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Gene selection from microarray data for cancer classification - A machine learning approach
(Elsevier, 2005) Wang, Yu; Tetko, Igor V.; Hall, Mark A.; Frank, Eibe; Facius, Axel; Mayer, Klaus F.X.; Mewes, Hans W.
A DNA microarray can track the expression levels of thousands of genes simultaneously. Previous research has demonstrated that this technology can be useful in the classification of cancers. Cancer microarray data normally contains a small number of samples which have a large number of gene expression levels as features. To select relevant genes involved in different types of cancer remains a challenge. In order to extract useful gene information from cancer microarray data and reduce dimensionality, feature selection algorithms were systematically investigated in this study. Using a correlation-based feature selector combined with machine learning algorithms such as decision trees, nave Bayes and support vector machines, we show that classification performance at least as good as published results can be obtained on acute leukemia and diffuse large B-cell lymphoma microarray data sets. We also demonstrate that a combined use of different classification and feature selection approaches makes it possible to select relevant genes with high confidence. This is also the first paper which discusses both computational and biological evidence for the involvement of zyxin in leukaemogenesis.
‘Returning to normal?’: Bourdieu, systems thinking, and online teaching post-COVID-19
(University of Newcastle, 2025) Richardson, Anthony; Herb, Annika; Lloyd, Clare; Richardson, Anthony; Corino, Maria-Teresa
The COVID-19 pandemic and resultant transition to online teaching was a profound shock for universities and their stakeholders (teachers, students, and administrators). Bourdieu’s concept of hysteresis (systemic rupture) describes how such disruptions provide an opportunity to question and potentially reshape elements of our collective social reality. However, his work also explores how our shared sense of what is ‘normal’ tends to be deeply ingrained and resistant to change. As the pandemic fades into the background of our collective memory, many tertiary teachers may be tempted to view tertiary teaching as a rubber ball which can simply bounce back to ‘the way things were’. But the Complex Adaptive Systems (CAS) which underpin our social reality do not behave like rubber balls. The Panarchy (Adaptive Cycle) heuristic offers a useful lens for understanding how the resilience of such systems lies in their ability to adapt when faced with challenges like the pandemic. Such disruptions can ripple through interconnected parts of the system, leading to changes which persist even after the initial crisis has passed. Such systems do not ‘bounce back’ unchanged after such shocks. The longing to return to pre-pandemic norms in university teaching is both personally understandable and sociologically explicable by reference to Bourdieu’s concepts of habitus and field. Yet the disruption caused by COVID may be precisely the kind of transformative event that the panarchy model captures well. The changes triggered by the pandemic may endure beyond its official end, reshaping systems in ways we did not anticipate. In this sense, our systems are not always resilient in the way we want them to be.
Classroom perceptions of physics and the introduction of technological applications
(The University of Waikato, 1987) Jones, Alister; Liley, Bruce; Osborne, Roger
This study explores the classroom perceptions of physics held by both teachers and students. A method of introducing technological applications into the classroom based on the generative learning model is investigated. Students’ views of school physics were examined by interviews with 60 7th form (17-18 years) students and surveys with 426 6th form (16-17 years) and 168 7th form physics students. The interviews and surveys showed that physics students generally had negative perceptions of school physics. The students ascribed these perceptions mainly to the apparent lack of relevance. The study also examined the students’ reasons for studying physics at secondary school and university. The major reasons given were career choice and interest. There were significant gender differences in career choice. The initial career destination of New Zealand physics graduates was also investigated. The ideas of the generative learning model and mini-theories were used as a theoretical base for the introduction of technological applications. One of the important aspects of these models is the learner’s existing knowledge (which includes interests). The students’ interests in technological applications were explored by interviews (40 students) and surveys (500 students). The results indicated that students were interested in applications within their own environment, directly involving people and aspects which corresponded to their intended careers and anticipated needs. There were gender differences in interest. Students were generally not interested in ‘school’ physics or domestic applications. Teachers’ approaches to the teaching and learning of school physics were examined by interviews (12) and their views on the introduction of technological applications were investigated by surveys (204). The findings were consistent with a transmission view of teaching and an overloaded syllabus. In a small study possible ways of introducing technological applications were examined. A new teaching strategy, based on the generative learning model, was developed for the two 7th form physics topics of electrical capacitance and the Doppler effect. These strategies were initially trialled with two classes and then with other classes at two other schools. The classes were observed throughout the trials and teacher and student interviews were undertaken. Compared with the previous teaching programmes the students were generally very positive about the approaches. The reasons students gave for being more positive were; the introduction of technological applications that they were interested in and could relate to, the experiments. individual projects, the class discussions and being able to explore ideas for themselves. They were also more confident to attempt traditional physics problems. The implications of the findings for teaching and learning, the curriculum and further research are discussed in the final chapter.
