Development of Imaging Mass Spectrometry Analysis of Lipids in Biological and Clinically Relevant Applications

La spectrométrie de masse mesure la masse des ions selon leur rapport masse sur charge. Cette technique est employée dans plusieurs domaines et peut analyser des mélanges complexes. L’imagerie par spectrométrie de masse (Imaging Mass Spectrometry en anglais, IMS), une branche de la spectrométrie de masse, permet l’analyse des ions sur une surface, tout en conservant l’organisation spatiale des ions détectés. Jusqu’à présent, les échantillons les plus étudiés en IMS sont des sections tissulaires végétales ou animales. Parmi les molécules couramment analysées par l’IMS, les lipides ont suscité beaucoup d'intérêt. Les lipides sont impliqués dans les maladies et le fonctionnement normal des cellules; ils forment la membrane cellulaire et ont plusieurs rôles, comme celui de réguler des événements cellulaires. Considérant l’implication des lipides dans la biologie et la capacité du MALDI IMS à les analyser, nous avons développé des stratégies analytiques pour la manipulation des échantillons et l’analyse de larges ensembles de données lipidiques. La dégradation des lipides est très importante dans l’industrie alimentaire. De la même façon, les lipides des sections tissulaires risquent de se dégrader. Leurs produits de dégradation peuvent donc introduire des artefacts dans l’analyse IMS ainsi que la perte d’espèces lipidiques pouvant nuire à la précision des mesures d’abondance. Puisque les lipides oxydés sont aussi des médiateurs importants dans le développement de plusieurs maladies, leur réelle préservation devient donc critique. Dans les études multi-institutionnelles où les échantillons sont souvent transportés d’un emplacement à l’autre, des protocoles adaptés et validés, et des mesures de dégradation sont nécessaires. Nos principaux résultats sont les suivants : un accroissement en fonction du temps des phospholipides oxydés et des lysophospholipides dans des conditions ambiantes, une diminution de la présence des lipides ayant des acides gras insaturés et un effet inhibitoire sur ses phénomènes de la conservation des sections au froid sous N2. A température et atmosphère ambiantes, les phospholipides sont oxydés sur une échelle de temps typique d’une préparation IMS normale (~30 minutes). Les phospholipides sont aussi décomposés en lysophospholipides sur une échelle de temps de plusieurs jours. La validation d’une méthode de manipulation d’échantillon est d’autant plus importante lorsqu’il s’agit d’analyser un plus grand nombre d’échantillons. L’athérosclérose est une maladie cardiovasculaire induite par l’accumulation de matériel cellulaire sur la paroi artérielle. Puisque l’athérosclérose est un phénomène en trois dimension (3D), l'IMS 3D en série devient donc utile, d'une part, car elle a la capacité à localiser les molécules sur la longueur totale d’une plaque athéromateuse et, d'autre part, car elle peut identifier des mécanismes moléculaires du développement ou de la rupture des plaques. l'IMS 3D en série fait face à certains défis spécifiques, dont beaucoup se rapportent simplement à la reconstruction en 3D et à l’interprétation de la reconstruction moléculaire en temps réel. En tenant compte de ces objectifs et en utilisant l’IMS des lipides pour l’étude des plaques d’athérosclérose d’une carotide humaine et d’un modèle murin d’athérosclérose, nous avons élaboré des méthodes «open-source» pour la reconstruction des données de l’IMS en 3D. Notre méthodologie fournit un moyen d’obtenir des visualisations de haute qualité et démontre une stratégie pour l’interprétation rapide des données de l’IMS 3D par la segmentation multivariée. L’analyse d’aortes d’un modèle murin a été le point de départ pour le développement des méthodes car ce sont des échantillons mieux contrôlés. En corrélant les données acquises en mode d’ionisation positive et négative, l’IMS en 3D a permis de démontrer une accumulation des phospholipides dans les sinus aortiques. De plus, l’IMS par AgLDI a mis en évidence une localisation différentielle des acides gras libres, du cholestérol, des esters du cholestérol et des triglycérides. La segmentation multivariée des signaux lipidiques suite à l’analyse par IMS d’une carotide humaine démontre une histologie moléculaire corrélée avec le degré de sténose de l’artère. Ces recherches aident à mieux comprendre la complexité biologique de l’athérosclérose et peuvent possiblement prédire le développement de certains cas cliniques. La métastase au foie du cancer colorectal (Colorectal cancer liver metastasis en anglais, CRCLM) est la maladie métastatique du cancer colorectal primaire, un des cancers le plus fréquent au monde. L’évaluation et le pronostic des tumeurs CRCLM sont effectués avec l’histopathologie avec une marge d’erreur. Nous avons utilisé l’IMS des lipides pour identifier les compartiments histologiques du CRCLM et extraire leurs signatures lipidiques. En exploitant ces signatures moléculaires, nous avons pu déterminer un score histopathologique quantitatif et objectif et qui corrèle avec le pronostic. De plus, par la dissection des signatures lipidiques, nous avons identifié des espèces lipidiques individuelles qui sont discriminants des différentes histologies du CRCLM et qui peuvent potentiellement être utilisées comme des biomarqueurs pour la détermination de la réponse à la thérapie. Plus spécifiquement, nous avons trouvé une série de plasmalogènes et sphingolipides qui permettent de distinguer deux différents types de nécrose (infarct-like necrosis et usual necrosis en anglais, ILN et UN, respectivement). L’ILN est associé avec la réponse aux traitements chimiothérapiques, alors que l’UN est associé au fonctionnement normal de la tumeur.

