Changes in species abundance and richness, stand structure, and species responses to habitat characteristics including disturbance intensity, were investigated in 28 permanent sample plots (PSP) covering a total area of about 6.2 hectares of subtropical rainforests in north-east New South Wales, Australia. The disturbance that occurred over 36 years previously varied from unlogged (controls), through single-tree selection (light), moderate selection and repeated single-tree selection to intensive (heavy) logging. Multivariate and univariate approaches were used to investigate changes in various plant groups, including all vascular plants, regenerating species (trees and understorey species > 1.3 m in height and < 10 cm diameter at 1.3 m above the ground level (dbh)), juvenile trees (regenerating species capable of attaining at least 10 cm dbh), and trees ¡Ý 10 cm dbh. In addition, dynamic parameters (recruitment, growth and mortality) were estimated using hierarchical multilevel modelling and parameter estimates used to simulate behaviour of the subtropical rainforest tree species in unlogged and logged stands, both within and beyond the range of available data.Chronological post-disturbance responses and changes in species abundance and richness as well as stand structure for trees ¡Ý 10 cm dbh were investigated using 20 PSP in a bid to better understand rainforest post-disturbance regeneration. The results portrayed minor and gradual ecological changes in the undisturbed controls analogous with natural forest dynamics where the changes were not significant. In logged sites, initial gradual changes were followed with more rapid and significant changes.In both unlogged and logged stands, the changes proceeded through three clearly identifiable stages. The first two stages lasted between 5 and 15 years each. In the initial stage, the number of individuals decreased in species with high frequency mainly in the shade tolerant species, with little or no change in species richness. In the second stage, species abundance and richness changed due to localised species turnover, replacement and losses with very little recruitment, and the numbers of both speciesand individuals declined to minima. In the third stage, due to recruitment beyond the 10 cm dbh, the net loss of species and trees ¡Ý 10 cm dbh were halted and reversed, and species diversity and abundance began to return to pre-disturbance levels.Species abundance and diversity for both shade tolerant and intolerant species in less intensively logged sites (single-tree selection logging) have recovered to levels comparable with that observed in the controls, but more intensively logged sites have not recovered to similar levels. Increased logging intensity was associated with increased and decreased densities in the shade intolerant and ¨Ctolerant species respectively. It was evident that stand structure in logged sites had yet to recover to levels comparable with that of unlogged controls. It appears the restoration of floristic diversity to levels similar to that of intact primary forest takes considerably less time than structural recovery. Changes in regeneration patterns in a subtropical rainforest in north-east New South Wales were investigated for a 13-year period during the 3rd and 4th decades following repeated single-tree selection logging. Multivariate and univariate analyses results showed that there were no significant differences in floristic assemblages within and between censuses; however, two contrasting trends of changes in plant groups were detected. In trees ¡Ý 10 cm dbh, the stem density and species richness increased in shade tolerant group, and while stem density increased in the shade intolerant group, species richness decreased during the study period. Amongst smaller sized species including trees (< 10 cm dbh), a general decrease in species richness was observed along with significant changes in stem densities (P = 0.03) with the number of individuals in the shade tolerant species increasing, while that of both shade intolerant and vine species decreased. Excluding the vines and understorey species from the broader regenerating species group, revealed a decrease in species richness in juvenile canopy tree, and a significant change in densities (P = 0.004) with the number of individuals in shade tolerant increasing, while that of shade intolerant trees decreased. A comparison between the canopy trees ¡Ý 10 cm dbh and juvenile canopy trees group showed that these groups were tending towards similar floristic assemblages. These results suggest gradual replacement of shade intolerant by shade tolerant species as stands were tending toward later stages of recovery within the regeneration. The results also show that the inclusion of regenerating species in long-term studies is both complementary to the larger plant component and more revealing of both trends and changes.Species-specific estimates of shade tolerance and size structure at maturity derived from observations on 23 plots were used to intuitively group 277 vascular plant species into 3 main groups including full floristic (all together), shade tolerant and intolerant groups. The shade tolerant and intolerant groups were further grouped into smaller plants groups depending on the development stage and maximum size at maturity. These groups included regenerating species, juvenile trees, and trees ¡Ý 10 cm dbh. Multivariate analyses of these nominated groups revealed that floristic assemblages were significantly associated with environmental gradients based on simple site characteristics.At the landscape (larger) scale, the floristic assemblages were significantly different between low (200-400), mid (400-700) and high altitude (over 700 meters above sea level). In addition, abundance of shade tolerant species including Doryphora sassafras Endl, Orites excelsa R.Br and Caldcluvia paniculosa (F.Muell) Hoogland was positively correlated with the altitudinal gradient. At the smaller (local) scale, intensively logged sites where large gaps were created had recovered their species richness, but effects of past logging were evident in trees ¡Ý 10 cm dbh, especially trees greater than 50 cm dbh where species abundance in shade tolerant decreased significantly. Less intensively logged sites at mid altitude where a few stems were removed had recovered their species richness in respect to trees ¡Ý 10 cm dbh, but the small gaps created may have healed quickly for appreciable regeneration response to occur, as juvenile trees component was significantly different to that of the (unlogged) controls.The abundance of shade intolerant and juvenile shade tolerant tree species increased in concert with levels of disturbance and abundance of shade intolerant species such as Duboisia myoporoides R.Br, Acacia melanoxylon R.Br, Rubus moorei F.Muell and R. hilli F.Muell was positively correlated with the disturbance gradient. Increase in number of individuals of certain tree species was positively correlated with both disturbance intensity and topography (mid slope through lower slope to creek/gully), but negatively correlated with aspect (NE - NW). We concluded that logged sites are yet to recover their pre-logging stand structure and rainforest tree species were found in sites where favourable recruitment and growth conditions were the encountered. These results show that logged sites had not yet regenerated to the pre-logging stand structure. They also show that habitat characteristics including history of disturbance and topography can influence the floristic assemblages in the sub-tropical rainforests at both the small (local) and large (geographic) scales. This supports the environmental control model that states ¡°species are found at sites where they encounter favourable living conditions¡±. Site characteristics as surrogate for some of these favourable living conditions were identified as useful potential variables to investigate the rainforest dynamic parameters (growth, recruitment and mortality) in both logged and unlogged stands.A quantitative model was developed using over 3 decades of data to describe and simulate the dynamics including recruitment, growth and mortality in unlogged stands and others subjected to different silvicultural regimes in uneven-aged mixed-species subtropical rainforests of north-eastern New South Wales. Hierarchical multilevel regression analyses including Poisson, Binomial and multinomial logit regression were used to estimate the rainforest dynamic parameters based on the assumption that trees perform differently in space and time, thus there are variations at both the plot and tree by measurement levels.Variations at the tree level required the botanical identity of trees to species level, and then the species-specific size at maturity and shade tolerance were used to classify species into 5 groups, each consisting of species with similar ecological characteristics. These groups were labelled as emergent and shade tolerant main canopy, shade tolerant mid canopy, shade tolerant understoreys, moderate shade tolerant and persistent, and shade intolerant pioneer tree species. Significant variables at the plot level including site characteristics such as topography (elevation, slope and aspect), and past disturbance were used as explanatory variables in species group models. The final model is as a classical matrix management-oriented model with an ecological touch and maximum size-dependent parameters of ingrowth and outgrowth. The model provides a tool to simulate stand performance after logging and to assess silvicultural prescriptions before they are applied in these types of forests.The simulations indicate that full recovery following a logging intensity where 47% of the overstorey basal area is removed with a checkerboard of logged and unlogged patches (group selection) on a 120-year cycle could enable sustainable timber production without compromising the ecological integrity in these forests. Following single-tree selection (33%), recovery takes about 150 years, and more intensive harvesting practices where 50-78% overstorey basal area is removed may take 180-220 years to recover. Pre-harvest climber cutting coupled with poisoning of non-timber species followed by intensive logging of merchantable trees would allow logging on a 300-year cycle. Shorter logging cycles may lead to changes in the forest structure and floristic composition where the overall species density is low with higher density of shade intolerant species.

