Dissertations / Theses on the topic 'Microscopy tools'
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Mignard-Debise, Lois. "Tools for the paraxial optical design of light field imaging systems." Thesis, Bordeaux, 2018. http://www.theses.fr/2018BORD0009/document.
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L'imagerie plénoptique est souvent présentée comme une révolution par rapport à l'imagerie standard. En effet, elle apporte plus de contrôle à l'utilisateur sur l'image finale puisque les dimensions spatiales et angulaires du champ de lumière offrent la possibilité de changer le point de vue ou de refaire la mise au point après coup ainsi que de calculer la carte de profondeur de la scène. Cependant, cela complique le travail du concepteur optique du système pour deux raisons. La première est qu'il existe une multitude d'appareils de capture plénoptique différents, chacun avec sa propre spécificité. La deuxième est qu'il n'existe pas de modèle qui relie le design de la caméra à ses propriétés optiques d'acquisition et qui puisse guider le concepteur dans sa tâche. Cette thèse répond à ces observations en proposant un modèle optique du premier ordre pour représenter n'importe quel appareil d'acquisition plénoptique. Ce modèle abstrait une caméra plénoptique par un réseau équivalent de caméras virtuelles existant en espace objet et qui effectue un échantillonnage identique de la scène. Ce modèle est utilisé pour étudier et comparer plusieurs caméras plénoptiques ainsi qu'un microscope plénoptique monté en laboratoire, ce qui révèle des lignes directrices pour la conception de systèmes plénoptiques. Les simulations du modèle sont aussi validées par l'expérimentation avec une caméra et le microscope plénoptiqueLight field imaging is often presented as a revolution of standard imaging. Indeed, it does bring more control to the user over the final image as the spatio-angular dimensions of the light field offer the possibility to change the viewpoint and refocus after the shot and compute the scene depth map.However, it complicates the work of the optical designer of the system for two reasons. The first is that there exist a multitude of different light field acquisition devices, each with its own specific design. The second is that there is no model that relates the camera design to its optical properties of acquisition and that would guide the designer in his task. This thesis addresses these observations by proposing a first-order optical model to represent any light field acquisition device. This model abstracts a light field camera as en equivalent array of virtual cameras that exists in object space and that performs the same sampling of the scene. The model is used to study and compare several light field cameras as well as a light field microscope setup which reveals guidelines for the conception of light field optical systems. The simulations of the model are also validated through experimentation with a light field camera and a light field microscope that was constructed in our laboratory
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Reeve, James Edward. "Functional dyes as tools for neurophysiology." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:8d8e7fa1-0f1d-4ff5-9f90-6915b15c1ad4.
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The aim of the project described in this thesis is to synthesise new functional molecules which interact with light for neurophysiological applications. In particular, I describe a family of amphiphilic porphyrins with large first hyperpolarisabilities which are used as SHG contrast agents and voltage-sensitive probes. In addition I detail a methodological microscopy tool and a novel caged form of a neuronal ion-channel antagonist. Chapter 1 introduces the key concepts underlying the use of dyes as SHG contrast agents. In particular it focuses on aspects of molecular design, covering both the amphiphilicity and nolinearity required by the target molecule. It covers quantification of the nonlinear properties of SHG stains, then surveys a number of examples which showcase the flexibility of SHG imaging as a biomedical technique. Chapter 2 describes a family of amphiphilic porphyrins with large first hyperpolarisabilities. Working from the structure-property relationships identified in Chapter 1, we fully characterise these dyes and demonstrate that they can be used in SHG imaging. We demonstrate that these molecules may also be tuned by complexation of a metal ion which can modulate their photophysical and solubility behaviour. Chapter 3 provides a description of how to determine the orientational distribution of dipolar dyes in a membrane by multiphoton microscopy. We measure the signal intensity of the dye in a model membrane system then find distributional moments which lead to the distribution itself. Chapter 4 explores whether off-axis contributions to the first hyperpolarisability tensor can significantly augment the dominant on-axis contribution from the main dipolar charge-transfer band. We synthesise and characterise a series of cis-donor cis-acceptor porphyrin compounds and explore their biophysical characteristics. Chapter 5 is the culmination of this project and after discussing method development, goes on to show how we measure the voltage sensitivity of an amphiphilic porphyrin SHG dye. We compare the archetypal porphyrin dye chromophore with three commercially available styryl dyes and demonstrate that our dye has greater sensitivity and a more rapid response. Chapter 6 describes a side project, the use of a photolabile cage to protect MK801, a neuronal ion-channel antagonist. By developing a water soluble photolabile cage using molecular design techniques, we are able to release MK801 in neurons with precise spatiotemporal control, allowing us to pinpoint the locus of two key neurophysiological processes.
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Bola, Sampol Raúl. "Development of optical tools for biological applications based on acousto-optic technology." Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/672264.
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To ensure progress in the field of biomedicine and drug development, it is essential to keep improving the equipment needed to carry out most of the experiments. With better tools, scientists can be more efficient, increasing the quality and volume of collected data from biological samples. At the same time, these tools should offer enough flexibility to adapt to new protocols and experiments.
Among all the tools used in cell biology laboratories, photonic technology is the most popular, since it is considered a non-invasive technique, being fully compatible with living samples. The work done in this thesis focuses on the development of two optical tools with great applicability in the field of cell biology: an optical trapping and force measurement system and a novel and flexible confocal microscopy unit. The combination of both apparatus will allow biologists to manipulate and measure forces inside living cells, while providing high contrast visualization of the specimen in real time. Both technologies share the same light modulator element: an acousto-optic deflector (AOD).
AODs are diffractive devices that use mechanical waves to deflect an incident beam of light with extreme precision and speed (in the kilohertz to megahertz range). Despite being developed in the 30s, their full potential has not been exploited until now. During the thesis, I have carried out a thorough study of the AOD properties, culminating in a new way to understand and use these devices: the acousto-optic holography (AOH). With slight modifications in the control electronics, these devices can be used in the same way as a full complex spatial light modulator. With this new approach, AODs can project arbitrary light patterns and scanning schemes, going beyond their main application as pure beam deflectors.
Incorporating AODs in an optical trapping system allows generating multiple stable optical traps through time multiplexing a single laser beam, catching and manipulating a plurality of objects at the same time. This scheme also allows synchronizing the laser position with a force measurement system based on direct momentum changes, being able to address single object information.
The optical trapping system developed in the first half of this thesis has been used to perform controlled oscillations, as well as measure the response force, in a variety of situations. It has been employed to obtain information about the mechanical properties of some biological structures, such as the cellular cytoskeleton or in active gels of tubulin bundles.
Second, focusing on acousto-optic holography, the thesis presents a new confocal microscope concept: the programmable array microscope, which serves as the starting point for a new generation of solid-state digital microscopes. This new concept proposes eliminating all the mechanical and mobile elements of conventional microscopes and replacing them with fully programmable elements. Specifically, it proposes eliminating the physical ”pinhole” and motorized scanning systems, thus resulting in a very flexible device.
The prototype allows the projection of an infinity of structured light patterns at high speeds to produce high-quality reconstructions. Given the high degree of flexibility, this new solid-state microscope can implement multiple imaging modes that can adapt to the needs of each experiment and/or sample. Apart from implementing already existing techniques, the prototype allows the investigation of new imaging modes and smart scanning schemes. These new modes aim to extract sample information more efficiently, faster, or at a higher resolution.
The thesis details the entire development process of the prototype, both in the optomechanical design, the generation of lighting patterns and scanning schemes. Regarding the confocal filtering part, we present two different solutions. First, we present a set of new image processing algorithms that take advantage of our flexible illumination system. Then, we provide the development of a custom and flexible camera module that allows arbitrary pixel reading.
Finally, with the same technology, two different paths have been explored in the field of super-resolution. On the one hand, the confocal system has been adapted for the parallelization of STED microscopy, speeding up the capture process and presenting promising first results. On the other hand, we have explored computational strategies based on deep learning that allow the recovery of high frequencies. This allows the observation of fine structures well beyond the diffraction limit barrier.Per poder garantir l’avanç de les ciències de la vida, amb la gran repercussió a la salut mundial que això comporta, és important anar millorant les eines amb les quals els científics (especialment els biòlegs) desenvolupen els experiments, podent així millorar la quantitat i el volum de les dades extretes. Amb noves eines, els investigadors poden desenvolupar i dissenyar nous experiments que proporcionin informació rellevant sobre l’estudi i la comprensió de molts processos cel·lulars i malalties. La tesi tracta sobre el desenvolupament de dos sistemes òptics amb gran aplicació en el camp de la biologia, ambdues basades en un element modulador de llum comú, els deflectors acusto-òptics (AODs). El AODs són dispositius totalment analògics, on s’utilitzen ones acústiques per poder modular i deflectar un làser amb una gran precisió i velocitat. A la primera part, s’explica el desenvolupament d’un sistema d’atrapament òptic i mesura de força. El sistema permet atrapar i manipular, de manera estable, múltiples objectes, així com realitzar oscil·lacions controlades. Al mateix temps, el sistema és totalment compatible amb mesura de forces per canvis de moment. Tot això permet paral·lelitzar experiments a l’interior cel·lular de manera totalment invasiva, oferint informació sobre les propietats mecàniques de diverses estructures biològiques. A la segona part, es presenta una nova forma d’entendre i utilitzar aquests dispositius: l’holografia acusto-òptica. Mitjançant la generació de senyals acústiques complexes, els AODs permeten projectar patrons de llum arbitraris, més enllà del seu ús principal com a deflectors làser. Això porta al desenvolupament d’un nou microscopi confocal, totalment programable i sense elements mecànics o mòbils. El microscopi permet projectar una infinitat de patrons de llum estructurada, per tal d’obtenir reconstruccions d’alta qualitat a centenars d’imatges per segon. Aquesta nova plataforma de microscòpia d’estat sòlid, permet investigar i implementar una infinitat de maneres d’imatge, per adaptar-se a les necessitats de cada experiment i / o mostra.
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Logan, Savannah. "Imaging Vibrio Cholerae Invasion and Developing New Tools for 3D Microscopy of Live Animals." Thesis, University of Oregon, 2019. http://hdl.handle.net/1794/24524.
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All animals harbor microorganisms that interact with each other and with their hosts. These microorganisms play important roles in health, disease, and defense against pathogens. The microbial communities in the intestine are particularly important in preventing colonization by pathogens; however, this defense mechanism and the means by which pathogens overcome it remain largely unknown. Moreover, while the composition of animal-associated microbial communities has been studied in great depth, the spatial and temporal dynamics of these communities has only recently begun to be explored.
Here, we use a transparent model organism, larval zebrafish, to study how a human pathogen, Vibrio cholerae, invades intestinal communities. We pay particular attention to a bacterial competition mechanism, the type VI secrection system (T6SS), in this process. In vivo 3D fluorescence imaging and differential contrast imaging of transparent host tissue allow us to establish that V. cholerae can use the T6SS to modulate the intestinal mechanics of its host to displace established bacterial communities, and we demonstrate that one part of the T6SS apparatus, the actin crosslinking domain, is responsible for this function.
Next, we develop an automated high-throughput light sheet fluorescence microscope to allow rapid imaging of bacterial communities and host cells in live larval zebrafish. Light sheet fluorescence microscopy (LSFM) has been limited in the past by low throughput and tedious sample preparation, and our new microscope features an integrated fluidic circuit and automated positioning and imaging to address these issues and allow faster collection of larger datasets, which will considerably expand the use of LSFM in the life sciences. This microscope could also be used for future experiments related to bacterial communities and the immune system.
The overarching theme of the work in this dissertation is the use and development of advanced imaging techniques to make new biological discoveries, and the conclusions of this work point the way toward understanding pathogenic invasion, maximizing the use of LSFM in the life sciences, and gaining a better grasp of host-associated bacterial community dynamics.
This dissertation includes previously published and unpublished co-authored material.
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Baker, Ryan. "IMAGING AND ANALYSIS OF LARVAL ZEBRAFISH GUT MOTILITY, AND AUTOMATED TOOLS FOR 3D MICROSCOPY." Thesis, University of Oregon, 2018. http://hdl.handle.net/1794/23133.
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Nearly all individual members of the animal kingdom have gastrointestinal tracts which feature unique cellular compositions, geometries, and temporal dynamics. These guts are distinct enough from one another, even across siblings or even across the same individual at different points in space and time, that defining meaningful scientific representations of those features is difficult. Studying these guts is also innately challenging as it requires accessing to the insides of the enclosed 3D volumes.
