307 research outputs found

    UMSL Bulletin 2023-2024

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    The 2023-2024 Bulletin and Course Catalog for the University of Missouri St. Louis.https://irl.umsl.edu/bulletin/1088/thumbnail.jp

    UMSL Bulletin 2022-2023

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    The 2022-2023 Bulletin and Course Catalog for the University of Missouri St. Louis.https://irl.umsl.edu/bulletin/1087/thumbnail.jp

    Recommended Implementation of Quantitative Susceptibility Mapping for Clinical Research in The Brain: A Consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group

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    This article provides recommendations for implementing quantitative susceptibility mapping (QSM) for clinical brain research. It is a consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group. While QSM technical development continues to advance rapidly, the current QSM methods have been demonstrated to be repeatable and reproducible for generating quantitative tissue magnetic susceptibility maps in the brain. However, the many QSM approaches available give rise to the need in the neuroimaging community for guidelines on implementation. This article describes relevant considerations and provides specific implementation recommendations for all steps in QSM data acquisition, processing, analysis, and presentation in scientific publications. We recommend that data be acquired using a monopolar 3D multi-echo GRE sequence, that phase images be saved and exported in DICOM format and unwrapped using an exact unwrapping approach. Multi-echo images should be combined before background removal, and a brain mask created using a brain extraction tool with the incorporation of phase-quality-based masking. Background fields should be removed within the brain mask using a technique based on SHARP or PDF, and the optimization approach to dipole inversion should be employed with a sparsity-based regularization. Susceptibility values should be measured relative to a specified reference, including the common reference region of whole brain as a region of interest in the analysis, and QSM results should be reported with - as a minimum - the acquisition and processing specifications listed in the last section of the article. These recommendations should facilitate clinical QSM research and lead to increased harmonization in data acquisition, analysis, and reporting

    Measuring blood flow and pulsatility with MRI: optimisation, validation and application in cerebral small vessel disease

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    Cerebral small vessel disease (SVD) is the breakdown of the small blood vessels of the brain, leading to many cases of stroke and dementia. The pathophysiology of SVD is largely unknown, although several mechanisms have been suggested. One such mechanism is the role of increased blood flow pulsatility into the brain, caused by vessel stiffening, leading to damage of the microvasculature. Magnetic resonance imaging (MRI) allows us to non-invasively measure blood flow and velocity using a technique called phase contrast-MRI – traditionally used with 2D slices across the vessel(s) of interest. An advanced form of phase-contrast MRI, known as 4D flow, has emerged in recent years that allows for a volume of data to be acquired, containing velocity information in all directions. However, to keep scan times practical when collecting this amount of data, spatiotemporal resolution has to be sacrificed. The main aim of this thesis was to assess 4D flow’s capabilities, including comparing it to the more well-established 2D method in healthy volunteers, patients, and phantom experiments, so as to better understand its role in investigating SVD. Another aim was to learn more about the role of flow and pulsatility in SVD development in patients using data acquired in the longitudinal Mild Stroke Study 3 (MSS3). Firstly, I systematically reviewed studies that have assessed the human brain using 4D flow. Across 61 relevant studies, I found a general consensus for the current use of the technique in this context. I then optimised the Siemens prototype 4D flow sequence (N = 11 healthy volunteers), testing different parameters to find the combination that best balanced scan quality and duration. I then assessed the test-retest repeatability and intra-rater reliability of both 2D and 4D methods (N = 11 healthy volunteers), as well as differences between them. Following this, I performed the same 4D-2D comparison on SVD patients (N = 10). Absolute flow measurements using 4D flow were shown to have moderate repeatability and reliability, while flow pulsatility measurements showed acceptable repeatability and reliability. Furthermore, 2D arterial pulsatility was measured higher than with 4D, while 4D often measured higher flow rates than 2D. 4D flow was shown to be feasible when used on SVD patients, with no noticeable issues caused by potential patient movement. Flow data analysis from the longitudinal SVD study MSS3 showed that intracranial pulsatility is associated with cross-sectional SVD lesion volume but not longitudinal lesion growth, with stronger associations seen in the arteries of the neck compared to the venous sinuses

    Chemometric tools for automated method-development and data interpretation in liquid chromatography

