The work focuses on Monte Carlo simulations for finding the optimal back scatter time-of-flight spectrometer design for concept testing at the NESSA facility at Uppsala University. The spectrometer consists of two scintillator detectors, D1 (placed in a neutron beam) and D2 (placed in front of D1), at some distance from each other. A fraction of the neutrons that impinge on D1 back scatter into D2 and information on the neutron energy distribution is acquired using the time-of-flight method. For the given constraints on geometry, resolution and efficiency a best resolution was found to be 6.6% with a corresponding efficiency of 1E-4 which gives a sufficient count rate for a neutron generator producing 1E+11 neutrons/s. In order to achieve a minimum of 10 000 counts/h with the same setup a D2 with an area of at least 7 cm^2 is required.

Tissue biopsy and swab culture are the gold standards for diagnosing tissue infection; these tests require significant time, diagnostic costs, and resources. Towards earlier and specific diagnosis of infection, a non-destructive, rapid, and mobile detection device is described to distinguish bacterial species via light scatter spectra from the surface of an infected tissue, reagent-free. Porcine skin and human cadaveric skin models of wound infection were used with a 650 nm LED and an angular photodiode array to detect bacterial infections on the tissue surface, which can easily be translated to a typical CMOS array or smartphone. Tissue samples were inoculated with Escherichia coli, Salmonella Typhimurium, or Staphylococcus aureus and backscatter was collected from 100 degrees to 170 degrees in 10 degrees increments; each bacterial species resulted in unique Mie scatter spectra. Distinct Mie scatter spectra were obtained from epidermis (intact skin model) and dermis (wound model) samples, as well as from porcine and human cadaveric skin samples. Interactions between bacterial colonies and lipid particles within dermis samples generated a characteristic Mie scatter spectrum, while the lipid itself did not contribute to such characteristic spectrum as corroborated with body lotion experiments. The designed angular photodiode array is able to immediately and non-destructively detect tissue bacterial infection and identify the species of infection within three seconds, which could greatly improve point of care diagnostics and antibiotic treatments.

Abstract This study was carried out to investigate in vivo the changes of the human lens autofluorescence (AF) with aging and cataractogenesis. Measurements were performed in the blue-green AF range (495 nm/520 nm) using a fluorometer designed, built and now clinically tested in our department. 43 random eyes of 43 healthy volunteers aged 6-86 years, five of each decade, were studied for effects of aging and 84 eyes of 84 patients with cortical, nuclear, posterior subcapsular or mixed lens opacities were studied for differences of various cataract types. The results were compared with the back light scatter values obtained by the commercially available Interzeag Lens Opacity Meter 701. Also AF and back light scatter of the lens were measured from 122 smoking males aged 57 to 76 years who participated in a cancer prevention study. The results were compared with the widely used subjective lens opacities classification system, LOCS III. In addition data was collected from 30 randomly chosen eyes of as many subjects with varying degrees of yellow-brown lens coloration in an otherwise healthy eye. We studied the influence of lens yellowing expressed by means of lens AF on visibility of retinal nerve fiber layer in black-and-white images. Lens AF profile consists of anterior and posterior peaks and a central plateau. The height of the anterior peak was used as a measure of the maximum AF value. The square root of the ratio between the posterior and the anterior AF peaks was used for estimating the lens transmission. Our technique was highly reproducible. The coefficient of variation was 3.9% for maximum AF and 2.9% for the lens transmission index. Both the maximum AF and light scatter were exponentially increased with age (r = 0.95 and 0.94, respectively; p < 0.0001). According to the regression line of AF begins to increase in early childhood. It appears by extrapolation to be absent at birth. In contrast light scatter in the lens was present even in young children. The lens transmission for blue-green light, determined from the lens AF curve, was almost unchanging with age up to 60 years. Thereafter it decreased rapidly and the interindividual variation increased.In cataractous lenses the mean AF and scatter values differed statistically significantly from those of age matched healthy controls. The highest AF values were measured in nuclear cataracts where AF was also related to visual acuity and an increasing yellow-brown colour of the nucleus. About half of the total variation of the transmission index values could be accounted for by changes in nuclear colour as assessed by the LOCS III grading system. The transmission index provided a more precise prediction about nuclear colour and opalescence than age or light scatter did. In cortical cataracts the AF curve was low and flattened and the maximum AF value was significantly lower than in the age matched control eyes. The highest light scatter values were measured from cortical cataracts, but the correlation between LOCS III cortical grades and light scatter values was rather weak. Posterior subcapsular cataracts cannot be quantified either with AF or with light scatter measurements. Lens yellowing, expressed as lens AF, had an actual effect on retinal nerve fiber layer visibility. AF measurements provided a better prediction about the visibility score than age or visual acuity did. The results of the present study indicate that the lens autofluorescence measurement may be a useful additional tool together with a subjective grading system in the follow-up of optical changes occurring in the nuclear region of the lens.