The work presented here describes tools and methodologies designed to address these difficulties. To investigate gut motility, we constructed a combined light sheet fluorescence and differential interference contrast microscope to obtain videos of larval zebrafish (Danio rerio) gut motility and to obtain 3D information about nearby fluorescently tagged cells. Using advanced computer vision algorithms, we quantified aspects of zebrafish gut motility which have never before been characterized, then used that information to identify the effects of different genetic, chemical, and physiological states of zebrafish gut motility. Finally, we designed and constructed an instrument for automating 3D microscopy for future studies.
This dissertation includes previously published and unpublished co-authored material.
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Vathalloor, Mathew Manoj. "Neuron guidance and nano-neurosurgery using optical tools." Doctoral thesis, Universitat Politècnica de Catalunya, 2009. http://hdl.handle.net/10803/33075.
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Jones, Debbie. "Fluorescence spectroscopy and microscopy as tools for monitoring redox transformations of uranium in biological systems." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/fluorescence-spectroscopy-and-microscopy-as-tools-for-monitoring-redox-transformations-of-uranium-in-biological-systems(e5420e94-b96e-4ee1-be63-1a3363672014).html.
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The immobilisation of uranium is an important issue within the nuclear industry due to contaminated land from accidental spillage, weapons testing or mining activities. Within the environment uranium is most commonly found in the +VI oxidation state as the mobile uranyl cation [UO2]2+. Alternatively, the +IV oxidation state can also be found in the environment, forming either an insoluble crystalline uraninite phase, or a more soluble molecular uranium(IV) species. Many endogenous subsurface bacteria can bind and accumulate actinide ions through biosorption and can reduce mobile uranyl(VI) species down to immobile uranium(IV) compounds and mineral phases. This work presents an investigation into the bioreduction process by two anaerobic Gram-negative bacteria, Geobacter sulfurreducens and Shewanella oneidensis MR-1. Luminescence spectroscopy is used to monitor the intensity of uranyl(VI) emission in situ over the course of a 24 hour bioreduction experiment with uranyl(VI) acetate as the electron acceptor and either acetate or lactate as the electron donor. An increase in intensity of the emission around hour three or four during the reduction, followed by an overall decrease, is attributed as the disproportionation of an unstable uranyl(V) intermediate. The role of inner and outer membrane c-typecytochromes as well as flavin secretion is also investigated using three deletion mutants of the S. oneidensis bacteria, which shows that in their absence, the reduction of uranyl(VI) does not occur over the course of 24 hours. The emission of uranium(IV) is also investigated during bioreduction in phosphate media and results show that emission can be observed in aqueous solutions at pH 7 pointing to the presence of a molecular product. One photon confocal and two photon fluorescence microscopy has been utilised for the very first time to directly optically image the bioreduction of uranyl(VI) in combination with luminescence lifetime mapping. The sorption of uranyl(VI) onto the surface of the bacteria with differing lifetimes indicates a direct interaction between uranyl(VI) and surface bound c-type cytochromes, since this variation was not observed in mutant S. oneidensis strains where the cytochromes were not present. Combined, these results have established the applicability of optical spectroscopy and microscopyin tracking the bioreduction of uranium in situ.
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Rosenthal, Malte [Verfasser]. "Clickmers and Aptamers as versatile tools for drug testing and fluorescence microscopy techniques / Malte Rosenthal." Bonn : Universitäts- und Landesbibliothek Bonn, 2020. http://d-nb.info/1224270592/34.
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ALMEIDA, FILHO AMERICO de. "Influencia da preparacao previa de amostras de aco AISI H 13 no comportamento a nitretacao." reponame:Repositório Institucional do IPEN, 1999. http://repositorio.ipen.br:8080/xmlui/handle/123456789/10775.
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Made available in DSpace on 2014-10-09T12:43:52Z (GMT). No. of bitstreams: 0Made available in DSpace on 2014-10-09T14:10:26Z (GMT). No. of bitstreams: 1 06769.pdf: 4275325 bytes, checksum: f2158eb766fa7886249500f40de27cec (MD5)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Dissertacao (Mestrado)
IPEN/D
Instituto de Pesquisas Energeticas e Nucleares, IPEN-CNEN/SP
FAPESP:97/04424-5
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Hernández-Neuta, Iván. "Nucleic acid analysis tools : Novel technologies and biomedical applications." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-146334.
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Nucleic acids are fundamental molecules of living organisms functioning essentially as the molecular information carriers of life. From how an organism is built to how it responds to external conditions, all of it, can be found in the form of nucleic acid sequences inside every single cell of every life form on earth. Therefore, accessing these sequences provides key information regarding the molecular identity and functional state of any living organism, this is very useful for areas like biomedicine, where accessing and understanding these molecular signatures is the key to develop strategies to understand, treat and diagnose diseases. Decades of research and technological advancements have led to the development of a number of molecular tools and engineering technologies that allow accessing the information contained in the nucleic acids. This thesis provides a general overview of the tools and technologies available for nucleic acid analysis, and proposes an illustrative concept on how molecular tools and emergent technologies can be combined in a modular fashion to design methods for addressing different biomedical questions. The studies included in this thesis, are focused on the particular use of the molecular tools named: padlock and selector probes, rolling circle amplification, and fluorescence detection of single molecules in combination with microfluidics and portable microscopy. By using this combination, it became possible to design and demonstrate novel approaches for integrated nucleic acid analysis, inexpensive digital quantification, mobile-phone based diagnostics and the description of viral infections. These studies represent a step forward towards the adoption of the selected group of tools and technologies, for the design and building of methods that can be used as powerful alternatives to conventional tools used in molecular diagnostics and virology.At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 1: Manuscript.
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Kamberger, Robert [Verfasser], and J. [Akademischer Betreuer] Korvink. "Manufacturing Methods for Magnetic Resonance Microscopy Tools with Application to Neuroscience / Robert Kamberger ; Betreuer: J. Korvink." Karlsruhe : KIT-Bibliothek, 2017. http://d-nb.info/1135266255/34.
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López, Conesa Lluís. "Advanced TEM imaging tools for materials science." Doctoral thesis, Universitat de Barcelona, 2015. http://hdl.handle.net/10803/395195.
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Being able to directly relate the final properties with the intimate structure provides a unique insight into the functionality of materials and devices, especially when compared to the necessarily statistical nature of the information that can be retrieved by macroscopic measurements. In particular, the scale reduction associated with the Nanoscience and Nanotechnology revolution demands characterization tools capable of reaching an unprecedented resolution, in a wide range of fields, not only for standard quality control, but in order to understand the properties of matter at the nanoscale. Going from bigger to smaller devices, but also from elemental building blocks (even atoms) to bigger assemblies, basic properties and device functionalities meet. With its ability to provide different kinds of information at a very high spatial resolution, state-of-the-art TEM and related techniques are in the core of this multidisciplinary and rapidly growing field.
The first major topic is related to the assessment of local atomic ordering/disordering phenomena in functional materials. A series of rare earth niobates (RE3NbO7) will be studied in order to understand the microstructural origin of their proton conduction properties, that make them excellent candidates to be used as electrode materials in solid oxide fuel cells. Also, single crystals of the tetragonal tungsten bronze (TTB) Sr0.33Ba0.66Nb2O6 (SBN-67) will be studied by different TEM techniques in order to assess the possible short range structural and/or chemical disorder. These features are thought to be responsible for the observed macroscopic uniaxial polarization vector of the material as well as its relaxor properties.
A second major topic of interest will be the phenomena taking place at interfaces. This includes the characterization of a set of LaNiO3 perovskite thin films grown on different substrates (LAO, LSAT, STO, YAO). The effect of the substrate-induced compressive/tensile strain, given by lattice mismatch, on the structure of the films will be assessed and related to the observed electric transport properties.
The interfaces in a GaN/InAlN multilayered system designed as a Bragg reflector for laser cavities applications will be investigated in order to account for a lower than expected reflectivity of the devices. The presence of structural defects and the detection of intergrowth of wurtzite and zinc blende phases of GaN in thin films will be addressed.
Also regarding interfaces and strain conditions, the characterization of the free surface of Nb2O5 nanorods, as a key point for their humidity sensing properties. Expanding on this, the strain state of Nb2O5 when grown on SnO2 nanowires will also be studied. The coupling of the sensing capabilities of Nb2O5 with the electrical transport properties of SnO2 is of particular interest for functional sensing devices. Therefore, defects at the interface and strain state are of capital interest in order to understand the band structure alignment of the system.
Interfaces in lower dimensionality systems will also be studied, as in the case of Ag@Fe3O4 dimers for applications in magnetoplasmonics. The epitaxial quality,
strain, and the possible chemical diffusion through the contact surface of the two phases of the dimer are key aspects in order to properly tailor their optical properties.
The last major topic is the mapping of magnetic fields at the nanoscale. The magnetic configurations of different geometric arrangements of magnetite Fe3O4 nanocubes will be studied. This characterization is aimed at obtaining enhanced responses in magnetic hyperthermia treatments for cancer.
Given the strong interrelationship between the problems under study, the chapter structure follows the dimensionality of the systems under study (3D, 2D, 1D and 0D systems).La reducció en l'escala espacial associada a la revolució de la Nanociència i la Nanotecnologia fa necessari comptar amb una sèrie d'eines capaces d'assolir una resolució sense precedents en una gran varietat d'àress, ja no tan sols com a control de qualitat, sinó per tal d'entendre les propietats de la matèria a la nanoescala. La correlació de la configuració estructural, la composició química i les distribucions de càrrega amb les propietats funcionals és imprescindible pel disseny de nous dispositius, tant des de la perspectiva 'top down' (reducció de les dimensions dels dispositius) com de la perspectiva 'bottom up' (fabricació d'estructures complexes a partir de blocs més petits, fins i tot àtoms). La capacitat de la Microscòpia Electrònica de Transmissió (TEM) de proporcionar diferents tipus d'informació amb una alta resolució espacial, situa les tècniques avançades de TEM com a peça clau en el desenvolupament d'aquest camp multidisciplinari i creixent. L'objectiu principal d'aquesta tesi ha estat l'aplicació de tècniques quantitatives d'imatge TEM per la resolució de problemes en ciència dels materials. La tesi cobreix un espectre ampli pel que fa al tipus de materials estudiats i els seus camps d'aplicació. El Capítol 1 presenta una introducció general a la teoria de formació d'imatge aplicada a la microscopia TEM. S'hi exposen els diferents fenòmens d'interacció electró-matèria que són responsables dels diferents tipus de contrast que es poden trobar a les imatges TEM. El Capítol 2 presenta les tècniques experimentals que es faran servir en la caracterització dels materials, en concret la simulació d'imatges d'alta resolució (HRTEM), l'holografia electrònica i l'anàlisi de la fase geomètrica (GPA). S'hi pot trobar una descripció del marc teòric i dels fonaments experimentals, juntament amb un resum dels resultats més recents en aquests camps. Els resultats experimentals s'agrupen en els capítols posteriors segons la dimensionalitat dels sistemes estudiats. En ordre decreixent de dimensionalitat s'hi inclouen: materials massius (3D), capes primes (2D), nanofils (1D) i nanopartícules (1D).
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Diederich, Benedict [Verfasser], Rainer [Gutachter] Heintzmann, and Christian [Gutachter] Eggeling. "Democratizing microscopy by introducing innovative Open-Source hard and software tools / Benedict Diederich ; Gutachter: Rainer Heintzmann, Christian Eggeling." Jena : Friedrich-Schiller-Universität Jena, 2021. http://d-nb.info/1239177542/34.
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Woringer, Maxime. "Tools to analyze single-particle tracking data in mammalian cells." Electronic Thesis or Diss., Sorbonne université, 2019. http://www.theses.fr/2019SORUS419.
