While much is known about the attachment of the chlamydiae to the host cell and intracellular events during the developmental cycle, little is known about the mechanism(s) by which elementary bodies exit the cell. In this report, we use the guinea-pig conjunctival model of Chlamydia caviae infection to present in vivo ultrastructural evidence supporting two mechanisms for release of chlamydiae from the mucosal epithelia. Four days after infection, histopathologic observation shows an intense infiltration of polymorphonuclear leukocytes (PMN) in the conjunctival epithelium. Using transmission electron microscopy, a gradient-directed PMN response to chlamydiae-infected epithelial cells was observed. As PMN infiltration intensifies, epithelial hemidesmosome/integrin/focal adhesion adherence with the basal lamina is disconnected and PMNs literally lift off and release infected superficial epithelia from the mucosa. Many of these infected cells appear to be healthy with intact microvilli, nuclei, and mitochondria. While lysis of some infected cells occurs with release of chlamydiae into the extracellular surface milieu, the majority of infected cells are pushed off the epithelium. We propose that PMNs play an active role in detaching infected cells from the epithelium and that these infected cells eventually die releasing organisms but, in the process, move to new tissue sites via fluid dynamics.

No description available.

<p> The fatigue softening behaviour of copper single crystals was investigated as a function of temperature. Copper crystals, prestrained in tension, were softened by "push-pull" cycling at constant plastic strain amplitude, in the low amplitude range, and the cyclic stress-strain curves determined at various temperatures. Transmission electron microscopy was employed to determine the detailed microstructural changes which occured during softening while X-ray and slip line observations were utilized to indicate the overall structural changes on a macroscopic scale. The results were correlated and a rationale, based on dipole production, proposed for the observed softening behaviour. </p> / Thesis / Master of Science (MSc)

Supporting videos attached / The nanoscale structure of fully dense human cortical bone is explored using advanced transmission electron microscopy (TEM) techniques. Studies of fully dense cortical bone are rare because of the sample preparation challenges. In this work, cryogenic ion milling is compared favourably with traditional ultramicrotoming methods because of the clearer imaging results and better preservation of biological structures in the ion milled samples. Ion milled samples were prepared parallel, perpendicular and at a 45 degree angle to the long axis of a human femur. The samples are cooled with liquid nitrogen while being milled to prevent heating damage to the bone structure. Bright-field and dark-field imaging show that mineral mainly occurs as 65 nm wide, 5 nm thick mineral structures, external to the collagen fibrils, and with the long axis of the mineral running parallel to the fibrils. In samples cut parallel to the long axis of the bone, the mineral structures have their c-axes aligned with the collagen fibril long axis. In these sections the mineral structures extend up to 200 nm and are grouped into stripe-like bunches, 53 nm apart. Samples cut perpendicular to the long axis of the bone show open areas roughly 45 nm in diameter. These open areas are assumed to be the location of collagen fibrils within the structure and are tangentially surrounded by 65 nm wide, 5 nm thick mineral structures. On average, there are 22 nm of mineral structures between adjoining collagen fibrils. Samples cut at 45 degrees to the long axis of the bone confirm that the open structure seen in the perpendicular section is not an artefact of sample preparation. By tilting the sample, the 45 degree sample shows the structure of both the parallel and perpendicular sections. The parallel structure strongly resembles images of embryonic bone and other mineralized tissues seen in the literature, so the perpendicular open structure is not caused by sample preparation. An examination of ultramicrotoming’s effect on mineral structure size compared with that of ion milling shows that the mineral structures in ion milled samples are twice as long as in ultramicrotomed samples, indicating that bone mineral may be damaged by the forces applied to the complex composite structure existing in fully dense cortical bone. Using energy dispersive X-ray spectroscopy (EDXS) results and a simplified model of the locations of mineral within the collagen/mineral framework, a calculation of the percentage of external mineral was performed. The result showed that 80+_ 6 % of the mineral in fully dense cortical bone must be external to the collagen fibrils to obtain the EDXS results. Finally, Z-contrast tomography, based on the use of high angle annular darkfield (HAADF) imaging, was used to prepared tomographic reconstructions of the external mineral in fully dense cortical bone. Unlike bright-field tomography, the Z-contrast technique allows examination of crystalline materials as the contrast in HAADF images is mass-thickness dependent instead of diffraction based. These reconstructions again showed the mineral tangentially surrounding 50 nm diameter cylindrical holes, assumed to be the location of collagen fibrils in all directions. This work shows the importance of mineral that is external to the collagen fibrils to the nanoscale structure of fully dense cortical bone. / Thesis / Doctor of Philosophy (PhD)

