A Bayesian spatial random effects model characterisation of tumour heterogeneity implemented using Markov chain Monte Carlo (MCMC) simulation

The focus of this study is the development of a statistical modelling procedure for characterising intra-tumour heterogeneity, motivated by recent clinical literature indicating that a variety of tumours exhibit a considerable degree of genetic spatial variability. A formal spatial statistical model has been developed and used to characterise the structural heterogeneity of a number of supratentorial primitive neuroecto-dermal tumours (PNETs), based on diffusionweighted magnetic resonance imaging. Particular attention is paid to the spatial dependence of diffusion close to the tumour boundary, in order to determine whether the data provide statistical evidence to support the proposition that water diffusivity in the boundary region of some tumours exhibits a deterministic dependence on distance from the boundary, in excess of an underlying random 2D spatial heterogeneity in diffusion. Tumour spatial heterogeneity measures were derived from the diffusion parameter estimates obtained using a Bayesian spatial random effects model. The analyses were implemented using Markov chain Monte Carlo (MCMC) simulation. Posterior predictive simulation was used to assess the adequacy of the statistical model. The main observations are that the previously reported relationship between diffusion and boundary proximity remains observable and achieves statistical significance after adjusting for an underlying random 2D spatial heterogeneity in the diffusion model parameters. A comparison of the magnitude of the boundary-distance effect with the underlying random 2D boundary heterogeneity suggests that both are important sources of variation in the vicinity of the boundary. No consistent pattern emerges from a comparison of the boundary and core spatial heterogeneity, with no indication of a consistently greater level of heterogeneity in one region compared with the other. The results raise the possibility that DWI might provide a surrogate marker of intra-tumour genetic regional heterogeneity, which would provide a powerful tool with applications in both patient management and in cancer research

Intercomparison of phenological transition dates derived from the PhenoCam Dataset V1.0 and MODIS satellite remote sensing

Phenology is a valuable diagnostic of ecosystem health, and has applications to environmental monitoring and management. Here, we conduct an intercomparison analysis using phenological transition dates derived from near-surface PhenoCam imagery and MODIS satellite remote sensing. We used approximately 600 site-years of data, from 128 camera sites covering a wide range of vegetation types and climate zones. During both “greenness rising” and “greenness falling” transition phases, we found generally good agreement between PhenoCam and MODIS transition dates for agricultural, deciduous forest, and grassland sites, provided that the vegetation in the camera field of view was representative of the broader landscape. The correlation between PhenoCam and MODIS transition dates was poor for evergreen forest sites. We discuss potential reasons (including sub-pixel spatial heterogeneity, flexibility of the transition date extraction method, vegetation index sensitivity in evergreen systems, and PhenoCam geolocation uncertainty) for varying agreement between time series of vegetation indices derived from PhenoCam and MODIS imagery. This analysis increases our confidence in the ability of satellite remote sensing to accurately characterize seasonal dynamics in a range of ecosystems, and provides a basis for interpreting those dynamics in the context of tangible phenological changes occurring on the ground

Statistical Curve Analysis: Developing Methods and Expanding Knowledge in Health

The analysis of curves can be claimed to be the core of most scientific ventures. In this dissertation, we focus on the statistical aspect of this type of analysis. Here, the curves originate from health and food-related areas and include improvements in blood glucose measurements, classification of moles, measurements of parameters during liver transplants in pigs, and data from the monitoring of the quality of fish. More specifically, the statistical curve analysis consists of several perspectives were all have some kind of in- trinsic comparison effort. However, the main approaches in these studies are related to regression and the problem of finding suitable critical regions. The regression part consists of robust nonlinear regression and linear mixed models while the critical regions are found through classification and hypothesis testing in scale-space. By improving the critical decision boundaries through e.g. the Bonferroni correction of scale-space maps in Paper I, and developing features to improve decisions regarding the classification of moles in Paper II, we were able to obtain high sensitivity and specificity in the developed systems. Re- gression was an integral part of the classification effort in Paper II, the improvement of blood glucose measurements in Paper III, and the statistical analysis of parameters measured during liver transplantation in pigs in Paper IV. Paper I is focused on maximizing sensitivity and specificity when detecting a significant change in the data. Here as in Paper II hyperspectral images are the source of data. The developed method produces a scale-space, where significant changes can be detected. Paper II aims to maximize sensitivity, specificity, and precision in the classification of moles. This is accomplished through curves from subimages obtained from each channel of the hyperspectral images. These curves show characteristic features from three important classes of moles. By using these features through the regression of these curves, we accomplish high sensitivity, specificity, and precision in the classification pursuit. In Paper III, we introduce a novel method for improving blood glucose estimation from continuous glucose measurements by using deconvolution. First, regression is used to estimate the parameters in the convolution kernel. Thereafter this response function was deconvolved through regression. In this way, we can estimate blood glucose from subcutaneous measurements. This gives a new method for controlling blood glucose levels which is of great importance for type 1 diabetes patients during and after exercise to avoid hypoglycemia. Testing two different methods in liver transplantation of pigs, where the statistical analysis of curves was done through the application of linear mixed models, is the focus of Paper IV. An important output of this work is that the two treatments can be statistically distinguished through the use of linear mixed models

Detection of leek rust disease under field conditions using hyperspectral proximal sensing and machine learning

