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.

Factors affecting vaccine handling and storage practices among immunization service providers in Ibadan, Oyo State, Nigeria.

Background: Improper handling has been identified as one of the major reasons for the decline in vaccine potency at the time of administration. Loss of potency becomes evident when immunised individuals contract the diseases the vaccines were meant to prevent. Objective: Assessing the factors associated with vaccine handling and storage practices. Methods: This was a cross-sectional study. Three-stage sampling was used to recruit 380 vaccine handlers from 273 health facilities from 11 Local Government areas in Ibadan. Data was analysed using SPSS version 16 Results: Seventy-three percent were aware of vaccine handling and storage guidelines with 68.4% having ever read such guidelines. Only 15.3% read a guideline less than 1 month prior to the study. About 65.0% had received training on vaccine management. Incorrect handling practices reported included storing injections with vaccines (13.7%) and maintaining vaccine temperature using ice blocks (7.6%). About 43.0% had good knowledge of vaccine management, while 66.1% had good vaccine management practices. Respondents who had good knowledge of vaccine handling and storage [OR=10.0, 95%CI (5.28 – 18.94), p < 0.001] and had received formal training on vaccine management [OR=5.3, 95%CI (2.50 – 11.14), p< 0.001] were more likely to have good vaccine handling and storage practices. Conclusion: Regular training is recommended to enhance vaccine handling and storage practices.

PI Toolset Methodology for Virtual Enterprise Performance Assessment and Governance

Part 16: Performance Measurement Systems

Trauma in critically ill children : transfusion and osmotherapy practices

Les accidents sont la cause la plus fréquente de décès chez l’enfant, la plupart du temps à cause d’un traumatisme cranio-cérébrale (TCC) sévère ou d’un choc hémorragique. Malgré cela, la prise en charge de ces patients est souvent basée sur la littérature adulte. Le mannitol et le salin hypertonique (3%) sont des traitements standards dans la gestion de l’hypertension intracrânienne, mais il existe très peu d’évidence sur leur utilité en pédiatrie. Nous avons entrepris une revue rétrospective des traumatismes crâniens sévères admis dans les sept dernières années, pour décrire l’utilisation de ces agents hyperosmolaires et leurs effets sur la pression intracrânienne. Nous avons établi que le salin hypertonique est plus fréquemment utilisé que le mannitol, qu’il ne semble pas y avoir de facteurs associés à l’utilisation de l’un ou l’autre, et que l’effet sur la pression intracrânienne est difficile à évaluer en raison de multiples co-interventions. Il faudra mettre en place un protocole de gestion du patient avec TCC sévère avant d’entreprendre des études prospectives. La transfusion sanguine est employée de façon courante dans la prise en charge du patient traumatisé. De nombreuses études soulignent les effets néfastes des transfusions sanguines suggérant des seuils transfusionnels plus restrictifs. Malgré cela, il n’y a pas de données sur les transfusions chez l’enfant atteint de traumatismes graves. Nous avons donc entrepris une analyse post-hoc d’une grosse étude prospective multicentrique sur les pratiques transfusionnelles des enfants traumatisés. Nous avons conclu que les enfants traumatisés sont transfusés de manière importante avant et après l’admission aux soins intensifs. Un jeune âge, un PELOD élevé et le recours à la ventilation mécanique sont des facteurs associés à recevoir une transfusion sanguine aux soins intensifs. Le facteur le plus prédicteur, demeure le fait de recevoir une transfusion avant l’admission aux soins, élément qui suggère probablement un saignement continu. Il demeure qu’une étude prospective spécifique des patients traumatisés doit être effectuée pour évaluer si une prise en charge basée sur un seuil transfusionnel restrictif serait sécuritaire dans cette population.

Geochemical Assessment and Separation of Source Waters in the Upper Boulder River Watershed Near Boulder, MT

Environmental samples were collected at three surface water sites between 5/21/2011 and 11/21/2014 along the Upper Boulder River near Boulder Montana. The sites were located at Bernice (within the mountain block), near the High Ore drainage (near the mountain block/basin transition), and at the USGS Gauging Station near Boulder, Montana (within the basin). The parameters measured in the field were SC, temperature, and alkalinity with occasional pH measurements. We collected samples for anions, cations, and stable isotopes in the catchment. We identified endmembers by sampling snow and groundwater and determined from available data an approximate endmember for rain, snow, and groundwater. We used temporal and spatial variations of water chemistry and isotopes to generate an endmember mixing model. Groundwater was found to always be an important contributor to river flow and could increase by nearly an order of magnitude during large snowmelt events. This resulted in groundwater comprising ~20% of total river flow during snowmelt at all sites. At peak snowmelt we observed that near surface water contributions to the river were from a mixture of rain and snow. Soil water, though not sampled, was hypothesized to be an important part of the hydrologic story. If so, the endmember contributions determined in this study may be different. Groundwater may have the highest variation depending on water chemistry of shallow soil water.