Directing for the 360 degree frame : developing a directorial approach to performance capture

What happens when the traditional framing mechanisms of our performance environments are removed and we are forced as directors to work with actors in digital environments that capture performance in 360 degrees? As directors contend with the challenges of interactive performance, the emergence of the online audience and the powerful influence of the games industry, how can we approach the challenges of directing work that is performance captured and presented in real time using motion capture and associated 3D imaging software? The 360 degree real time capture of performance, while allowing for an unlimited amount of framing potential, demands a unique and uncompromisingly disciplined style of direction and performance that has thus far remained unstudied and unquantified. By a close analysis of the groundbreaking work of artists like Robert Zemeckis and the Wetta Digital studio it is possible to begin to quantify what the technical requirements and challenges of 360 degree direction might be, but little has been discovered about the challenges of communicating the unlimited potential of framing and focus to the actors who work with these directors within these systems. It cannot be argued that the potential of theatrical space has evolved beyond the physical and moved into a more accessible virtual and digitised form, so how then can we direct for this unlimited potential and where do we place the focus of our directed (and captured) performance?

Social implications of radical technology adoption within the livestock industry - a design investigation: Innovating disruptive technologies in traditional marketplaces

This thesis presents a design investigation into how traditional technology-orientated markets can use design led innovation (DLI) strategies in order to achieve better market penetration of disruptive products. In a review of the Australian livestock industry, considering historical information and present-day trends, a lack of socio-cultural consideration was identified in the design and implementation of products and systems, previously been taken to market. Hence the adoption of these novel products has been documented as extremely slow. Classical diffusion models have typically been used in order to implement these products. However, this thesis poses that it is through the strategic intent of design led innovation, where heavily technology-orientated markets (such as the Australian livestock industry), can achieve better final adoption rates. By considering a range of external factors (business models, technology and user needs), rather than focusing design efforts solely on the technology, it is argued that using DLI approach will lead to disruptive innovations being made easier to adopt in the Australian livestock industry. This thesis therefore explored two research questions: 1. What are the social inhibitors to the adoption of a new technology in the Australian livestock industry? 2. Can design be used to gain a significant feedback response to the proposed innovation? In order to answer these questions, this thesis used a design led innovation approach to investigate the livestock industry, centring on how design can be used early on in the development of disruptive products being taken to market. This thesis used a three stage data collection programme, combining methods of design thinking, co-design and participatory design. The first study found four key themes to the social barriers of technology adoption; Social attitudes to innovation, Market monitoring, Attitude to 3D imaging and Online processes. These themes were built upon through a design thinking/co-design approach to create three ‘future scenarios’ to be tested in participant workshops. The analysis of the data collection found four key socio-cultural barriers that inhibited the adoption of a disruptive innovation in the Australian livestock industry. These were found to be a lack of Education, a Culture of Innovation, a Lack of Engagement and Communication barriers. This thesis recommends five key areas to be focused upon in the subsequent design of a new product in the Australian livestock industry. These recommendations are made to business and design managers looking to introduce disruptive innovations in this industry. Moreover, the thesis presents three design implications relating to stakeholder attitudes, practical constraints and technological restrictions of innovations within the industry.

