Transmission electron tomography: quality assessment and enhancement for three-dimensional imaging of nanostructures

Nanotechnology has revolutionised humanity's capability in building microscopic systems by manipulating materials on a molecular and atomic scale. Nan-osystems are becoming increasingly smaller and more complex from the chemical perspective which increases the demand for microscopic characterisation techniques. Among others, transmission electron microscopy (TEM) is an indispensable tool that is increasingly used to study the structures of nanosystems down to the molecular and atomic scale. However, despite the effectivity of this tool, it can only provide 2-dimensional projection (shadow) images of the 3D structure, leaving the 3-dimensional information hidden which can lead to incomplete or erroneous characterization. One very promising inspection method is Electron Tomography (ET), which is rapidly becoming an important tool to explore the 3D nano-world. ET provides (sub-)nanometer resolution in all three dimensions of the sample under investigation. However, the fidelity of the ET tomogram that is achieved by current ET reconstruction procedures remains a major challenge. This thesis addresses the assessment and advancement of electron tomographic methods to enable high-fidelity three-dimensional investigations. A quality assessment investigation was conducted to provide a quality quantitative analysis of the main established ET reconstruction algorithms and to study the influence of the experimental conditions on the quality of the reconstructed ET tomogram. Regular shaped nanoparticles were used as a ground-truth for this study. It is concluded that the fidelity of the post-reconstruction quantitative analysis and segmentation is limited, mainly by the fidelity of the reconstructed ET tomogram. This motivates the development of an improved tomographic reconstruction process. In this thesis, a novel ET method was proposed, named dictionary learning electron tomography (DLET). DLET is based on the recent mathematical theorem of compressed sensing (CS) which employs the sparsity of ET tomograms to enable accurate reconstruction from undersampled (S)TEM tilt series. DLET learns the sparsifying transform (dictionary) in an adaptive way and reconstructs the tomogram simultaneously from highly undersampled tilt series. In this method, the sparsity is applied on overlapping image patches favouring local structures. Furthermore, the dictionary is adapted to the specific tomogram instance, thereby favouring better sparsity and consequently higher quality reconstructions. The reconstruction algorithm is based on an alternating procedure that learns the sparsifying dictionary and employs it to remove artifacts and noise in one step, and then restores the tomogram data in the other step. Simulation and real ET experiments of several morphologies are performed with a variety of setups. Reconstruction results validate its efficiency in both noiseless and noisy cases and show that it yields an improved reconstruction quality with fast convergence. The proposed method enables the recovery of high-fidelity information without the need to worry about what sparsifying transform to select or whether the images used strictly follow the pre-conditions of a certain transform (e.g. strictly piecewise constant for Total Variation minimisation). This can also avoid artifacts that can be introduced by specific sparsifying transforms (e.g. the staircase artifacts the may result when using Total Variation minimisation). Moreover, this thesis shows how reliable elementally sensitive tomography using EELS is possible with the aid of both appropriate use of Dual electron energy loss spectroscopy (DualEELS) and the DLET compressed sensing algorithm to make the best use of the limited data volume and signal to noise inherent in core-loss electron energy loss spectroscopy (EELS) from nanoparticles of an industrially important material. Taken together, the results presented in this thesis demonstrates how high-fidelity ET reconstructions can be achieved using a compressed sensing approach.

The Comparison of Under-Five-Children’s Nutrition Status Among Ethnic Groups in North of Iran, 1998 - 2013; Results of a Three Stages Cross-Sectional Study

