that the cohomology
of this cosimplicial space is a free simplicial resolution of the H(R)-algebra of X.
For R = Fp,  the finite field on p elements, this cosimplicial resolution fits the E2
page of a spectral sequence and give convergence results under certain finiteness
restrictions on X. For R = Z, the integers, a similar result is not obtained and
the reasons for this are given.
DOI: 10.4225/03/58b8dc7ae8af9
title: New “clickable” reagents for bioconjugate chemistry

description: Bioorthogonal “click” chemistries represent a small but growing class of reliable “spring-loaded” reactions that occur exclusively between a pair of specific reaction partners, without interference from any of the native functional groups found in biological systems. These chemistries can be used to efficiently introduce a whole host of entities into biomolecules, ranging from targeting groups through to detectable molecules and functionalities that alter biodistribution characteristics.
This thesis describes the synthesis, utilisation and assessment of five new “clickable” imaging probes, spanning three different designs, with each bearing an alkyne functionality to facilitate highly-site specific tagging of azide-bearing (bio)molecules via the Cu(I)-catalysed click reaction. The first set of tags are luminescent terbium(III) complexes incorporating cyclen-based chelators. Their utility for luminescent labelling was demonstrated though successful click conjugation to a small model azide compound as well as E.coli aspartate/glutamate-binding protein incorporating a genetically encoded p-azido-L-phenylalanine or p-(azidomethyl)-L-phenylalanine residue. Upon conjugation, one of the complexes displayed a significant luminescent enhancement (“light-up” effect), providing a simple indicator of successful ligation. The tags should prove useful for time-gated assay luminescence applications. A second set of tags, also cyclen-based, were designed for potential bimodal imaging applications. These feature a fluorescent alkynyl-napthalimide group for optical detection, and a chelated Gd(III) ion to provide image contrast in MRI. As proof-of-concept, one of the complexes was clicked to a lipidated cell-penetrating peptide and uptake into tongue squamous carcinoma cells successfully visualised by fluorescence microscopy. The naphthalimide group was also found to impart photo-cytotoxic activity to the tagged peptide, suggesting that the tag may be a useful prototype building block for the production of theranostic agents. The final class of tags, based upon the TACN macrocycle, were designed for chelation of the radionuclide 64Cu and thereby the production of radiolabelled conjugates for imaging of tumours via positron emission tomography. Model 64Cu chelates proved to be highly stable under physiological conditions, including in the presence of serum. By clicking one of the tags to a fluorescently-labelled bombesin peptide, a radiotracer designed for targeted imaging of prostate cancer was produced and evaluated in a small animal model. Although the peptide conjugate ultimately proved to have poor biodistribution characteristics, the “clickable” tags should prove useful for the development of better performing PET tracers in the future.