京都大学 / 新制・課程博士 / 博士(医学) / 甲第23073号 / 医博第4700号 / 新制||医||1049(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 溝脇 尚志, 教授 黒田 知宏, 教授 増永 慎一郎 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DGAM

京都大学 / 新制・課程博士 / 博士(工学) / 甲第23215号 / 工博第4859号 / 新制||工||1758(附属図書館) / 京都大学大学院工学研究科物質エネルギー化学専攻 / (主査)教授 大江 浩一, 教授 近藤 輝幸, 教授 深澤 愛子 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Stimulated Raman scattering (SRS) imaging is a chemical imaging scheme that can visualize cellular content based on intrinsic chemical bond vibrations. To resolve chemicals with overlapping Raman bands, spectroscopic SRS platforms have been developed. To date, endeavors on high-speed instrumentation have achieved spectral acquisition at the microsecond level, enabling in vivo imaging of cells and tissues. Nevertheless, due to the extremely small Raman cross-sections, the current performance of SRS is bounded by a design space that trades off speed, signal fidelity, and spectral bandwidth. The lack of tailored data mining algorithms further limits the chemical information one can extract from the spectroscopic images. My thesis work focuses on developing computational SRS imaging approaches to break the physical tradeoffs and novel data analytical tools to decipher essential chemical information from stimulated Raman spectroscopic images. Utilizing data redundancy of spectroscopic images, we developed two compressive sensing schemes to improve the imaging speed by one order of magnitude without information loss. To break the sensitivity limit, we proposed an ultrafast spectroscopic SRS system and further integrated it with a deep neural network to synergistically achieve microsecond level imaging in the fingerprint region. To improve the chemical specificity and content levels, we implemented a sparsity-regularized spectral unmixing algorithm, realizing multiplexed imaging of up to six major metabolites in a cell. Finally, enabled by advances in low-exposure imaging and spectral unmixing, longitudinal imaging of biofuel synthesis in live cells with sophisticated chemical information is demonstrated. / 2022-09-24T00:00:00Z

Background. Major depressive disorder (MDD) is a leading cause of death and disability worldwide, and many individuals with MDD will experience treatment-resistant depression (TRD). TRD can lead to the development of suicidal ideation and behaviours, and up to 30% of people with refractory depression will attempt suicide at some point in their life. A neurobiological understanding of suicide is lacking, and neuroimaging markers of illness may elucidate the relationship between suicidal ideation and attempt. Diffusion tensor imaging (DTI) is a particularly sensitive neuroimaging modality that quantifies the microstructural integrity of white matter tracts, which may be useful in the investigation of psychiatric disease. The source of white matter changes may be further elucidated using free water imaging to isolate signal specific to the fibre tract and quantify the fractional volume of the free water compartment. Methodology. For this study, data were obtained from N=36 outpatients with TRD (n=20 suicide ideators and n=16 suicide attempters). Clinical characteristics of the patient sample were examined using clinician-rated and self-report questionnaires of depression and suicidal ideation severity. Whole-brain analysis of DTI data was conducted using tract-based spatial statistics (TBSS) via FMRIB Software Library (FSL) to identify between-group differences in white matter microstructure between suicide ideators and attempters. Free water imaging correction was applied through estimation of a constrained bi-tensor model via an in house MatLab-based script developed at Harvard University. Between-group differences of suicide ideators versus attempters were identified at a family-wise error (FWE) corrected significance threshold of p≤0.05. Subsequent exploratory analyses were performed at an uncorrected significance threshold of p≤0.01. Results. Suicide attempters had greater family history of suicide attempt, higher self-reported suicidal ideation severity, and were more likely to have received overnight treatment in a psychiatric facility in the past. TBSS revealed elevated mean diffusivity (MD), axial diffusivity (AD) and free water (FW) in suicide attempters compared to suicide ideators (thresholded p=<0.05, family-wise error corrected). Subsequent exploratory analyses revealed reduced fractional anisotropy (FA) and elevated radial diffusivity (RD) in fronto-thalamo-limbic white matter tracts of suicide attempters (thresholded p=<0.01, uncorrected). Free water correction appeared to increase detection of fractional anisotropy changes and suppress spurious differences in axial and radial diffusivity. Conclusion. The identification of significantly altered diffusion metrics in suicide attempters compared to suicide ideators suggests white matter pathology in TRD and suicide attempt. The effect of free water correction on diffusion metrics and the elevation of free water itself provide evidence toward the source of anisotropic changes. Future investigations to explore the combined impact of these measures in suicide and depression are recommended.