<p>Biological treatment optimization aim at improving radiation therapy by accounting for the radiobiological tumour and normal tissues response properties when optimizing the dose delivery. Generally traditional methods, using only dosimetrical measures, disregard the nonlinear radiation response of different tumours and normal tissues. The accumulated knowledge on tissue response to radiation, in the form of more accurate dose response relations, cell survival models and their associated biological parameters, alongside with the tools for biological treatment plan optimization, has allowed the present investigation on the potential merits of biologically based treatment optimization in radiation therapy.</p><p>With a more widespread implementation of intensity modulated radiation therapy in the clinic, there is an increasing demand for faster and safer treatment delivery techniques. In this thesis biological treatment plan optimization, using the probability to achieve complication free tumour control as the quantifier for treatment outcome, was applied to radiation therapy of early breast cancer and advanced cervix cancer. It is shown that very conformal dose distributions can generally be produced with 3 or 4 optimally orientated coplanar intensity modulated beams, without having clinically significant losses in treatment outcome from the optimal dose distribution.</p><p>By using exhaustive search methods, the optimal coplanar beam directions for intensity modulated photon beams for early breast cancer and the optimal non-coplanar directions for an advanced cervix cancer were investigated. Although time consuming, exhaustive search methods have the advantage of revealing most features involving interactions between a small number of beams and how this may influence the treatment outcome. Thus phase spaces may serve as a general database for selecting an almost optimal treatment configuration for similar patients. Previous knowledge acquired with physically optimized uniform beam radiation therapy may not apply when intensity modulated biological optimization is used. Thus unconventional treatment directions were sometimes found.</p>

