This report adresses the problem of software correction of spatially variant blur in digital images. The problem arises when the camera optics contains flaws, when the scene contains multiple moving objects with different relative motion or the camera itself is i.e. rotated. Compensation through deconvolving is impossible due to the shift-variance in the PSF hence alternative methods are required. There are a number of suggested methods published. This report evaluates two methods

In this thesis, after a general introduction, we first review some differential geometry to provide the mathematical background needed to derive the key equations in cosmology. Then we consider the Robertson-Walker geometry and its relationship to cosmography, i.e., how one makes measurements in cosmology. We finally connect the Robertson-Walker geometry to Einstein's field equation to obtain so-called cosmological Friedmann-Lemaître models. These models are subsequently studied by means of potential diagrams.

This thesis examines the synthesis, photophysical properties, and sensory responses of hydroxy-substituted 1,4-distyryl-2,5-bis(arylethynyl)benzenes (Cruciforms, XFs). These two-dimensional cross-conjugated materials possess spatially separated frontier molecular orbitals (FMOs). This spatial separation allows the HOMO and LUMO to be addressed independently by analytes, which leads to significant changes in their absorption and emission. These properties allow XFs to be utilized for the detection of various analytes. These studies highlight the benefits of utilizing XFs for the development of advanced functional solid state materials for sensory applications.

It is well known that cells in tissues display a large heterogeneity in gene expression due to differences in cell lineage origin and variation in the local environment at different sites in the tissue, a heterogeneity that is difficult to study by analyzing bulk RNA extracts from tissue. Recently, genome-wide transcriptome analysis technologies have enabled the analysis of this variation with single-cell resolution. In order to link the heterogeneity observed at molecular level with the morphological context of tissues, new methods are needed which achieve an additional level of information, such as spatial resolution. In this thesis I describe the development and application of padlock probes and rolling circle amplification (RCA) as molecular tools for spatially-resolved transcriptome analysis. Padlock probes allow in situ detection of individual mRNA molecules with single nucleotide resolution, visualizing the molecular information directly in the cell and tissue context. Detection of clinically relevant point mutations in tumor samples is achieved by using padlock probes in situ, allowing visualization of intra-tumor heterogeneity. To resolve more complex gene expression patterns, we developed in situ sequencing of RCA products combining padlock probes and next-generation sequencing methods. We demonstrated the use of this new method by, for the first time, sequencing short stretches of transcript molecules directly in cells and tissue. By using in situ sequencing as read-out for multiplexed padlock probe assays, we measured the expression of tens of genes in hundreds of thousands of cells, including point mutations, fusions transcripts and gene expression level. These molecular tools can complement genome-wide transcriptome analyses adding spatial resolution to the molecular information. This level of resolution is important for the understanding of many biological processes and potentially relevant for the clinical management of cancer patients. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

My research on the new concepts for spectrometer has been focused on the development of true multi-dimensional spectrometers, which use a multi-dimensional [two-dimensional (2D) or 3D] mapping of the spectral information into space. I showed that by combining a simple dispersive element (a volume hologram) formed in very inexpensive polymers with a basic Fabry-Perot interferometer, we can form a spectrometer with ultra-high resolution over a large spectral bandwidth, which surpasses all conventional spectrometers. I strongly believe that the extension of this mapping into three dimensions by using synthetic nanophotonic structures with engineered dispersion can further improve the performance and reduce the overall spectrometer size into the micron regime. The need for efficient modeling and simulation tools comes from the sophisticated nature of the new 3D nanophotonic structures, which makes their simple analysis using well-known simple formulas for the propagation of the electromagnetic fields in bulk materials impossible. In my Ph.D. research, I developed new approximate modeling tools for both the modeling of incoherent sources in nanophotonics, and for the propagation of such optical beams inside the 3D nanophotonic structures of interest with several orders of magnitude improvement in the simulation speed for practical size devices without sacrificing accuracy. To enable new dispersive properties using a single nanophotonic structure, I have focused in my Ph.D. research into polymer-based 3D photonic crystals, which can be engineered using their geometrical features to demonstrate unique dispersive properties in three dimensions that cannot be matched by any bulk material even with orders of magnitude larger sizes. I have demonstrated the possibilities of using a very compact structure for wavelength demultiplexing and also for spectroscopy without adding any other device.