Schwertmannite, a ferric oxyhydroxysulfate mineral typically found under acidic, high sulfate and iron aqueous conditions, such as acid mine drainage environments, was studied using analytical high resolution transmission electron microscopy (HRTEM). HRTEM offers advantages over bulk techniques such as powder x-ray diffraction and pair distribution function (PDF) analysis of synchrotron data, in its ability to discern multiple phases within poorly crystalline nanominerals. Based on extensive HRTEM observations of both natural and synthetic schwertmannite samples, the authors suggest that schwertmannite should not be described as a single phase mineral with a repeating unit cell, but as a polyphasic nanomineral with crystalline areas spanning less than a few nanometers within an amorphous matrix. The few visible lattice fringes observable in both natural and synthetic schwertmannite agree well with d-spacings of goethite (and jarosite in natural samples) implying that the transformation from schwertmannite to these phases occurs as a gradual structural reordering at the nanoscale. In the synthetic study, the complete transformation from schwertmannite to goethite nanorods and nanoparticles within 24 hours at 75°C was observed, indicating a low energetic barrier to schwertmannite's phase transformation. We also found that amorphous silica can be intimately entrained within natural schwertmannite, and that high concentrations of arsenic can be held in close association of nanocrystalline regions of the mineral. / Ph. D.

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.

abstract: In this dissertation research, conventional and aberration-corrected (AC) transmission electron microscopy (TEM) techniques were used to evaluate the structural and compositional properties of thin-film semiconductor compounds/alloys grown by molecular beam epitaxy for infrared photo-detection. Imaging, diffraction and spectroscopy techniques were applied to TEM specimens in cross-section geometry to extract information about extended structural defects, chemical homogeneity and interface abruptness. The materials investigated included InAs1-xBix alloys grown on GaSb (001) substrates, InAs/InAs1-xSbx type-II superlattices grown on GaSb (001) substrates, and CdTe-based thin-film structures grown on InSb (001) substrates. The InAsBi dilute-bismide epitaxial films were grown on GaSb (001) substrates at relatively low growth temperatures. The films were mostly free of extended defects, as observed in diffraction-contrast images, but the incorporation of bismuth was not homogeneous, as manifested by the lateral Bi-composition modulation and Bi-rich surface droplets. Successful Bi incorporation into the InAs matrix was confirmed using lattice expansion measurements obtained from misfit strain analysis of high-resolution TEM (HREM) images. Analysis of averaged intensity line profiles in HREM and scanning TEM (STEM) images of the Ga-free InAs/InAs1-xSbx type-II strained superlattices indicated slight variations in layer thickness across the superlattice stack. The interface abruptness was evaluated using misfit strain analysis of AC-STEM images, electron energy-loss spectroscopy and 002 dark-field imaging. The compositional profiles of antimony across the superlattices were fitted to a segregation model and revealed a strong antimony segregation probability. The CdTe/MgxCd1-xTe double-heterostructures were grown with Cd overflux in a dual-chamber molecular beam epitaxy with an ultra-high vacuum transfer loadlock. Diffraction-contrast images showed that the growth temperature had a strong impact on the structural quality of the epilayers. Very abrupt CdTe/InSb interfaces were obtained for epilayers grown at the optimum temperature of 265 °C, and high-resolution imaging using AC-STEM revealed an interfacial transition region with a width of a few monolayers and smaller lattice spacing than either CdTe or InSb. / Dissertation/Thesis / Doctoral Dissertation Materials Science and Engineering 2017

During recent years, new types of materials have been discovered with unique properties. One family of such materials are two-dimensional materials, which include graphene and MXene. These materials are stronger, more flexible, and have higher conductivity than other materials. As such they are highly interesting for new applications, e.g. specialized in vivo drug delivery systems, hydrogen storage, or as replacements of common materials in e.g. batteries, bulletproof clothing, and sensors. The list of potential applications is long for these new materials. As these materials are almost entirely made up of surfaces, their properties are strongly influenced by interaction between their surfaces, as well as with molecules or adatoms attached to the surfaces (surface groups). This interaction can change the materials and their properties, and it is therefore imperative to understand the underlying mechanisms. Surface groups on two-dimensional materials can be studied by Transmission Electron Microscopy (TEM), where high energy electrons are transmitted through a sample and the resulting image is recorded. However, the high energy needed to get enough resolution to observe single atoms damages the sample and limits the type of materials which can be analyzed. Lowering the electron energy decreases the damage, but the image resolution at such conditions is severely limited by inherent imperfections (aberrations) in the TEM. During the last years, new TEM models have been developed which employ a low acceleration voltage together with aberration correction, enabling imaging at the atomic scale without damaging the samples. These aberration-corrected TEMs are important tools in understanding the structure and chemistry of two-dimensional materials. In this thesis the two-dimensional materials graphene and Ti3C2Tx MXene have been investigated by low-voltage, aberration-corrected (scanning) TEM. High temperature annealing of graphene covered by residues from the synthesis is studied, as well as the structure and surface groups on single and double Ti3C2Tx MXene. These results are important contributions to the understanding of this class of materials and how their properties can be controlled.