<p>One of the most used irradiation techniques in modern radiation therapy is step-and-shoot IMRT. The accuracy of this technique when delivering complex dose distributions strongly depends on the size of the subfields. The aims of this study is to determine the minimum size of subfields that can be used efficiently in Step-and-Shoot IMRT, to investigate the validation process for beam delivery and treatment planning dose calculations, and to find recommendations for practical clinical implementations.</p><p>Two different detectors, a CC04 ion chamber and a SFD stereotactic diode, have been used for measuring head scatter factors in air (Sc), total output factors (Scp) and dose profiles in water for a wide range of field sizes. The measurements were compared to calculations done with a pre-release version of the Nucletron MasterPlanTM v 3.1 treatment planning system that employs a novel, high resolution fluence modelling for both its pencil beam and collapsed cone dose calculation algorithms. Collimator settings were explicitly checked using FWHM film measurements with a build-up sheet of tungsten placed close to the treatment head to reduce the influence from lateral electron transport and geometrical penumbra. An analysis of the influence and sensitivity of Scp for small fields with respect to the linear accelerator source size and shape was also made.</p><p>The measurements with the ionization chamber and the stereotactic diode showed good agreements with each other and with the treatment planning system calculations for field sizes larger than 2×2 cm2. For small field sizes, measurements with different detectors yielded different results. Calculations showed agreements with measurements with the smallest detector, provided careful field size calibration and commissioning of calculation parameters. Uncertainties in collimator settings and source characteristics were shown to yield large uncertainties in Scp for fields smaller than 2×2 cm2.</p><p>The treatment planning system was found to properly handle small subfields but results were very sensitive to uncertainties in source size, as well as calibration and reproducibility of the collimator settings. Therefore if subfields smaller than 2×2 cm2 are to be used in IMRT extra care should be taken to determine the source characteristics and to calibrate the collimators. The volume of the detectors used for validation of such small fields and the loss of charged particle equilibrium conditions also have to be taken into consideration.</p>