Evaluation of MegaVoltage Cone Beam CT image quality with an unmodified Elekta Precise Linac and EPID : a feasibility study

In order to increase the accuracy of patient positioning for complex radiotherapy treatments various 3D imaging techniques have been developed. MegaVoltage Cone Beam CT (MVCBCT) can utilise existing hardware to implement a 3D imaging modality to aid patient positioning. MVCBCT has been investigated using an unmodified Elekta Precise linac and 15 iView amorphous silicon electronic portal imaging device (EPID). Two methods of delivery and acquisition have been investigated for imaging an anthropomorphic head phantom and quality assurance phantom. Phantom projections were successfully acquired and CT datasets reconstructed using both acquisition methods. Bone, tissue and air were 20 clearly resolvable in both phantoms even with low dose (22 MU) scans. The feasibility of MegaVoltage Cone beam CT was investigated using a standard linac, amorphous silicon EPID and a combination of a free open source reconstruction toolkit as well as custom in-house software written in Matlab. The resultant image quality has 25 been assessed and presented. Although bone, tissue and air were resolvable 2 in all scans, artifacts are present and scan doses are increased when compared with standard portal imaging. The feasibility of MVCBCT with unmodified Elekta Precise linac and EPID has been considered as well as the identification of possible areas for future development in artifact correction techniques to 30 further improve image quality.

MegaVoltage Cone Beam Computed Tomography with a standard medical linear accelerator

Accurate patient positioning is vital for improved clinical outcomes for cancer treatments using radiotherapy. This project has developed Mega Voltage Cone Beam CT using a standard medical linear accelerator to allow 3D imaging of the patient position at treatment time with no additional hardware required. Providing 3D imaging functionality at no further cost allows enhanced patient position verification on older linear accelerators and in developing countries where access to new technology is limited.

Cone beam computed tomography in oral radiology

In dentistry, basic imaging techniques such as intraoral and panoramic radiography are in most cases the only imaging techniques required for the detection of pathology. Conventional intraoral radiographs provide images with sufficient information for most dental radiographic needs. Panoramic radiography produces a single image of both jaws, giving an excellent overview of oral hard tissues. Regardless of the technique, plain radiography has only a limited capability in the evaluation of three-dimensional (3D) relationships. Technological advances in radiological imaging have moved from two-dimensional (2D) projection radiography towards digital, 3D and interactive imaging applications. This has been achieved first by the use of conventional computed tomography (CT) and more recently by cone beam CT (CBCT). CBCT is a radiographic imaging method that allows accurate 3D imaging of hard tissues. CBCT has been used for dental and maxillofacial imaging for more than ten years and its availability and use are increasing continuously. However, at present, only best practice guidelines are available for its use, and the need for evidence-based guidelines on the use of CBCT in dentistry is widely recognized. We evaluated (i) retrospectively the use of CBCT in a dental practice, (ii) the accuracy and reproducibility of pre-implant linear measurements in CBCT and multislice CT (MSCT) in a cadaver study, (iii) prospectively the clinical reliability of CBCT as a preoperative imaging method for complicated impacted lower third molars, and (iv) the tissue and effective radiation doses and image quality of dental CBCT scanners in comparison with MSCT scanners in a phantom study. Using CBCT, subjective identification of anatomy and pathology relevant in dental practice can be readily achieved, but dental restorations may cause disturbing artefacts. CBCT examination offered additional radiographic information when compared with intraoral and panoramic radiographs. In terms of the accuracy and reliability of linear measurements in the posterior mandible, CBCT is comparable to MSCT. CBCT is a reliable means of determining the location of the inferior alveolar canal and its relationship to the roots of the lower third molar. CBCT scanners provided adequate image quality for dental and maxillofacial imaging while delivering considerably smaller effective doses to the patient than MSCT. The observed variations in patient dose and image quality emphasize the importance of optimizing the imaging parameters in both CBCT and MSCT.