Background: Despite improvements in child health, malnutrition still remains one of the main public health challenges in Iran. Objectives: The aim of this study was to compare under nutrition among under-five children with regard to ethnicity in rural area in north Iran. Patients and Methods: In three cross-sectional studies 7575 subjects in three time-periods including 2339 children in 1998, 2749 in 2004, and 2487 in 2013, were evaluated. All under-five-children in 20 out of 118 villages were chosen by random sampling and assessed. Under nutrition was defined as underweight, stunting and wasting lower than -2 SD (Z < -2 SD). Results: Generally, stunting was declined 17.1% and underweight and wasting were increased 0.9% and 1%, respectively during 15 years (1998 - 2013). Underweight increased 0.5% in Fars-natives and 3.2% in Turkmans and it was decreased 0.9% in Sistanis. Statistical difference in Turkman children among the three stages of the study was significant (P = 0.001). Stunting has decreased 28.7% in Fars-natives and 35.1% in Sistanis, it was increased 9.3% in Turkman group. Statistical differences among three stages in inter-ethnic groups were significant (P = 0.001 for all). Compared the group with good economic status, the odds ratio was 1.831 in poor economic group (P = 0.001). The risk of under nutrition in Sistanis was 1.754 times more than in Fars-natives (P = 0.001). Conclusions: Under nutrition remains one of the main health problems in under-five-year children in north Iran being more common in Sistani children. Stunting in Sistani children deeply decreased while in Turkman children slightly increased during the 15-year period study. Poor economic status is a risk factor for under nutrition in this area.

The minimum number of measurements for colour, sparkle, and graininess characterisation in gonio-apparent panels

Materials with new visual appearances have emerged over the last few years. In the automotive industry in particular there is a growing interest in materials with new effect finishes, such as metallic, pearlescent, sparkle, and graininess effects. Typically, for solid colours the mean of three measurements with repetitions is sufficient to obtain a representative measurement for colour characterisation. However, gonio-apparent panels have non-homogeneous colours, and there are no studies that recommend the minimum number of repetitions for colour, sparkle, and graininess characterisation of this type of panel. We assume that colour panels incorporating special-effect pigments in their colour recipes will require a higher minimum number of measurements than solid colour panels. Therefore, the purpose of this study is to verify this assumption by using a multiangle BYK-mac spectrophotometer, given that it is currently the only commercial device that can measure colour, sparkle, and graininess values simultaneously. In addition, a possible methodology is given for establishing the minimum number of measurements when characterising gonio-apparent materials using a specific instrument, able to be implemented in future instruments when determining multiple appearance attributes (colour, gloss, sparkle, etc.) for many coloration technologies. Thus, we studied the minimum number of measurements needed to characterise the colour, sparkle, and graininess of three types of sample with solid, metallic, and pearlescent coatings respectively. Twenty measurements were made at twenty random positions (different target areas) of 90 samples. The minimum number of measurements for all these variables was determined on the basis of the point at which the cumulative mean value became constant. Thus, applying new statistical tools, it is clearly shown that metallic and pearlescent panels require more colour measurements than solid panels, in particular when geometries are being measured in a specular direction. As regards texture (sparkle and graininess), more measurements are needed for graininess than for sparkle, and more for metallic panels than for pearlescent panels.

Three Essays on a Longitudinal Analysis of Business Start-ups using the Kauffman Firm Survey

This dissertation focused on the longitudinal analysis of business start-ups using three waves of data from the Kauffman Firm Survey. The first essay used the data from years 2004-2008, and examined the simultaneous relationship between a firm’s capital structure, human resource policies, and its impact on the level of innovation. The firm leverage was calculated as, debt divided by total financial resources. Index of employee well-being was determined by a set of nine dichotomous questions asked in the survey. A negative binomial fixed effects model was used to analyze the effect of employee well-being and leverage on the count data of patents and copyrights, which were used as a proxy for innovation. The paper demonstrated that employee well-being positively affects the firm's innovation, while a higher leverage ratio had a negative impact on the innovation. No significant relation was found between leverage and employee well-being. The second essay used the data from years 2004-2009, and inquired whether a higher entrepreneurial speed of learning is desirable, and whether there is a linkage between the speed of learning and growth rate of the firm. The change in the speed of learning was measured using a pooled OLS estimator in repeated cross-sections. There was evidence of a declining speed of learning over time, and it was concluded that a higher speed of learning is not necessarily a good thing, because speed of learning is contingent on the entrepreneur's initial knowledge, and the precision of the signals he receives from the market. Also, there was no reason to expect speed of learning to be related to the growth of the firm in one direction over another. The third essay used the data from years 2004-2010, and determined the timing of diversification activities by the business start-ups. It captured when a start-up diversified for the first time, and explored the association between an early diversification strategy adopted by a firm, and its survival rate. A semi-parametric Cox proportional hazard model was used to examine the survival pattern. The results demonstrated that firms diversifying at an early stage in their lives show a higher survival rate; however, this effect fades over time.