Metropolitan reform and decision making: Dove-Myer Robinson’s challenge to local body morphological fundamentalism
(The University of Waikato, 1987) Edgar, John Timothy; Barber, Laurie; Hart, Philip
The capacity of New Zealand local bodies to perceive their geographical identities and political autonomy as enduringly useful and to jealously protect these against proposals for structural change is studied in this thesis. This self protective guardianship is termed morphological fundamentalism. The latter word is derived from a theological description of the evangelical movement that considered the truth of the Bible to be unchanging and applicable to any age, while “morphological” pertains to the biological study of form and structure. Taken together, the words denote a dogmatic assumption of structural unalterability. The effect of this determined defence of local body geographical and political integrity has been to contain administrative change despite the emergence of urban and metropolitan communities from the country’s colonial settlement. This thesis is concerned first with a challenge to New Zealand local body morphological fundamentalism posed by Dove-Myer Robinson, Mayor of Auckland 1959-1965, 1968-1980 who campaigned for the reform of metropolitan government and the establishment of an Auckland Regional Authority. The thesis is concerned secondly with Robinson’s continued challenge to morphological fundamentalism after the Auckland Regional Authority is established and his failure to become an authoritative metropolitan decision maker. The first part of this study of Dove-Myer Robinson’s political career is intended to identify the strength of morphological fundamentalism in Greater Auckland and the urgency for reform there of the local body structure, which consisted of thirty two different municipalities of counties and twenty special purpose bodies. Robinson’s role in promoting the Auckland Regional Authority concept, his choice of overseas models for the authority, the reactions of local and central government politicians to his proposals and the vexed progress of legislation establishing the Auckland Regional Authority are assessed. Dove-Myer Robinson played a leading role in Auckland City politics, beginning with his entry into the Brown’s Island Drainage controversy in 1944. He became an Auckland City Councillor in 1952, Chairman of the Auckland and Suburban Drainage Board in 1953 and Mayor of Auckland City in 1959. Then in 1960 he began his struggle for the creation of a Greater Auckland Authority, able to coalesce metropolitan opinion and promulgate major metropolitan and regional development. This thesis outlines the reputation Robinson brought to his reform campaign. Robinson was an independent political figure who developed a personal following amongst Aucklanders as well as a strong populist appeal in the working class areas of the city. As such he was unacceptable to the Greater Auckland local body Establishment and particularly to the ruling Citizens’ and Ratepayers’ Association on the Auckland City Council. His Jewish and working class origins, his wartime activities, his personal life and his personality were also considered dubious by his opponents. This study demonstrates the effects Robinson’s personal reputation had on those involved in the metropolitan reform process. It also explains how these factors developed into a feud between Robinson and the two political associations on the Auckland City Council - the Citizens’ and Ratepayers’ Association and the Labour Party. The culmination of the feud - the mayor’s loss of office in the 1965 municipal elections - is linked to his loss of position on the fledgling Auckland Regional Authority and his three year exile from political influence on the body. The second part of this thesis assesses Robinson’s declining ability to influence the metropolitan decision making carried out by the Auckland Regional Authority. This study portrays the changing nature of Robinson’s battle against morphological fundamentalism during which the mayor became frustrated and finally thwarted by the strength of that mentality. After the establishment of the Auckland Regional Authority, it was only a matter of time before morphological fundamentalism was again taken up by the municipal local bodies to protect the political authority and pre-eminence they had enjoyed in the preceding local government structure. In deference to the attitudes associated with the preceding Auckland local government - parochial jealousies and rivalries, consultation between municipalities and inter-municipal agreement on large works, resentment of the central city and timidity in relations with central government - succeeding Auckland Regional Authority chairmen, H.D. Lambie and T.H. Pearce had developed a “benign” regionalism for the Auckland Regional Authority. Its limited objectives were designed to pre-empt any challenge to the body and let the municipal bodies see the body as an extension of their own authority, successfully implementing objectives they had wanted but had not been able to agree on funding. In effect, morphological fundamentalism was being allowed to win by default. Robinson’s rapid rail proposals however, challenged this limited conception of the Auckland Regional Authority and placed strains on the capacity of the Auckland Regional Authority to make decisions that enjoyed widespread support amongst its members and the municipal local bodies. In the face of this challenge, the municipal local bodies became openly defensive of their political authority and Robinson clashed with them, and lost. A brief study of the two overseas examples Robinson most closely modelled his authority upon is made to elucidate the problems Robinson had in challenging the residual morphological fundamentalism after the Auckland Regional Authority was established. The thesis concludes by assessing the impact Robinson had on local body morphological fundamentalism and to what extent his own political methods and reputation had facilitated his challenge.
