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Dissertation
Experimentele opstelling voor het modelleren van responsies van een levend organisme

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Towards Individualised Model-based Monitoring: From Biology to Technology

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One of the main obstacles in applying engineering approaches to biological processes remains dealing with inter- and intra-individual differences. Therefore, it is highly challenging to accurately monitor their individual state (cfr. personalised medicine). The general objective of this PhD is to develop a framework for individualised model-based monitoring for biological processes, as inspired by control engineering concepts. The presented approach addresses four main topics: i) the biological process itself (i.e. bio-process), ii) the process model, iii) model-based features and iv) individualised change detection based on individual thresholds. In order to explore the general objective, six different case studies (cell, embryo, animal, human) were examined: i) individualised monitoring of activity and body weight in the activity-based anorexia rat model, ii) individualised model-based monitoring of interleukin-6 for early detection of infection in pigs, iii) model-based monitoring of heart rate and blood cytokine time series for early detection of infections in critically ill patients, iv) model-based monitoring of mGluR-dependent synaptic plasticity in hippocampal brain slices of rat, v) individualised monitoring of hippocampal theta oscillations and individualised electrical stimulation in the mesencephalic reticular formation for real-time closed-loop suppression of locomotion in rat and vi) individualised model-based monitoring of chicken embryo status during incubation based on eggshell temperature and micro-environmental air temperature. The results showed that the individual bio-processes involved (individual structure, individual dynamics, bio-signals) can be considered as the biological equivalents of clever-designed control engineering components by defining actuator and homeostatic variables for each of the six case studies (case studies i-vi). Although biological processes are known to contain many nonlinearities, compact individual linear models (general Box-Jenkins models) could be used for the specific individualised monitoring applications of the case studies. By using these models we obtained good approximations of the individual bio-process dynamics (case studies ii, iii, iv and vi), since biological systems often show relatively simple responses (expressing the crucial dominant processes that ascertain healthy internal homeostatic or homeodynamic conditions) when exposed to perturbations as illustrated by the bio-processes of the case studies. In addition, we were able to uncover information about the underlying mechanisms/state by applying data-based mechanistic modelling approaches (i.e. case studies iv and vi). Based on the results, we suggest three different model-based features (model parameter changes, changes in model order and changes in the noise model). In addition, more than 20 other generic metrics from the fields of complex systems science, change detection and control engineering were identified that can be used while analysing individual time series (case studies i-vi). This list of metrics can be used for all individual bio-processes in the design of model-based monitoring application. Based on the specific case studies, three possible approaches were proposed for model-based monitoring of bio-processes based on individual thresholds (e.g. case studies v and vi): 1) individual thresholds based on (sub-)population information, 2) individual thresholds based on universal laws and insights from control engineering, complex systems science and biology and 3) individual thresholds based on individual serial baseline measurements, which can be considered as the most individualised way. To conclude, this thesis has led to some innovative individualised monitoring applications based on each of the six specific case studies. Until now the existence of general frameworks for individualised model-based monitoring of biological processes is limited. Each specific case contributed to the development of such general framework inspired by control engineering concepts. The presented general approach could be used in a broad range of application domains, thus stressing the generic power of the suggested framework for individualized model-based monitoring of (complex) bio-processes.

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Dissertation
Field potentials and behavior analysis in rat models of abnormal brain cavities and compulsion