<p>Optical fibre sensors can be used to measure a wide variety of properties. In some cases they have replaced conventional electronic sensors due to their possibility of performing measurements in environments suffering from electromagnetic disturbance, or in harsh environments where electronics cannot survive. In other cases they have had less success mainly due to the higher cost involved in fibre-optic sensor systems. Intensity modulated fibre-optic sensors normally require only low-cost monitoring systems principally based on light emitting diodes and photo diodes. The sensor principle itself is very simple when based on coupling between fibres, and coupling based intensity modulated sensors have found applications over a long time, mainly within position and vibration sensing. In this thesis new concepts and applications for intensity modulated fibre-optic sensors based on coupling between fibres are presented. From a low-cost and standard component perspective alternative designs are proposed and analyzed in order to find improved performance. The development of a sensor for an industrial temperature sensing application, involving aspects on multiplexing and fibre network installation, is presented. Optical time domain reflectometry (OTDR) is suggested as an efficient technique for multiplexing several coupling based sensors, and sensor network installation with blown fibre in micro ducts is proposed as a flexible and cost-efficient alternative to traditional cabling. A new sensor configuration using a fibre to a multicore fibre coupling and an image sensor readout system is proposed. With this system a high-performance sensor setup with a large measurement range can be realised without the need for precise fibre alignment often needed in coupling based sensors involving fibres with small cores. The system performance is analyzed theoretically with complete system simulations on different setups. An experimental setup is made based on standard fibre and image acquisition components, and differences from the theoretical performance are analyzed. It is shown that sub-µm accuracy should be possible to obtain, being the theoretical limit, and it is further suggested that the experimental performance is mainly related to two error sources: core position instability and differences between the real and the expected optical power distribution. Methods to minimize the experimental error are proposed and evaluated.</p>

<p>KTH, Division of Neuronic Engineering, have a finite element model of the head. However, this model does not contain detailed modeling of the brain. This thesis project consists of finding a method to extract brain tissues from T1-weighted MR images of the head. The method should be automatic to be suitable for patient individual modeling.</p><p>A summary of the most common segmentation methods is presented and one of the methods is implemented. The implemented method is based on the assumption that the probability density function (pdf) of an MR image can be described by parametric models. The intensity distribution of each tissue class is modeled as a Gaussian distribution. Thus, the total pdf is a sum of Gaussians. However, the voxel values are also influenced by intensity inhomogeneities, which affect the pdf. The implemented method is based on the expectation-maximization algorithm and it corrects for intensity inhomogeneities. The result from the algorithm is a classification of the voxels. The brain is extracted from the classified voxels using morphological operations.</p>

<p>The Earth’s surface contains of 71% oceans and a large part of the global carbon cycle takes place in the oceans. In the aquatic environment, the sediment-water interface plays an important role for the mineralisation of organic material. One factor that can affect the mineralisation is resuspension. Resuspension cause mixing of surface sediments and bottom water and result in a redistribution of the sediment when it settles again. Resuspension also increases the transport of oxygen into the sediment, reduces the diffusive boundary layer surrounding particles, and enhance the nutrient uptake. Resuspension can be induced by both wave action and bottom currents and is a common physical process in both shallow coastal areas and in the deep ocean. Human impacts, such as dredging and trawling, can also cause resuspension.</p><p>The effect of resuspension on mineralisation of organic material was studied in two experiments ex situ during December to April 2004/2005. The aim for Experiment 1 was to investigate how the intensity of the resuspension event affects the degradation rate. The aim for Experiment 2 was to investigate how different concentrations of resuspended sediment affect the degradation rate of organic matter. Sediment samples were collected in December and late March at a marine field station, Askö, Sweden. Sediment and bottom water were transferred to and incubated in sealed bottles. For Experiment 1, resuspension was created in bottles with a specially designed rotary table, creating different intensity of water movements. In Experiment 2, bottles with different concentrations of sediment were put on an ordinary rotary table. The mineralisation rates were in both experiments monitored by daily sampling of sediment-water slurry, and analysed for total inorganic carbon by a gas chromatography with a thermal detector, GC-TCD.</p><p>Results from Experiment 1 did not show any clear patterns regarding inorganic carbon formation. Experiment 2 did show clear patterns for two of six replicates of mineralisation of organic material. For these replicates the mineralisation rate were low according to previous studies. However, the sediment concentration seems to not affect the mineralisation rate. For both experiments, valuable information on how to better design experiments to investigate the importance of resuspension and the effect of mineralisation of organic material was yielded. Hence, further studies are needed to continue the investigation of the importance of resuspension for the mineralisation rate of organic material, and its impacts on the nutrient fluxes in the oceans.</p>