Thesis (MSc (Radiography))--Cape Peninsula University of Technology, 2019 / Introduction: Traumatic brain injury (TBI) is frequently associated with mortality and morbidity in low-income countries. Computed Tomography Brain (CTB) imaging aid in the management of patients by accurately exploring primary and secondary brain injuries following trauma. However, there is controversy among researchers on the benefits of follow-up CTB imaging (FCTBI) amongst patients presenting with TBI showing a normal baseline scan. As such, in an attempt to address the contention, the primary focus of this research study was to explore the role of FCTBI with regards to the clinical status of such patients. The secondary focus was to determine the timing of performing FCTBI post TBI. Method: A retrospective cross sectional quantitative design was conducted for this research study. A total sampling strategy was employed on medical records of 85 patients treated at the research site in Zimbabwe. Data were collected over a two year period. Adult patients between the ages of 18 and 75, with TBI and who had a normal first CTBI1 (primary scan done upon hospital admission) were included in this research study. The evolution of different types of brain pathology diagnosed on FCTBI in affected patients were recorded on data collection sheets. An analysis then followed to establish whether the sample patients had developed any neurological complications. Results: The study showed that in 85 patients with TBI, 36% recorded abnormal radiological findings on FCTBI with subdural haematoma (19%) being the most common intracranial lesion followed by intracerebral haemorrhage (8%), subarachnoid haemorrhage (6%) and lastly, pneumocephalus and epidural haematoma (1% respectively). The most frequent causal mechanism of trauma was road traffic accidents (RTAs) at 58%. Males with TBI comprised a higher proportion (53%) than did females (47%). The performance of CTBI1 at 8 hours post trauma occurrence, within a recommended hospital observation period of 20 hours post trauma occurrence, may provide sufficient time for lesions to evolve and thus determine the appropriate patient management. The young adult age group of 26-35 years was found to be more susceptible to TBI. Conclusion: FCTBI was found to be of value in timely detection of evolving intracranial lesions which enabled appropriate management of patients. The current study recommends that patients who exhibit a declining Glasgow Coma Scale (GCS) score and deteriorating neurological status undergo a FCTBI.

Co-registering images of different modalities, termed intermodal image registration, is an important tool in improving our understanding of how certain features detectable in one modality might manifest in the other. However, structural changes – usually the result of tissue processing or noise in image acquisition – can make matching difficult. In this thesis, I outline a pre-processing protocol for co-registration of paired histological sections and MRI scans as well as discuss different co-registration strategies using the rabbit larynx as a model system.

Poisoning is common and carries considerable morbidity and mortality. Two to three patients are admitted to the Emergency Unit at Groote Schuur Hospital every day with drug overdose. As absorption occurs in the small intestine the rates at which ingested poisons pass into and through the small bowel are important factors in determining the amount of poison potentially available for absorption. Although the effects of pharmacological doses of many drugs on gastric emptying and motility are known, information on the effects of higher doses is limited. I investigated patients who took overdoses of certain commonly used drugs to determine their effects on gastric emptying and motility and small intestinal transit. The study was divided into two parts. One hundred and four patients were studied in Part 1. These patients took overdoses of tricyclic antidepressants (n = 31), carbamazepine (n = 15), phenytoin (n = 12), paracetamol (n = 29) and opioid-paracetamol mixtures (n = 17). They received standard hospital management of which sorbitol was not a part. Part 2 consisted of sixty-one patients who had sorbitol added to their treatment. These patients had taken overdoses of the tricyclic antidepressants (n = 15), carbamazepine (n = 7), phenytoin (n = 8), paracetamol (n = 13) and opioid-paracetamol mixtures (n = 18). The effects of sorbitol on gastric emptying and small intestinal transit were evaluated. A third study-the paracetamol control test was done on 5 healthy volunteers. Each subject was studied twice; the first time after taking 1 G of paracetamol and the second time after no drug ingestion.