An increasing demand for food, and in particular animal products, is putting high pressure on natural resources, often at places distant from the consumption. Nitrogen and phosphorus are essential nutrients in food production but an excessive use can cause environmental impacts such as eutrophication that can harm ecosystems services vital to local communities. This study developed sub-national spatially explicit N and P footprints that were extended with an assessment of nutrient leaching risk and risk of impact on biodiversity. The consumption of N and P in Brazilian soybean production at municipal level was estimated for the whole of Brazil as well as for UK soybean demand. This was then combined with the risk of nutrient leaching (Nrisk and Prisk) and species richness (Nbio and Pbio). The results showed high Nbio and Pbio in Mato Grosso, Paraná, and Rio Grande do Sul. The same analysis of the effects of UK soybean demand showed a higher risk of impacts in Rondônia and less in Paraná and Rio Grande do Sul compared to total Brazilian soybean production. A municipal case study showed that the demand of Brazilian soybean in the UK, EU, and China generated different spatial patterns of impact risks at municipal level. Spatially explicit footprints that also encompass risks of impacts are important for being able to identify the responsible consumer and parts of the supply chain where sustainability interventions will be most effective. There are several opportunities for future development within this research field as data availability is continuingly increasing.

The spatially distributed adaptive array is defined and analyzed. It is applied to both time division multiple access (TDMA) and code division multiple access (CDMA) cellular networks to improve the outage probability at either the base station or mobiles. In a TDMA network, the distributed array consists of three sub-arrays at alternate corners of a hexagonal cell. It is shown analytically that the SINR of combined beamforming of the distributed sub-arrays is greater than or equal to the SIR or independent beamforming of the sub-arrays. Closed form solutions are derived for estimating the BER performance of Rayleigh fading mobile signals received at a distributed adaptive array with combined beamforming of the sub-arrays. The simulated TDMA uplink outage probability of multiple same-cell co-channel users in a fading environment is compared between conventional, spatially distributed arrays with independent beamforming of the sub-arrays and combined beamforming of the sub-arrays. The effect of the antenna element spacing, number of elements and angular spread is also investigated. Spatially distributed arrays are formed in a CDMA network on the downlink with arrays in multi-way soft handoff with the mobiles. The outage probability performance of combined beamforming of the arrays in handoff is compared to independent beamforming of the arrays as well as to conventional sectorized antennas. The range between mobiles and distributed sub-arrays in the case of a spatially distribu-ted array can be larger than between conventional center cell arrays and mobiles. Therefore, the effect of interference on the range increase relative to an omni antenna of adaptive and phased arrays in a multipath environment for both narrowband and wideband spread spectrum systems is investigated. An analytical model for predicting the asymptotic range limitation of phased arrays when the angular spread exceeds the array beamwidth is derived. / Thesis (PhD (Electronic Engineering))--University of Pretoria, 2006. / Electrical, Electronic and Computer Engineering / unrestricted

The subject of this bachelor thesis is the design of the spatially adaptable 3D printer for Contour Crafting. Aiming to apply megascale aditive technology in a field of construction industry.