<p>In the human body, turbulent flow is associated with many complications. Turbulence typically occurs downstream from stenoses and heart valve prostheses and at branch points of arteries. A proper way to study turbulence may enhance the understanding of the effects of stenoses and improve the functional assessment of damaged heart valves and heart valve prostheses.</p><p>The methods of today for studying turbulence in the human body lack in either precision or speed. This thesis exploits a magnetic resonance imaging (MRI) phenomenon referred to as signal loss in order to develop a method for estimating turbulence intensity in blood flow.</p><p>MRI measurements were carried out on an appropriate flow phantom. The turbulence intensity results obtained by means of the proposed method were compared with previously known turbulence intensity results. The comparison indicates that the proposed method has great potential for estimation of turbulence intensity.</p>

<p>A common technique to evaluate load paths in complex structures is to perform FE-calculations with relative large elements. This procedure gives no information regarding stress concentrations at e.g. holes or radius but this phenomenon can later on be investigated in details with local individual submodels. Displacements is taken from the global model and used to analyse stress concentrations and crack driving parameters in the submodel.</p><p>Today, the crack controlling stress intensity factors are in general cases obtained from handbook solutions of elementary cases. This method requires engineering judgements in a conservative manner and one way to improve the solution is to model the crack in its correct surroundings in a local three-dimensional submodel.</p><p>This master thesis is focused on the development of an automated support for analysing three-dimensional cracks in submodels. The results from a global Nastran model can be imported to Trinitas and used for a more accurate stress and fatigue life analysis in a local model. Here a three-dimensional crack tip subdomain can be generated inside an eight point brick volume. The crack tip subdomain is specially designed and adjusted for accurate determination of stress intensity factors along the crack front. For example, all points are adjusted with respect to the brick volume and the crack size, triangular wedge elements are applied around the crack tip, the midpoints for these elements are moved to quarter points and the crack front is curved. The crack tip subdomain is validated against several reference cases and shows sufficiently good results with respect to the stress intensity factor.</p><p>Finally, the automated crack tip subdomain generation is applied to a geometrically complex part of a main wing carry-through bulkhead of a fighter aircraft in order to show the applicability of the procedure in an industrial environment.</p>

This paper describes two methods for constructing a depth map from images. Each method has two stages. First, one or more needle maps are determined using a pair of images. This process employs either the Marr-Poggio-Grimson stereo and shape-from-shading, or, instead, photometric stereo. Secondly, a depth map is constructed from the needle map or needle maps computed by the first stage. Both methods make use of an iterative relaxation method to obtain the final depth map.

Previous studies have shown growth hormone and therapeutic low intensity pulsed ultrasound can enhance mandibular growth separately. The aim of this study is to evaluate the concomitant effect of both of these applications on mandibular growth in rat. Methods: 24 male Sprague Dawley rats were divided into four groups, 6 in each. Groups 1, 2, 3, and 4 were designated as untreated control, recombinant rat growth hormone, Low Intensity Pulsed Ultrasound, and combination of both groups respectively. After 21 days of daily treatment on mandibular condylar, mandibles from euthanized rats are dissected, and scanned by MicroComputed Tomography to measure the mandibular bone volume, bone surface area, and condylar bone mineral density. Also Real-time Polymerase Chain Reaction was performed on the extracted livers’ C-fos, C-jun, and IGF-1 genes expressions. Results: Groups 2, 3 and 4 showed significant (p<0.05) growth stimulation when compared to the untreated control group. However, there was no statistical significant difference between groups 2, 3 and 4 with regard to bone volume or surface area. Conversely, condylar bone mineral density for group 4 was significantly reduced than groups 1, 2, and 3. Rats’ weights were not significantly different among the treatment groups after the treatment was performed. Additionally, gene expression study showed that the expression of C-jun, in harvested livers for Group 4 was less than that of Group 2 showing fewer side effects. Conclusion: When growth hormone was applied to rats’ mandible together with therapeutic ultrasound, preferential increase in bone volume, and surface area occurred with the expense of condylar bone mineral density and with less potential side effects. / Pharmaceutical Science