title: Real time analysis of cataract surgery videos using deep learning

authors: Whitten, Jesse

subjects: Deep learning

abstract: A deep learning framework is proposed that classifies surgical instruments within cataract surgery videos and generates clinical summary reports, proving objective reporting and analysis. This framework is run in real time on an embedded system, potentially allowing real time feedback directly in a clinical environment. To evaluate this framework, a novel dataset of 39 cataract surgery videos is sampled at different frame rates and labeled with 10 surgical instrument classes. This dataset is used to train and evaluate several image classification deep learning model architectures: ResNet-50, ResNet-152 and InceptionV3. An Nvidia Jetson Nano 4GB embedded system is used to operate an optimised variation of the framework, evaluating the accuracy and representation of clinical summary reports. It was found that the deep learning models provided a maximum mean predictive AUC score of 0.982 and a sensitivity of 0.968 on hold out test videos. The Jetson Nano was demonstrated to provide accurate and representative clinical summary reports with a video frame rate of 6 frames per second, completing in real time. These results show that the deep learning framework is viable for integration into the clinical environment, automatically providing clinical summary reports containing objective assessment statistics, video annotations and graphical timeline visualisations of cataract removal surgeries.

text: Real time analysis of cataract surgery videos using deep learning A deep learning framework is proposed that classifies surgical instruments within cataract surgery videos and generates clinical summary reports, proving objective reporting and analysis. This framework is run in real time on an embedded system, potentially allowing real time feedback directly in a clinical environment. To evaluate this framework, a novel dataset of 39 cataract surgery videos is sampled at different frame rates and labeled with 10 surgical instrument classes. This dataset is used to train and evaluate several image classification deep learning model architectures: ResNet-50, ResNet-152 and InceptionV3. An Nvidia Jetson Nano 4GB embedded system is used to operate an optimised variation of the framework, evaluating the accuracy and representation of clinical summary reports. It was found that the deep learning models provided a maximum mean predictive AUC score of 0.982 and a sensitivity of 0.968 on hold out test videos. The Jetson Nano was demonstrated to provide accurate and representative clinical summary reports with a video frame rate of 6 frames per second, completing in real time. These results show that the deep learning framework is viable for integration into the clinical environment, automatically providing clinical summary reports containing objective assessment statistics, video annotations and graphical timeline visualisations of cataract removal surgeries.

year: 2022

title: Clonal cell proliferation in the mammary gland

authors: Jacobson, Gregory M.

