Introduction to Realistic Neural Modeling

This document corresponds to the tutorial on realistic neural modeling given by David Beeman at WAM-BAMM*05, the first annual meeting of the World Association of Modelers (WAM) Biologically Accurate Modeling Meeting (BAMM) on March 31, 2005 in San Antonio, TX. Part I - Introduction to Realistic Neural Modeling for the Beginner: This is a general overview and introduction to compartmental cell modeling and realistic network simulation for the beginner. Although examples are drawn from GENESIS simulations, the tutorial emphasizes the general modeling approach, rather than the details of using any particular simulator. Part II - Getting Started with Modeling Using GENESIS: This builds upon the background of Part I to describe some details of how this approach is used to construct cell and network simulations in GENESIS. It serves as an introduction and roadmap to the extended hands-on GENESIS Modeling Tutorial.

Realistic Single Cell Modeling – from Experiment to Simulation

This tutorial gives a step by step explanation of how one uses experimental data to construct a biologically realistic multicompartmental model. Special emphasis is given on the many ways that this process can be imprecise. The tutorial is intended for both experimentalists who want to get into computer modeling and for computer scientists who use abstract neural network models but are curious about biological realistic modeling. The tutorial is not dependent on the use of a specific simulation engine, but rather covers the kind of data needed for constructing a model, how they are used, and potential pitfalls in the process.

Fuzzy Multi-Objective Linear Programming and Simulation Approach to the Development of Valid and Realistic Master Production Schedule

Master production schedule (MPS) plays an important role in an integrated production planning system. It converts the strategic planning defined in a production plan into the tactical operation execution. The MPS is also known as a tool for top management to control over manufacture resources and becomes input of the downstream planning levels such as material requirement planning (MRP) and capacity requirement planning (CRP). Hence, inappropriate decision on the MPS development may lead to infeasible execution, which ultimately causes poor delivery performance. One must ensure that the proposed MPS is valid and realistic for implementation before it is released to real manufacturing system. In practice, where production environment is stochastic in nature, the development of MPS is no longer simple task. The varying processing time, random event such as machine failure is just some of the underlying causes of uncertainty that may be hardly addressed at planning stage so that in the end the valid and realistic MPS is tough to be realized. The MPS creation problem becomes even more sophisticated as decision makers try to consider multi-objectives; minimizing inventory, maximizing customer satisfaction, and maximizing resource utilization. This study attempts to propose a methodology for MPS creation which is able to deal with those obstacles. This approach takes into account uncertainty and makes trade off among conflicting multi-objectives at the same time. It incorporates fuzzy multi-objective linear programming (FMOLP) and discrete event simulation (DES) for MPS development.

Generating Realistic Camera Shake for Virtual Scenes

When depicting both virtual and physical worlds, the viewer's impression of presence in these worlds is strongly linked to camera motion. Plausible and artist-controlled camera movement can substantially increase scene immersion. While physical camera motion exhibits subtle details of position, rotation, and acceleration, these details are often missing for virtual camera motion. In this work, we analyze camera movement using signal theory. Our system allows us to stylize a smooth user-defined virtual base camera motion by enriching it with plausible details. A key component of our system is a database of videos filmed by physical cameras. These videos are analyzed with a camera-motion estimation algorithm (structure-from-motion) and labeled manually with a specific style. By considering spectral properties of location, orientation and acceleration, our solution learns camera motion details. Consequently, an arbitrary virtual base motion, defined in any conventional animation package, can be automatically modified according to a user-selected style. In an animation package the camera motion base path is typically defined by the user via function curves. Another possibility is to obtain the camera path by using a mixed reality camera in motion capturing studio. As shown in our experiments, the resulting shots are still fully artist-controlled, but appear richer and more physically plausible.

White matter microstructure alterations of the medial forebrain bundle in melancholic depression

BACKGROUND The medial forebrain bundle (MFB) is a key structure of the reward system and connects the ventral tegmental area (VTA) with the nucleus accumbens (NAcc), the medial and lateral orbitofrontal cortex (mOFC, lOFC) and the dorsolateral prefrontal cortex (dlPFC). Previous diffusion tensor imaging (DTI) studies in major depressive disorder point to white matter alterations of regions which may be incorporated in the MFB. Therefore, it was the aim of our study to probe white matter integrity of the MFB using a DTI-based probabilistic fibre tracking approach. METHODS 22 patients with major depressive disorder (MDD) (12 melancholic-MDD patients, 10 non-melancholic-MDD patients) and 21 healthy controls underwent DTI scans. We used a bilateral probabilistic fibre tracking approach to extract pathways between the VTA and NACC, mOFC, lOFC, dlPFC respectively. Mean fractional anisotropy (FA) values were used to compare structural connectivity between groups. RESULTS Mean-FA did not differ between healthy controls and all MDD patients. Compared to healthy controls melancholic MDD-patients had reduced mean-FA in right VTA-lOFC and VTA-dlPFC connections. Furthermore, melancholic-MDD patients had lower mean-FA than non-melancholic MDD-patients in the right VTA-lOFC connection. Mean-FA of these pathways correlated negatively with depression scale rating scores. LIMITATIONS Due to the small sample size and heterogeneous age group comparisons between melancholic and non-melancholic MDD-patients should be regarded as preliminary. CONCLUSIONS Our results suggest that the melancholic subtype of MDD is characterized by white matter microstructure alterations of the MFB. White matter microstructure is associated with both depression severity and anhedonia.