An Analysis of the Factors that Influence Regional Economic Development Cooperation

This dissertation is a comparative case study of regional cooperation in the field of economic development. In the 21st century global economy, proponents of regionalism have put forth fresh arguments for collective action. A regional approach to economic development activity presents a classic social dilemma: How can local officials collectively improve the economic prospects of a region, and remain autonomous to act in the best interest of the local community? This research examines the role of social capital in overcoming this social dilemma. Three (3) comparable Metropolitan Statistical Areas (MSAs) form the empirical basis of this research. The Houston MSA, the Atlanta MSA and the Miami MSA present distinct variations of regionalized economic development activity. This dissertation seeks to explain this disparity in the dependent variable. The hypothesis is that accrued social capital is crucial to obtaining economic development cooperative agreements. This qualitative research utilized secondary demographic and economic databases, survey instruments, interviews, field observations, and a review of legislative and administrative decisions to formulate a clear understanding of the factors influencing the current state of regional economic development cooperation within each region. The study concludes that the legislative and executive decisions of state government exert inordinate influence on the capacity of local officials to cooperate regionally for economic development purposes.

Understanding the Impact of the Property Tax Appeal Process on Assessment Uniformity: Procedures, Structures, and Outcomes

Property taxes serve as a vital revenue source for local governments. The revenues derived from the property tax function as the primary funding source for a variety of critical local public service systems. Property tax appeal systems serve as quasi-administrative-judicial mechanisms intended to assure the public that property tax assessments are correct, fair, and equitable. Despite these important functions, there is a paucity of empirical research related to property tax appeal systems. This study contributes to property tax literature by identifying who participates in the property tax appeal process and examining their motivations for participation. In addition, the study sought to determine whether patterns of use and success in appeal systems affected the distribution of the tax burden. Data were collected by means of a survey distributed to single-family property owners from two Florida counties. In addition, state and county documents were analyzed to determine appeal patterns and examine the impact on assessment uniformity, over a three-year period. The survey data provided contextual evidence that single-family property owners are not as troubled by property taxes as they are by the conduct of local government officials. The analyses of the decision to appeal indicated that more expensive properties and properties excluded from initial uniformity analyses were more likely to be appealed, while properties with homestead exemptions were less likely to be appealed. The value change analyses indicated that appeals are clustered in certain geographical areas; however, these areas do not always experience a greater percentage of the value changes. Interestingly, professional representation did not increase the probability of obtaining a reduction in value. Other relationships between the variables were discovered, but often with weak predictive ability. Findings from the assessment uniformity analyses were also interesting. The results indicated that the appeals mechanisms in both counties improved assessment uniformity. On average, appealed properties exhibited greater horizontal and vertical inequities, as compared to non-appealed properties, prior to the appeals process. After, the appeal process was completed; the indicators of horizontal and vertical equity were largely improved. However, there were some indications of regressivity in the final year of the study.

Investigating the Roles and Requirements, Manifestations and Management of Metadata in the Creation of Reliable and Preservation of Authentic Electronic Entities Created by Dynamic, Interactive and Experiential Systems: Report on the Work and Findings of the Interpares 2 Description Cross Domain Group