Stable isotope stratigraphy of deep-sea cores from the Southwest Pacific region: aspects of late Quaternary palaeoceanography
(The University of Waikato, 1988) Cuthbertson, Alison Macauley; Hendy, Chris H.; Nelson, Campbell S.
¹⁸O/¹⁶O and ¹³C/¹²C ratios of calcareous planktonic and benthic foraminifera from the Late Quaternary section of deep-sea sediment cores from the Tasman Sea and Southwest Pacific Ocean have been determined in this study. The core sites cover a latitudinal range from the equator to 49°S, and samples were provided by the Ocean Drilling Program and the New Zealand Oceanographic Institute. In most cases the cores were sampled at 10cm intervals. Generally, attention has been focused on the latest Quaternary (stages 1 to 5) glacial-interglacial oscillations of the δ¹⁸O and δ¹³C record, and aspects of their palaeoceanographic significance. Some longer sequences of core were also studied. Of the Southwest Pacific Ocean cores, 594 yielded the most detailed record for the past 130ky. Located just south of the Subtropical Convergence it has proved particularly sensitive to substage climatic fluctuations. In addition the high sedimentation rate (averaging ~13cm/ky) has reduced smoothing by bioturbation. Core 594 has yielded one of the most detailed isotopic records available world-wide for stages 1 to 6. Concurrent carbonate analysis by Cooke (1988) has revealed a similarly detailed carbonate record whose rises and falls are more or less synchronous with the isotopic record. To the west of New Zealand Core 593 was analysed to 44m sub-bottom depth and a clear record of isotopic fluctuations back to the 55/56 stage boundary was obtained. Sites 593 and 594 have thus provided useful isotopic reference curves for the Southwest Pacific region. Consistent changes in the planktonic δ¹³C record of some of the cores may reflect variations in CaCO₃ productivity linked to cyclical glacial-interglacial fluctuations. Glacial benthic δ¹³C results support a decreased volume of NADW production. Resumption of NADW flow is marked in many cases by a transient drop in δ¹³C values before rising to interglacial values as the relatively stagnant, isotopically lighter water is “flushed” from Deep Water flow paths. AABW appears to dominate during glacial periods. A northern shift of the Subtropical Convergence east of New Zealand is suggested (and supported by micropalaeontological data; Cooke, 1988), with a more restricted shift in the Tasman Sea. Interglacial Deep Waters appear to be dominated during interglacial times by AABW, whilst NADW is dominant in the Tasman Sea. Planktonic δ¹³C results suggest a more southerly position of the Subtropical Divergence in the Tasman Sea during interglacial periods. Lead-lag relationships in the δ¹³O signal between surface and bottom-dwelling foraminifera over Termination Iᴀ reveal a pattern of meltwater circulating first to the surface waters at higher latitudes, and to bottom waters at lower latitude sites. A modification of the meltwater “lid” is proposed, with the lid extending only partially across the ocean surface, and not into equatorial regions.