WOMEN, CYCLING, AND THE PUBLIC SPHERE: HOW DISCURSIVE AND COMMUNITY PRACTICES AFFECT ENGAGEMENT

This thesis considers the impact that discursive and community practices have on women’s access to the public sphere by examining female cyclists and a cycling community in Miami, Florida via interviews and observation. In the interviews, female cyclists frequently reported fears for their safety, including concern over harassment, when riding in public space. I interviewed participants of the cycling community and observed Emerge Miami’s meetings and events, where publicly organized cycling excursions were a major component. Using the theoretical and methodological lenses of Feminist Critical Discourse Analysis and Communities of Practice, I examined the interviews to understand how participants discursively framed and contextualized gender-based harassment. I found two meta-discourse frames in operation: a normative frame (that essentially accepted the status quo) and a feminist frame (that challenged the “naturalness” of women’s harassment as just what one had to live with). The feminist frame offered a pathway for women to exert control over their experiences and alter the cultural understanding of harassment’s meaning and effect. The local community practices of Emerge Miami also challenged the normative frames that often silence women, employing explicitly invitational practices, which demonstrates how local discursive and social activity can impact and increase women’s involvement by creating a more accessible space for women to engage with their local cycling community.

Trauma in critically ill children : transfusion and osmotherapy practices

Les accidents sont la cause la plus fréquente de décès chez l’enfant, la plupart du temps à cause d’un traumatisme cranio-cérébrale (TCC) sévère ou d’un choc hémorragique. Malgré cela, la prise en charge de ces patients est souvent basée sur la littérature adulte. Le mannitol et le salin hypertonique (3%) sont des traitements standards dans la gestion de l’hypertension intracrânienne, mais il existe très peu d’évidence sur leur utilité en pédiatrie. Nous avons entrepris une revue rétrospective des traumatismes crâniens sévères admis dans les sept dernières années, pour décrire l’utilisation de ces agents hyperosmolaires et leurs effets sur la pression intracrânienne. Nous avons établi que le salin hypertonique est plus fréquemment utilisé que le mannitol, qu’il ne semble pas y avoir de facteurs associés à l’utilisation de l’un ou l’autre, et que l’effet sur la pression intracrânienne est difficile à évaluer en raison de multiples co-interventions. Il faudra mettre en place un protocole de gestion du patient avec TCC sévère avant d’entreprendre des études prospectives. La transfusion sanguine est employée de façon courante dans la prise en charge du patient traumatisé. De nombreuses études soulignent les effets néfastes des transfusions sanguines suggérant des seuils transfusionnels plus restrictifs. Malgré cela, il n’y a pas de données sur les transfusions chez l’enfant atteint de traumatismes graves. Nous avons donc entrepris une analyse post-hoc d’une grosse étude prospective multicentrique sur les pratiques transfusionnelles des enfants traumatisés. Nous avons conclu que les enfants traumatisés sont transfusés de manière importante avant et après l’admission aux soins intensifs. Un jeune âge, un PELOD élevé et le recours à la ventilation mécanique sont des facteurs associés à recevoir une transfusion sanguine aux soins intensifs. Le facteur le plus prédicteur, demeure le fait de recevoir une transfusion avant l’admission aux soins, élément qui suggère probablement un saignement continu. Il demeure qu’une étude prospective spécifique des patients traumatisés doit être effectuée pour évaluer si une prise en charge basée sur un seuil transfusionnel restrictif serait sécuritaire dans cette population.