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    The thesis explores the challenges and advancements in the field of liquid chromatography (LC), particularly focusing on complex sample analysis using high-resolution mass spectrometry (MS) and two-dimensional (2D) LC techniques. The research addresses the need for efficient optimization and data-handling strategies in modern LC practice. The thesis is divided into several chapters, each addressing specific aspects of LC and polymer analysis. Chapter 2 provides an overview of the need for chemometric tools in LC practice, discussing methods for processing and analyzing data from 1D and 2D-LC systems and how chemometrics can be utilized for method development and optimization. Chapter 3 introduces a novel approach for interpreting the molecular-weight distribution and intrinsic viscosity of polymers, allowing quantitative analysis of polymer properties without prior knowledge of their interactions. This method correlates the curvature parameter of the Mark-Houwink plot with the polymer's structural and chemical properties. Chapters 4 and 5 focus on the analysis of cellulose ethers (CEs), essential in various industrial applications. A new method is presented for mapping the substitution degree and composition of CE samples, providing detailed compositional distributions. Another method involves a comprehensive 2D LC-MS/MS approach for analyzing hydroxypropyl methyl cellulose (HPMC) monomers, revealing subtle differences in composition between industrial HPMC samples. Chapter 6 introduces AutoLC, an algorithm for automated and interpretive development of 1D-LC separations. It uses retention modeling and Bayesian optimization to achieve optimal separation within a few iterations, significantly improving the efficiency of gradient LC separations. Chapter 7 focuses on the development of an open-source algorithm for automated method development in 2D-LC-MS systems. This algorithm improves separation performance by refining gradient profiles and accurately predicting peak widths, enhancing the reliability of complex gradient LC separations. Chapter 8 addresses the challenge of gradient deformation in LC instruments. An algorithm based on the stable function corrects instrument-specific gradient deformations, enabling accurate determination of analyte retention parameters and improving data comparability between different sources. Chapter 9 introduces a novel approach using capacitively-coupled-contactless-conductivity detection (C4D) to measure gradient profiles without adding tracer components. This method enhances inter-system transferability of retention models for polymers, overcoming the limitations of UV-absorbance detectable tracer components. Chapter 10 discusses practical choices and challenges faced in the thesis chapters, highlighting the need for well-defined standard samples in industrial polymer analysis and emphasizing the importance of generalized problem-solving approaches. The thesis identifies future research directions, emphasizing the importance of computational-assisted methods for polymer analysis, the utilization of online reaction modulation techniques, and exploring continuous distributions obtained through size-exclusion chromatography (SEC) in conjunction with triple detection. Chemometric tools are recognized as essential for gaining deeper insights into polymer chemistry and improving data interpretation in the field of LC

    ATR-FTIR Spectroscopy-Linked Chemometrics:A Novel Approach to the Analysis and Control of the Invasive Species Japanese Knotweed

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    Japanese knotweed (Reynoutria japonica), an invasive plant species, causes negative environmental and socio-economic impacts. A female clone in the United Kingdom, its extensive rhizome system enables rapid vegetative spread. Plasticity permits this species to occupy a broad geographic range and survive harsh abiotic conditions. It is notoriously difficult to control with traditional management strategies, which include repetitive herbicide application and costly carbon-intensive rhizome excavation. This problem is complicated by crossbreeding with the closely related species, Giant knotweed (Reynoutria sachalinensis), to give the more vigorous hybrid, Bohemian knotweed (Fallopia x Bohemica) which produces viable seed. These species, hybrids, and backcrosses form a morphologically similar complex known as Japanese knotweed ‘sensu lato’ and are often misidentified. The research herein explores the opportunities offered by advances in the application of attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy-linked chemometrics within plant sciences, for the identification and control of knotweed, to enhance our understanding of knotweed biology, and the potential of this technique. ATR-FTIR spectral profiles of Japanese knotweed leaf material and xylem sap samples, which include important biological absorptions due to lipids, proteins, carbohydrates, and nucleic acids, were used to: identify plants from different growing regions highlighting the plasticity of this clonal species; differentiate between related species and hybrids; and predict key physiological characteristics such as hormone concentrations and root water potential. Technical advances were made for the application of ATR-FTIR spectroscopy to plant science, including definition of the environmental factors that exert the most significant influence on spectral profiles, evaluation of sample preparation techniques, and identification of key wavenumbers for prediction of hormone concentrations and abiotic stress. The presented results cement the position of concatenated mid-infrared spectroscopy and machine learning as a powerful approach for the study of plant biology, extending its reach beyond the field of crop science to demonstrate a potential for the discrimination between and control of invasive plant species
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