Rust disease is an important problem for leek cultivation worldwide. It reduces market value and in extreme cases destroys the entire harvest. Farmers have to resort to periodical full-field fungicide applications to prevent the spread of disease, once every 1 to 5 weeks, depending on the cultivar and weather conditions. This implies an economic cost for the farmer and an environmental cost for society. Hyperspectral sensors have been extensively used to address this issue in research, but their application in the field has been limited to a relatively low number of crops, excluding leek, due to the high investment costs and complex data gathering and analysis associated with these sensors. To fill this gap, a methodology was developed for detecting leek rust disease using hyperspectral proximal sensing data combined with supervised machine learning. First, a hyperspectral library was constructed containing 43,416 spectra with a waveband range of 400-1000 nm, measured under field conditions. Then, an extensive evaluation of 11 common classifiers was performed using the scikit-learn machine learning library in Python, combined with a variety of wavelength selection techniques and preprocessing strategies. The best performing model was a (linear) logistic regression model that was able to correctly classify rust disease with an accuracy of 98.14%, using reflectance values at 556 and 661 nm, combined with the value of the first derivative at 511 nm. This model was used to classify unlabelled hyperspectral images, confirming that the model was able to accurately classify leek rust disease symptoms. It can be concluded that the results in this work are an important step towards the mapping of leek rust disease, and that future research is needed to overcome certain challenges before variable rate fungicide applications can be adopted against leek rust disease

Perfluorocarbon Enhanced Glasgow Oxygen Level Dependent (GOLD) magnetic resonance metabolic imaging identifies the penumbra following acute ischemic stroke

The ability to identify metabolically active and potentially salvageable ischaemic penumbra is crucial for improving treatment decisions in acute stroke patients. Our solution involves two complementary novel MRI techniques (Glasgow Oxygen Level Dependant (GOLD) Metabolic Imaging), which when combined with a perfluorocarbon (PFC) based oxygen carrier and hyperoxia can identify penumbra due to dynamic changes related to continued metabolism within this tissue compartment. Our aims were (i) to investigate whether PFC offers similar enhancement of the second technique (Lactate Change) as previously demonstrated for the T2*OC technique (ii) to demonstrate both GOLD metabolic imaging techniques working concurrently to identify penumbra, following administration of Oxycyte® (O-PFC) with hyperoxia. Methods: An established rat stroke model was utilised. Part-1: Following either saline or PFC, magnetic resonance spectroscopy was applied to investigate the effect of hyperoxia on lactate change in presumed penumbra. Part-2; rats received O-PFC prior to T2*OC (technique 1) and MR spectroscopic imaging, which was used to identify regions of tissue lactate change (technique 2) in response to hyperoxia. In order to validate the techniques, imaging was followed by [14C]2-deoxyglucose autoradiography to correlate tissue metabolic status to areas identified as penumbra. Results: Part-1: PFC+hyperoxia resulted in an enhanced reduction of lactate in the penumbra when compared to saline+hyperoxia. Part-2: Regions of brain tissue identified as potential penumbra by both GOLD metabolic imaging techniques utilising O-PFC, demonstrated maintained glucose metabolism as compared to adjacent core tissue. Conclusion: For the first time in vivo, enhancement of both GOLD metabolic imaging techniques has been demonstrated following intravenous O-PFC+hyperoxia to identify ischaemic penumbra. We have also presented preliminary evidence of the potential therapeutic benefit offered by O-PFC. These unique theranostic applications would enable treatment based on metabolic status of the brain tissue, independent of time from stroke onset, leading to increased uptake and safer use of currently available treatment options

Image analysis and statistical inference in neuroimaging with R

R is a language and environment for statistical computing and graphics. It can be considered an alternative implementation of the S language developed in the 1970s and 1980s for data analysis and graphics (Becker and Chambers, 1984; Becker et al., 1988). The R language is part of the GNU project and offers versions that compile and run on almost every major operating system currently available. We highlight several R packages built specifically for the analysis of neuroimaging data in the context of functional MRI, diffusion tensor imaging, and dynamic contrast-enhanced MRI. We review their methodology and give an overview of their capabilities for neuroimaging. In addition we summarize some of the current activities in the area of neuroimaging software development in R

Developing a New Algorithm to Detect Right Thumb Fingernail in Healthy Human

Due to significant challenges faced by traditional methods of personal identification like fingerprinting, eye scanning, and voice recognition, new techniques are needed. One such approach involves the use of human nail images for identification and access to personal identification programs and electronic patient files. A novel algorithm, which consists of three stages, has been proposed utilizing the HSV color space detection algorithm, grayscale contrast optimization algorithm, nail segmentation, and image smoothing with a Gaussian filter. This method reduces tested image data and preserves the primary image structure, and has the potential to surpass the accuracy of traditional methods, providing an additional layer of security in personal identification programs and electronic patient files. Nail image detection can be conducted remotely and accessed through standard cameras or smartphones, making it a more hygienic and convenient option than physical contact methods such as fingerprinting or eye scanning. Moreover, the use of nail images for personal identification has several other benefits, especially in situations where traditional methods are not feasible, such as in individuals with skin conditions that prevent fingerprinting. The success of the proposed algorithm in detecting nail images for personal identification has implications beyond individual security and can be applied in different fields, including healthcare and forensic science, to improve identification accuracy and prevent fraud. For example, the use of nail images could help prevent identity theft in healthcare settings, where sensitive information is stored and exchanged