Metadata that is associated with either an information system or an information object for purposes of description, administration, legal requirements, technical functionality, use and usage, and preservation, plays a critical role in ensuring the creation, management, preservation and use and re-use of trustworthymaterials, including records. Recordkeeping1 metadata, of which one key type is archival description, plays a particularly important role in documenting the reliability and authenticity of records and recordkeeping systemsas well as the various contexts (legal-administrative, provenancial, procedural, documentary, and technical) within which records are created and kept as they move across space and time. In the digital environment, metadata is also the means by which it is possible to identify how record components – those constituent aspects of a digital record that may be managed, stored and used separately by the creator or the preserver – can be reassembled to generate an authentic copy of a record or reformulated per a user’s request as a customized output package.Issues relating to the creation, capture, management and preservation of adequate metadata are, therefore, integral to any research study addressing the reliability and authenticity of digital entities, regardless of the community, sector or institution within which they are being created. The InterPARES 2 Description Cross-Domain Group (DCD) examined the conceptualization, definitions, roles, and current functionality of metadata and archival description in terms of requirements generated by InterPARES 12. Because of the needs to communicate the work of InterPARES in a meaningful way across not only other disciplines, but also different archival traditions; to interface with, evaluate and inform existing standards, practices and other research projects; and to ensure interoperability across the three focus areas of InterPARES2, the Description Cross-Domain also addressed its research goals with reference to wider thinking about and developments in recordkeeping and metadata. InterPARES2 addressed not only records, however, but a range of digital information objects (referred to as “entities” by InterPARES 2, but not to be confused with the term “entities” as used in metadata and database applications) that are the products and by-products of government, scientific and artistic activities that are carried out using dynamic, interactive or experiential digital systems. The nature of these entities was determined through a diplomatic analysis undertaken as part of extensive case studies of digital systems that were conducted by the InterPARES 2 Focus Groups. This diplomatic analysis established whether the entities identified during the case studies were records, non-records that nevertheless raised important concerns relating to reliability and authenticity, or “potential records.” To be determined to be records, the entities had to meet the criteria outlined by archival theory – they had to have a fixed documentary format and stable content. It was not sufficient that they be considered to be or treated as records by the creator. “Potential records” is a new construct that indicates that a digital system has the potential to create records upon demand, but does not actually fix and set aside records in the normal course of business. The work of the Description Cross-Domain Group, therefore, addresses the metadata needs for all three categories of entities.Finally, since “metadata” as a term is used today so ubiquitously and in so many different ways by different communities, that it is in peril of losing any specificity, part of the work of the DCD sought to name and type categories of metadata. It also addressed incentives for creators to generate appropriate metadata, as well as issues associated with the retention, maintenance and eventual disposition of the metadata that aggregates around digital entities over time.

Collaborative governance of smart cities: addressing multiple relations of actors involved

This dissertation aims to contribute to the discourse on the governance of smart cities (SC) by examining the collaborative relationships between various actors involved in developing and implementing SC initiatives. Poorly organized collaboration can lead to conflicts and misunderstandings, resulting in failures in realizing such complex technological initiatives. Hence, capturing the main elements of SC collaboration becomes essential for understanding how they should be developed and managed. However, the topic has been limitedly explored in prior research, with fragmented studies on narrow aspects related to the SC governance. Using Russia as an empirical setting, the study focuses on the interplay of both government and non-governmental stakeholders in constructing collaborative relationships within SC, covering both vertical and horizontal dimensions of their interaction. The overarching goal of this research is to understand how collaborative governance unfolds in the SC context by stating two guiding research questions: 1) who are the dominant actors in SC and what are their roles? 2) what are the relationships forged among them? The dissertation investigates the SC initiatives across three different cities – Moscow, Saint Petersburg, and Perm – in a format of empirical illustration as well as an in-depth case study. The dissertation provides three main contributions. First, it strengthens the link between the SC domain, public governance, and literature on cross-sectoral collaboration by highlighting ‘urban smartness’ as a source for generating multiple values. Second, the thesis offers novel view on the strategic development paths which conceptually shape the SC framework. It connects the techno-centric and human-centric perspectives of SC by showing that they are naturally linked, rather than mutually exclusive. Third, the study illustrates that SC initiatives are contextually dependent, and this dependence covers specificities of public governance, including underlying informal mechanisms, which influence the inception, development, and management of SC in the organizational realms.

Petroleomics By Electrospray Ionization Ft-icr Mass Spectrometry Coupled To Partial Least Squares With Variable Selection Methods: Prediction Of The Total Acid Number Of Crude Oils.