Le système des noyaux de la base est principalement impliqué dans le contrôle et l'apprentissage moteur.Le rôle de la voie cortico-striatale a été et est toujours fortement étudié mais le striatum reçoit aussides afférences excitatrices du thalamus, souvent considéré comme un simple relais entre les noyaux dela base et le cortex, formant ainsi des boucles de structures sous-corticales. Les principales afférencesthalamostriatales glutamatergiques proviennent des noyaux thalamiques intralaminaires et forment descontacts synaptiques avec les deux types de neurones efférents GABAergiques du striatum (i- et d-MSNs) et les interneurones cholinergiques (INCs). Le complexe thalamique intralaminaire peut sedistinguer en une partie rostrale (ILTr) contenant les noyaux centrolatéral (CL), paracentral (PC) etcentral médial (CeM) et une partie caudale (ILTc) formée du noyau parafasciculaire (Pf) chez lerongeur (équivalent du complexe parafasciculaire-centromedian chez le primate). Le complexe thalamiqueintralaminaire est souvent considéré comme une structure fonctionnelle homogène, cependant de plus enplus d’études mettent en évidence des différences anatomiques, électrophysiologiques et fonctionnelles desparties rostrales et caudales de l’intralaminaire. Le noyau intralaminaire caudal est de mieux en mieuxdécrit et sa projection striatale se montre impliquée principalement dans la réponse aux stimuli sensorielsainsi que dans la flexibilité motrice. Des données obtenues par Marco Diana et collaborateurs à l’EcoleNationale Supérieure (Paris) apportent un éclairage nouveau sur l'importance du noyau intralaminairerostral, en particulier le noyau centrolatéral, dans le contrôle du mouvement, en montrant que la stimulationoptogénétique de la projection glycinergique/GABAergique ponto-intralaminaire thalamique inhibe les neu-rones thalamiques et provoque une hypolocomotion. Ces résultats indiquent que la suppression de laprojection thalamique sur le striatum mène à une perturbation de la fonction des ganglions de la base.Cette dernière décennie se caractérise par une explosion de nouvelles techniques aussi bien dans lesdomaines d’imagerie que dans les techniques de manipulation génique d’animaux permettant de répondreà certaines questions qui ne pouvaient techniquement pas trouver de réponse jusqu’ici. Ce travail dethèse a pour but de mieux comprendre l’importance des afférences du thalamus intralaminaire sur lestriatum, en particulier sa partie rostrale, qui, de manière surprenante, sont très mal caractérisées. Deplus, les noyaux thalamiques intralaminaires sont un relais entre le cervelet et le striatum, par conséquent,l'analyse de ces connexions pourrait améliorer notre compréhension des maladies neurodégénératives tellesque la maladie de Parkinson impliquant à la fois les noyaux gris centraux et le cervelet, mais dont lesinteractions fonctionnelles n'ont pas encore été décryptées.La première partie de ce travail de thèse consiste en une étude anatomique détaillée des projections duthalamus intralaminaire sur le striatum, en particulier sur ses principales sous-populations (d- et i-MSNs,INCs) et sous-régions (dorso-latéral=DLS, dorso-médian=DMS), par l’utilisation combinée d’un marquagerétrograde monosynaptique et d’une technique de transparisation (« clearing ») permettant par la suitede réaliser une imagerie complète du cerveau à l’aide d’un microscope à feuille de lumière. Les analysesanatomiques réalisées ont permis de confirmer l’existence de projections directes des noyaux thalamiquesintralaminaires sur le striatum dorsal, celles-ci présentant un pattern d’innervation préférentiel pour lesINCs (DMS>DLS) suivi par les dMSNs (DLS>DMS). Les cibles postsynaptiques des projectionsthalamostriatales sont similaires aux projections dopaminergiques, suggérant une interaction étroite entreces afférences.La seconde partie de cette thèse, vise a mieux comprendre l’importance fonctionnelle des connexionsthalamostriatales mises en évidence précédemment dans la locomotion spontanée. Pour cela deux ap-proches seront utilisées: une approche modifiant l’activité de ces neurones par l’utilisation de techniquescomme l’optogénétique et la chémogénétique et une approche descriptive par une technique d’imageriecalcique permettant d’enregistrer l’activité neuronale en temps réel sur des animaux libres de se mouvoir.Les résultats obtenus montrent que l’inhibition de l’ensemble des neurones de l’ILTr est nécessaire pourobserver un phénotype moteur d’hypolocomotion. La mise en place d’un système de détection de motricitéfine et l’enregistrement de l’activité calcique des neurones striataux, nous permettront, à l’avenir, de mieux identifier le type de comportement moteur impliqué dans cette hypolocomotion ainsi que d’évaluer l’impactde cette inhibition thalamique sur l’activité des neurones striataux. / Doctorat en Sciences biomédicales et pharmaceutiques (Médecine) / info:eu-repo/semantics/nonPublished