abstract: The primary aim of this thesis was to classify the nature of the clonal expansion of cells that gives rise to bovine and murine mammary epithelia. It is generally assumed that the mammary gland is derived from the outgrowth of mammary-determined stem cell progeny, and that this expansion produces a mixture of cellular clones throughout the gland. Molecular techniques that enable the 'visualization' of the size and distribution of these clones will lead to a better appreciation of mammary gland development and architecture. 
In female mammals, the simplest 'mark' of clonality is provided by the inactivation of one or the other of the two X chromosomes. This event occurs early in embryogenesis and gives rise to stem cells that propagate this mark in progeny cells throughout the life of the animal. Two approaches, that utilized X-inactivation as a mark of clonality, were investigated, 1) naturally occurring X-linked gene polymorphisms in cattle, and 2) artificially introduced X-linked transgenes in mice. 
The first part of this thesis deals with the isolation and utilization of polymorphic markers on the bovine X-chromosome as markers of clonality. Such expressed genetic markers are essential if one is to distinguish which of the two X-chromosomes is active in a given cell. Two X-linked bovine genes, glucose-6-phosphate dehydrogenase (g6pd) and the X-inactive specific transcript (Xist) were selected for sequencing and SNP detection. As no specific sequence data was available for these genes, a bovine lambda genomic DNA library was screened. The G6PD clone selected from a lambda library was shown to be a pseudogene and therefore not useful for the present study. Another clone, that hybridized with an Xist gene probe, was shown to actually represent a bovine Huntingtin Associated Protein 1 like (Hap1-like) pseudogene, making it of no utility in this study. However, screening of regions of exon 1 of the Xist gene by direct PCR and sequencing, led to the discovery of an informative G↔T single nucleotide polymorphism (SNP). The variation, which was found in frequencies of 0.8 and 0.2 for 'G' and 'T' variants respectively (32% of females are heterozygous), was used in a number of different ways in order to assess the clonal profile of small 'blocks' of the gland (≤30 mm3). In these preliminary experiments, RT-PCR analysis of Xist expression patterns within each of the small blocks (each comprising around 3 X 107 cells) showed general heterogeneity but the experiments were not conclusive. Limitations of the experimental methods used are discussed and suggestions of alternative approaches, that will offer higher resolution, are presented. 
A second experimental approach, involving mice with a reporter transgene construct introduced into the X-chromosome (H253), was also used. The transgene consisted of 14 tandem repeats of a lacZ nuclear-localized reporter gene coupled with a mouse 3-hydroxyl-3-methylglutaryl coenzyme A reductase (hmgcr) promoter (Tam and Tan, 1992). A number of researchers had already utilized this transgenic model, and had confirmed that the cellular patterns of lacZ expression reflected actual X-inactivation patterns in a number of tissues. While carrying out initial investigations to ascertain the utility of this reporter system in investigations of the mammary gland it was discovered that the usual description of hmgcr as a 'house-keeping' gene is somewhat of a misnomer, as some tissues in the mouse show very strong patterns of lacZ expression while others gave minimal, or no, detectable expression. Furthermore, transgene expression was observed to increase during pregnancy and it was concluded that this effect was almost certainly a response to increased estrogen levels at this time. 
Whole mount analysis of five mouse mammary glands from transgenic animals revealed heterogeneous patterns of lacZ staining, indicating that mammary epithelia is generally polyclonal. In total, 42% of terminal buds and alveoli displayed a single lacZ staining pattern. Analysis of these staining patterns induct termini indicated that the majority of individual alveoli are derived from two or three division competent (stem) cells.