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Brain damage is caused by loss or deterioration of brain cells and it is a prevalent type of injury that may be fatal, or may result in severe impairments, with devastating consequences on the quality of life of survivors. Loss of neural cells may lead to the formation of abnormal brain cavities (aBC), that are most often the result of stroke and traumatic brain injuries (TBI), but can also occur after surgical resection of tumors or abscesses. The chronic debilitating symptoms caused by neuronal damage are currently untreatable and largely depend on the degree and location of damage. In this work, we investigated the potential of neuromodulation as a treatment option, driven in a novel target - directly within the aBC wall, so as to alter aBC-related symptoms, and to improve behavioral outcome after neurological damage. We used a generic model for brain damage, developed in a rat model. A foldable electrode array was implanted against the aBC wall, in a motor cortical rat model. The electrode implant was used both to interact with neural populations as well as record their activity. Much of the current understanding about motor system function is based on correlations between brain and behavioral tasks. Thus, the general objective of this thesis was to develop algorithms that identify behavioral and neural signal features with multiple aims: (i) to validate the aBC wall as a target for recording meaningful brain activity, (ii) to better quantify motor impairments and (iii) to investigate how modulating brain activity can improve behavioral outcome. In a first step, we recorded electrical brain activity, as field potentials (FPs) on the surface of motor cortical aBC of freely moving rats. We showed that FPs are dominated by oscillatory activity in the theta range (4-9 Hz) and gamma range (30-100 Hz) and can be an informative biomarker for behavioral features, as it allowed us to discriminate between behavioral state: active versus resting. In a second step, we analyzed in detail impairment state. We developed an automated computer algorithm for analyzing reaching and grasping in impaired animals, subsequent to induction of a motor cortical aBC. The algorithm automatically tracks the movement of the rat's forelimb using image processing methods. We classified endpoint behavior, achieving accuracy rates of 86%-92%. With this extended analysis we captured perturbation of skill after a motor cortical lesion was induced. Kinematics of reaching revealed that rats developed individual strategies to achieve the task. In a third phase, we used the automatic algorithm to evaluate kinematics and endpoint outcome of skilled reaching during stimulation in different targets within the lesion wall. We stimulated either over the entire 16-electrode array (non-selective stimulation) or over subsets of electrodes (selective stimulation), proving that both strategies could alter kinematics of movement, with selective stimulation being at least as effective as non-selective stimulation. Neurostimulation has been proven effective in the past recent years in treating psychiatric disorders. Finally, we used a rat model of obsessive compulsive disorder (OCD) in which deep brain stimulation was used to diminish compulsive symptoms. We showed that responders to deep brain stimulation presented specific brain modulations in the frequency bands of delta (1- 4 Hz), theta (4-8 Hz), beta (12-30 Hz), and lower gamma (30-45 Hz) that were otherwise not present in the non-responders or in the control subjects. Our strategy is not limited by the cause of insult, be it ischemic stroke or traumatic brain injury, and allows direct interaction with the lesion wall via an invasive array of electrodes that can be used both for stimulation and for recording brain electrical activity. Access to neural activity allowed us to investigate neural mechanisms that may be relevant for impaired brain function, both in rat models of motor disability and psychiatric disorders. Finally, our strategy aims for an individual-focus treatment, that circumvents patient-dependent differences like severity and location of the brain damage.

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Book
Bioreactors and process monitoring for scale-up of stem cell production
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Year: 2016 Publisher: Leuven KU Leuven. Faculty of Bioscience Engineering

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For almost two decades it is claimed that cell-based therapies will revolutionize the field of medicine. Albeit major scientific breakthroughs that present cells as the active ingredient of a clinical therapy are succeeding each other at increasing speed, today only few of these research successes are able to materialise their full clinical potential and develop into a widely available commercial cell-based treatment. Besides the remaining scientific challenges (e.g. exact mechanisms of action), costly product development, and a complex regulatory and reimbursement landscape, it is hypothesised that the lack of automated, controlled and cost-effective production strategies forms a major hurdle towards a wide-spread clinical translation of cell based therapies. This work therefore aims at creating enabling tools and knowledge for monitored and controlled large-scale stem cell production, with the ultimate goal of facilitating the manufacturing of qualitative and cost-effective cell-based therapies. Flask-based cell expansion processes are currently still the gold standard despite the disadvantage of their limited scale-up and automation potential. In a first phase the translation from flask-based cell production processes to a bioreactor-based process was investigated, without adversely influencing the properties of the cells. In parallel to the bioreactor-based scale-up, this work describes how the data from these bioreactor processes can be utilised to non-invasively monitor critical process parameters in real-time, then utilise this information for process control strategies that enable more informed process decisions, ultimately leading to an improved product quality.

