Digital image processing for prognostic and diagnostic clinical pathology

When digital imaging and image processing methods are applied to clinical diagnostic and prognostic needs, the methods can be seen to increase human understanding and provide objective measurements. Most current clinical applications are limited to providing subjective information to healthcare professionals rather than providing objective measures. This Thesis provides detail of methods and systems that have been developed both for objective and subjective microscopy applications. A system framework is presented that provides a base for the development of microscopy imaging systems. This practical framework is based on currently available hardware and developed with standard software development tools. Image processing methods are applied to counter optical limitations of the bright field microscope, automating the system and allowing for unsupervised image capture and analysis. Current literature provides evidence that 3D visualisation has provided increased insight and application in many clinical areas. There have been recent advancements in the use of 3D visualisation for the study of soft tissue structures, but its clinical application within histology remains limited. Methods and applications have been researched and further developed which allow for the 3D reconstruction and visualisation of soft tissue structures using microtomed serial histological sections specimens. A system has been developed suitable for this need is presented giving considerations to image capture, data registration and 3D visualisation, requirements. The developed system has been used to explore and increase 3D insight on clinical samples. The area of automated objective image quantification of microscope slides presents the allure of providing objective methods replacing existing objective and subjective methods, increasing accuracy and rsducinq manual burden. One such existing objective test is DNA Image Ploidy which seeks to characterise cancer by the measurement of DNA content within individual cell nuclei, an accepted but manually burdensome method. The main novelty of the work completed lies in the development of an automated system for DNA Image Ploidy measurement, combining methods for automatic specimen focus, segmentation, parametric extraction and the implementation of an automated cell type classification system. A consideration for any clinical image processing system is the correct sampling of the tissue under study. VVhile the image capture requirements for both objective systems and subjective systems are similar there is also an important link between the 3D structures of the tissue. 3D understanding can aid in decisions regarding the sampling criteria of objective tests for as although many tests are completed in the 2D realm the clinical samples are 3D objects. Cancers such as Prostate and Breast cancer are known to be multi-focal, with areas of seeming physically, independent areas of disease within a single site. It is not possible to understand the true 3D nature of the samples using 2D micro-tomed sections in isolation from each other. The 3D systems described in this report provide a platform of the exploration of the true multi focal nature of disease soft tissue structures allowing for the sampling criteria of objective tests such as DNA Image Ploidy to be correctly set. For the Automated DNA Image Ploidy and the 3D reconstruction and visualisation systems, clinical review has been completed to test the increased insights provided. Datasets which have been reconstructed from microtomed serial sections and visualised with the developed 3D system area presented. For the automated DNA Image Ploidy system, the developed system is compared with the existing manual method to qualify the quality of data capture, operational speed and correctness of nuclei classification. Conclusions are presented for the work that has been completed and discussion given as to future areas of research that could be undertaken, extending the areas of study, increasing both clinical insight and practical application

Platforms: The Sequel

In this article, the authors discuss recent developments on sales and use tax reporting and collection obligations imposed on platforms that facilitate taxable sales of tangible personal property or services

Non-structural carbohydrate profiles and ratios between soluble sugars and starch serve as indicators of productivity for a bioenergy grass

There is a pressing need to find a sustainable alternative to fossil fuels that will not compromise food security or require extensive use of agrochemicals. Miscanthus is a perennial energy grass predominantly used for combustion but with the current advancement of ligno-cellulosic fermentation technologies there is an interest in using Miscanthus for bioethanol production. Currently, the only commercially grown genotype of Miscanthus is M.× giganteus; a high yielding, interspecific hybrid of M. sacchariflorus and M. sinensis. As M.× giganteus is a sterile triploid, it cannot be used as a parent so Miscanthus breeding effort is focused on producing new interspecific varieties that out-perform M.× giganteus. The carbohydrate profiles of four genotypes of Miscanthus, including M. sacchariflorus (Sac-5), M.× giganteus (Gig-311), M. sinensis (Sin-11) and M. sinensis (Goliath), were characterized at replicated field sites in Aberystwyth, West Wales and Harpenden, south-east England. Our hypothesis was that a distinctive carbohydrate profile underlies enhanced biomass accumulation. Biomass accumulation is greatest when day-lengths and solar intensity are highest; so, observations were made in the middle of UK summer (July) for 2 years. Gig-311 had a greater abundance of fructose in its stems at both sites, and both Gig-311 and Sac-5 had low abundance of starch. At both sites, the highest yielding genotype was Gig-311 and Sac-5 was also high yielding at Harpenden, but performed comparatively poorly at Aberystwyth. At both sites Gig-311 had a distinctly high concentration of fructose, low starch and a high ratio of soluble sugars: starch, and at Harpenden, Sac-5 was similar. We conclude that the abundance of starch and fructose and a greater partitioning of soluble sugars, relative to starch, are candidate biomarkers of productivity in Miscanthus