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Ce travail présente des outils pour analyser la régulation de la transcription dans les cellules eucaryotes, en particulier pour le suivi de facteurs de transcription (TF) individuels dans les cellules de mammifères. Un noyau de cellule eucaryote est complexe et contient de nombreuses molécules (ADN, ARN, protéines, ATP, etc). Ces molécules interagissent avec des TF et influencent la transcription. Certaines de ces interactions peuvent être étudiées par des techniques de biochimie. La plupart, en particulier les interactions faibles, non covalentes, sont invisibles par ces méthodes. La microscopie de cellules vivantes et le suivi de molécules uniques (SPT en anglais) sont de plus en plus utilisées pour étudier ces phénomènes. L'inférence des paramètres biophysiques d'un facteur de transcription, par exemple son coefficient de diffusion, son nombre de sous-populations ou son temps de résidence sur l'ADN sont cruciaux pour comprendre sa dynamique et son influence sur la transcription. Des outils validés et précis sont donc nécessaires pour analyser les données de SPT. Pour être utile, un outil de SPT doit être non seulement validé, mais aussi accessible à des non-programmeurs. Ils doivent aussi tenir compte des biais expérimentaux présents dans les données. Nous proposons un outil d'analyse de SPT, qui se fonde sur l'estimation du propagateur de la diffusion. Ce outil a été validé et est accessible par une interface web. Nous avons montré qu'il donne des résultats proches de l'état de l'art. Il a été testé dans deux cadres : (1) l'étude de la diffusion augmentée par la catalyse enzymatique in vitro et (2) l'analyse de la dynamique du TF c-Myc dans des cellules de mammifèresThis work aims at providing tools to dissect the regulation of transcription in eukaryotic cells, with a focus on single-particle tracking of transcription factors in mammalian cells. The nucleus of an eukeryotic cell is an extremely complex medium, that contains a high concentration of macromolecules (DNA, RNA, proteins) and other small molecules (ATP, etc). How these molecules interact with transcription factors, and thus influence transcription rates is an area of intense investigations. Although some of these interactions can be captured by regular biochemistry, many of them, including weak, non-covalent interactions remain undetected by these methods. Live-cell imaging and single-particle tracking (SPT) techniques are increasingly used to characterize such effects. The inference of biophysical parameters of a given transcription factor (TF), such as its diffusion constant, the number of subpopulations or its residence time on DNA, are crucial to understanding how TF dynamics and transcription intertwine. Accurate and validated SPT analysis tools are needed. To be used by the community, SPT tools should not only be carefully validated, but also be easily accessible to non-programmers. They should also be designed to take into account known biases of the imaging techniques. In this work, we first propose a tool, accessible through a web interface, based on the modeling of the diffusion propagator. We validate it extensively and show that it exhibits state-of-the art performance. We apply this tool to two experimental settings: (1) the study of catalysis-enhanced diffusion in-vitro and (2) the analysis of the dynamics of the c-Myc transcription factor in mammalian cells
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Ebai, Tonge. "Development of Enhanced Molecular Diagnostic Tools for Protein Detection and Analysis." Doctoral thesis, Uppsala universitet, Molekylära verktyg, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-320380.
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Improved diagnosis, prognosis and disease follow-up is a fundamental procedure and a constant challenge in medicine. Among the different molecular biomarkers, proteins are the essential regulatory component in blood; hence, by developing enhanced specific and sensitive molecular tools will gives great insight into the different processes in disease treatment. In this thesis, we build on the proximity ligation assay to develop and apply new adaptable methods to facilitate protein detection. In paper I, I present a variant of the proximity ligation assay (we call PLARCA) using micro titer plate for detection and quantification of protein using optical density as readout in the fluorometer. PLARCA detected femtomolar levels of these proteins in patient samples, which was considerably below the detection threshold for ELISA. In paper II, we developed and adapted a new method into the in situ PLA methods for detection and identification of extracellular vesicles (EVs) using flow cytometry as readout (a method we call ExoPLA). We identified five target proteins on the surface of the Evs and using three colors, we identified the EV using flow cytometer. In paper III, we aim to improve the efficiency of in situ PLA by creating and developing new designs and versions of the assay we called Unfold probes Through comparison of detection of protein using in situ PLA versus Unfold probes, we observed considerable decrease in non-specific signals, and also a lower detection threshold. In paper IV, we describe the development of a solid phase proximity extension (sp-PEA) assay for protein detection and quantification. We compared detection of IL-8, TNF-alpha, IL-10 and IL-6 using spPEA and PEA; spPEA demonstrations over 2 orders of magnitudes in the lower detection concentrations by decreased in background noise.
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Xu, Daxue. "Analyses of Particulate Contaminants in Semiconductor Processing Fluids." Thesis, University of North Texas, 1998. https://digital.library.unt.edu/ark:/67531/metadc500968/.
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Particle contamination control is a critical issue for the semiconductor industry. In the near future, this industry will be concerned with the chemical identities of contaminant particles as small as 0.01 pm in size. Therefore, analytical techniques with both high chemical sensitivity and spatial resolution are required. Transmission electron microscopy (TEM) provides excellent spatial resolution and yields structural and compositional information. It is rarely used, however, due to the difficulty of sample preparation. The goals of this research are to promote the use of TEM as an ultrafine particle analysis tool by developing new sample preparation methods, and to exploit the new TEM techniques for analysis of particles in semiconductor processing fluids. A TEM methodology for the analysis of particulate contaminants in fluids with an elemental detectability limit as low as 0.1 part per trillion (ppt), and a particle concentration detectability limit as low as 1 particle/ml for particles greater than 0.2 pm was developed and successfully applied to the analysis of particles in HF, H202, de-ionized (DI) water, and on the surface of an electronic device. HF samples from three manufacturers were examined. For HF (B), the maximum particle concentration was 8.3 x 103 particles/ml. Both a viscous material and lath-shaped particles were observed. The Sb concentration was less than 0.6 part per billion (ppb). HF (C) was the cleanest. CaF2 and TiO2 particles were identified in HF (D). For H2 02, iron and tin oxides and hydroxides were identified. The maximum particle concentration was 990 particles/ml. The Sn and Fe concentrations were less than 0.3 ppb. Spherical and dendritic particles were observed. For DI water, spherical and dendritic particles (<2 particles/ml), and particles containing Fe or Si with concentrations less than 0.1 ppt were observed. Contaminants on an electronic device surface were also analyzed. Clusters of small particles were determined to be a mixture of aluminum oxides and aluminum silicates.
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Watabe, Tetsuya. "Booster, a Red－Shifted Genetically Encoded Förster Resonance Energy Transfer (FRET) Biosensor Compatible with Cyan Fluorescent Protein/Yellow Fluorescent Protein-Based FRET Biosensors and Blue Light-Responsive Optogenetic Tools." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263527.
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Grah, Joana Sarah. "Mathematical imaging tools in cancer research : from mitosis analysis to sparse regularisation." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/273243.
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This dissertation deals with customised image analysis tools in cancer research. In the field of biomedical sciences, mathematical imaging has become crucial in order to account for advancements in technical equipment and data storage by sound mathematical methods that can process and analyse imaging data in an automated way. This thesis contributes to the development of such mathematically sound imaging models in four ways: (i) automated cell segmentation and tracking. In cancer drug development, time-lapse light microscopy experiments are conducted for performance validation. The aim is to monitor behaviour of cells in cultures that have previously been treated with chemotherapy drugs, since atypical duration and outcome of mitosis, the process of cell division, can be an indicator of successfully working drugs. As an imaging modality we focus on phase contrast microscopy, hence avoiding phototoxicity and influence on cell behaviour. As a drawback, the common halo- and shade-off effect impede image analysis. We present a novel workflow uniting both automated mitotic cell detection with the Hough transform and subsequent cell tracking by a tailor-made level-set method in order to obtain statistics on length of mitosis and cell fates. The proposed image analysis pipeline is deployed in a MATLAB software package called MitosisAnalyser. For the detection of mitotic cells we use the circular Hough transform. This concept is investigated further in the framework of image regularisation in the general context of imaging inverse problems, in which circular objects should be enhanced, (ii) exploiting sparsity of first-order derivatives in combination with the linear circular Hough transform operation. Furthermore, (iii) we present a new unified higher-order derivative-type regularisation functional enforcing sparsity of a vector field related to an image to be reconstructed using curl, divergence and shear operators. The model is able to interpolate between well-known regularisers such as total generalised variation and infimal convolution total variation. Finally, (iv) we demonstrate how we can learn sparsity promoting parametrised regularisers via quotient minimisation, which can be motivated by generalised Eigenproblems. Learning approaches have recently become very popular in the field of inverse problems. However, the majority aims at fitting models to favourable training data, whereas we incorporate knowledge about both fit and misfit data. We present results resembling behaviour of well-established derivative-based sparse regularisers, introduce novel families of non-derivative-based regularisers and extend this framework to classification problems.
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Schulte, Lukas [Verfasser], Holger [Akademischer Betreuer] Stark, Holger [Gutachter] Stark, and Ralf [Gutachter] Ficner. "New Computational Tools for Sample Purification and Early-Stage Data Processing in High-Resolution Cryo-Electron Microscopy / Lukas Schulte ; Gutachter: Holger Stark, Ralf Ficner ; Betreuer: Holger Stark." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2019. http://d-nb.info/1175204889/34.
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Luther, Ilse. "Semen characteristics of free-ranging African elephants (Loxodonta africana) and Southern white rhinoceros (Ceratotherium simum simum) using Computer-aided sperm analysis, Electron microscopy and Genomics as diagnostic tools." University of the Western Cape, 2016. http://hdl.handle.net/11394/5443.
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Philosophiae Doctor - PhDThe survival of free-ranging (in situ) African elephant and Southern white rhinoceros populations are currently being challenged on a daily basis in Africa. Reproductive health is considered a vital component of species conservation. Conservation of the last mega land mammals may ultimately require intervention by breeding management or combined with assisted reproductive technologies (ART). There is a strong case for gathering baseline information, both physiological and biological, of any species, as opportunities arise. During this study a total number of 21 ejaculates collected over two seasons from 12 free-ranging African elephant bulls were characterised, as well as 10 ejaculates collected from 10 free-ranging Southern white rhinoceros bulls from two populations. Ejaculates were collected from adult bulls by means of electroejaculation under anaesthesia. Routine semen analysis was combined with Computer-aided sperm analysis (CASA), Computer-aided sperm morphology analysis (CASMA), Transmission electron microscopy (TEM) and Genomics as diagnostic tools. Additionally, sperm functionality within different media was investigated and sperm subpopulation classification according to the motion pattern displayed. The results presented is based on the evaluation and classification of ≈ 45 000 individual African elephant spermatozoa and ≈ 18 000 individual Southern white rhinoceros spermatozoa. The average elephant ejaculate contained a total number of 47 x 10⁹ spermatozoa (volume of 56 ± 38mL x concentration of 818 ± 750 x 10⁶/mL) that recorded a total motility of 81 ± 29% of which 62 ± 26% were progressively motile. CASA recorded velocities for curvilinear velocity (VCL 241 ± 58μm/s), straight-line velocity (VSL 173 ± 181μm/s) and average path velocity (VAP 201 ± 54μm/s), and kinematics at straightness of track (STR 86 ± 85%), linearity of track (LIN 67 ± 16%), amplitude of lateral head displacement (ALH 4 ± 0.75μm) and beat cross frequency (BCF 21 ± 3Hz). Structural analysis revealed 68 ± 11% of the spermatozoa were viable (intact plasma membrane) and 77 ± 11% maintained acrosome integrity. Ejaculates contained 55 ± 14% morphologically normal spermatozoa, CASMA measured sperm head lengths at 6.83 ± 0.26μm and width 3.32 ± 0.18μm (total head area of 20.17 ± 1.96μm²) of which 38.95 ± 0.92% is covered by an acrosomal cap. The average rhinoceros ejaculate contained a total number of 1.1 x 10⁹ spermatozoa (volume of 24 ± 24mL x concentration of 83 ± 96 x 10⁶/mL) that recorded a total motility at 82 ± 8% of which 28 ± 23% were progressively motile. CASA recorded velocities for VCL (85 ± 29μm/s), VSL (44 ± 25μm/s) and VAP (69 ± 30μm/s, and kinematics at STR (63 ± 14%), LIN (51 ± 16%), ALH (2 ± 0.16μm) and BCF (16 ± 6Hz). Structural analysis revealed 73 ± 10% of the spermatozoa were viable (intact plasma membrane) and 76 ± 4% maintained acrosome integrity. Ejaculates contained 62 ± 14% morphologically normal spermatozoa, CASMA measured sperm head lengths at 5.5 ± 0.17μm and width 2.9 ± 0.19μm (total head area of 14.8 ± 1.43μm²) of which 36.3 ± 0.59% is covered by an acrosomal cap. Based on a Boolean argument and CASA data exploration it was possible to derive elephant and rhinoceros CASA cut-off criteria to sort between activated and hyperactivated motile spermatozoa. For the genomic component of this study, the CatSper1 (Loxodonta africana) gene was identified,sequenced and verified in a free-ranging (natural) African elephant population. Multivariate analysis(MVA) was applied to examine the associations between the semen and sperm parameters and the traits they accounted for in this study. Our understanding of wildlife reproductive sciences can substantially progress as the analytical techniques applied and the combination thereof is expanded. This investigation presents a new set of comprehensive semen and sperm threshold values for future investigations.
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Alaoui, Lasmaili Karima El. "Caractérisation au moyen d'outils mathématiques des effets vasculaires du bevacizumab à des fins d'optimisation des protocoles thérapeutiques dans le cas des tumeurs cérébrales." Thesis, Université de Lorraine, 2017. http://www.theses.fr/2017LORR0023/document.