Gravity-induced coronal plane joint moments in adolescent idiopathic scoliosis

Background Adolescent Idiopathic Scoliosis is the most common type of spinal deformity, and whilst the risk of progression appears to be biomechanically mediated (larger deformities are more likely to progress), the detailed biomechanical mechanisms driving progression are not well understood. Gravitational forces in the upright position are the primary sustained loads experienced by the spine. In scoliosis they are asymmetrical, generating moments about the spinal joints which may promote asymmetrical growth and deformity progression. Using 3D imaging modalities to estimate segmental torso masses allows the gravitational loading on the scoliotic spine to be determined. The resulting distribution of joint moments aids understanding of the mechanics of scoliosis progression. Methods Existing low-dose CT scans were used to estimate torso segment masses and joint moments for 20 female scoliosis patients. Intervertebral joint moments at each vertebral level were found by summing the moments of each of the torso segment masses above the required joint. Results The patients’ mean age was 15.3 years (SD 2.3; range 11.9 – 22.3 years); mean thoracic major Cobb angle 52° (SD 5.9°; range 42°-63°) and mean weight 57.5 kg (SD 11.5 kg; range 41 – 84.7 kg). Joint moments of up to 7 Nm were estimated at the apical level. No significant correlation was found between the patients’ major Cobb angles and apical joint moments. Conclusions Patients with larger Cobb angles do not necessarily have higher joint moments, and curve shape is an important determinant of joint moment distribution. These findings may help to explain the variations in progression between individual patients. This study suggests that substantial corrective forces are required of either internal instrumentation or orthoses to effectively counter the gravity-induced moments acting to deform the spinal joints of idiopathic scoliosis patients.

Simultaneous multilayer scanning and detection for multiphoton fluorescence microscopy

Fast three-dimensional (3D) imaging requires parallel optical slicing of a specimen with an efficient detection scheme. The generation of multiple localized dot-like excitation structures solves the problem of simultaneous slicing multiple specimen layers, but an efficient detection scheme is necessary. Confocal theta detection (detection at 90 degrees to the optical axis) provides a suitable detection platform that is capable of cross-talk-free fluorescence detection from each nanodot (axial dimension approximate to 150 nm). Additionally, this technique has the unique feature of imaging a specimen at a large working distance with super-resolution capabilities. Polarization studies show distinct field structures for fixed and fluid samples, indicating a non-negligible field-dipole interaction. The realization of the proposed imaging technique will advance and diversify multiphoton fluorescence microscopy for numerous applications in nanobioimaging and optical engineering.

Raman spectroscopy explores molecular structural signatures of hidden materials in depth: Universal Multiple Angle Raman Spectroscopy

Non-invasive 3D imaging in materials and medical research involves methodologies such as X-ray imaging, MRI, fluorescence and optical coherence tomography, NIR absorption imaging, etc., providing global morphological/density/absorption changes of the hidden components. However, molecular information of such buried materials has been elusive. In this article we demonstrate observation of molecular structural information of materials hidden/buried in depth using Raman scattering. Typically, Raman spectroscopic observations are made at fixed collection angles, such as, 906, 1356, and 1806, except in spatially offset Raman scattering (SORS) (only back scattering based collection of photons) and transmission techniques. Such specific collection angles restrict the observations of Raman signals either from or near the surface of the materials. Universal Multiple Angle Raman Spectroscopy (UMARS) presented here employs the principle of (a) penetration depth of photons and then diffuse propagation through non-absorbing media by multiple scattering and (b) detection of signals from all the observable angles.