Characterization of chilling-shock responses in four genotypes of Miscanthus reveals the superior tolerance of M. × giganteus compared with M. sinensis and M. sacchariflorus

Abstract Background and Aims The bioenergy grass Miscanthus is native to eastern Asia. As Miscanthus uses C4 photosynthesis, the cooler temperatures experienced in much of northern Europe are expected to limit productivity. Identification of genetic diversity in chilling tolerance will enable breeders to generate more productive varieties for these cooler regions. Characterizing the temporal relationships between photosynthesis, carbohydrate and molecular expression of relevant genes is key to understanding genotypic differences in tolerance or sensitivity. Methods To characterize chilling responses in four Miscanthus genotypes, plants were exposed to a sudden reduction in temperature. The genotypes studied comprised of two M. sinensis, one M. sacchariflorus and one inter-species hybrid, M. × giganteus. Changes in photosynthesis (Asat), carbohydrate composition and the expression of target transcripts were observed following chilling-shock. After 4 d the decline in leaf elongation rate (LER) in the different genotypes was measured. Results Following chilling-shock the greatest decline in Asat was observed in M. sacchariflorus and one M. sinensis genotype. Carbohydrate concentrations increased in all genotypes following chilling but to a lesser extent in M. sacchariflorus. Two stress inducible genes were most highly expressed in the genotypes that experienced the greatest declines in Asat and LER. Miscanthus × giganteus retained the highest Asat and was unique in exhibiting no decline in LER following transfer to 12 °C. Conclusions Miscanthus × giganteus exhibits a superior tolerance to chilling shock than other genotypes of Miscanthus. The absence of sucrose accumulation in M. sacchariflorus during chilling-shock suggests an impairment in enzyme function. A candidate transcription factor, MsCBF3, is most highly expressed in the most sensitive genotypes and may be a suitable molecular marker for predicting chilling sensitivity

Effects of a free school breakfast programme on children\u27s attendance, academic achievement and short-term hunger: results from a stepped-wedge, cluster randomised controlled trial

BACKGROUND: Free school breakfast programmes (SBPs) exist in a number of high-income countries, but their effects on educational outcomes have rarely been evaluated in randomised controlled trials. METHODS: A 1-year stepped-wedge, cluster randomised controlled trial was undertaken in 14 New Zealand schools in low socioeconomic resource areas. Participants were 424 children, mean age 9±2 years, 53% female. The intervention was a free daily SBP. The primary outcome was children\u27s school attendance. Secondary outcomes were academic achievement, self-reported grades, sense of belonging at school, behaviour, short-term hunger, breakfast habits and food security. RESULTS: There was no statistically significant effect of the breakfast programme on children\u27s school attendance. The odds of children achieving an attendance rate <95% was 0.76 (95% CI 0.56 to 1.02) during the intervention phase and 0.93 (95% CI 0.67 to 1.31) during the control phase, giving an OR of 0.81 (95% CI 0.59 to 1.11), p=0.19. There was a significant decrease in children\u27s self-reported short-term hunger during the intervention phase compared with the control phase, demonstrated by an increase of 8.6 units on the Freddy satiety scale (95% CI 3.4 to 13.7, p=0.001). There were no effects of the intervention on any other outcome. CONCLUSIONS: A free SBP did not have a significant effect on children\u27s school attendance or academic achievement but had significant positive effects on children\u27s short-term satiety ratings. More frequent programme attendance may be required to influence school attendance and academic achievement

Effects of a free school breakfast programme on school attendance, achievement, psychosocial function, and nutrition: a stepped wedge cluster randomised trial

<p>Abstract</p> <p>Background</p> <p>Approximately 55,000 children in New Zealand do not eat breakfast on any given day. Regular breakfast skipping has been associated with poor diets, higher body mass index, and adverse effects on children's behaviour and academic performance. Research suggests that regular breakfast consumption can improve academic performance, nutrition and behaviour. This paper describes the protocol for a stepped wedge cluster randomised trial of a free school breakfast programme. The aim of the trial is to determine the effects of the breakfast intervention on school attendance, achievement, psychosocial function, dietary habits and food security.</p> <p>Methods/Design</p> <p>Sixteen primary schools in the North Island of New Zealand will be randomised in a sequential stepped wedge design to a free before-school breakfast programme consisting of non-sugar coated breakfast cereal, milk products, and/or toast and spreads. Four hundred children aged 5-13 years (approximately 25 per school) will be recruited. Data collection will be undertaken once each school term over the 2010 school year (February to December). The primary trial outcome is school attendance, defined as the proportion of students achieving an attendance rate of 95% or higher. Secondary outcomes are academic achievement (literacy, numeracy, self-reported grades), sense of belonging at school, psychosocial function, dietary habits, and food security. A concurrent process evaluation seeks information on parents', schools' and providers' perspectives of the breakfast programme.</p> <p>Discussion</p> <p>This randomised controlled trial will provide robust evidence of the effects of a school breakfast programme on students' attendance, achievement and nutrition. Furthermore the study provides an excellent example of the feasibility and value of the stepped wedge trial design in evaluating pragmatic public health intervention programmes.</p> <p>Trial Registration Number</p> <p>Australian New Zealand Clinical Trials Registry (ANZCTR) - ACTRN12609000854235</p