text: Clonal cell proliferation in the mammary gland The primary aim of this thesis was to classify the nature of the clonal expansion of cells that gives rise to bovine and murine mammary epithelia. It is generally assumed that the mammary gland is derived from the outgrowth of mammary-determined stem cell progeny, and that this expansion produces a mixture of cellular clones throughout the gland. Molecular techniques that enable the 'visualization' of the size and distribution of these clones will lead to a better appreciation of mammary gland development and architecture. 
In female mammals, the simplest 'mark' of clonality is provided by the inactivation of one or the other of the two X chromosomes. This event occurs early in embryogenesis and gives rise to stem cells that propagate this mark in progeny cells throughout the life of the animal. Two approaches, that utilized X-inactivation as a mark of clonality, were investigated, 1) naturally occurring X-linked gene polymorphisms in cattle, and 2) artificially introduced X-linked transgenes in mice. 
The first part of this thesis deals with the isolation and utilization of polymorphic markers on the bovine X-chromosome as markers of clonality. Such expressed genetic markers are essential if one is to distinguish which of the two X-chromosomes is active in a given cell. Two X-linked bovine genes, glucose-6-phosphate dehydrogenase (g6pd) and the X-inactive specific transcript (Xist) were selected for sequencing and SNP detection. As no specific sequence data was available for these genes, a bovine lambda genomic DNA library was screened. The G6PD clone selected from a lambda library was shown to be a pseudogene and therefore not useful for the present study. Another clone, that hybridized with an Xist gene probe, was shown to actually represent a bovine Huntingtin Associated Protein 1 like (Hap1-like) pseudogene, making it of no utility in this study. However, screening of regions of exon 1 of the Xist gene by direct PCR and sequencing, led to the discovery of an informative G↔T single nucleotide polymorphism (SNP). The variation, which was found in frequencies of 0.8 and 0.2 for 'G' and 'T' variants respectively (32% of females are heterozygous), was used in a number of different ways in order to assess the clonal profile of small 'blocks' of the gland (≤30 mm3). In these preliminary experiments, RT-PCR analysis of Xist expression patterns within each of the small blocks (each comprising around 3 X 107 cells) showed general heterogeneity but the experiments were not conclusive. Limitations of the experimental methods used are discussed and suggestions of alternative approaches, that will offer higher resolution, are presented. 
A second experimental approach, involving mice with a reporter transgene construct introduced into the X-chromosome (H253), was also used. The transgene consisted of 14 tandem repeats of a lacZ nuclear-localized reporter gene coupled with a mouse 3-hydroxyl-3-methylglutaryl coenzyme A reductase (hmgcr) promoter (Tam and Tan, 1992). A number of researchers had already utilized this transgenic model, and had confirmed that the cellular patterns of lacZ expression reflected actual X-inactivation patterns in a number of tissues. While carrying out initial investigations to ascertain the utility of this reporter system in investigations of the mammary gland it was discovered that the usual description of hmgcr as a 'house-keeping' gene is somewhat of a misnomer, as some tissues in the mouse show very strong patterns of lacZ expression while others gave minimal, or no, detectable expression. Furthermore, transgene expression was observed to increase during pregnancy and it was concluded that this effect was almost certainly a response to increased estrogen levels at this time. 
Whole mount analysis of five mouse mammary glands from transgenic animals revealed heterogeneous patterns of lacZ staining, indicating that mammary epithelia is generally polyclonal. In total, 42% of terminal buds and alveoli displayed a single lacZ staining pattern. Analysis of these staining patterns induct termini indicated that the majority of individual alveoli are derived from two or three division competent (stem) cells.

year: 2004

title: Interface of gender and culture

authors: Tamasese, Kiwi

subjects: Maori

abstract: I greet you in the soothing waters of the Pacific. The birth waters of Hawai’i to the North, island of the dream time, and Aotearoa, to the south. Papua New Guinea to the West and Marquesas to the East.  These islands are the gathering places of the world’s largest Continent, the Pacific. We of this continent know that her birth waters are our connection.  We also know that she is woman identified. It is no surprise therefore that from Hawai’i to the north to Aotearoa in the south the positioning of women in each of these societies bears a different story to that of the women of the continent of Europe.  This reality lived out in Hawai’i means women shared with men the ultimate leadership of peoples.  This location of women power is named Kuhinanui. Many remarkable women of Hawai’i occupied this position.  From times of peace throughout to the first clash with imposed new culture, women of Hawai’i led, bled, struggled, defied and kept the kukui of self belief burning. Genealogically Hawai’i is connected to her other sisters throughout the Pacific.  The story of Kuhinanui Liliuokalani is poignant.

text: Interface of gender and culture I greet you in the soothing waters of the Pacific. The birth waters of Hawai’i to the North, island of the dream time, and Aotearoa, to the south. Papua New Guinea to the West and Marquesas to the East.  These islands are the gathering places of the world’s largest Continent, the Pacific. We of this continent know that her birth waters are our connection.  We also know that she is woman identified. It is no surprise therefore that from Hawai’i to the north to Aotearoa in the south the positioning of women in each of these societies bears a different story to that of the women of the continent of Europe.  This reality lived out in Hawai’i means women shared with men the ultimate leadership of peoples.  This location of women power is named Kuhinanui. Many remarkable women of Hawai’i occupied this position.  From times of peace throughout to the first clash with imposed new culture, women of Hawai’i led, bled, struggled, defied and kept the kukui of self belief burning. Genealogically Hawai’i is connected to her other sisters throughout the Pacific.  The story of Kuhinanui Liliuokalani is poignant.

year: 1993