Natural ventilation and indoor air quality in educational buildings: experimental assessment and improvement strategies

Indoor environmental conditions in classrooms, in particular temperature and indoor air quality, influence students’ health, attitude and performance. In recent years, several studies regarding indoor environmental quality of classrooms were published and natural ventilation proved to have great potential, particularly in southern European climate. This research aimed to evaluate indoor environmental conditions in eight schools and to assess their improvement potential by simple natural ventilation strategies. Temperature, relative humidity and carbon dioxide concentration were measured in 32 classrooms. Ventilation performance of the classrooms was characterized using two techniques, first by fan pressurization measurements of the envelope airtightness and later by tracer gas measurements of the air change rate assuming different envelope conditions. A total of 110 tracer gas measurements were made and the results validated ventilation protocols that were tested afterward. The results of the ventilation protocol implementation were encouraging and, overall, a decrease on the CO2 concentration was observed without modifying the comfort conditions. Nevertheless, additional measurements must be performed for winter conditions.

Towards a smart semi-active prosthetic leg: preliminary assessment and testing

This paper presents a development of a semi-active prosthetic knee, which can work in both active and passive modes based on the energy required during the gait cycle of various activities of daily livings (ADLs). The prosthetic limb is equipped with various sensors to measure the kinematic and kinetic parameters of both prosthetic limbs. This prosthetic knee is designed to be back-drivable in passive mode to provide a potential use in energy regeneration when there negative energy across the knee joint. Preliminary test has been performed on transfemoral amputee in passive mode to provide some insight to the amputee/prosthesis interaction and performance with the designed prosthetic knee.

Determinants of environmental accounting and reporting practices in portuguese local entities

Purpose – The purpose of this paper is to develop environmental accounting and reporting practices (EARPs) by Portuguese local entities and their determining factors. Design/methodology/approach – Data were obtained through a postal survey. In order to measure the degree of development of environmental accounting and reporting practices index was developed, which reflects the extent to which a set of eight EARPs have been implemented by the 69 Portuguese local entities included in the sample. Three variables are considered in this study as possible factors that drive the development of environmental management practices (EMPs) by local entities, namely, size of entity, accounting framework, degree of development of EMPs. Findings – Results indicate the degree of development of EARPs in Portuguese local entities is low. Additionally, accounting regulation and the degree of development of EMPs are explaining factors of the degree of development of environmental accounting practices in Portuguese local entities. Originality/value – This study adds to the international research on environmental accounting in public sector by providing empirical data from a country, Portugal, where empirical evidence is still relatively limited.

By-catch and discarding practices in five Algarve (southern Portugal) metiers

The catches and discards of trawlers, seiners and trammel netters were studied in the Algarve (southern Portugal) using observers onboard commercial fishing vessels. Species diversity was high, with 236 species recorded as occasionally, frequently or regularly discarded. Mean discard rates per trip were 0.13, 0.20, 0.27, 0.62 and 0.70, respectively, for trammel nets, demersal purse seines, pelagic purse seines, fish trawls and crustacean trawls, with high variability in terms of discard volume and discard rate, This was especially so for se ncrs where from 0 to 100% of the total catch might be discarded. No significant relationships were found between discard quantity or discard rate and characteristics of the fishing vessels sampled within each metier (total length, TAB, hp, kW). Based on the above discard rates and the official landings, it was estimated that in 1996, Algarve trawlers discarded 9000-13000 tonnes (t) while seiners discarded 5500-8200 t. Discarding practices in these fisheries are reviewed and the reasons for discarding are presented by species and metier basis. The results support the need for more studies on the factors contributing to discarding, variability in discard quantities and rates, the fate of discards and their importance to the marine ecosystem, and on ways of reducing by-catch and discarding in these fisheries.

mHealth-based Methods for Neuromotor Assessment and Rehabilitation

Recent years observed massive growth in wearable technology, everything can be smart: phones, watches, glasses, shirts, etc. These technologies are prevalent in various fields: from wellness/sports/fitness to the healthcare domain. The spread of this phenomenon led the World-Health-Organization to define the term 'mHealth' as "medical and public health practice supported by mobile devices, such as mobile phones, patient monitoring devices, personal digital assistants, and other wireless devices". Furthermore, mHealth solutions are suitable to perform real-time wearable Biofeedback (BF) systems: sensors in the body area network connected to a processing unit (smartphone) and a feedback device (loudspeaker) to measure human functions and return them to the user as (bio)feedback signal. During the COVID-19 pandemic, this transformation of the healthcare system has been dramatically accelerated by new clinical demands, including the need to prevent hospital surges and to assure continuity of clinical care services, allowing pervasive healthcare. Never as of today, we can say that the integration of mHealth technologies will be the basis of this new era of clinical practice. In this scenario, this PhD thesis's primary goal is to investigate new and innovative mHealth solutions for the Assessment and Rehabilitation of different neuromotor functions and diseases. For the clinical assessment, there is the need to overcome the limitations of subjective clinical scales. Creating new pervasive and self-administrable mHealth solutions, this thesis investigates the possibility of employing innovative systems for objective clinical evaluation. For rehabilitation, we explored the clinical feasibility and effectiveness of mHealth systems. In particular, we developed innovative mHealth solutions with BF capability to allow tailored rehabilitation. The main goal that a mHealth-system should have is improving the person's quality of life, increasing or maintaining his autonomy and independence. To this end, inclusive design principles might be crucial, next to the technical and technological ones, to improve mHealth-systems usability.