The images in positron emission tomography (PET) represent three dimensional dynamic distributions of biologically interesting molecules labelled with positron emitting radionuclides (radiotracers). Spatial localisation of the radio-tracers is achieved by detecting in coincidence two collinear photons which are emitted when the positron annihilates with an ordinary electron. In order to obtain quantitatively accurate images in PET, it is necessary to correct for the effects of photon attenuation within the subject being imaged. These corrections can be obtained using singles-mode photon transmission scanning. Although suitable for small animal PET, these scans are subject to high amounts of contamination from scattered photons. Currently, no accurate correction exists to account for scatter in these data. The primary purpose of this work was to implement and validate an analytical scatter correction for PET transmission scanning. In order to isolate the effects of scatter, we developed a simulation tool which was validated using experimental transmission data. We then presented an analytical scatter correction for singles-mode transmission data in PET. We compared our scatter correction data with the previously validated simulation data for uniform and non-uniform phantoms and for two different transmission source radionuclides. Our scatter calculation correctly predicted the contribution from scattered photons to the simulated data for all phantoms and both transmission sources. We then applied our scatter correction as part of an iterative reconstruction algorithm for simulated and experimental PET transmission data for uniform and non-uniform phantoms. We also tested our reconstruction and scatter correction procedure using transmission data for several animal studies (mice, rats and primates). For all studies considered, we found that the average reconstructed linear attenuation coefficients for water or soft-tissue regions of interest agreed with expected values to within 4%. Using a 2.2 GHz processor, the scatter correction required between 6 to 27 minutes of CPU time (without any code optimisation) depending on the phantom size and source used. This extra calculation time does not seem unreasonable considering that, without scatter corrections, errors in the reconstructed attenuation coefficients were between 18 to 45% depending on the phantom size and transmission source used. / Science, Faculty of / Physics and Astronomy, Department of / Graduate

The RTT80 cone beam x-ray computed tomography system, developed by Rapiscan Systems Ltd, uses switched x-ray sources and fixed offset detector rings to remove the time consuming mechanical rotations of earlier imaging systems. This system produces three-dimensional images in real time. A Geant4 Monte Carlo simulation has been developed to investigate scattered radiation in the uncollimated detector machine, showing high levels of scatter behind highly attenuating objects. A new scatter correction method is proposed which estimates scatter to each detector, in each projection, from 1cm³ voxels of the computerised object. The scatter distributions from different materials are pre-determined using a Geant4 Monte Carlo simulation. The intensity of scatter from each voxel is based on measured data. The method is applied to two simulated test objects, a water box simulated with a monoenergetic input spectrum and a test suitcase simulated with a polyenergetic spectrum. The test suitcase is broken down into separate components to analyse the method further. The results show that the method performs well for low attenuating objects, but the results are sensitive to the intensity values. However, the method provides a good basis for a scatter correction method.

This study investigated primary seed dispersal of !nara (Acanthosicyos horridus) by Blackbacked Jackals (Canis mesomelas) and secondary seed dispersal by scatter-hoarding hairyfooted gerbils (Gerbilliscus (Gerbillurus) spp.) in the central Namib Desert. This was accomplished by examining visitation rates and fruit removal of !nara melons, primarily by jackals. In addition, I determined the viability and germination rate of !nara seeds collected from jackal scat. The results indicate that jackals were the dominant species to visit !nara (93.3%) and the only !nara frugivores recorded by camera traps over two !nara fruiting seasons. There was no difference in the viability of ingested seeds and control seeds, but germination rates of ingested !nara seeds were significantly higher (50.4%) than control !nara seeds (34%). This component of the study suggests that Black-backed Jackals are the main primary dispersers of !nara seeds in the central Namib Desert. I furthermore examined secondary seed dispersal by tracking !nara seeds to determine whether scatter-hoarding hairyfooted gerbils were caching or consuming seeds. I recorded the distance moved, depth of seed burial, recovery rate and the habitats in which seeds were buried in three habitat types. Hairyfooted gerbils removed 100% !nara seeds from experimental sites and cached 60.3 % of all the !nara seeds removed. The gerbils frequently retrieved the buried caches within two days (77% of the time) and re-cached them elsewhere. The majority of caches were in the open areas (83%) and only consisted of one (39%) or two seeds (45%). Only 1.7% of the cached seeds were not retrieved by the gerbils during the 30-day observation periods. !Nara seeds were moved an average distance of 29.1±1.6 m and buried at an average depth of 4±0.2 cm. Although there is high probability of cache retrieval, some of the cached seeds survived. As gerbil caches are at favourable locations for plant establishment, and as it is more likely that buried seeds will survive until suitable conditions for germination and seedling establishment, seed dispersal by hairy-footed gerbils is advantageous to !nara plants. Therefore, hairy-footed gerbil species in the central Namib Desert contributed to secondary seed dispersal of !nara. The combined interaction of endozoochory by Black-backed Jackals (Canis mesomelas) and synzoochory by hairy-footed gerbils (Gerbillurus spp.) in dispersing seeds of !nara plants (Acanthosicyos horridus) in the central Namib Desert suggest diplochory is highly likely.

There was a large radar campaign during 2007 and 2008, the International Polar Year (IPY),and at that time the EISCAT Svalbard Radar was operated and measured the ionosphere continuouslyat most times. This report presents statistical results from an electron enhancementpoint of view. Until now there has been some research into the field and results based on theions in the ionosphere, and the enhancements we refer to as Naturally enhanced ion acousticlines (NEIALs). Plasma line data from May 2007 to February 2008 has been analysed inorder to find and classify enhancements as NEIALs have been classified but with respect tothe electron distribution instead of the ion distribution. A method of detection was developedin order to differentiate the enhancements from the background with a relation between theminimum and maximum power of each measured dump. Results show that there is a largedifference between the downshifted plasma lines and the upshifted plasma lines, both has arange distribution peak at 180 km and the upshifted plasma line has another peak at 230 kmwhich the downshifted plasma line does not. The occurrence rate of the enhancements was1.64 % for the downshifted plasma line and 4.69 % for the upshifted plasma line. Threedifferent types of enhancements are classified using the variance distribution for the peakfrequency of that detected dump, Single, Profile, and Diffuse. The Single enhancements havea bit different spectral, range, and time of day distributions than of the Profile and Diffusedistributions. The Diffuse classifications are mostly wrong classifications and aliasing and itis very similar to Profile enhancements as seen by its distribution.

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