High resolution quantitative computed tomography-based assessment of trabecular microstructure and strength estimates by finite-element analysis of the spine, but not DXA, reflects vertebral fracture status in men with glucocorticoid-induced osteoporosis

High-resolution quantitative computed tomography (HRQCT)-based analysis of spinal bone density and microstructure, finite element analysis (FEA), and DXA were used to investigate the vertebral bone status of men with glucocorticoid-induced osteoporosis (GIO). DXA of L1–L3 and total hip, QCT of L1–L3, and HRQCT of T12 were available for 73 men (54.6±14.0years) with GIO. Prevalent vertebral fracture status was evaluated on radiographs using a semi-quantitative (SQ) score (normal=0 to severe fracture=3), and the spinal deformity index (SDI) score (sum of SQ scores of T4 to L4 vertebrae). Thirty-one (42.4%) subjects had prevalent vertebral fractures. Cortical BMD (Ct.BMD) and thickness (Ct.Th), trabecular BMD (Tb.BMD), apparent trabecular bone volume fraction (app.BV/TV), and apparent trabecular separation (app.Tb.Sp) were analyzed by HRQCT. Stiffness and strength of T12 were computed by HRQCT-based nonlinear FEA for axial compression, anterior bending and axial torsion. In logistic regressions adjusted for age, glucocorticoid dose and osteoporosis treatment, Tb.BMD was most closely associated with vertebral fracture status (standardized odds ratio [sOR]: Tb.BMD T12: 4.05 [95% CI: 1.8–9.0], Tb.BMD L1–L3: 3.95 [1.8–8.9]). Strength divided by cross-sectional area for axial compression showed the most significant association with spine fracture status among FEA variables (2.56 [1.29–5.07]). SDI was best predicted by a microstructural model using Ct.Th and app.Tb.Sp (r2=0.57, p<0.001). Spinal or hip DXA measurements did not show significant associations with fracture status or severity. In this cross-sectional study of males with GIO, QCT, HRQCT-based measurements and FEA variables were superior to DXA in discriminating between patients of differing prevalent vertebral fracture status. A microstructural model combining aspects of cortical and trabecular bone reflected fracture severity most accurately.

Responses of lung cells to realistic exposure of primary and aged carbonaceous aerosols

Diesel exhaust and wood burning are important sources of ambient atmospheric particles due to increasing numbers of diesel cars and the importance of wood as a source of renewable energy. Inhalation is the predominant route of entry and uptake for fine and ultrafine particles into the body. Health effects of atmospheric particles are still not completely understood. There is consistent evidence from epidemiology that particle exposure contributes to respiratory and cardiovascular diseases. This study aimed at examining acute responses of airway epithelial cells and luminal macrophages after exposure to freshly emitted and photochemically aged carbonaceous aerosols under realistic atmospheric conditions. In addition to a bronchial epithelial cell line advanced cell cultures namely fully differentiated respiratory epithelia and primary surface macrophages were used. Our results demonstrate that a single exposure of the cells to realistic particle doses of 0.3–3 ng diesel or 3–9 ng wood aerosol per cm2 cell surface induces small, particle-specific responses. The release of interleukin-6 and -8 was found to be decreased in differentiated airway epithelia but not in the other cell models studied. Aerosol exposure decreased macrophage phagocytic activity by 45–90%. Cell and tissue integrity remained unaffected. Overall, primary and aged particles from the same combustion induced similar responses in the cell models tested, whereby particles from diesel exhaust affected the cells more than those from wood combustion.

Scaling relations between trabecular bone volume fraction and microstructure at different skeletal sites

In this study, we investigated the scaling relations between trabecular bone volume fraction (BV/TV) and parameters of the trabecular microstructure at different skeletal sites. Cylindrical bone samples with a diameter of 8mm were harvested from different skeletal sites of 154 human donors in vitro: 87 from the distal radius, 59/69 from the thoracic/lumbar spine, 51 from the femoral neck, and 83 from the greater trochanter. μCT images were obtained with an isotropic spatial resolution of 26μm. BV/TV and trabecular microstructure parameters (TbN, TbTh, TbSp, scaling indices (< > and σ of α and αz), and Minkowski Functionals (Surface, Curvature, Euler)) were computed for each sample. The regression coefficient β was determined for each skeletal site as the slope of a linear fit in the double-logarithmic representations of the correlations of BV/TV versus the respective microstructure parameter. Statistically significant correlation coefficients ranging from r=0.36 to r=0.97 were observed for BV/TV versus microstructure parameters, except for Curvature and Euler. The regression coefficients β were 0.19 to 0.23 (TbN), 0.21 to 0.30 (TbTh), −0.28 to −0.24 (TbSp), 0.58 to 0.71 (Surface) and 0.12 to 0.16 (<α>), 0.07 to 0.11 (<αz>), −0.44 to −0.30 (σ(α)), and −0.39 to −0.14 (σ(αz)) at the different skeletal sites. The 95% confidence intervals of β overlapped for almost all microstructure parameters at the different skeletal sites. The scaling relations were independent of vertebral fracture status and similar for subjects aged 60–69, 70–79, and >79years. In conclusion, the bone volume fraction–microstructure scaling relations showed a rather universal character.