This thesis explores theoretical aspects of scanning transmission electron microscopy (STEM) and the comparison of simulation with experiment. / The long standing contrast mismatch problem between theory and experiment in conventional high resolution transmission electron microscopy (HRTEM) is examined using the principle of reciprocity and bright field scanning transmission electron microscopy (BFSTEM). It is found that quantitative agreement between theoretical and experimental images is possible provided that theory suitably accounts for the spatial incoherence of the source, and that experimental images are placed on an absolute scale with respect to the incident beam current. Agreement between theory and experimental image contrast is found to be independent of specimen thickness and probe defocus. / Core-loss electron energy-loss spectroscopy (EELS) is a powerful experimental tool with the potential to provide atomic-resolution information about the electronic structure at defects and interfaces in materials and nanostructures. Interpretation, however, is nonintuitive due to the nonlocal ionization potential. Novel improvements in microscope design and operating environment have enabled two dimensional chemical maps. This has permitted a more thorough theoretical analysis. This thesis compares experimental STEM EELS images of LaMnO3, BiSrMnO3 and Si samples to the relevant theoretical simulations. Image features which at first appear counter intuitive are discussed and explained with the accompanying theoretical simulations. It is demonstrated, using a sample of SrTiO3, that more direct interpretation of atomic resolution chemical maps is possible when using energy dispersive x-ray spectroscopy (EDS) in STEM. / This thesis considers extending chemical mapping in STEM EELS to three dimensions using depth sectioning. It explores, theoretically, the feasibility to depth section zone-axis aligned crystals that contain embedded impurities. In STEM EELS this is found to be possible for point defects but not for larger extended objects such as nanoparticles. / The theory describing the mechanism by which contrast is obtained in elastic scanning confocal electron microscopy (SCEM) is developed. It is shown that there is no first order phase contrast in SCEM and thus low image contrast. Finally, energy filtered scanning transmission electron microscopy (EFSCEM) is developed theoretically. The fundamental equation describing image formation is derived and an efficient computation method is developed to allow the rapid calculation of EFSCEM images.

The research carried out here employed analytical and imaging transmission electron microscopy and scanning transmission electron microscopy to gain a good understanding of local structure and composition of semiconductor nanocrystals and quantum dots for electronics and optoelectronics applications. One of the world's most advanced analytical scanning transmission electron microscopes in the field, the Daresbury SuperSTEM, was used to scrutinise the structure and composition of the samples. Three nanostructure systems are investigated in this thesis: 1. Structures consisting of Ge-nanocrystals (NCs) in alumina. Here HRTEM suggests relaxed and twinned smaller NCs grown annealed at lower temperature compared to elongated non-faulty bigger NCs annealed at higher temperature. HRTEM also suggests a polycrystalline structure of the matrix. 2. With regards to the InAs/GaAs quantum dots (QD) the study aims in particular at elucidating QD formation by investigating samples grown with and without growth interrupt (GI). Diffraction contrast TEM shows formation of buried dots in the sample prepared with GI whereas for the sample without GI the immediate growth of GaAs after InAs inhibits diffusion and segregation of In adotoms, and no footprint of buried dots has been observed. HRTEM and HAADF show coherent QDs in the sample with GI and abrupt InAs/GaAs interfaces in the sample without GI. In executing energy electron loss spectroscopy (EELS) and geometric phase analysis (GPA) the distribution of In in InGaAs/GaAs QDs has been obtained in samples grown in the critical thickness regime for quantum dot formation. The highest In percentage achieved in the dots grown with a nominal fraction of 100% was ~70%. EELS shows variations in the In concentration within the QD structure and wetting layer 3. In the case of Er-doped Si-NCs in silica this research tries to provide an understanding of structure, composition and position of excess Si and Er in the silica matrix of materials prepared under different growth conditions and to correlate this information with the PL emission, all with the aim to find preparation routes for optimum optical efficiency for applications of this materials system in silicon photonics. High spatial correlation between Si-NCs, Er and O in the Er and Si co-implanted sample with strong indication of an Er-oxide/Si core-shell structure had been found. The lack of an Er-oxide plasmon indicates, however, that the shell structure and its interface with the SiNCs is highly defective and a likely cause for non-radiative recombination. The sample with similar excess Er and Si concentrations but prepared in a two-stage implantation and annealing process shows a 10 times improvement in the optical emission. Here no spatial correlation between Er and Si-NCs was found in core loss EELS. EELS and HAADF evidenced more highly, near-atomically dispersed Er in the matrix with no formation of a core-shell structure as compared to the co-implanted sample. No footprint of Er-silicide plasmon was observed by low loss valence band EELS investigation in the co-implanted sample.