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L’objectif principal de ce travail de thèse a été de caractériser les effets de l’anti-VEGF Bevacizumab (Avastin) sur le réseau vasculaire tumoral in vivo, au cours du temps, à l’aide du modèle de la chambre dorsale chez la souris nude. Les images du réseau vasculaire tumoral acquises par microscopie intravitale ont été analysées par un algorithme de traitement d’images développé au sein de notre équipe, permettant de mettre en évidence les modifications morphologiques induites par le traitement et d’isoler des paramètres discriminants de la « normalisation » vasculaire, par comparaison à un réseau vasculaire sain. La période de « normalisation » vasculaire détectée par notre outil a été confortée par l’analyse de la fonctionnalité des vaisseaux sanguins au cours du temps, in vivo et par une analyse immunohistochimique des vaisseaux sanguins tumoraux et du tissu tumoral. A travers des essais préliminaires in vivo, en regard des résultats de ce travail concernant une fenêtre de "normalisation", nous avons cherché à vérifier l'hypothèse d'un bénéfice d'un traitement anti-VEGF préalablement à la thérapie photodynamique (PDT) sur des tumeurs de glioblastome xénogreffées en sous-cutané et en chambre dorsale. L'efficacité de la PDT est décrite comme étant dépendante d'une d'oxygénation tumorale suffisante et d'une distribution maximale de l'agent photosensibilisant au coeur des tumeurs. Parallèlement à ces travaux, nous avons cherché en équipe pluridiscilinaire à développer un modèle mathématique de la réponse au bevacizumab à partir de données biologiques réelles obtenues sur le même modèle in vivo et permettant pour l'avenir de simuler les réponses à différentes doses et différentes durées de traitement, toujours à des fins d'optimisation des protocoles thérapeutiquesThe main aim of this work was to characterize the effects of the anti-VEGF Bevacizumab (Avastin) on the tumor vascular network, in vivo, over time, thanks to the skin fold chamber model on the nude mouse. Images of the vascular network obtained using intravital microscopy were analyzed par a dedicated image processing algorithm developed within our research team, allowing to highlight the morphological modifications induced by the treatment and to isolate discriminating parameters of the vascular "normalization", by comparison to healthy vascular networks. Le vascular "normalization" period detected with our tool was comforted by the analysis of the functionality of the blood vessels over time, in vivo and by an immunohistochemical analysis of the blood vessels and of the tumor tissue. In preliminary in vivo experiments, we tried to verify the hypothesis of the benefits of an anti-VEGF treatment prior to photodynamic therapy (PDT) on glioblastoma xenografts implanted subcutaneously or in the skin fold chamber. The efficacy of PDT is described as being dependent on tumor oxygenation and on the distribution of the photosensitizing agent within the tumor. In paralel to this work, we tried as a pluridisciplinary team to develop a mathematical model of the tumor response to bevacizumab using biological data obtained on the same in vivo model et that will allow in the future to simulate the response for different doses and different treatment durations, for the optimization of therapeutic protocols
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Raman, Purnima. "Freeze drying microscopy as a tool to study sublimation kinetics." Thesis, Loughborough University, 2015. https://dspace.lboro.ac.uk/2134/18316.
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Freeze-drying is the process of removal of water or organic solvent from a desired product by means of sublimation at a low temperature and low pressure. It is commonly employed for drying samples which are heat labile and require sensitive treatment, and is mainly used in the pharmaceutical and food industries. It is an expensive process, requiring vacuum, refrigeration and long cycle times, but does yield quality benefits due to the low temperatures involved and the porous nature of the product. Reducing drying times is important to manufacturers, and this depends on optimising rates of heat and mass transfer in the system without the sample losing its porous structure. However, freeze drying is difficult to study experimentally due to the low temperatures and pressures involved. The quality of the final product mainly depends on the sublimation rate and an optimum lyophilisation requires identification of the parameters which influence the process. The main aim of this study is to employ freeze drying microscopy (FDM) as a useful tool to identify these process parameters and help optimise primary drying phase of the freeze drying process for two systems: lactose (relevant to pharmaceuticals) and coffee (the most widely freeze-dried food product). This equipment allows the movement of sublimation fronts to be directly visualised in-situ under carefully controlled (and isothermal conditions), but has scarcely been used in the literature for this purpose. An image analysis method is developed to automatically track the movement of sublimation fronts, and the frontal data fitted to a simple mass transfer model employing surface and bulk resistances. Initial experiments with lactose solution show poor reproducibility in nucleation temperatures during the freezing step and thus primary drying rates. To improve reproducibility, a small amount of silver iodide (AgI) was added to samples which acts as a nucleating agent and increases the nucleation temperature. This addition of AgI also increases the mean ice crystal size in the samples and are easily visible under the freeze-drying microscope, and in many cases show a distinct orientation with respect to direction of sublimation front. Furthermore, the orientation greatly influences sublimation rates, being approximately factor of two faster when crystals are oriented in the direction of mass transfer. FDM experiments with coffee were less straightforward as nucleation temperatures could not be reliably controlled, even with AgI added. Nevertheless there was a clear decrease of bulk resistance with increasing nucleation temperature. An experimental programme was then undertaken to examine the impact of initial solid content, cooling rate, the addition of an annealing step, freeze drying temperature and aeration (for coffee samples). Frontal data were fitted to a simple mass transfer model comprising surface and bulk (per unit depth) resistances and good fits to data were obtained. FDM experiments with lactose and coffee clearly showed the presence of a surface resistance which could also be seen as a surface layer which was devoid of ice crystals (and hence not porous when sublimed). The edge resistance first increased and then decreased with solids content. The resistance per unit depth increased exponentially with solids content, so much so that there is an optimal solids content (around 10% solids) in relation of the rate of production of dried material. Cooling rates were mainly found to affect the surface resistance rather than bulk resistance and this may be due to different levels of surface drying when the samples are being cooled for different lengths of time. Annealing substantially changed the ice crystal sizes, and had a beneficial effect on freeze drying rates and had a similar effect to adding AgI. Freeze drying rates also increased with increasing temperature approximately in line with the saturated vapour pressure (SVP) of ice which is widely held to constitute the driving force for mass transfer. It was possible to make drying time calculations for conventional vial (lactose) and tray (coffee) drying using the frontal rate data obtained from FDM. For 10% lactose and 10% coffee (annealed) there was good agreement between the vial and tray data and predictions based on a microstructure oriented parallel to the direction of mass transfer. This was the only case where agreement was found, but also the only case where directionality was observed in FDM. The much faster drying times observed in the vial and tray experiments are thus attributed to directional solidification occurring in these systems, and this was borne out by SEM imaging. Aeration of the coffee samples was also found to substantially reduce drying times. The influence of microstructure on freeze drying rates is thus very clear.
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Aljamal, Mohammad Abdulraheem. "Comparison of Microscopic and Mesoscopic Traffic Modeling Tools for Evacuation Analysis." Thesis, Virginia Tech, 2017. http://hdl.handle.net/10919/79592.
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Evacuation processes can be evaluated using different simulation models. However, recently, microscopic simulation models have become a more popular tool for this purpose. The objectives of this study are to model multiple evacuation scenarios and to compare the INTEGRATION microscopic traffic simulation model against the MATSim mesoscopic model. Given that the demand was the same for both models, the comparison was achieved based on three indicators: estimated evacuation time, average trip duration, and average trip distance. The results show that the estimated evacuation times in both models are close to each other since the Origin-Destination input file has a long tail distribution and so the majority of the evacuation time is associated when travelers evacuate and not the actual evacuation times. However, the evaluation also shows a considerable difference between the two models in the average trip duration. The average trip duration using INTEGRATION increases with increasing traffic demand levels and decreasing roadway capacity. On the other hand, the average trip duration using MATSim decreases with increasing traffic demand and decreasing the roadway capacity. Finally, the average trip distance values were significantly different in both models. The conclusion showed that the INTEGRATION model is more realistic than the MATSim model for evacuation purposes. The study concludes that despite the large execution times of a microscopic traffic simulation, the use of microsimulation is a worthwhile investment.Master of Science
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Wan, Yong. "Fluorender, an interactive tool for confocal microscopy data visualization and analysis." Thesis, The University of Utah, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3592436.
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Confocal microscopy has become a popular imaging technique in biology research in recent years. It is often used to study three-dimensional (3D) structures of biological samples. Confocal data are commonly multichannel, with each channel resulting from a different fluorescent staining. This technique also results in finely detailed structures in 3D, such as neuron fibers. Despite the plethora of volume rendering techniques that have been available for many years, there is a demand from biologists for a flexible tool that allows interactive visualization and analysis of multichannel confocal data. Together with biologists, we have designed and developed FluoRender. It incorporates volume rendering techniques such as a two-dimensional (2D) transfer function and multichannel intermixing. Rendering results can be enhanced through tone-mappings and overlays. To facilitate analyses of confocal data, FluoRender provides interactive operations for extracting complex structures. Furthermore, we developed the Synthetic Brainbow technique, which takes advantage of the asynchronous behavior in Graphics Processing Unit (GPU) framebuffer loops and generates random colorizations for different structures in single-channel confocal data. The results from our Synthetic Brainbows, when applied to a sequence of developing cells, can then be used for tracking the movements of these cells. Finally, we present an application of FluoRender in the workflow of constructing anatomical atlases.
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Wong, Tsz-wai Terence, and 黃子維. "Optical time-stretch microscopy: a new tool for ultrafast and high-throughput cell imaging." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hub.hku.hk/bib/B5066234X.
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The exponential expansion in the field of biophotonics over the past half-century has been leading to ubiquitous basic science investigations, ranging from single cell to brain networking analysis. There is also one biophotonics technology used in clinic, which is optical coherence tomography, mostly for high-speed and high-resolution endoscopy. To keep up such momentum, new biophotonics technologies should be aiming at improving either the spatial resolution or temporal resolution of optical imaging. To this end, this thesis will address a new imaging technique which has an ultra-high temporal resolution. The applications and its cost-effective implementations will also be encompassed.
In the first part, I will introduce an entirely new optical imaging modality coined as optical time-stretch microscopy. This technology allows ultra-fast real-time imaging capability with an unprecedented line-scan rate (~10 million frames per second). This ultrafast microscope is renowned as the world’s fastest camera. However, this imaging system is previously not specially designed for biophotonics applications. Through the endeavors of our group, we are able to demonstrate this optical time-stretch microscopy for biomedical applications with less biomolecules absorption and higher diffraction limited resolution (<2 μm). This ultrafast imaging technique is particularly useful for high-throughput and high-accuracy cells/drugs screening applications, such as imaging flow cytometry and emulsion encapsulated drugs imaging.
In the second part, two cost-effective approaches for implementing optical time-stretch confocal microscopy are discussed in details. We experimentally demonstrate that even if we employ the two cost-effective approaches simultaneously, the images share comparable image quality to that of captured by costly specialty 1μm fiber and high-speed ( >16 GHz bandwidth) digitizer. In other words, the cost is drastically reduced while we can preserve similar image quality.
At the end, I will be wrapping up my thesis by concluding all my work done and forecasting the future challenges concerning the development of optical time-stretch microscopy. In particular, three different research directions are discussed.published_or_final_version
Electrical and Electronic Engineering
Master
Master of Philosophy
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Allwell-Brown, Gbemisola. "Individual and household-level determinants of malaria infection in under-5 children from north-west and southern Nigeria : A cross-sectional comparative study based on the 2015 Nigeria Malaria Indicator Survey." Thesis, Uppsala universitet, Internationell mödra- och barnhälsovård (IMCH), 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-324360.
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Introduction Nigeria has the highest malaria burden worldwide. The 2010 and 2015 Nigeria Malaria Indicator Surveys (NMIS) suggest an improvement in malaria indicators, with the North West zone lagging behind. This study aimed to identify the individual and household-level malaria determinants in north-west and southern Nigeria, using Rapid Diagnostic Testing (RDT) and microscopy for malaria diagnosis. Methods Data on 3,358 children aged 6-59 months from north-west and southern Nigeria from the 2015 NMIS was used. The two populations were compared using chi-square tests, and logistic regression analysis was done for determinants of malaria infection, based on RDT and microscopic malaria test results. Results Malaria prevalence by RDT in the north-west and south was 55.8% and 29.2%, respectively (37.0% and 14.9%, respectively by microscopy). In both populations, a higher age, positive RDT in an additional household member and rural residence increased the odds of malaria infection; while higher education of the head of household and greater household wealth lowered the odds of malaria infection. Household clustering of RDT-positive cases appeared to be stronger in the south compared to the north-west. There were no statistically significant differences between the results using RDT or microscopy. Conclusion Irrespective of the diagnostic tool used, malaria determinants were similar in north-west and southern Nigeria. However, poorer social circumstances were observed in the north-west, and may account for the delayed progress in malaria control in the region. There may be a need to intensify malaria control efforts, particularly in the north-west, while awaiting socio-economic development.