Limbic white matter microstructure plasticity reflects recovery from depression

BACKGROUND White matter microstructure alterations of limbic and reward pathways have been reported repeatedly for depressive episodes in major depressive disorder (MDD) and bipolar disorder (BD). However, findings during remission are equivocal. It was the aim of this study to investigate if white matter microstructure changes during the time course of clinical remission. METHODS Fifteen depressed patients (11 MDD, 4 BD) underwent diffusion-weighted MRI both during depression, and during remission following successful antidepressive treatment (average time interval between scans=6 months). Fractional anisotropy (FA) was sampled along reconstructions of the supero-lateral medial forebrain bundle (slMFB), the cingulum bundle (CB), the uncinate fasciculus (UF), the parahippocampal cingulum (PHC) and the fornix. Repeated measures ANCOVAs controlling for the effect of age were calculated for each tract. RESULTS There was a significant main effect of time (inter-scan interval) for mean-FA for the right CB and for the left PHC. For both pathways there was a significant time×age interaction. In the right CB, FA increased in younger patients, while FA decreased in older patients. In the left PHC, a reverse pattern was seen. FA changes in the right CB correlated positively with symptom reductions. Mean-FA of UF, slMFB and fornix did not change between the two time points. LIMITATIONS All patients were medicated, sample size, and lack of control group. CONCLUSIONS Right CB and left PHC undergo age-dependent plastic changes during the course of remission and may serve as a state marker in depression. UF, slMFB and FO microstructure remains stable.

White matter matters: a multimodal approach to investigate white matter microstructure and metabolism

White matter connects different brain areas and applies electrical insulation to the neuron’s axons with myelin sheaths in order to enable quick signal transmission. Due to its modulatory properties in signal conduction, white matter plays an essential role in learning, cognition and psychiatric disorders (Fields, 2008a). In respect thereof, the non-invasive investigation of white matter anatomy and function in vivo provides the unique opportunity to explore the most complex organ of our body. Thus, the present thesis aimed to apply a multimodal neuroimaging approach to investigate different white matter properties in psychiatric and healthy populations. On the one hand, white matter microstructural properties were investigated in a psychiatric population; on the other hand, white matter metabolic properties were assessed in healthy adults providing basic information about the brain’s wiring entity. As a result, three research papers are presented here. The first paper assessed the microstructural properties of white matter in relation to a frequent epidemiologic finding in schizophrenia. As a result, reduced white matter integrity was observed in patients born in summer and autumn compared to patients born in winter and spring. Despite the large genetic basis of schizophrenia, accumulating evidence indicates that environmental exposures may be implicated in the development of schizophrenia (A. S. Brown, 2011). Notably, epidemiologic studies have shown a 5–8% excess of births during winter and spring for patients with schizophrenia on the Northern Hemisphere at higher latitudes (Torrey, Miller, Rawlings, & Yolken, 1997). Although the underlying mechanisms are unclear, the seasonal birth effect may indicate fluctuating environmental risk factors for schizophrenia. Thus, exposure to harmful factors during foetal development may result in the activation of pathologic neural circuits during adolescence or young adulthood, increasing the risk of schizophrenia (Fatemi & Folsom, 2009). While white matter development starts during the foetal period and continues until adulthood, its major development is accomplished by the age of two years (Brody, Kinney, Kloman, & Gilles, 1987; Huang et al., 2009). This indicates a vulnerability period of white matter that may coincide with the fluctuating environmental risk factors for schizophrenia. Since microstructural alterations of white matter in schizophrenia are frequently observed, the current study provided evidence for the neurodevelopmental hypothesis of schizophrenia. In the second research paper, the perfusion of white matter showed a positive correlation between white matter microstructure and its perfusion with blood across healthy adults. This finding was in line with clinical studies indicating a tight coupling between cerebral perfusion and WM health across subjects (Amann et al., 2012; Chen, Rosas, & Salat, 2013; Kitagawa et al., 2009). Although relatively little is known about the metabolic properties of white matter, different microstructural properties, such as axon diameter and myelination, might be coupled with the metabolic demand of white matter. Furthermore, the ability to detect perfusion signal in white matter was in accordance with a recent study showing that technical improvements, such as pseudo-continuous arterial spin labeling, enabled the reliable detection of white matter perfusion signal (van Osch et al., 2009). The third paper involved a collaboration within the same department to assess the interrelation between functional connectivity networks and their underlying structural connectivity.