Negative-ion mode electrospray ionization, ESI(-), with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was coupled to a Partial Least Squares (PLS) regression and variable selection methods to estimate the total acid number (TAN) of Brazilian crude oil samples. Generally, ESI(-)-FT-ICR mass spectra present a power of resolution of ca. 500,000 and a mass accuracy less than 1 ppm, producing a data matrix containing over 5700 variables per sample. These variables correspond to heteroatom-containing species detected as deprotonated molecules, [M - H](-) ions, which are identified primarily as naphthenic acids, phenols and carbazole analog species. The TAN values for all samples ranged from 0.06 to 3.61 mg of KOH g(-1). To facilitate the spectral interpretation, three methods of variable selection were studied: variable importance in the projection (VIP), interval partial least squares (iPLS) and elimination of uninformative variables (UVE). The UVE method seems to be more appropriate for selecting important variables, reducing the dimension of the variables to 183 and producing a root mean square error of prediction of 0.32 mg of KOH g(-1). By reducing the size of the data, it was possible to relate the selected variables with their corresponding molecular formulas, thus identifying the main chemical species responsible for the TAN values.

Comparative Cytogenetics Of Physalaemus albifrons And Physalaemus Cuvieri Species Groups (anura, leptodactylidae).

Recently, Physalaemus albifrons (Spix, 1824) was relocated from the Physalaemus cuvieri group to the same group as Physalaemus biligonigerus (Cope, 1861), Physalaemus marmoratus (Reinhardt & Lütken, 1862) and Physalaemus santafecinus Barrio, 1965. To contribute to the analysis of this proposition, we studied the karyotypes of Physalaemus albifrons, Physalaemus santafecinus and three species of the Physalaemus cuvieri group. The karyotype of Physalaemus santafecinus was found to be very similar to those of Physalaemus biligonigerus and Physalaemus marmoratus, which were previously described. A remarkable characteristic that these three species share is a conspicuous C-band that extends from the pericentromeric region almost to the telomere in the short arm of chromosome 3. This characteristic is not present in the Physalaemus albifrons karyotype and could be a synapomorphy of Physalaemus biligonigerus, Physalaemus marmoratus and Physalaemus santafecinus. The karyotype of Physalaemus santafecinus is also similar to those of Physalaemus marmoratus and Physalaemus biligonigerus owing to the presence of several terminal C-bands and the distal localization of the NOR in a small metacentric chromosome. In contrast, the Physalaemus albifrons karyotype has no terminal C-bands and its NOR is located interstitially in the long arm of submetacentric chromosome 8. The NOR-bearing chromosome of Physalaemus albifrons very closely resembles those found in Physalaemus albonotatus (Steindachner, 1864), Physalaemus cuqui Lobo, 1993 and some populations of Physalaemus cuvieri Fitzinger, 1826. Additionally, the Physalaemus albifrons karyotype has an interstitial C-band in chromosome 5 that has been exclusively observed in species of the Physalaemus cuvieri group. Therefore, we were not able to identify any chromosomal feature that supports the reallocation of Physalaemus albifrons.

Micromorphology Of The Dental Pulp Is Highly Preserved In Cancer Patients Who Underwent Head And Neck Radiotherapy.

Teeth are often included in the radiation field during head and neck radiotherapy, and recent clinical evidence suggests that dental pulp is negatively affected by the direct effects of radiation, leading to impaired sensitivity of the dental pulp. Therefore, this study aimed to investigate the direct effects of radiation on the microvasculature, innervation, and extracellular matrix of the dental pulp of patients who have undergone head and neck radiotherapy. Twenty-three samples of dental pulp from patients who finished head and neck radiotherapy were analyzed. Samples were histologically processed and stained with hematoxylin-eosin for morphologic evaluation of the microvasculature, innervation, and extracellular matrix. Subsequently, immunohistochemical analysis of proteins related to vascularization (CD34 and smooth muscle actin), innervation (S-100, NCAM/CD56, and neurofilament), and extracellular matrix (vimentin) of the dental pulp was performed. The morphologic study identified preservation of the microvasculature, nerve bundles, and components of the extracellular matrix in all studied samples. The immunohistochemical analysis confirmed the morphologic findings and showed a normal pattern of expression for the studied proteins in all samples. Direct effects of radiotherapy are not able to generate morphologic changes in the microvasculature, innervation, and extracellular matrix components of the dental pulp in head and neck cancer patients.