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Nyflött, Åsa. "Development of an Image Processing Tool for Fluorescence Microscopy Analysis of Paper Chemistry." Thesis, Karlstads universitet, Fakulteten för teknik- och naturvetenskap, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:kau:diva-6990.
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Paper making today is, to some extent, based on empirical knowledge. It is wellknown that fines, pH, charge and ion strength affect the manufacture of paper. One way of extending knowledge of the mechanisms of paper chemistry is to follow the trajectories of fines and additives in the paper suspension to gather information as to the manner in which they react. Four tracking algorithms adapted to the needs of this particular problem were implemented in order to track particles effciently. The tracking algorithms include two variants of the well-known "Lucas-Kanade algorithm" and template matching techniques based on cross-correlation and least squares matching. Although these techniques are similar in principle, the actual tracking can nevertheless differ; the Lucas-Kanade algorithms were found to be more invariant to noise, whereas the cross-correlation and least squares methods are more rapid to execute in Matlab. The tracking methods have been evaluated using a simulator to generate image sequences of synthetic particles moving according to Brownian motion. Tracking has also been evaluated on microscope images of real latex particles where the results have been compared to manual tracking. Tracking of both the simulated particles and the latex particles resulted in similar results when compared to known position and manual tracking, respectively.Tillverkning av papper är till en viss del baserad på empirisk kunskap. Välkänt är att finmaterial, pH värde, laddning och jonstyrka påverkar de papperskemiska mekanismerna och därmed flertalet pappersegenskaper vid tillverkning av papper. En möjlighet att utveckla kunskaperna inom papperskemiska mekanismerar att studera finmaterial och additiv i en pappers suspension for att samla in informationom reaktionsmekanismer. Fyra trackningalgoritmer ar vidareutvecklade i syftet att möjliggöra studier kring papperskemiska mekanismer. Trackningalgoritmerna inkluderar två varianter av den välkända "Lucas-Kanade" algoritm och två template-baserade metoder: korskorrelation och minsta kvadratmetoden. Samtliga metoder bygger på samma princip, men trots detta kan resultaten från trackningen skilja mellan metoderna. Lucas-Kanade algoritmerna är mer oberoende av brus medan korskorrelationen och minsta kvadratmetoden exekveras snabbare i Matlab. Trackning metoderna utvärderades med hjälp av en simulator som genererar bildsekvenser av syntetiska partiklar med en Brownsk rörelse. Trackningen har även använts på mikroskopibilder av rörelsebanor på verkliga suspenderade latex partiklar, varvid trackningresultatet har jämförts med manuell trackning. De genererade bildsekvensernapa de simulerade partiklarna har kända rörelsebanor som är jämförbara med rörelsebanor for latex partiklarna.
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Tavakoli, Mitra. "Corneal confocal microscopy : a novel non-invasive diagnostic tool for assessing peripheral neuropathies." Thesis, University of Manchester, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.492280.
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Corneal confocal microscopy (GCM) is a novel non-invasive in vivo imaging clinical technique for the study of corneal cellular structure. It provides images of all layers of the cornea which are comparable to in-vitro histochemical techniques. In the series of studies presented in this thesis we have evaluated the considerable potential of GGM to quantify corneal nerve morphology in a range of clinical conditions characterised by small fibre damage. The results indicate that the widest application of GCM may well be in the field of peripheral metabolic (diabetes, Fabry disease) and other causes of neuropathies. Thus CCM may provide a means to identify patients at risk, follow progression and measure therapeutic response in not only diabetic neuropathy but also a range of other neuropathies.
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Jaouen, Kévin. "Backside absorbing layer microscopy : a new tool for the investigation of 2D materials." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS296/document.
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La microscopie optique sur substrats antireflets est un outil de caractérisation simple et puissant qui a notamment permis l'isolation du graphène en 2004. Depuis, le domaine d'étude des matériaux bidimensionnels (2D) s'est rapidement développé, tant au niveau fondamental qu'appliqué. Ces matériaux ultraminces présentent des inhomogénéités (bords, joints de grains, multicouches, etc.) qui impactent fortement leurs propriétés physiques et chimiques. Ainsi leur caractérisation à l'échelle locale est primordiale. Cette thèse s'intéresse à une technique récente de microscopie optique à fort contraste, nommée BALM, basée sur l'utilisation originale de couches antireflets très minces (2-5 nm) et fortement absorbantes (métalliques). Elle a notamment pour but d'évaluer les mérites de cette technique pour l'étude des matériaux 2D et de leur réactivité chimique. Ainsi, les différents leviers permettant d'améliorer les conditions d'observation des matériaux 2D ont tout d'abord été étudiés et optimisés pour deux matériaux modèles : l'oxyde de graphène et les monocouches de MoS₂. L'étude de la dynamique de dépôt de couches moléculaires a notamment permis de montrer à la fois l'extrême sensibilité de BALM pour ce type de mesures et l'apport significatif des multicouches antireflets pour l'augmentation du contraste lors de l'observation des matériaux 2D. L'un des atouts principaux de BALM venant de sa combinaison à d'autres techniques, nous nous sommes particulièrement intéressés au couplage de mesures optiques et électrochimiques pour lesquelles le revêtement antireflet sert d'électrode de travail. Nous avons ainsi pu étudier optiquement la dynamique de réduction électrochimique de l'oxyde de graphène (GO), l'électro-greffage de couches minces organiques par réduction de sels de diazonium sur le GO et sa forme réduite (r-GO), ainsi que l'intercalation d'ions métalliques entre feuillets de GO. En combinant versatilité et fort-contraste, BALM est ainsi établi comme un outil prometteur pour l'étude des matériaux 2D et en particulier pour la caractérisation locale et in situ de leur réactivité chimique et électrochimiqueOptical microscopy based on anti-reflective coatings is a simple yet powerful characterization tool which notably allowed the first observation of graphene in 2004. Since then, the field of two-dimensional (2D) materials has developed rapidly both at the fundamental and applied levels. These ultrathin materials present inhomogeneities (edges, grain boundaries, multilayers, etc.) which strongly impact their physical and chemical properties. Thus their local characterization is essential. This thesis focuses on a recent enhanced-contrast optical microscopy technique, named BALM, based on ultrathin (2-5 nm) and strongly light-absorbing (metallic) anti-reflective layers. The goal is notably to evaluate the benefits of this technique for the study of 2D materials and their chemical reactivity. The various levers to improve 2D materials observation were investigated and optimized for two model materials: graphene oxide and MoS₂ monolayers. The investigation of molecular layer deposition dynamic notably showed the extreme sensitivity of BALM for such measurements and the significant contribution of multilayers anti-reflective coatings to enhance contrast during the observation of 2D materials. One of the main assets of BALM comes from its combination to other techniques. We particularly considered the coupling between optical measurements and electrochemistry for which the anti-reflective layer serves as working electrode. We investigated optically the dynamic of electrochemical reduction of Graphene Oxide (GO), the electrografting of organic layers by diazonium salts reduction on GO and its reduced form (rGO), as well as the intercalation of metallic ions within GO sheets. By combining versatility and high-contrast, BALM is established as a promising tool for the study of 2D materials, especially for the local and in situ characterization of their chemical and electrochemical reactivity
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Gonçalves, Bruno Filipe Pimparel. "Digital imaging processing tools for neuronal images." Master's thesis, Universidade de Aveiro, 2012. http://hdl.handle.net/10773/10584.
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Mestrado em Biomedicina MolecularOs neurónios são celulas especializadas do Sistema Nervoso, cujas funções se baseiam na correta formação de três compartimentos subcelulares primários – corpo celular, axónio e dendrites – e na rede neuronal que formam para passar a informação entre si. A análise quantitativa das características destas estruturas pode ser usada para estudar a relação entre a morfologia e função neuronal, e monitorizar alterações que ocorram em células individuais ou ao nível da rede, que se possam correlacionar com doenças neurológicas. Nesta tese foi efetuada uma pesquisa de ferramentas digitais disponíveis dedicadas ao processamento e análise de imagens neuronais, com enfoque na sua aplicabilidade para analisar as nossas bioimagens neuronais de fluorescência adquiridas no dia-a-dia. Nos programas selecionados (NeuronJ, NeurphologyJ e NeuriteQuant) foi primeiro avaliada a necessidade de preprocessamento, e os programas foram subsequentemente utilizados em conjuntos de imagens de culturas primárias de córtex de rato para comparar a sua eficácia no processamento destas bioimagens. Os dados obtidos com os vários programas foram comparados com a análise manual usando o ImageJ como ferramenta de análise. Os resultados demonstraram que o programa que aparenta funcionar melhor com as nossas imagens de fluorescência é o NeuriteQuant, porque é automático e dá resultados globalmente semelhantes aos da análise manual, especialmente na avaliação do Comprimento das Neurites por célula. Uma das desvantagens é que a quantificação da ramificação das neurites não dá resultados satisfatórios e deve continuar a ser realizada manualmente. Também realizamos uma pesquisa de ferramentas de processamento de imagem dedicada a imagens de contraste de fase, mas poucos programas foram encontrados. Estas imagens são mais fáceis de obter e mais acessíveis economicamente, contudo são mais difíceis de analisar devido às suas características intrínsecas. Para contornar esta lacuna, estabeleceu-se e otimizou-se uma sequência de processamento e análise para melhor extrair informação neuronal relevante de imagens de contraste de fase utilizando o programa ImageJ. A sequência desenvolvida, na forma de uma macro do ImageJ designada NeuroNet, foi aplicada a imagens de contraste de fase de culturas neuronais em diferentes dias de diferenciação, na presença ou ausência de um inibidor farmacológico, com o objetivo de responder a uma questão científica. A macro NeuroNet desenvolvida provou ser útil para analisar estas bioimagens, existindo contudo espaço para ser aperfeiçoada.
Neurons are specialized cells of the Nervous System, with their function being based on the formation of the three primary sub cellular compartments – soma, axons, and dendrites – and on the neuritic network they form to contact and pass information to each other. The quantitative analysis of the characteristics of these structures can be used to study the relation between neuronal morphology and function, and to monitor distortions occurring in individual cells or at the network level that may correlate with neurological diseases. In this thesis a survey of freely available digital tools dedicated to neuronal images processing and analysis was made with an interest in their applicability to analyse our routinely acquired neuronal fluorescent bioimages. The selected program´ (NeuronJ, NeurphologyJ and NeuriteQuant) preprocessing requirements were first evaluated, and the programs were subsequently applied to a set of images of rat cortical neuronal primary cultures in order to compare their effectiveness in bioimage processing. Data obtained with the various programs was compared to the manual analysis of the images using the ImageJ analysis tool. The result show that the program that seems to work better with our fluorescence images is NeuriteQuant, since it is automatic and gives overall results more similar to the manual analysis. This is particularly true for the evaluation of the Neurite Length per Cell. One of the drawbacks is that the quantification of neuritic ramification does not give satisfactory results and is better to be performed manually. We also performed a survey of digital image processing tools dedicated to phase contrast microphotographs, but very few programs were found. These images are easier to obtain and more affordable in economic terms, however they are harder to analyse due to their intrinsic characteristics. To surpass this gap we have established and optimized a sequence of steps to better extract relevant information of neuronal phase contrast images using ImageJ. The work-flow developed, in the form of an ImageJ macro named NeuroNet, was then used to answer a scientific question by applying it to phase contrast images of neuronal cultures at different differentiating days, in the presence or absence of a pharmacological inhibitor. The developed macro NeuroNet proved to be useful to analyse the images however there is still space to improvement.
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Turner, Ian James. "AFM investigations of critical interactions in the Bacillus primosome and Cryogenic AFM : a new tool for structural biology." Thesis, University of Nottingham, 2006. http://eprints.nottingham.ac.uk/10188/.
