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- Grytsan, Andrii, 1986-
(författare)
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Abdominal aortic aneurysm inception and evolution - A computational model
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Abdominal aortic aneurysm (AAA) is characterized by a bulge in the abdominal aorta. AAA development is mostly asymptomatic, but such a bulge may suddenly rupture, which is associated with a high mortality rate. Unfortunately, there is no medication that can prevent AAA from expanding or rupturing. Therefore, patients with detected AAA are monitored until treatment indication, such as maximum AAA diameter of 55 mm or expansion rate of 1 cm/year. Models of AAA development may help to understand the disease progression and to inform decision-making on a patient-specific basis. AAA growth and remodeling (G&R) models are rather complex, and before the challenge is undertaken, sound clinical validation is required.In Paper A, an existing thick-walled model of growth and remodeling of one layer of an AAA slice has been extended to a two-layered model, which better reflects the layered structure of the vessel wall. A parameter study was performed to investigate the influence of mechanical properties and G&R parameters of such a model on the aneurysm growth.In Paper B, the model from Paper A was extended to an organ level model of AAA growth. Furthermore, the model was incorporated into a Fluid-Solid-Growth (FSG) framework. A patient-specific geometry of the abdominal aorta is used to illustrate the model capabilities.In Paper C, the evolution of the patient-specific biomechanical characteristics of the AAA was investigated. Four patients with five to eight Computed Tomography-Angiography (CT-A) scans at different time points were analyzed. Several non-trivial statistical correlations were found between the analyzed parameters.In Paper D, the effect of different growth kinematics on AAA growth was investigated. The transverse isotropic in-thickness growth was the most suitable AAA growth assumption, while fully isotropic growth and transverse isotropic in-plane growth produced unrealistic results. In addition, modeling of the tissue volume change improved the wall thickness prediction, but still overestimated thinning of the wall during aneurysm expansion.
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- Hantke, Max Felix, 1984-
(författare)
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Coherent Diffractive Imaging with X-ray Lasers
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The newly emerging technology of X-ray free-electron lasers (XFELs) has the potential to revolutionise molecular imaging. XFELs generate very intense X-ray pulses and predictions suggest that they may be used for structure determination to atomic resolution even for single molecules. XFELs produce femtosecond pulses that outrun processes of radiation damage and permit the study of structures at room temperature and of structural dynamics.While the first demonstrations of flash X-ray diffractive imaging (FXI) on biological particles were encouraging, they also revealed technical challenges. In this work we demonstrated how some of these challenges can be overcome. We exemplified, with heterogeneous cell organelles, how tens of thousands of FXI diffraction patterns can be collected, sorted, and analysed in an automatic data processing pipeline. We improved image resolution and reduced problems with missing data. We validated, described, and deposited the experimental data in the Coherent X-ray Imaging Data Bank.We demonstrated that aerosol injection can be used to collect FXI data at high hit ratios and with low background. We reduced problems with non-volatile sample contaminants by decreasing aerosol droplet sizes from ~1000 nm to ~150 nm. We achieved this by adapting an electrospray aerosoliser to the Uppsala sample injector. Mie scattering imaging was used as a diagnostic tool to measure positions, sizes, and velocities of individual injected particles.XFEL experiments generate large amounts of data at high rates. Preparation, execution, and data analysis of these experiments benefits from specialised software. In this work we present new open-source software tools that facilitates prediction, online-monitoring, display, and pre-processing of XFEL diffraction data.We hope that this work is a valuable contribution in the quest of transitioning FXI from its first experimental demonstration into a technique that fulfills its potentials.
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- Silverstein, David N.
(författare)
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Investigations of neural attractor dynamics in human visual awareness
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- What we see, how we see it and what emotions may arise from stimuli has long been studied by philosophers, psychologists, medical doctors and neuroscientists. This thesis work investigates a particular view on the possible dynamics, utilizing computational models of spiking neural attractor networks. From neurological studies on humans and other primates, we know visual perception and recognition of objects occur partly along the visual ventral stream, from V1 to V2, V4, IT and downstream to other areas. This visual awareness can be both conscious and unconscious and may also trigger an emotional response. As seen from many psychophysical experiments in backward masking (BM) and attentional blink (AB), some spatial and temporal dynamics can determine what becomes visually conscious and what does not. To explore this computationally, biophysical models of BM and AB were implemented and simulated to mimic human experiments, with the assumption that neural assemblies as attractor networks activate and propagate along the ventral stream and beyond. It was observed that attractor interference between percepts in sensory and associative cortex can occur during this activity. During typical human AB experimental trials in which two expected target symbols amongst distractors are presented less than 500 ms apart, the second target is often not reported as seen. When simulating this paradigm as two expected target neural attractors amongst distractors, it was observed in the present work that an initial attractor in associative cortex can impede the activation and propagation of a following attractor, which mimics missing conscious perception of the second target. It was also observed that simulating the presence of benzodiazepines (GABA agonists) will slow cortical dynamics and increase the AB, as previously shown in human experiments.During typical human BM experimental trials in which a brief target stimulus is followed by a masking stimulus after a short interval of less than 100 ms, recognition of the target can be impaired when in close spatial proximity. When simulating this paradigm using a biophysical model of V1 and V2 with feedforward and feedback connections, attractor targets were activated in V1 before imposition of a proximal metacontrast mask. If an activating target attractor in V1 is quiesced enough with lateral inhibition from a mask, or not reinforced by recurrent feedback from feedforward activation in V2, it is more likely to burn out before becoming fully active and progressing through V2 and beyond. BM was also simulated with an increasing stimulus interval and with the presence and absence of feedback activity. This showed that recurrent feedback diminishes BM effects and can make conscious perception more likely.To better understand possible emotional components of visual perception and early regulation, visual signaling pathways to the amygdala were investigated and proposed for emotional salience and the possible onset of fear. While one subcortical and likely unconscious pathway (before amydala efferent signaling) was affirmed via the superior colliculus and pulvinar, four others traversed through the ventral stream. One traversed though IT on recognition, another via the OFC on conditioning, and two other possibly conscious pathways traversed though the parietal and then prefrontal cortex, one excitatory pathway via the ventral-medial area and one regulatory pathway via the ventral-lateral area. Predicted latencies were determined for these signaling pathways, which can be experimentally testable. The conscious feeling of fear itself may not occur until after interoceptive inspection.A pathology of attractor dynamics was also investigated, which can occur from the presence of a brain tumor in white matter. Due to degradation from tumor invasion of white matter projections between two simulated neocortical patches, information transfer between separate neural attractors degraded, leading first to recall errors and later to epileptic-like activity. Neural plasticity could partially compensate up to a point, before transmission failure. This suggests that once epileptic seizures start in glioma patients, compensatory plasticity may already be exhausted. Interestingly, the presence of additional noise could also partially compensate for white matter loss.
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