Acousto-optic (AO) sensing and imaging (AOI) is a dual-wave modality that combines ultrasound with diffusive light to measure and/or image the optical properties of optically diffusive media, including biological tissues such as breast and brain. The light passing through a focused ultrasound beam undergoes a phase modulation at the ultrasound frequency that is detected using an adaptive interferometer scheme employing a GaAs photorefractive crystal (PRC). The PRC-based AO system operating at 1064 nm is described, along with the underlying theory, validating experiments, characterization, and optimization of this sensing and imaging apparatus. The spatial resolution of AO sensing, which is determined by spatial dimensions of the ultrasound beam or pulse, can be sub-millimeter for megahertz-frequency sound waves.A modified approach for quantifying the optical properties of diffuse media with AO sensing employs the ratio of AO signals generated at two different ultrasound focal pressures. The resulting “pressure contrast signal” (PCS), once calibrated for a particular set of pressure pulses, yields a direct measure of the spatially averaged optical transport attenuation coefficient within the interaction volume between light and sound. This is a significant improvement over current AO sensing methods since it produces a quantitative measure of the optical properties of optically diffuse media without a priori knowledge of the background illumination. It can also be used to generate images based on spatial variations in both optical scattering and absorption. Finally, the AO sensing system is modified to monitor the irreversible optical changes associated with the tissue heating from high intensity focused ultrasound (HIFU) therapy, providing a powerful method for noninvasively sensing the onset and growth of thermal lesions in soft tissues. A single HIFU transducer is used to simultaneously generate tissue damage and pump the AO interaction. Experimental results performed in excised chicken breast demonstrate that AO sensing can identify the onset and growth of lesion formation in real time and, when used as feedback to guide exposure parameters, results in more predictable lesion formation. / Bernard M. Gordon Center for Subsurface and Imaging Systems (CenSSIS) via the NSF ERC award number EEC-9986821.

Imaging of multiple cells has rapidly multiplied the rate of data acquisition as well as our knowledge of the complex dynamics within the mammalian brain. The process of data acquisition has been dramatically enhanced with highly affordable, sensitive image sensors enable high-throughput detection of neural activity in intact animals. Genetically encoded calcium sensors deliver a substantial boost in signal strength and in combination with equally critical advances in the size, speed, and sensitivity of image sensors available in scientific cameras enables high-throughput detection of neural activity in behaving animals using traditional wide-field fluorescence microscopy. However, the tremendous increase in data flow presents challenges to processing, analysis, and storage of captured video, and prompts a reexamination of traditional routines used to process data in neuroscience and now demand improvements in both our hardware and software applications for processing, analyzing, and storing captured video. This project demonstrates the ease with which a dependable and affordable wide-field fluorescence imaging system can be assembled and integrated with behavior control and monitoring system such as found in a typical neuroscience laboratory. An Open-source MATLAB toolbox is employed to efficiently analyze and visualize large imaging data sets in a manner that is both interactive and fully automated. This software package provides a library of image pre-processing routines optimized for batch-processing of continuous functional fluorescence video, and additionally automates a fast unsupervised ROI detection and signal extraction routine. Further, an extension of this toolbox that uses GPU programming to process streaming video, enabling the identification, segmentation and extraction of neural activity signals on-line is described in which specific algorithms improve signal specificity and image quality at the single cell level in a behaving animal. This project describes the strategic ingredients for transforming a large bulk flow of raw continuous video into proportionally informative images and knowledge.