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In this thesis for the first AFM has been employed for the high resolution imaging of a protein assembly. The DnaB-DnaG Helicase-Primase interaction in Bacillus is the key reaction that causes the switch from primase mode to polymerisation mode. This assembly was imaged using the AFM to a sub-molecular resolution revealing structural detail of the interaction. It is shown that the binding of the primase causes the structure of the helicase to switch from a hexamer to a trimer of dimers with one primase molecule bound to each dimer; also the existance of sub-populations with one and two primases bound suggests a sequential mode of binding. Recently crystallography data has been published that confirms the structural observations generated by AFM here. This is the first time that AFM and crystallography data have been used concurrently to solve the molecular structure of a protein assembly and it shows the potential application of AFM for sub-molecular resolution imaging of other protein assemblies. The role of DnaD in the Bacillus primosome is well established, however, its exact function was unknown. In this thesis AFM was applied to help solve this biomolecular problem, it revealed that DnaD has a pivotal role in early primosome assembly, opening up the DNA allowing other components of the cascade to bind. DnaD was shown to cause supercoiled DNA to adopt an open circular formation; this reaction was shown to be both reversible and universally applicable to all sequences of DNA. Comparisons are made between the role of DnaD and the roles of the histone-like proteins H-NS and HU. These experiments show that AFM can be applied to the imaging of proteins and their interactions with DNA and used to solve biomolecular problems that other techniques cannot solve. The design and implementation of a novel cryogenic AFM system for the imaging of biomolecules at subzero temperatures was executed. Preliminary results show that such a system has the potential to reduce the two main intrinsic effects limiting current AFM imaging; sample softness and thermal motion. The application of AFM in this thesis shows its strength as a tool in molecular biology not only for the high resolution imaging of proteins and protein assemblies but also as a technique that can be uniquely applied to solve biomolecular problems. This thesis also shows for the first time that AFM can be applied to generate sub-molecular resolution of protein assemblies. The strength of the AFM data when combined with crystallography data shows that AFM is a very powerful tool for the imaging of protein assemblies; it could even become the technique of choice
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Maggiano, Corey. "CONFOCAL LASER SCANNING MICROSCOPY AS A TOOL FOR THE INVESTIGATION OF TETRACYCLINE FLUORESCENCE IN ARCHAEOLOGICALHUMAN BONE." Master's thesis, University of Central Florida, 2005. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/2752.
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Fluorochromes such as tetracycline have been used to label bone for histomorphometric analysis, measuring bone formation, growth, maintenance, and pathology. More recently, similar fluorescence has been observed in ancient human bone. Attributed to tetracycline (TC) exposure, this phenomenon could affect various aspects of health during life and/or preservation of remains postmortem. Standard epifluorescence microscopy is the most common tool employed in the analysis of these labels. Though valuable, this technique is limited by its inability to penetrate bone three-dimensionally and its inclusion of out-of-focus light, possibly disrupting accurate analysis. Confocal Laser Scanning Microscopy (CLSM) has been demonstrated as a valuable tool for three-dimensional histology. Its application to the study of compact bone fluorescence has been lacking, especially in archaeological and forensic sciences. In the following two papers, modern TC-controlled bone is compared to well preserved archaeological bone recovered from the Dakhleh Oasis, Egypt, using both standard wide-field and more modern confocal techniques for imaging and analysis. Spectral analysis via CLSM shows that both modern and ancient fluorescent labels in bone share the exact same fluorescence emission peak at 525 nm. Differences in the shape of the spectral curve and photobleaching characteristics are discussed. In addition, CLSM's high-resolution two- and three-dimensional imaging capabilities (in polarized light, scattered light, and fluorescence light) are found to increase the flexibility and creativity of investigations into the occurrence of tetracycline labels in archaeological bone and could have added benefits for modern medical and anatomical experimentation.M.S.
Department of Biology
Arts and Sciences
Biology
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Vieker, Henning [Verfasser]. "Helium Ion Microscopy: a new tool to analyze and modify nanoscale objects / Henning Vieker." Bielefeld : Universitätsbibliothek Bielefeld, 2014. http://d-nb.info/1064382134/34.
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Hermann, Martin, Oliver Nussbaumer, Ralf Knöfler, Paul Hengster, Walter Nussbaumer, and Werner Streif. "Real-Time Live Confocal Fluorescence Microscopy as a New Tool for Assessing Platelet Vitality." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-136619.
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Background: Assessment of platelet vitality is important for patients presenting with inherited or acquired disorders of platelet function and for quality assessment of platelet concentrates. Methods: Herein we combined live stains with intra-vital confocal fluorescence microscopy in order to obtain an imaging method that allows fast and accurate assessment of platelet vitality. Three fluorescent dyes, FITC-coupled wheat germ agglutinin (WGA), tetramethylrhodamine methyl ester perchlorate (TMRM) and acetoxymethylester (Rhod-2), were used to assess platelet morphology, mitochondrial activity and intra-platelet calcium levels. Microscopy was performed with a microlens-enhanced Nipkow spinning disk-based system allowing live confocal imaging. Results: Comparison of ten samples of donor platelets collected before apheresis and platelets collected on days 5 and 7 of storage showed an increase in the percentage of Rhod-2positive platelets from 3.6 to 47 and finally to 71%. Mitochondrial potential was demonstrated in 95.4% of donor platelets and in 92.5% of platelets stored for 7 days. Conclusion: Such fast and accurate visualization of known key parameters of platelet function could be of relevance for studies addressing the quality of platelets after storage and additional manipulation, such as pathogen inactivation, as well as for the analysis of inherited platelet function disordersHintergrund: Die Vitalitätsbestimmung von Blutplättchen ist sowohl für die Analyse angeborener Plättchendefekte als auch für die Qualitätsbestimmung von Plättchenkonzentraten von zentraler Bedeutung. Methoden: In der vorliegenden Arbeit stellen wir eine Methode vor, die mittels einer Kombination von Vitalfarbstoffen und konfokaler «Real time»-Mikroskopie neue Einblicke in die Vitalitätsbestimmung lebender Plättchen ermöglicht. Mittels der Zugabe von FITC-gekoppeltem Weizenkeimlektin (WGA), Tetramethylrhodamin-Methylesterperchlorat (TMRM) und Acetoxymethylester (Rhod-2) wurde bei lebenden Blutplättchen deren Morphologie, mitochondriale Aktivität und Veränderungen im Calcium-Haushalt im Rahmen der Lagerung analysiert. Für die Mikroskopie wurde ein Nipkow-System gewählt, das eine konfokale Mikroskopie lebender Zellen ermöglicht. Ergebnisse: Der Vergleich von 10 humanen Blutplättchenproben zu Beginn bzw. nach 5 und 7 Tagen Lagerung zeigte einen Anstieg der Rhod-2-positiven Plättchen von 3,6 über 47 auf 71%. Die Anzahl der Blutplättchen mit TMRM-positiven Mitochondrien hingegen lag vor der Lagerung bei 95,4% und nach den 7 Tagen Lagerung bei 92,5%. Schlussfolgerung: Die hier vorgestellte Methodik der Bildgebung zur Bestimmung vitaler Parameter von Blutplättchen eignet sich als ergänzende Analysemodalität für eine bessere Bestimmung der Blutplättchenqualität
Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich
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Hermann, Martin, Oliver Nussbaumer, Ralf Knöfler, Paul Hengster, Walter Nussbaumer, and Werner Streif. "Real-Time Live Confocal Fluorescence Microscopy as a New Tool for Assessing Platelet Vitality." Karger, 2010. https://tud.qucosa.de/id/qucosa%3A26667.
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Background: Assessment of platelet vitality is important for patients presenting with inherited or acquired disorders of platelet function and for quality assessment of platelet concentrates. Methods: Herein we combined live stains with intra-vital confocal fluorescence microscopy in order to obtain an imaging method that allows fast and accurate assessment of platelet vitality. Three fluorescent dyes, FITC-coupled wheat germ agglutinin (WGA), tetramethylrhodamine methyl ester perchlorate (TMRM) and acetoxymethylester (Rhod-2), were used to assess platelet morphology, mitochondrial activity and intra-platelet calcium levels. Microscopy was performed with a microlens-enhanced Nipkow spinning disk-based system allowing live confocal imaging. Results: Comparison of ten samples of donor platelets collected before apheresis and platelets collected on days 5 and 7 of storage showed an increase in the percentage of Rhod-2positive platelets from 3.6 to 47 and finally to 71%. Mitochondrial potential was demonstrated in 95.4% of donor platelets and in 92.5% of platelets stored for 7 days. Conclusion: Such fast and accurate visualization of known key parameters of platelet function could be of relevance for studies addressing the quality of platelets after storage and additional manipulation, such as pathogen inactivation, as well as for the analysis of inherited platelet function disorders.Hintergrund: Die Vitalitätsbestimmung von Blutplättchen ist sowohl für die Analyse angeborener Plättchendefekte als auch für die Qualitätsbestimmung von Plättchenkonzentraten von zentraler Bedeutung. Methoden: In der vorliegenden Arbeit stellen wir eine Methode vor, die mittels einer Kombination von Vitalfarbstoffen und konfokaler «Real time»-Mikroskopie neue Einblicke in die Vitalitätsbestimmung lebender Plättchen ermöglicht. Mittels der Zugabe von FITC-gekoppeltem Weizenkeimlektin (WGA), Tetramethylrhodamin-Methylesterperchlorat (TMRM) und Acetoxymethylester (Rhod-2) wurde bei lebenden Blutplättchen deren Morphologie, mitochondriale Aktivität und Veränderungen im Calcium-Haushalt im Rahmen der Lagerung analysiert. Für die Mikroskopie wurde ein Nipkow-System gewählt, das eine konfokale Mikroskopie lebender Zellen ermöglicht. Ergebnisse: Der Vergleich von 10 humanen Blutplättchenproben zu Beginn bzw. nach 5 und 7 Tagen Lagerung zeigte einen Anstieg der Rhod-2-positiven Plättchen von 3,6 über 47 auf 71%. Die Anzahl der Blutplättchen mit TMRM-positiven Mitochondrien hingegen lag vor der Lagerung bei 95,4% und nach den 7 Tagen Lagerung bei 92,5%. Schlussfolgerung: Die hier vorgestellte Methodik der Bildgebung zur Bestimmung vitaler Parameter von Blutplättchen eignet sich als ergänzende Analysemodalität für eine bessere Bestimmung der Blutplättchenqualität.
Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.
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Bergmann, Stephan [Verfasser]. "Optimizing single molecule localization microscopy as a tool in chemistry, biology, and physics / Stephan Bergmann." Bielefeld : Universitätsbibliothek Bielefeld, 2020. http://d-nb.info/1204561869/34.
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Christou, Nina-Eleni. "Development of NMR as a tool for the structural and dynamic high-resolution characterization of phototranformable fluorescent proteins." Thesis, Université Grenoble Alpes, 2020. http://www.theses.fr/2020GRALY051.