Screening The Life Cycle Of Schistosoma Mansoni Using High-resolution Mass Spectrometry.

Schistosomiasis is a common tropical disease caused by Schistosoma species Schistosomiasis' pathogenesis is known to vary according to the worms' strain. Moreover, high parasitical virulence is directly related to eggs release and granulomatous inflammation in the host's organs. This virulence might be influenced by different classes of molecules, such as lipids. Therefore, better understanding of the metabolic profile of these organisms is necessary, especially for an increased potential of unraveling strain virulence mechanisms and resistance to existing treatments. In this report, direct-infusion electrospray high-resolution mass spectrometry (ESI(+)-HRMS) along with the lipidomic platform were employed to rapidly characterize and differentiate two Brazilian S. mansoni strains (BH and SE) in three stages of their life cycle: eggs, miracidia and cercariae, with samples from experimental animals (Swiss/SPF mice). Furthermore, urine samples of the infected and uninfected mice were analyzed to assess the possibility of direct diagnosis. All samples were differentiated using multivariate data analysis, PCA, which helped electing markers from distinct lipid classes; phospholipids, diacylglycerols and triacylglycerols, for example, clearly presented different intensities in some stages and strains, as well as in urine samples. This indicates that biochemical characterization of S. mansoni may help narrowing-down the investigation of new therapeutic targets according to strain composition and aggressiveness of disease. Interestingly, lipid profile of infected mice urine varies when compared to control samples, indicating that direct diagnosis of schistosomiasis from urine may be feasible.

New Microsatellite Markers For Wild And Commercial Species Of Passiflora (passifloraceae) And Cross-amplification.

• We developed the first microsatellites for Passiflora setacea and characterized new sets of markers for P. edulis and P. cincinnata, enabling further genetic diversity studies to support the conservation and breeding of passion fruit species. • We developed 69 microsatellite markers and, in conjunction with assessments of cross-amplification using primers available from the literature, present 43 new polymorphic microsatellite loci for three species of Passiflora. The mean number of alleles per locus was 3.1, and the mean values of the expected and observed levels of heterozygosity were 0.406 and 0.322, respectively. • These microsatellite markers will be valuable tools for investigating the genetic diversity and population structure of wild and commercial species of passion fruit (Passiflora spp.) and may be useful for developing conservation and improvement strategies by contributing to the understanding of the mating system and hybridization within the genus.

Oxidative Stress And Susceptibility To Mitochondrial Permeability Transition Precedes The Onset Of Diabetes In Autoimmune Non-obese Diabetic Mice.

Beta cell destruction in type 1 diabetes (TID) is associated with cellular oxidative stress and mitochondrial pathway of cell death. The aim of this study was to determine whether oxidative stress and mitochondrial dysfunction are present in T1D model (non-obese diabetic mouse, NOD) and if they are related to the stages of disease development. NOD mice were studied at three stages: non-diabetic, pre-diabetic, and diabetic and compared with age-matched Balb/c mice. Mitochondria respiration rates measured at phosphorylating and resting states in liver and soleus biopsies and in isolated liver mitochondria were similar in NOD and Balb/c mice at the three disease stages. However, NOD liver mitochondria were more susceptible to calcium-induced mitochondrial permeability transition as determined by cyclosporine-A-sensitive swelling and by decreased calcium retention capacity in all three stages of diabetes development. Mitochondria H2O2 production rate was higher in non-diabetic, but unaltered in pre-diabetic and diabetic NOD mice. The global cell reactive oxygen species (ROS), but not specific mitochondria ROS production, was significantly increased in NOD lymphomononuclear and stem cells in all disease stages. In addition, marked elevated rates of 2',7'-dichlorodihydrofluorescein (H2DCF) oxidation were observed in pancreatic islets from non-diabetic NOD mice. Using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) and lipidomic approach, we identified oxidized lipid markers in NOD liver mitochondria for each disease stage, most of them being derivatives of diacylglycerols and phospholipids. These results suggest that the cellular oxidative stress precedes the establishment of diabetes and may be the cause of mitochondrial dysfunction that is involved in beta cell death.