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Dissertation
Health effects of exposure to green space, airborne pollen and air pollution A mobile health study on adults with tree pollen allergy

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Over the past decades the prevalence of pollen allergy has increased. This trend is expected to continue due to ongoing urbanization, climate change and increasing air pollution. In order to mitigate urban heat and improve air quality in the city, urban green space has been promoted. Urban green spaces have been associated with numerous health benefits. Contact with the natural environment strengthens the human microbiome and immune system. Green spaces promote an active lifestyle and provide mental health benefits. By improving the air quality, green spaces can also contribute to better respiratory health. However, urban vegetation is also a source of airborne pollen.The literature provides contradicting results regarding the effects of green space on the health of pollen allergy patients. These contradictions stem from the complex interactions between environmental factors, as well as from a heterogeneity in approaches when it comes to exposure studies. To properly study the health effects from exposure to green space on the health of people with pollen allergy we need detailed spatial data on green space and the allergenic trees within these greenspaces. In addition, we need insights in the effects of local vegetation on local pollen composition. Until now, the majority of exposure studies relied on exposure within various buffers around the residence. Nevertheless, a significant share of exposure takes place outside the residential area and pollen and air pollutant concentrations vary in time and space. In order to define exposure more realistically there is need for a method that can account for the spatiotemporal aspect of personal exposure.Nevertheless, the first step towards an exposure analysis is the generation of a distribution model of potential allergenic trees. For Flanders a database with validated observations of vascular plants at a 1 km resolution is available (Florabank). The observations can be combined with environmental covariates (soil characteristics, land use, habitat type) in a species distribution model. We modelled habitat suitability for 13 wind-pollinated tree genera. Genus-specific thresholds were used to obtain presence-absence maps. By summing the 13 presence-absence maps we obtained a tree diversity map at genus-level. We find that summing binary maps does not result in an overestimation of diversity when the study area is urbanized (Flanders) and the spatial resolution is coarse (1 km). The obtained diversity map can be used to determine exposure to biodiversity in health studies.In a second step, we studied the effects of local vegetation on the pollen composition. Although pollen can travel long distances, local vegetation contributes to local peak concentrations of pollen. Standardized pollen monitoring takes place at roof top level and measures a background level of pollen. Possible local peaks remain undetected, yet contribute to human pollen exposure. By mounting passive samplers at 2 m above the ground in 13 locations in Flanders we aimed to measure local pollen compositions during the tree pollen season (February-May) of 2017. The passive samplers successfully measured local pollen compositions characterized by 12 taxa. We used Non-metric Multidimensional Scaling (NMDS) to characterize each sampling site by its pollen composition. Then we use an indirect gradient analysis to associate the pollen composition with the land cover within a 20, 200, 500, 1000, 2000 and 5000 m radius around the sampling site. We found an urban-rural and wet-dry gradient associated with the first and second NMDS axis. Most of the associations were found for the land cover in a 1000-5000 m radius. This local scale effect is of importance for urban green management: urban forests at the edge of the city contribute to the pollen concentration within the city. In addition, we understand that environmental health studies require sufficiently large exposure radii.Thus, in the residential exposure study we determined garden cover, grassland cover and forest cover within a 1, 2 and 5 km radius around the residence of 157 adults with a tree pollen allergy. The density of allergenic trees (alder, hazel and birch) was derived from the regional forest inventories. We used a generalized linear models with a Poisson distribution to associate residential exposure to mental well-being (standardized questionnaires) and respiratory health (average symptom severity reported in a smartphone application). All green space types were protective for mental well-being, yet a risk factor for symptom severity. The density of allergenic trees in forests was a risk factor for mental well-being as well as symptom severity. We found that green space effects on health became smaller as the exposure radius increased.In an attempt to determine personal exposure more realistically, we used GPS data gathered by a smartphone application. We compared exposure between case-days with severe allergy symptoms and control-days without symptoms. We determined exposure by extracting green space cover, allergenic tree density, birch pollen levels and pollutant levels at the GPS point locations. For each day we could determine the average exposure taking into account spatiotemporal variability. Grassland cover, forest cover, alder density and hazel density protected against severe allergy symptoms. Birch density and birch pollen as well as pollutants (nitrogen dioxide (NO2), ozone (O3), and particulate matter < 10 µm (PM10)) were risk factors for severe allergy symptoms. For GPS tracks that were entirely within Flanders, we could calculate exposure to the tree diversity model at genus level. We found no associations between severe allergy symptoms and alpha-diversity of tree genera.This manuscript shows that adults with a tree pollen allergy experience mental and respiratory health benefits from exposure to green space, given that density of allergenic trees (birch) is low. GPS tracking allowed for a more realistic approximation of personal exposure. Although we did not identify a diversity effect, we do promote biodiverse urban green spaces in order to prevent domination of allergenic vegetation.