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La découverte de protéines fluorescentes photo-transformables (PTFP) au cours des dernières décennies a révolutionné le domaine de la microscopie optique. Les protéines fluorescentes réversiblement commutables (RSFP), en particulier, sont couramment utilisées pour les techniques de microscopie à super-résolution comme en RESOLFT (REversible Saturable OpticaL Fluorescence Transitions) par exemple. Par photoactivation, les RSFP passent d'un état "on" - fluorescent - à un état "off" - éteint - qui, combiné à des systèmes d'illumination avancés permet d'imager des composants cellulaires préalablement marqués à une résolution nanométrique. De nombreuses études cristallographiques sur les RSFP ont apporté des informations structurelles importantes et ont permis de dresser des hypothèses quant à leur comportement photo-physique. Elles ont également guidé l'ingénierie des protéines fluorescentes afin d'améliorer leur conception et leur utilisation in vivo. Cependant, les cristaux de ces protéines qui sont étudiées à des températures cryogéniques ne permettent pas de capturer la dynamique moléculaire des RSFP dans le but de comprendre, voir d'améliorer leur propriétés photo-physique. C'est pourquoi au cours de ma thèse, j'ai majoritairement utilisé la résonance magnétique nucléaire (RMN) en solution multidimensionnelle sur une RSFP verte - appelée rsFolder - afin de compléter et améliorer nos connaissances sur ces protéines. À l'aide d'un dispositif d'éclairage laser in situ portatif couplé au spectromètre RMN, j'ai pu extraire des informations dynamiques locales quantitatives concernant les états "on" et "off" fluorescents de rsFolder qui sont respectivement caractérisés par un chromophore en conformation cis et trans. Les signatures des résidus dans l'état "off" non fluorescent ont été identifiées à l'aide d'expériences de RMN d'échange induite par LASER. L'état "off" métastable de rsFolder apparaît plus dynamique dans l'échelle de temps de la milliseconde que l'état "on" fluorescent. La RMN a également permis de mettre en lumière quatre configurations du chromophore possible qui sont pH dépendante. De plus, j'ai observé pour la première fois l'isomérisation du chromophore induite par le pH cis-trans. Les valeurs dérivées de la RMN des énergies d'activation concernant l'isomérisation et les différences d'énergie libre entre le chromophore cis et trans ont permis de cartographier le paysage d'énergie libre de l'état fondamental de rsFolder à différents pH. Enfin, la comparaison de données de RMN et des mesures optiques sur rsFolder ainsi que sur différents mutants a mis en évidence le rôle important que la RMN peut jouer dans le domaine de l'ingénierie des RSFPs.Dans l'ensemble, mes travaux de thèse ont permis non seulement d'établir un système d'illumination in situ fiable, accompagné d'expériences de RMN pertinentes dans le but d'étudier les RSFP mais aussi de souligner l'importance de la dynamique moléculaire dans la compréhension des propriétés photo-physiques des RSFPsThe discovery of Phototransformable Fluorescent proteins (PTFPs) over the last decades has revolutionized the field of microscopy. Reversibly photo-switchable fluorescent proteins (RSFPs), in particular, are currently routinely used for Super Resolution Microscopy techniques, such as RESOLFT (REversible Saturable OpticaL Fluorescence Transitions). Photo-induced switching between a fluorescent "on"- and a dark "off"-state, in combination with advanced illumination schemes has allowed for imaging nanometer sized compartments in biological cells. Crystallographic studies of such RSFPs have provided useful mechanistic explanations for their photophysical behaviour and has guided fluorescent protein engineering into designing better tags. However, the crystal forms of such proteins studied at cryogenic temperatures fail to capture dynamics present in RSFPs which could potentially play a significant role in their photophysics. So far, only a single NMR study for the RSFP Dronpa has been reported in the literature (Mizuno, 2008). During my PhD thesis, I was able to complement crystallographic studies of rsFolder, a green RSFP, with a dynamic perspective using multidimensional solution NMR spectroscopy.Using a portable in-situ laser illumination device coupled with the NMR spectrometer, I was able to extract quantitative local dynamic information for both the fluorescent "on"- and "off"-states of rsFolder, characterized by a primarily cis and trans chromophore, respectively. NMR signatures of residues in the non-fluorescent "off"-state were identified using LASER-driven Exchange NMR experiments. The metastable photo-induced "off"-state of rsFolder appears more dynamic on the millisecond timescale than the fluorescent "on"-state. NMR investigations of the chromophore resulted in the deciphering of four configurations, populated in a pH-dependent fashion. Moreover, pH-induced cis-trans isomerization of the chromophore was observed, in the absence of light. NMR-derived values of activation energies for isomerization and free energy differences between the cis and trans chromophore enabled the mapping of the ground-state free energy landscape of rsFolder at different pH values and buffer compositions. Lastly, comparing NMR observables with optical measurements on rsFolder and mutants highlights the potential role that NMR can play in the field of RSFP engineering. Altogether, my PhD work yielded in not only a reliable in-situ illumination set-up accompanied with relevant NMR experiments to study RSFPs, but also highlighted the importance of dynamics in understanding RSFPs' photophysical properties
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Wendland, Kristin [Verfasser]. "Semi-automated fluorescence microscopy and automated image analysis as a tool to study neuronal survival / Kristin Wendland." Berlin : Medizinische Fakultät Charité - Universitätsmedizin Berlin, 2021. http://d-nb.info/124154090X/34.
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Fries, Ryan. "Evaluating the impacts of accelerated incident clearance tools and strategies by harnessing the power of microscopic traffic simulation." Connect to this title online, 2007. http://etd.lib.clemson.edu/documents/1181669446/.
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GOUVEA, CRISTOL DE PAIVA. "DUAL BEAM MICROSCOPY AS A MODIFICATION AND CHARACTERIZATION TOOL OF ORGANIC SEMICONDUCTOR THIN FILMS AND FOR DEVICE FABRICATION." PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO, 2016. http://www.maxwell.vrac.puc-rio.br/Busca_etds.php?strSecao=resultado&nrSeq=29615@1.
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PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIROCOORDENAÇÃO DE APERFEIÇOAMENTO DO PESSOAL DE ENSINO SUPERIOR
PROGRAMA DE SUPORTE À PÓS-GRADUAÇÃO DE INSTS. DE ENSINO
PROGRAMA DE EXCELENCIA ACADEMICA
Nesta tese de doutoramento apresentamos a técnica de microscopia de feixe duplo (MEV e FIB) como uma ferramenta modificadora das propriedades físico-química dos semicondutores orgânicos, a qual pode ser eficaz para alterar e controlar a mobilidade dos portadores de carga nestes materiais semicondutores. Neste caso, filmes finos e dispositivos orgânicos, principalmente à base de tiofeno, foram bombardeados com diferentes doses de íons de Ga com objetivo de induzir modificações na estrutura polimérica a partir das diversas interações entre o íon e o polímero. As propriedades dos filmes finos e dos dispositivos bombardeados foram caracterizadas através das técnicas de UV-Vis, Espectroscopia Raman e CELIV, as quais indicaram a existência de dois regimes de comportamentos governados pela dose de íons empregada. Técnicas avançadas de microscopia eletrônica indicaram a formação de uma estrutura tipo grafítica, em torno de 50 nm da superfície do bombardeamento, decorrente da interação entre os íons de gálio e a camada polimérica. A possibilidade de construir dispositivos orgânicos intercalados com camadas grafíticas pode ser explorada de forma a construir arquiteturas mais eficientes, explorando a alta resolução espacial que a técnica FIB proporciona.
In this doctoral thesis we presented the dual-beam microscopy (SEM and FIB) technique as a modifier tool of physicochemical properties of the organic semiconductors, which it can be effective to change and control the charge carrier mobility into these semiconductor materials. In this case, organic devices and thin films, especially at thiophene base, were bombarded with different Ga ion doses in order to induce modification in the polymeric structure from the various interactions between the ion and the polymer. The bombarded thin films and devices properties were characterized by UV-Vis, Raman spectroscopy and CELIV techniques, which indicated the existence of two behavior regimes governed by the ion dose employed. Advanced electron microscopy techniques indicated the formation of a graphitic structure, around 50 nm from the surface bombardment, resulting of the interaction between the gallium ions and the polymer layer. The possibility to fabricate organic devices interspersed with graphitic layers can be exploited in order to construct more efficient architectures, using the high spatial resolution of the FIB technique.
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Axelsson, Eva, and Therese Wilson. "Microscopic simulation as an evaluation tool for the road safety of vulnerable road users." Thesis, Linköpings universitet, Kommunikations- och transportsystem, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-130010.
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Traffic safety has traditionally been measured by analyzing historical accident data, which is a reactive method where a certain number of accidents must occur in order to identify the safety problem. An alternative safety assessment method is to use proximal safety indicators that are defined as measures of accident proximity, which is considered a proactive method. With this method it is possible to detect the safety problem before the accidents have happened. To be able to detect problems in traffic situations in general, microscopic simulation is commonly used. In these models it may be possible to generate representative near-accidents, measured by proximal safety indicator techniques. A benefit of this would be the possibility to experiment with different road designs and evaluate the traffic safety level before reconstructions of the road infrastructure. Therefore has an investigation been performed to test the possibility to identify near-accidents (conflicts) in a microscopic simulation model mimicking the Traffic Conflict Technique developed by Hydén (1987). In order to perform the investigation a case study has been used where an intersection in the city center of Stockholm was studied. The intersection has been rebuilt, which made it possible to perform a before and after study. For the previous design there was a traffic safety assessment available which was carried out using the Traffic Conflict Technique. Microscopic simulation models representing the different designs of the intersection were built in PTV Vissim. In order to evaluate and measure the traffic safety in reality as well as in the microscopic simulation models, a traffic safety assessment was performed in each case. The traffic safety assessment in field for the present design was carried out as a part of this thesis. The main focus of this thesis was the road safety for vulnerable road users. The method to identify conflicts in the simulation model has been to extract raw data output from the simulation model and thereafter process this data in a Matlab program, aiming to mimic the Traffic Conflict Technique. The same program and procedure was used for both the previous and the present design of the intersection. The results from the traffic safety assessment in the simulation model have been compared to the results from the field study in order to evaluate how well microscopic simulation works as an evaluation tool for traffic safety in new designs. The comparison shows that the two methods of conflict identification cannot replace each other straight off. But with awareness of the differences between the methods, the simulation model could be used as an indication when evaluating the level of traffic safety in a road design.
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Kilani, Suha School of Medicine UNSW. "The use of polarised light microscopy as a non-invasive tool for early assessment of human oocytes and embryos." Awarded by:University of New South Wales. School of Medicine, 2007. http://handle.unsw.edu.au/1959.4/35247.
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The overall aim was to evaluate a non-invasive technique for the assessment of oocytes and embryos using polarized light microscopy (PolScope-LC) with the goal of improving success rates in IVF. A literature review revealed little validation of the PolScope techniques in published work. A reproducible and accurate method for measuring the zona pellucida (ZP) thickness and density involving the PolScope computer software was validated by achieving low coefficient of variance and small inter/intra observer errors. Utilizing this method, 1477 oocytes from 211 stimulated cycles were analysed in this thesis. Results showed that increasing age has an adverse effect on the ZP thickness and density. Study of extended culturing of embryos showed that the ZP starts thinning as early as day 3 and embryos tend to have denser zonas over time. Standardisation of timing of PolScope observations in relation to the meiotic spindle was studied. Metaphase II oocytes were examined sequentially in culture from aspiration until microinjection using the PolScope The spindle is a highly dynamic structure that can appear and disappear over time in culture. A visible spindle was detected in 58% of the oocytes immediately after aspiration. This percentage increased until it stabilised at 39-40hrs post hCG and then declined significantly. Average spindle signal intensity increased over time reaching its peak at 39-40hrs post hCG, then declined significantly by 40.5hrs post hCG. The importance of spindle presence and morphology was investigated by following up embryos created after sperm injection at 39-40hrs post hCG. There was a significant relationship between normal meiotic spindle shape and density and embryo quality. A higher percentage of ???usable??? embryos, and all of pregnancies, arose from oocytes with a normal barrel shaped spindle. Finally, the impact of two issues related to spindle formation - the type of hCG used to trigger oocyte maturation and the site of microinjection during ICSI were assessed using the PolScope. The results showed a biological difference in spindle formation and embryo quality between rhCG and uhCG. In a separate randomised trial embryo quality was better when injecting the sperm in the vegetal pole away from the spindle during ICSI. The results from this thesis suggest that PolScope, if appropriately applied, may assist in improving IVF outcome.
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Thevathasan, Jervis Vermal [Verfasser], and Jonas [Akademischer Betreuer] Ries. "Establishing single-molecule localization microscopy as a quantitative tool towards structural cell biology. / Jervis Vermal Thevathasan ; Betreuer: Jonas Ries." Heidelberg : Universitätsbibliothek Heidelberg, 2020. http://d-nb.info/122083629X/34.
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Holroyd, Dale. "Atomic force microscopy : a novel tool for the analysis of the mechanism of action of antimicrobial peptides on target membranes." Thesis, Stellenbosch : Stellenbosch University, 2003. http://hdl.handle.net/10019.1/53306.
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Thesis (MSc)--Stellenbosch University, 2003.ENGLISH ABSTRACT: Nanoscale visualisation of live cells and cellular components under physiological conditions has long been a goal in microscopy. The objective of this study was to validate the use of Atomic Force Microscopy (AFM) as a new tool in unravelling the mysteries of antimicrobial peptide mechanism of action. Using the simplest AFM imaging technique, we were able to analyse the influence of haemolytic melittin and anti-bacterial magainin 2 on different target membranes at nanometer resolution, without using fixing agents. First, magainin 2 was synthesised and purified by gel permeation chromatography and high performance liquid chromatography (HPLC). The purity of magainin 2 and melittin, isolated from bee venom (Sigma-Aldrich), was verified with electro spray ionisation mass spectrometry (ESI-MS). Second, dose-response experiments were used to determine the optimum peptide/target cell ratio that would allow interaction with the membrane without causing lysis. Third, peptide/target-cell samples were placed on silica plates and visualised using contact mode AFM. Images obtained of the cells before and after peptide treatment, showed distinct changes in cell membrane surface topology. We observed grooves, lesions, membrane collapse and vesiculation depending on the concentration, type of peptide and target-cell used, allowing us to make conclusions regarding the mechanism of action of melittin and magainin 2. In comparison with model membrane studies, our AFM results show that a peptide can function by more than one mechanism of action depending on the structural composition of the membrane, which appears to have specific segregated lateral organisation. Magainin 2 (non-toxic) selectively targets cell membranes using different mechanisms of action. In this way it can lyse bacterial membranes (anti-bacterial agent) using one mechanism, while using another mechanism to interact with mammalian cells at physiological concentrations, without destroying them. In contrast, melittin (toxic) is non-selective, and uses the same mechanism of interaction with bacterial and mammalian cells. In conclusion, we propose a new holistic model for the mechanism of action of antimicrobial peptides.