Life Cycle Thinking for sustainability assessment and decision-making in selected food supply chains in Costa Rica

The Agenda 2030 contains 17 integrated Sustainable Development Goals (SDGs). SDG 12 for Sustainable Consumption and Production (SCP) promotes the efficient use of resources through a systemic change that decouples economic growth from environmental degradation. The Food Systems (FS) pillar in SDG 12 entails paramount relevance due to its interconnection to many other SDGs, and even when being a crucial world food supplier, the Latin American and Caribbean (LAC) Region struggles with environmental and social externalities, low investment in agriculture, inequity, food insecurity, poverty, and migration. Life Cycle Thinking (LCT) was regarded as a pertinent approach to identify hotspots and trade-offs, and support decision-making process to aid LAC Region countries as Costa Rica to diagnose sustainability and overcome certain challenges. This thesis aimed to ‘evaluate the sustainability of selected products from food supply chains in Costa Rica, to provide inputs for further sustainable decision-making, through the application of Life Cycle Thinking’. To do this, Life Cycle Assessment (LCA), Life Cycle Costing (LCC), and Social Life Cycle Assessment (S-LCA) evaluated the sustainability of food-waste-to-energy alternatives, and the production of green coffee, raw milk and leafy vegetables, and identified environmental, social and cost hotspots. This approach also proved to be a useful component of decision-making and policy-making processes together with other methods. LCT scientific literature led by LAC or Costa Rican researchers is still scarce; therefore, this research contributed to improve capacities in the use of LCT in this context, while offering potential replicability of the developed frameworks in similar cases. Main limitations related to the representativeness and availability of primary data; however, future research and extension activities are foreseen to increase local data availability, capacity building, and the discussion of potential integration through Life Cycle Sustainability Assessment (LCSA).

The environmental DNA in the risk assessment and decision making processes for the invasive species management in agri-food sector, hydraulic security and biodiversity conservation

The use of environmental DNA (eDNA) analysis as a monitoring tool is becoming more and more widespread. The eDNA metabarcoding methods allow rapid community assessments of different target taxa. This work is focused on the validation of the environmental DNA metabarcoding protocol for biodiversity assessment of freshwater habitats. Scolo Dosolo was chosen as study area and three sampling points were defined for traditional and eDNA analyses. The gutter is a 205 m long anthropic canal located in Sala Bolognese (Bologna, Italy). Fish community and freshwater invertebrate metazoans were the target groups for the analysis. After a preliminary study in summer 2019, 2020 was devoted to the sampling campaign with winter (January), spring (May), summer (July) and autumn (October) surveys. Alongside with the water samplings for the eDNA study, also traditional fish surveys using the electrofishing technique were performed to assess fish community composition; census on invertebrates was performed using an entomological net and a surber sampler. After in silico analysis, the MiFish primer set amplifying a fragment of the 12s rRNA gene was selected for bony fishes. For invertebrates the FWHF2 + FWHR2N primer combination, that amplifies a region of the mitochondrial coi gene, was chosen. Raw reads were analyzed through a bioinformatic pipeline based on OBITools metabarcoding programs package and QIIME2. The OBITools pipeline retrieved seven fish taxa and 54 invertebrate taxa belonging to six different phyla, while QIIME2 recovered eight fish taxa and 45 invertebrate taxa belonging to the same six phyla as the OBITools pipeline. The metabarcoding results were then compared with the traditional surveys data and bibliographic records. Overall, the validated protocol provides a reliable picture of the biodiversity of the study area and an efficient support to the traditional methods.