A solution strategy to include the opening of the opercular slits in moving-mesh CFD models of suction feeding

The gill cover of fish and pre-metamorphic salamanders has a key role in suction feeding by acting as a one-way valve. It initially closes to avoid an inflow of water through the gill slits, after which it opens to allow outflow of the water that was sucked through the mouth into the expanded buccopharyngeal cavity. However, due to the inability of analytical models (relying on the continuity principle) to calculate a fluid flow through a shape-and-size-changing cavity with two openings, stringent boundary conditions had to be used in previously developed mathematical models after the moment of valve opening. By solving additionally for momentum conservation, computational fluid dynamics (CFD) has the capacity to dynamically simulate these flows, but this technique also faces complications to model a transition from closed to open valves. Here, I present a relatively simple solution strategy to incorporate valve opening, exemplified in an axisymmetrical model of a suction-feeding sunfish in ANSYS Fluent software. By controlling viscosity of a separately defined fluid entity at the opercular cavity region, early inflow can be blocked (high viscosity assigned) and later outflow can be allowed (changing viscosity to that of water). Finally, by analysing the CFD solution obtained for the sunfish model, a few new insights in the biomechanics of suction feeding will be discussed

Treatment of biodiesel wastewater using ferric chloride and ferric sulfate

The production of biodiesel through the transesterification method produces a large amount of wastewater that contains high level of chemical oxygen demand (COD) and oil and grease. In this study, coagulation was adopted to treat the biodiesel wastewater. Two types of coagulants were examined using standard jar test apparatus, i.e. ferric chloride and ferric sulfate. The effects of pH and coagulant dosage were examined at 150 rpm of rapid mixing and 20 rpm slow mixing and 30 min settling time, higher removal of SS (over 80%), colour (over 80%), COD (over 50%) and Oil and Grease (over 90%) were achieved at pH 6. Ferric Chloride was found to be superior was observed at reasonable lower amount of coagulant i.e. 300 mg/L. The result indicated that coagulation and flocculation process had contributed bigger roles in integrated treatment system

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

Surface networks

© Copyright CASA, UCL. The desire to understand and exploit the structure of continuous surfaces is common to researchers in a range of disciplines. Few examples of the varied surfaces forming an integral part of modern subjects include terrain, population density, surface atmospheric pressure, physico-chemical surfaces, computer graphics, and metrological surfaces. The focus of the work here is a group of data structures called Surface Networks, which abstract 2-dimensional surfaces by storing only the most important (also called fundamental, critical or surface-specific) points and lines in the surfaces. Surface networks are intelligent and “natural ” data structures because they store a surface as a framework of “surface ” elements unlike the DEM or TIN data structures. This report presents an overview of the previous works and the ideas being developed by the authors of this report. The research on surface networks has fou

The metaRbolomics Toolbox in Bioconductor and beyond

Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub

High-performance geometric vascular modelling

Image-based high-performance geometric vascular modelling and reconstruction is an essential component of computer-assisted surgery on the diagnosis, analysis and treatment of cardiovascular diseases. However, it is an extremely challenging task to efficiently reconstruct the accurate geometric structures of blood vessels out of medical images. For one thing, the shape of an individual section of a blood vessel is highly irregular because of the squeeze of other tissues and the deformation caused by vascular diseases. For another, a vascular system is a very complicated network of blood vessels with different types of branching structures. Although some existing vascular modelling techniques can reconstruct the geometric structure of a vascular system, they are either time-consuming or lacking sufficient accuracy. What is more, these techniques rarely consider the interior tissue of the vascular wall, which consists of complicated layered structures. As a result, it is necessary to develop a better vascular geometric modelling technique, which is not only of high performance and high accuracy in the reconstruction of vascular surfaces, but can also be used to model the interior tissue structures of the vascular walls.This research aims to develop a state-of-the-art patient-specific medical image-based geometric vascular modelling technique to solve the above problems. The main contributions of this research are:- Developed and proposed the Skeleton Marching technique to reconstruct the geometric structures of blood vessels with high performance and high accuracy. With the proposed technique, the highly complicated vascular reconstruction task is reduced to a set of simple localised geometric reconstruction tasks, which can be carried out in a parallel manner. These locally reconstructed vascular geometric segments are then combined together using shape-preserving blending operations to faithfully represent the geometric shape of the whole vascular system.- Developed and proposed the Thin Implicit Patch method to realistically model the interior geometric structures of the vascular tissues. This method allows the multi-layer interior tissue structures to be embedded inside the vascular wall to illustrate the geometric details of the blood vessel in real world