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Dissertation
Depression and burnout A different perspective Investigating the differences and similarities between these 21st century epidemics through data-based transfer function modelling

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To date, depression is the worldwide leading cause for disability and a considerable contributor to the global disease burden. In recent years, another disorder that shares certain traits with depression has been on the rise, namely burnout. Although the prevalence and disease burden of burnout is not nearly as great as that of depression, it has been escalating in the last decade. As a result, burnout has been receiving a lot of attention in the media and companies have started putting their resources to detect and prevent burnout in the workplace. Both disorders currently have a major impact on Western society and cannot be thought away and could thus be called '21st century epidemics'.Whereas available literature on depression is vast, literature on burnout is scarce and literature comparing depression to burnout is even more limited. There is still a lot to learn about burnout and how it compares to depression. This is especially true when it comes to studying the psychophysiology of both disorders. For instance, the search for biomarkers to quantify depression has been going on for several decades, whereas it has only just started for burnout. Although we haven't found a 'true biomarker' for depression yet, we already have a great knowledge of its physiology. This knowledge is lacking for burnout.The general aim of this PhD thesis was to study the psychophysiology of patients with burnout or depression and to compare both patient groups, as well as to compare them to healthy controls. For that purpose, a clinical study was set up where healthy controls, patients with burnout and patients with depression performed a combined physical and mental task. All participants cycled for half an hour and completed an arithmetic challenge of three minutes during cycling. The energy expenditure of the participants was measured via indirect calorimetry. Their heart rate was monitored with an ECG and with a wearable sports watch. Finally, the delivered biking power and the participants' core body acceleration were logged as well.Using data-based mechanistic input-output modelling with power as input and energy expenditure or heart rate as output, it was demonstrated that the energy expenditure and heart rate of healthy controls and patients with burnout or depression can be equivalently decomposed into a physical component and a mental component. A detailed study of the energy expenditure revealed that the energy metabolism of patients with burnout or depression is dysregulated and that this dysregulation seems to be more important for depressive patients. A thorough evaluation of the heart rate response showed that the link between power and heart rate is altered in patients with burnout or depression. Interestingly, we found that features derived from the mental component of energy expenditure or heart rate could not differentiate between the three subject groups, whereas features derived from the physical component could. Finally the data-based mechanistic input-output modelling approach was also successfully applied with activity (derived from acceleration) as input and heart rate from a sports watch as output. We found that the heart rate data of the sports watch were as accurate as the heart rate data of ECG. Additionally, we observed the same trends in the features obtained from the wearable data as the trends found in the features calculated from the reference data.Summarised, this PhD thesis first and foremost demonstrates the universality of the data-based mechanistic input-output modelling approach. Second, this work shows that during physical exercise the energy metabolism and the heart rate response of patients with burnout or depression is dysregulated. Third, the results of this research suggest that more research should be conducted on the physiological response of burnout patients and depressive patients to a physical exercise, rather than a mental exercise. Finally, this PhD illustrates that it is feasible to monitor the physiology of burnout and depression using wearable technology.

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Dissertation
Modelling of bioresponses to micro-environmental variables using dynamic data-based models.