Sequencing technologies and applications have pushed the limits and enabled novel studies of biological mechanisms, evolutionary relationships and communication networks between cells. The technical developments leading to single cell RNA-sequencing have enabled detection of rare cell populations while spatial resolution added insights into larger biological environments, like tissues and organs. Massively parallel sequencing has paved the way for integrated high-throughput analyses including that of studying gene expression, protein expression and mapping of microbial communities. This thesis starts with an introduction describing the technical and biological advancements made in recent years with focus on spatially resolved approaches. Then, a summary of recent accomplishments is presented, which enabled ongoing work in a novel field of spatial hostmicrobiome profiling. Lastly, the concluding remarks include both a future perspective and a short reflection on the current developments in the spatial multi-omics field. 16S sequencing is often used for taxonomic classification of bacteria. In Paper I, this sequencing technique was used to study the aerodigestive microbiome in pediatric lung transplant recipients. Many of these patients regretfully reject the organ after transplant, but the underlying cause is, in many cases, unknown. In this paper, multiple factors influencing rejection were examined including that of the aerodigestive microbiome. Pediatric lung transplant recipients often suffer from gastrointestinal dysmotility and the focus of this study was also to analyze changes in the microbiome in relation to irregular gastric muscle movements. The results showed that lung transplant recipients had, in general, lower microbial diversity in the gastric fluid and throat and also that the microbial overlap between lung and gastric sampling sites was significantly less in transplant recipients compared to controls. In addition, gastrointestinal dysmotility was shown to influence the gastric microbiome in lung transplant recipients, but, given the small sample size available in this study, the correlation to patient outcome could not be examined. Integrated analysis of the transcriptome and the antibody-based proteome in the same tissue section was enabled using the method developed in Paper II. Spatial Multi- Omics (SM-Omics) uses a barcoded glass array to capture mRNA and antibody-based expression of selected proteins in the same section. The antibody-based profiling of the tissue section was enabled by either immunofluorescence or DNA-barcoded antibodies that were then decoded by sequencing. The protocol was scaled-up using an automated liquidhandling system. Using this method, simultaneous profiling of the transcriptome and multiplexed protein values was determined in both the mouse brain cortex and mouse spleen. Results showed a high correlation in spatial pattern between gene expression and antibody measurements, independently of the antibody labelling technique. SM-Omics generates a high-plex multi-omics characterization of the tissue in a high throughput manner while exhibiting low technical variation. / Tekniker och applikationer som använder sekvensering har flyttat fram gränsernaoch tillåtit nya undersökningar av biologiska mekanismer, evolutionära släktskap ochkommunikationsnätverk mellan celler. De tekniska utvecklingarna som har lett fram tillRNA-sekvensering av enskilda celler har möjliggjort upptäckten av sällsynta cellpopulationer medan den rumsliga upplösningen har inneburit en ökad förståelse av störrebiologiska miljöer, såsom vävnader och organ. Massively parallel sequencing har banat vägför integrerade analyser med hög kapacitet, vilket inkluderar analys av genuttryck,proteinuttryck och kartläggning av bakteriella samhällen. Den här avhandlingen börjar meden introduktion som beskriver tekniska och biologiska framsteg som gjorts de senaste åren,med fokus på den rumsliga upplösningen. Sedan följer en summering av de senasteprestationerna som har möjliggjort det pågående arbetet i ett nytt fält som avhandlarrumslig profilering av bakterien och dess värd. Slutligen innehåller slutordet både ettframtida perspektiv samt en kort reflektion av den nuvarande utvecklingen inom fälten förrumslig mång-omik. 16S-sekvensering används ofta för att taxonomiskt klassificera bakterier. Dennasekvenseringsteknik användes i artikel I för att studera mikrobiomet i luft- ochmatspjälkningskanalen hos barn med transplanterad lunga. Dessvärre är det vanligt medavstötning av lungan efter transplantationen hos många av dessa patienter, men denunderliggande orsaken till avstötningen är, i många fall, okänd. I denna studie undersöktesflertalet faktorer, inklusive mikrobiomet i luft- och matspjälkningskanalen, som kan tänkaspåverka bortstötningen. Barn med transplanterad lunga lider ofta av störningar i magtarmkanalens rörelser och artikelns fokus var därmed även att analysera förändringar imikrobiomet i relation till dessa avvikande rörelser i mag-tarmkanalen. Resultatet visade attpatienter med transplanterad lunga generellt hade lägre bakteriell mångfald i magsaft ochhals, samt att det bakteriella överlappet mellan lunga och magsaft var signifikant mindre ipatienter med transplanterad lunga jämfört med kontrollerna. För övrigt visade det sig attstörningar i mag-tarmkanalens rörelser påverkade magsaftens mikrobiom hos patientermed transplanterad lunga, men på grund av studiens storlek på urvalet, kunde det inteundersökas hur detta korrelerade till utfallet hos patienterna. Integrerad analys av transkriptomet och antikroppsbaserad analys av proteomet isamma vävnadssnitt har möjliggjorts genom metoden som utvecklats i artikel II. SpatialMulti-Omics (SM-Omics) använder ett avkodningsbart mönster av korta DNA-segment påen glasyta för att fånga mRNA och antikroppsbaserat uttryck av utvalda proteiner frånsamma vävnadssnitt. Den antikroppsbaserade profileringen av vävnadssnittet uppnåddesgenom antingen immunofluorescens eller antikroppar märkta med DNA-segment somkunde avkodas genom sekvensering. Protokollet skalades upp genom ett automatiseratsystem för att behandla vätskor. Genom användning av denna metod kunde simultanprofilering av transkriptomet och flertalet proteiner uppnås i både hjärnbarken och mjältenhos en mus. Resultaten visade en hög korrelation i det rumsliga mönstret mellangenuttrycket och de antikroppsbaserade mätningarna, oberoende av hur antikropparnahade märkts. SM-Omics genererar en storskalig karaktärisering av vävnaden av flera omikermed hög kapacitet samtidigt som den har låg teknisk variation. / <p>QC 2021-02-02</p>

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