Radiation capture and conversion efficiencies of Miscanthus sacchariflorus, M. sinensis and their naturally occurring hybrid M. × giganteus

Miscanthus is a rhizomatous C4 grass of great interest as a biofuel crop because it has the potential to produce high yields over a wide geographical area with low agricultural inputs on marginal land less suitable for food production. At the moment, a clonal interspecific hybrid Miscanthusxgiganteus is the most widely cultivated and studied in Europe and the United States, but breeding programmes are developing newer more productive varieties. Here, we quantified the physiological processes relating to whole season yield in a replicated plot trial in Wales, UK. Light capture and conversion efficiency were parameterized for four carefully selected genotypes (M.sinensis, M.sacchariflorus and Miscanthusxgiganteus). Differences in the canopy architecture in mature stands as measured by the extinction coefficient (k) were small (0.55-0.65). Sensitivity analysis on a mathematical model of Miscanthus was performed to quantify the accumulative intercepted photosynthetically active radiation (iPAR) in the growing season using (i) k, (ii) variation in the thermal responses of leaf expansion rate, (iii) base temperature for degree days and (iv) date start of canopy expansion. A 10% increase in k or leaf area per degree day both had a minimal effect on iPAR (3%). Decreasing base temperature from 10 to 9 degrees C gave an 8% increase in iPAR. If the starting date for canopy expansion was the same as shoot emergence date, then the iPAR increases by 12.5%. In M.xgiganteus, the whole season above ground and total (including below ground) radiation-use efficiency (RUE) ranged from 45% to 37% higher than the noninterspecific hybrid genotypes. The greater yields in the interspecific hybrid M.xgiganteus are explained by the higher RUE and not by differences in iPAR or partitioning effects. Studying the mechanisms underlying this complex trait could have wide benefits for both fuel and food production

Відгук офіційного опонента доктора філологічних наук, професора Кузьменка В.І. на дисертацію Галича А.О. за темою Жанрові модифікації портретного дискурсу в документалістиці ХХ – ХХІ ст

У дисертації вперше в українському літературознавстві здійснено комплексне дослідження особливостей портретування в документальній літературі, осмислено його специфіку у творах різних жанрів, простежено складники портретних характеристик, визначено домінантні підходи до створення портретів. Удосконалено системну класифікацію портретів в українській документалістиці згідно з новітніми досягненнями літературознавства. Уточнено структуру, семіотику й семантику портрета в різних жанрах мемуарної, біографічної (автобіографічної) літератури. Набули подальшого розвитку модифікації портретів у документальних творах. Розширено й уточнено формулювання низки теоретичних понять, зокрема таких, як портрет, концентрований портрет, деконцентрований портрет, автопортрет, парний портрет, колективний портрет, оніричний портрет, некропортрет. Залучено до аналізу тексти, зокрема останніх літ, які досі не були предметом наукових студій, а також маловідомі архівні матеріали.У дисертації вперше в українському літературознавстві здійснено комплексне дослідження особливостей портретування в документальній літературі, осмислено його специфіку у творах різних жанрів, простежено складники портретних характеристик, визначено домінантні підходи до створення портретів. Удосконалено системну класифікацію портретів в українській документалістиці згідно з новітніми досягненнями літературознавства. Уточнено структуру, семіотику й семантику портрета в різних жанрах мемуарної, біографічної (автобіографічної) літератури. Набули подальшого розвитку модифікації портретів у документальних творах. Розширено й уточнено формулювання низки теоретичних понять, зокрема таких, як портрет, концентрований портрет, деконцентрований портрет, автопортрет, парний портрет, колективний портрет, оніричний портрет, некропортрет. Залучено до аналізу тексти, зокрема останніх літ, які досі не були предметом наукових студій, а також маловідомі архівні матеріали.У дисертації вперше в українському літературознавстві здійснено комплексне дослідження особливостей портретування в документальній літературі, осмислено його специфіку у творах різних жанрів, простежено складники портретних характеристик, визначено домінантні підходи до створення портретів. Удосконалено системну класифікацію портретів в українській документалістиці згідно з новітніми досягненнями літературознавства. Уточнено структуру, семіотику й семантику портрета в різних жанрах мемуарної, біографічної (автобіографічної) літератури. Набули подальшого розвитку модифікації портретів у документальних творах. Розширено й уточнено формулювання низки теоретичних понять, зокрема таких, як портрет, концентрований портрет, деконцентрований портрет, автопортрет, парний портрет, колективний портрет, оніричний портрет, некропортрет. Залучено до аналізу тексти, зокрема останніх літ, які досі не були предметом наукових студій, а також маловідомі архівні матеріали