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Artificial intelligence for pulmonary function tests
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ISBN: 9789461651945 Year: 2016 Volume: 701 Publisher: Leuven Leuven University Press

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The contribution of the cytoskeleton in cellular aggregation: a data-based modelling approach

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Micro-aggregates have several unique properties that make them suitable for tissue engineering: they are associated with increased cell viability, they enhance multilineage differentiation and they secrete trophic factors with an anti-inflammatory effect. In addition, micro-aggregates have the ability to fuse into one larger structure when brought into close contact. Hence, they are of great interest in bottom-up tissue engineering, in which large heterotypic tissues that mimic the native organisational tissue structure are gradually built up by using small units as building blocks. An important step for the application of micro-aggregates in tissue engineering is a complete understanding of their formation. During this formation, a change in cell morphology, determined by cell contractility and cortical tension, is required. These factors are both determined by the structure and functionality of the cytoskeleton. Therefore, the importance of different components of the cytoskeleton during the aggregation of hPDCs was studied by adding different inhibitors to the medium. In this thesis, Y-27632, a ROCK-inhibitor, and (S)-nitroblebbistatin, an inhibitor of MYH ATPase, were evaluated for their effect on aggregate formation. Two different aggregate sizes were tested since cell number might influence cell aggregation by affecting contact opportunities between cells and cell survival. The dynamics of the aggregation behaviour were captured using time-lapse microscopy. Area and circularity of the aggregates were extracted from the images and analysed using a data-based modelling approach. It is demonstrated that ROCK-inhibitor reduces compaction and slows down the formation of micro-aggregates compared to control conditions. Moreover, the effect of Y-27632 is found to be depended on aggregate size. Experiments with (S)-nitroblebbistatin were not coherent. Consequently, no conclusions concerning the contribution of myosin II to cellular aggregation could be made. In addition to time-lapse microscopy, aggregates treated with ROCK-inhibitor were imaged in confocal microscopy in order to quantify cell viability and visualise the actin network as well as the nucleus. Although this analysis did not reveal any statistically significant results, some clear trends are observed. First of all, it is stated that cells at the boundary have a higher volume compared to central cells. Secondly, it is seen that boundary cells have a tendency to become more spherical as the concentration of Y-27632 is increased. It is believed that a more complete insight in aggregate formation is the first step towards a better process control and thus would enhance the performance of the final engineered tissue.

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Dissertation
Stress Measurements of Youth Volleyball Players: the impact of coach interventions on stress levels and performance during training

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Technology has become indispensable in our daily life and has also found its way into the sports environment where it has proven its benefits. Sensors are implemented for measuring variables such as heart rate, blood pressure, speed and distance covered. One equally important but often forgotten variable in elite sport is the mental load of an athlete. Top performances cannot be reached when psychological aspects are unfavourable. This variable however remains difficult to measure, especially when using physiological signals. In this master’s thesis, a method is examined to establish an athlete’s mental state using real-time physiological measurements of the heart rate and the physical activity. Nine youth volleyball athletes were monitored during six trainings to assess the impact of coach interventions on their mental state. Athletic performance was established and the link with the obtained stress levels is explored. The possibility to simulate coach-related stressors is investigated and whether the extra stress generates a difference in heart rate-derived stress measures. Specific coach-related stress instants are examined more closely. The possibility to implement questionnaires is explored before summarizing the results and their link to competition. The mental HR, the raw HR, and the frequency analysis of the HRV showed no significant difference when comparing the two types of trainings. HR normalized to the physical activity suggested a higher value, around 20 bpm/m/s², in the stressful trainings. Match formats and services generated a higher mental HR (±15 bpm) compared to standard set, pass, and attack exercises. During the stress moments, specific responses were observed in all the different stress indicators. However, not all moments generated a response and not all indicators presented a response to the same stress instants. The performance during the stressful trainings appeared higher in the service exercises. Nevertheless, overall conclusions about the higher performance trend in the stressful environment could not be made and more data is needed to suggest individual trends. The results from the questionnaires were inconclusive, questioning the usefulness in underage athletes and whether a true discrepancy between the stressful and stressless training existed. We may conclude that it is hard to create a stressful environment during training but that the suggested stress indicators (especially the ones considering physical activity) could provide useful insight into specific stress moments.

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