Data re-engineering using formal transformations

This thesis presents and analyses a solution to the problem of formally re- engineering program data structures, allowing new representations of a program to be developed. The work is based around Ward's theory of program transformations which uses a Wide Spectrum Language, WSL, whose semantics were specially developed for use in proof of program transformations. The re-engineered code exhibits equivalent functionality to the original but differs in the degree of data abstraction and representation. Previous transformational re-engineering work has concentrated upon control flow restructuring, which has highlighted a lack of support for data restructuring in the maintainer's tool-set. Problems have been encountered during program transformation due to the lack of support for data re-engineering. A lack of strict data semantics and manipulation capabilities has left the maintainer unable to produce optimally re-engineered solutions. It has also hindered the migration of programs into other languages because it has not been possible to convert data structures into an appropriate form in the target language. The main contribution of the thesis is the Data Re-Engineering and Abstraction Mechanism (DREAM) which allows theories about type equivalence to be represented and used in a re-engineering environment. DREAM is based around the technique of "ghosting", a way of introducing different representations of data, which provides the theoretical underpinning of the changes applied to the program. A second major contribution is the introduction of data typing into the WSL language. This allows DREAM to be integrated into the existing transformation theories within WSL. These theoretical extensions of the original work have been shown to be practically viable by implementation within a prototype transformation tool, the Maintainer's Assistant. The extended tool has been used to re-engineer heavily modified, commercial legacy code. The results of this have shown that useful re-engineering work can be performed and that DREAM integrates well with existing control flow transformations

Hydrodynamic propulsion of human sperm

The detailed fluid mechanics of sperm propulsion are fundamental to our understanding of reproduction. In this paper, we aim to model a human sperm swimming in a microscope slide chamber. We model the sperm itself by a distribution of regularized stokeslets over an ellipsoidal sperm head and along an infinitesimally thin flagellum. The slide chamber walls are modelled as parallel plates, also discretized by a distribution of regularized stokeslets. The sperm flagellar motion, used in our model, is obtained by digital microscopy of human sperm swimming in slide chambers. We compare the results of our simulation with previous numerical studies of flagellar propulsion, and compare our computations of sperm kinematics with those of the actual sperm measured by digital microscopy. We find that there is an excellent quantitative match of transverse and angular velocities between our simulations and experimental measurements of sperm. We also find a good qualitative match of longitudinal velocities and computed tracks with those measured in our experiment. Our computations of average sperm power consumption fall within the range obtained by other authors. We use the hydrodynamic model, and a prototype flagellar motion derived from experiment, as a predictive tool, and investigate how sperm kinematics are affected by changes to head morphology, as human sperm have large variability in head size and shape. Results are shown which indicate the increase in predicted straight-line velocity of the sperm as the head width is reduced and the increase in lateral movement as the head length is reduced. Predicted power consumption, however, shows a minimum close to the normal head aspect ratio

The impact of immediate breast reconstruction on the time to delivery of adjuvant therapy: the iBRA-2 study

Background: Immediate breast reconstruction (IBR) is routinely offered to improve quality-of-life for women requiring mastectomy, but there are concerns that more complex surgery may delay adjuvant oncological treatments and compromise long-term outcomes. High-quality evidence is lacking. The iBRA-2 study aimed to investigate the impact of IBR on time to adjuvant therapy. Methods: Consecutive women undergoing mastectomy ± IBR for breast cancer July–December, 2016 were included. Patient demographics, operative, oncological and complication data were collected. Time from last definitive cancer surgery to first adjuvant treatment for patients undergoing mastectomy ± IBR were compared and risk factors associated with delays explored. Results: A total of 2540 patients were recruited from 76 centres; 1008 (39.7%) underwent IBR (implant-only [n = 675, 26.6%]; pedicled flaps [n = 105,4.1%] and free-flaps [n = 228, 8.9%]). Complications requiring re-admission or re-operation were significantly more common in patients undergoing IBR than those receiving mastectomy. Adjuvant chemotherapy or radiotherapy was required by 1235 (48.6%) patients. No clinically significant differences were seen in time to adjuvant therapy between patient groups but major complications irrespective of surgery received were significantly associated with treatment delays. Conclusions: IBR does not result in clinically significant delays to adjuvant therapy, but post-operative complications are associated with treatment delays. Strategies to minimise complications, including careful patient selection, are required to improve outcomes for patients

Cohort Profile: Burden of Obstructive Lung Disease (BOLD) study

The Burden of Obstructive Lung Disease (BOLD) study was established to assess the prevalence of chronic airflow obstruction, a key characteristic of chronic obstructive pulmonary disease, and its risk factors in adults (≥40 years) from general populations across the world. The baseline study was conducted between 2003 and 2016, in 41 sites across Africa, Asia, Europe, North America, the Caribbean and Oceania, and collected high-quality pre- and post-bronchodilator spirometry from 28 828 participants. The follow-up study was conducted between 2019 and 2021, in 18 sites across Africa, Asia, Europe and the Caribbean. At baseline, there were in these sites 12 502 participants with high-quality spirometry. A total of 6452 were followed up, with 5936 completing the study core questionnaire. Of these, 4044 also provided high-quality pre- and post-bronchodilator spirometry. On both occasions, the core questionnaire covered information on respiratory symptoms, doctor diagnoses, health care use, medication use and ealth status, as well as potential risk factors. Information on occupation, environmental exposures and diet was also collected

Data from: Analytical and clinical validation of a digital sequencing panel for quantitative, highly accurate evaluation of cell-free circulating tumor DNA

Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital SequencingTM is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient’s cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing

Light from the East: travel to China and Australian activism in the long Sixties

Throughout the "long Sixties" a diverse array of Australian activists traveled beyond what was popularly known as the "bamboo curtain" into the People's Republic of China (PRC). This paper will argue that they found not the monolithic "red menace" presented by media and government, but an often contradictory set of images mediated by their own political agendas and the changing nature of Chinese politics. More than useful idiots, these radicals took important political lessons from their Chinese counterparts, engaging in a largely unacknowledged process of transnational exchange. Through investigating three key groups of antipodean travelers - Communist Party members in the 1950s, student and worker revolutionaries in the late 1960s, and Indigenous activists in the early 1970s - it is possible to understand how not only their diverse political agendas, but also the changing realities of Chinese domestic and foreign politics, impacted on the lessons they took home. Drawing on memoirs, newspaper and magazine articles as well as archival sources, a light will be shone on this period of political and cultural exchange across seemingly impassable Cold War boundaries, illuminating Australia's often forgotten involvement in the Sixties experience

Lanman_2015

This file is a zipped folder containing the variants tables for each of the 165 matched tumor and liquid biopsy samples

patient_table

Table providing patient-level concordance information