利用受激发射损耗（STED）显微术突破远场衍射极限

远场光学显微镜受衍射极限分辩率的限制，而近场光学显微镜由于缺乏层析能力，则无法实现超分辨的三维成像，研究了既可突破远场光学显微术的衍射极限分辨率又可实现三维成像的成像技术——受激发射损耗（STED），综述了STED的分辨率与STED光的光强，延迟时间、光斑空间分布等主要参数的关系，以及该技术的最新进展和应用前景。

Temporal characteristic simulation for stimulated emission depletion microscopy

The imaging technology of stimulated emission depletion (STED) utilizes the nonlinearity relationship between the fluorescence saturation and the excited state stimulated depletion. It implements three-dimensional (3D) imaging and breaks the diffraction barrier of far-field light microscopy by restricting fluorescent molecules at a sub-diffraction spot. In order to improve the resolution which attained by this technology, the computer simulation on temporal behavior of population probabilities of the sample was made in this paper, and the optimized parameters such as intensity, duration and delay time of the STED pulse were given.

超分辨远场生物荧光成像——突破光学衍射极限

长期以来,远场光学荧光显微镜凭借其非接触、无损伤、可探测样品内部等优点,一直是生命科学中最常用的观测工具。但由于衍射极限的存在,使传统的宽场光学显微镜横向和纵向的分辨率分别仅约为230 nm和1000 nm。为了揭示细胞内分子尺度的动态和结构特征,提高光学显微镜分辨率成为生命科学发展的迫切要求,在远场荧光显微镜的基础上,科学家们已经发展出许多实用的提高分辨率甚至超越分辨率极限的成像技术。例如,采用横向结构光照明提高横向分辨率到约100 nm,利用纵向驻波干涉效应将纵向分辨率提高5~10倍。然而,直到在光学荧光显微镜中引入非线性效应后,衍射极限才被真正突破,如受激荧光损耗显微镜利用非线性效应实现了30~50 nm的三维分辨率。另外应用荧光分子之间能量转移共振原理以及单荧光分子定位技术也可以突破衍射极限,甚至可以将分子定位精度提高到几个纳米的量级。

An evaluation of volumetric interest points

This paper presents the first performance evaluation of interest points on scalar volumetric data. Such data encodes 3D shape, a fundamental property of objects. The use of another such property, texture (i.e. 2D surface colouration), or appearance, for object detection, recognition and registration has been well studied; 3D shape less so. However, the increasing prevalence of depth sensors and the diminishing returns to be had from appearance alone have seen a surge in shape-based methods. In this work we investigate the performance of several detectors of interest points in volumetric data, in terms of repeatability, number and nature of interest points. Such methods form the first step in many shape-based applications. Our detailed comparison, with both quantitative and qualitative measures on synthetic and real 3D data, both point-based and volumetric, aids readers in selecting a method suitable for their application. © 2011 IEEE.

A survey of terahertz applications in cultural heritage conservation science

The authors present a review of the advances that have been made to establish terahertz applications in the cultural heritage conservation sector over the last several years. This includes material spectroscopy, 2D and 3D imaging and tomographic studies, using a broad range of terahertz sources demonstrating the breadth and application of this burgeoning community.

Ordinal judgements of depth in monocularly- and binocularly-viewed photographs of complex natural scenes

This study investigated the contribution of stereoscopic depth cues to the reliability of ordinal depth judgments in complex natural scenes. Participants viewed photographs of cluttered natural scenes, either monocularly or stereoscopically. On each trial, they judged which of two indicated points in the scene was closer in depth. We assessed the reliability of these judgments over repeated trials, and how well they correlated with the actual disparities of the points between the left and right eyes' views. The reliability of judgments increased as their depth separation increased, was higher when the points were on separate objects, and deteriorated for point pairs that were more widely separated in the image plane. Stereoscopic viewing improved sensitivity to depth for points on the same surface, but not for points on separate objects. Stereoscopic viewing thus provides depth information that is complementary to that available from monocular occlusion cues.