AFRIKAANSE OPSOMMING: Nanoskaal visualiseering van lewende selle en sellulêre komponente onder fisiologiese toestande is al 'n geruime tyd 'n mikpunt in mikroskopie. Die doel van hierdie studie was om antimikrobiese peptiede se meganisme van werking op teikenselle op nanoskaalvlak met AFM te visualiseer. Sonder om fikseermiddels by te voeg, het ons die eenvoudigste AFM tegniek gebruik om die effek van hemolitiese melittien en anti-bakteriële magainin 2 op verskillende teikenselle, in nanometer resolusie, waar te neem. Eerstens is Magainin 2 gesintesiseer en gesuiwer met behulp van gelpermeasie chromatografie en hoë doeltreffenheid vloeistof chromatografie (HPLC). Die suiwerheid van magainin 2 en kommersiële bye gif melittien, is bevestig met behulp van elektrosproei-ionisasie massaspektrometrie (ESI-MS). Tweedens, is dosis-respons eksperimente gebruik om die optimale peptied/teikensel verhouding te bepaal voordat membraanliese plaasvind. Derdens, is peptied/teikensel monsters op silika plate gevisualiseer met gebruik van kontak AFM. Die beelde van die selle, voor en na peptied behandeling, het duidelike veranderinge in seltopologie getoon. Ons het groewe, letsels, membraaninstorting en vesikulasie, afhangende van die konsentrasie peptied en teikensel gebruik, waargeneem. Dit het ons toegelaat om tot gevolgtrekkings te kom aangaande die meganisme van werking van melittien en magainin 2. In ooreenstemming met model membraan studies, het ons AFM resultate gewys dat 'n peptied veelvoudige meganismes van werking kan hê, afhangend van die strukturele samestelling van die membraan, wat klaarblyklik laterale segregasie toon. Magainin 2 (nie-giftig) is selektief ten opsigte van teikenselle omdat dit gebruik maak van verskillende meganismes van werking op bakteriële en soogdier selle. In teenstelling is melittien (giftig) nie-selektief, en gebruik dieselfde meganisme van werking op bakteriële en soogdierselle. Ten slotte, stel ons 'n nuwe model vir die meganisme van werking voor.
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Amante, Joseph David. "Scanning Methods as Monitoring, Verification, and Accounting tools for CO₂ Sequestration in Unconventional Gas Reservoirs." Thesis, Virginia Tech, 2015. http://hdl.handle.net/10919/76047.
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Unconventional gas reservoirs in carbon dioxide sequestration activities is a relatively new and unexplored concept currently undergoing pilot scale testing. Sequestration has the potential for enhancing gas recovery while mitigating carbon dioxide to long term storage structures. Due to the extremely complex systems associated with these unconventional reservoirs, modeling becomes difficult to predict accurately. This thesis presents methods to increase the confidence of inferred parameter testing for unconventional reservoir sequestration in both seam coal bed methane wells and a shale wells. Various tests include the use of computed tomography coupled with Avizo modeling software, inductively coupled mass spectrometer fluid transport analysis, pressure transient build tests, liquid level detection, and desorption analysis coupled with cleat image analysis. Analyses of coals performed by both environmental scanning electron microscope (ESEM) and micro CT demonstrate that distributions of cleat porosity in coals are anisotropic and not correlated to the seam depth or location. ESEM is used with micro CT scanning to verify the results before and after the impregnation of the carbonic acid. The micro CT data in Avizo Fire© was used calculate an increase in cleat permeability by 25%. The increase of major flow pathways is caused by the dissolution of carbonates. Changes in the structures were observed qualitatively through ESEM and micro CT and quantitatively through Avizo and inductively coupled mass spectrometry. The results of comparative study between the cleat structures and the desorption of various seams indicate a trend in the cleat porosity and the desorption rate of the coals as well as the cleat porosity and the total gas in various seams.Master of Science
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Khadhraoui, Boutheina. "éco-extraction assistée par ultrasons des plantes médicinales : mécanisme(s), intensification et industrialisation ULTRASOUND TECHNOLOGY FOR FOOD PROCESSING, PRESERVATION AND EXTRACTION Histo-cytochemistry and scanning electron microscopy for studying spatial and temporal extraction of metabolites induced by ultrasound. Towards chain detexturation mechanism Microscopic imaging as a tool to target spatial and temporal extraction of bioactive compounds through ultrasound intensificationUltrason. Review of Alternative Solvents for Green Extraction of Food and Natural Green solvents for analytical chemistry." Thesis, Avignon, 2019. http://www.theses.fr/2019AVIG0715.
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Le retour à la naturalité a favorisé le développement des compléments alimentaires à base de ressources végétales qui apparaissent comme un réservoir quasi-infini de nutriments et de substances naturelles bioactives. Ceci fait de l’extraction solide/liquide une étape incontournable au sein des industries intéressées par ce type de molécules. Avec les préoccupations environnementale set sociétales, il est devenu nécessaire d’inventer et développer de nouveaux procédés qui répondent aux six principes de l’éco-extraction. Cette démarche a totalement inspiré cette thèse qui a pour principal objectif le développement d’une technique d’éco-extraction assistée par ultrasons en substitution de la technique conventionnelle. Ce travail a permis de montrer qu’il était possible d’intensifier l’extraction de composés d’intérêt en utilisant les ultrasons avec une meilleure sélectivité et de meilleurs rendements d’extraction. Une attention particulière a été accordée à la compréhension des mécanismes d’action des ultrasons via une étude macroscopique et microscopique approfondie des structures végétales. Cette investigation a prouvé que les ultrasons agissent différemment en fonction des structures végétales et de leurs propriétés morphologiques et chimiques qui leur confèrent un degré de résistance plus ou moins important face à l’action des ultrasons. Partant de ces résultats, l’étude macroscopique et microscopique a été définie comme un outil de décision pour une extraction ciblée. Cette variabilité a été aussi constatée à l’échelle industrielle prouvant davantage l’importance de l’analyse microscopique. Enfin, le procédé d’extraction par ultrasons a été adopté à l’échelle industrielle pour ses performances d’extraction et pour son empreinte environnementale significativement réduite par rapport au procédé CV. Ce travail a également conduit à des travaux complémentaires sur l’étude du potentiel de solubilisation des produits naturels en vue d’une utilisation pour l’extraction de composés végétaux difficiles à solubiliser dans l’eau. Des résultats prometteurs ont été obtenus en termes de pouvoirs de solubilisation et d’extraction notamment à partir de la matière végétale broyée. Les résultats de cette dernière partie soulèvent cependant des questions qui pourraient faire l’objet de futures recherches et de perspectives pour ce travail qui sont principalement liés à l’étude des problèmes liés au changement du solvant et au prétraitement de la matière première et de la faisabilité industrielle de ce nouveau procédéWith recent trends in the increasing interest to environmental, economic and safety considerations,extraction techniques have largely focused on finding solutions with sustainable and green values toimplement in food processing, cosmetic and pharmaceutical industries. In this context, new “green”extraction techniques were developed such as Ultrasound-Assisted Extraction (UAE). The mainobjective of this thesis is industrial implementation of this new process in substitution to theconventional (CV) process. It has been shown in this work that the extraction of compounds ofinterest from rosemary and other plant matrices could be intensified using ultrasound, and thatdifferent performance gain could be achieved according to the plant matrix structural properties.Indeed, macroscopic and microscopic investigation of untreated and treated raw materials provedthat US act through different mechanisms and its resulting impacts can be extremely limited by plantstructural morphological and chemical properties, especially those of the specialized structures.Significant variability in performance gain was also observed at the industrial scale. Overall, USappears as a promising technique with a significant performance gain in terms of extraction yield andselectivity. Moreover, this process presents low environmental footprint compared to the CV one.Finally, it has been shown that natural products, such as honey and fruit juices, can be used toimprove solubilization and extraction of molecules that are poorly soluble in water. Encouragingresults were obtained in terms of solubilization and extraction abilities, especially from ground rawmaterials. However, these results raise questions related to the feasibility of industrialimplementation of this new process
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Torres, Nogueira Luisa Maria. "Les lésions osseuses tranchantes (par scies) et tranchantes contondantes : analyse des mécanismes lésionnels et des instruments à l'origine de ces lésions." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0272/document.
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Ce travail expérimental s’est intéressé aux lésions osseuses produites par des scies et par une hachette, sur des échantillons humains et animaux. En ce qui concerne les scies, 170 faux départs ont été étudiés au stéréomicroscope en utilisant cinq scies différentes. Les scies universelles se comportent comme les scies à tronçonner, du fait de l’inclinaison vers l’arrière de chaque dent. La largeur minimum du faux départ permet de classer les lésions selon les catégories de Symes. Les profils convexes indiquent l’utilisation d’une scie universelle ou d’une scie à tronçonner. Les profils concaves sont beaucoup plus variés, et indiquent l’utilisation d’une scie à refendre. La forme des murs permet de déterminer le type d’avoyage sauf quand ils sont droits ou difficiles à analyser. Parmi les critères secondaires, l’aspect des stries au fond de la lésion s’est révélé de grande importance pour identifier le type d’avoyage. En ce qui concerne la hachette, nous avons utilisé un protocole standardisé produisant des lésions osseuses de petites dimensions. Le stéréomicroscope a constaté le caractère vertical des stries, qui s’explique par le mouvement vertical effectué par l’instrument au moment de l’impact. Le microscope électronique à balayage a permis de décrire parfaitement les lésions, de comprendre la surélévation des berges (« uprising ») et l’effet exercé à distance (« lateral pushing back »). La présence du latéral pushing back et de stries verticales permet d’affirmer que les lésions osseuses ont été produites par un instrument tranchant contondant. Ces caractères se pérennisent même après carbonisationIn this experimental work bone lesions produced by saws and a hatchet on human and animal samples were analyzed. With regard to the saws, 170 experimental false starts lesions were studied under stereomicroscope produced by five different saws. Universal saws behave like crosscut saws, because each tooth displays a tilt backwards. The minimum width of the kerf makes it possible to classify bone lesions according to Symes’ categories. Convex profiles indicate the use of a universal or crosscut saw. Concave profiles vary a great deal and indicate the use of a rip saw. The shape of the walls allows for determining the type of set except when they are straight or difficult to analyze. Among the secondary criteria, the appearance of the striae on the kerf floor is able to point the type of set. For the study of bone lesions by a hatchet a standardized device was used to produce small bone lesions. The stereomicroscope was able to observe the vertical striae explained by the vertical movement of the instrument at the time of impact. The scanning electron microscope allowed for a detailed analysis of bone lesions and made it possible to understand the uprising and the lateral pushing back. The presence of a lateral pushing back and of vertical striae is sufficient to determine that the bone lesions were achieved by a sharp blunt instrument. These characters are visible even after carbonization
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Doran, Marc C. "Nanoindentation as a Characterization Tool for Wear Resistance in Stainless Steels." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1462807632.
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Robson, Alex J. "Single particle tracking as a tool to investigate the dynamics of integrated membrane complexes in vivo." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:7769f80c-a56d-4513-9123-1d65ef8c9911.
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The last decade has seen substantial advances in single-molecule tracking methods with nano-metre level precision. A powerful tool in single-molecule tracking is fluorescence imaging. One particular application, total internal reflection microscopy, can capture biological processes at high contrast video rate imaging at the single-particle level. This thesis presents methodologically novel methods in analysing single particle tracking data. Presented here is an application of a Bayesian statistical approach that can discriminate between the different diffusive modes that appear with the presence of membrane architecture. This algorithm is denoted BARD; a Bayesian Analysis to Ranking Diffusion. These algorithms are applied to a total internal fluorescence microscopy based experimental data of a novel membrane probe in Escherichia coli. This probe is a plasmid expressed, non-native membrane integrating trans-membrane helix and thus acts as an ideal protein based probe under no specific native control. Two experiments were performed using a combination of varying helix probe size and growth temperature experiments effectively altering the transition temperature of the membrane. These data are suggestive of a passive partitioning of the helix protein into mobile and immobile domains that emerge from the underlying phase behaviour of the membrane.
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Hohner, Robin, and Ekengren André. "Study Of Belts Acting As A Positioning System For Interconnected Gripping Tools In Tube Filling Machines." Thesis, Linnéuniversitetet, Institutionen för maskinteknik (MT), 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-77221.
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The task performed in this assignment is to improve the reliability of Norden Machinery ABs product family. This is to be done by examining and replacing the belt used to stop the spreading of tubes from ingoing shipping crate to the infeed of the machine. The way that this was approached was by testing different candidates on a spectrum of their rigidity to find if a flexible or more rigid belt would perform better than the current context of the system. The testing was conducted for a period of 4 weeks and results were gathered by examining damages to the belts by the use of microscope. After the damage had been analyzed the conclusion was drawn that flexible alternatives seems to perform the task better than their rigid counterparts however more work is needed in the fields regarding the fastening and operation of the machine to use the best suited candidates derived from this test, the monolithic belt FMT-02TXCT-U1.