Can Immune Response Mechanisms Explain the Fecal Shedding Patterns of Cattle Infected with Mycobacterium avium Subspecies paratuberculosis?

Johne’s disease (JD) is a chronic disease in ruminants and is caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP). At late stages of the disease, MAP bacilli are shed via feces excretion and in turn create the potential for oral-fecal transmission. The role of the host immune response in MAP bacteria shedding patterns at different stages of JD is still unclear. We employed mathematical modeling to predict if the variation in MAP shedding could be correlated to the immune response in infected animals. We used a novel inverse modeling approach that assumed biological interactions among the antigen-specific lymphocyte proliferation response (cell-mediated response), antibody/humoral immune responses, and MAP bacteria. The modeling framework was used to predict and test possible biological interactions between the measured variables and returns only the essential interactions that are relevant in explaining the observed cattle MAP experimental infection data. Through confronting the models with data, we predicted observed effects (enhancement or suppression) and extents of interactions among the three variables. This analysis enabled classification of the infected cattle into three different groups that correspond to the unique predicted immune responses that are essential to explain the data from cattle within these groups. Our analysis highlights the strong and weak points of the modeling approach, as well as the key immune mechanisms predicted to be expressed in all animals and those that were different between animals, hence giving insight into how animals exhibit different disease dynamics and bacteria shedding patterns

On the homology of the Harmonic Archipelago

We calculate the singular homology and \v{C}ech cohomology groups of the Harmonic archipelago. As a corollary, we prove that this space is not homotopy equivalent to the Griffiths space. This is interesting in view of Eda's proof that the first singular homology groups of these spaces are isomorphic

Engineering the Outcoupling Pathways in Plasmonic Tunnel Junctions via Photonic Mode Dispersion for Low-Loss Waveguiding

Outcoupling of plasmonic modes excited by inelastic electron tunneling (IET) across plasmonic tunnel junctions (TJs) has attracted significant attention due to low operating voltages and fast excitation rates. Achieving selectivity among various outcoupling channels, however, remains a challenging task. Employing nanoscale antennas to enhance the local density of optical states (LDOS) associated with specific outcoupling channels partially addressed the problem, along with the integration of conducting 2D materials into TJs, improving the outcoupling to guided modes with particular momentum. The disadvantage of such methods is that they often involve complex fabrication steps and lack fine-tuning options. Here, we propose an alternative approach by modifying the dielectric medium surrounding TJs. By employing a simple multilayer substrate with a specific permittivity combination for the TJs under study, we show that it is possible to optimize mode selectivity in outcoupling to a plasmonic or a photonic-like mode characterized by distinct cutoff behaviors and propagation length. Theoretical and experimental results obtained with a SiO2-SiN-glass multilayer substrate demonstrate high relative coupling efficiencies of (62.77 ± 1.74)% and (29.07 ± 0.72)% for plasmonic and photonic-like modes, respectively. The figure-of-merit, which quantifies the tradeoff between mode outcoupling and propagation lengths (tens of μm) for both modes, can reach values as high as 180 and 140. The demonstrated approach allows LDOS engineering and customized TJ device performance, which are seamlessly integrated with standard thin film fabrication protocols. Our experimental device is well-suited for integration with silicon nitride photonics platforms.</p

Learning, Prediction and Planning with Approximate Forward Models

The capacity to build internal representations of the world provides an agent with the opportunity to use them to act in its surroundings more appropriately. These internal representations may capture complex associations and keep track of the state of the agent and the environment. One of the most striking aspects of this phenomenon is that the agent may manipulate these internal representations to consider the distant future, and to formulate plans likely to lead to beneficial outcomes. Our treatment in this thesis considers this particular class of agents referred to as model-based. The behaviour of these agents is not only contingent upon the current sensory stream and their memory, but also based on hypothetical future sensory streams that are produced from potential sequences of actions. Throughout this thesis, there are two main themes that we explore and that are fundamental for advancing our understanding of model-based agents. The first is the agent's uncertainty about its environment and how it influences its decision-making. There are multiple aspects one could investigate about this relation. We analyse two specific scenarios. The first illustrates how it is possible to harness the agent's uncertainty to devise error-correction schemes. In the second, a probability distribution that defines the agent's current model is used to derive intrinsic utility signals to guide behaviour. The other main theme that permeates this thesis is the question of what are the aspects of the external world that should be stored and represented by an internal model? This question has important consequences for the design of learning objectives. As we will see in this thesis, we start with perhaps the most conceptually intuitive way to frame a learning objective for acquiring a world model. Namely, the assumption that the agent must be able to predict as accurately as possible its future observations. From this starting point, we progress towards learning objectives that introduce additional prediction targets or constraints to aim for a compressed and more essential representation of an observation. This theme concludes by trying to gain some perspective on whether it is possible, and even desirable, to attempt to have an internal model that tries to map the external observations, as we start to consider information-theoretic notions of relevance. Our results show that these design choices can have a profound effect on performance, even when the planning machinery is identical, and demonstrate the importance of building world models aligned with the agent's behavioural objectives

Beside and behind the wheel : factors that influence driving stress and driving behavior

A large percentage of traffic accidents are due to human errors. Driving behavior and driving stress influence the probability of making these mistakes. Both are influenced by multiple factors, among which might be elements such as age, gender, sleeping hours, or working hours. The objective of this paper is to study, in a real scenario and without forcing the driver?s state, the relationship between driving behavior, driving stress, and these elements. Furthermore, we aim to provide guidelines to improve driving assistants. In this study, we used 1050 driving samples obtained from 35 volunteers. The driving samples correspond to regular commutes from home to the workplace. ANOVA and ANCOVA tests were carried out to check if there are significant differences in the four factors analyzed. Although the results show that driving behavior and driving stress are affected by gender, age, and sleeping hours, the most critical variable is working hours. Drivers with long working days suffer significantly more driving stress compared to other drivers, with the corresponding effect on their driving style. These drivers were the worst at maintaining the safety distance.5311-8814-F0ED | Sara Maria da Cruz Maia de Oliveira PaivaN/

X-ray microtomography provides new insights into vacuum impregnation of spinach leaves

Vacuum impregnation is used in the food industry to facilitate the impregnation of porous products with, e.g. firming, antioxidant, antimicrobial or cryoprotective agents. X-ray micro-tomography (CT) was used to study the process of vacuum impregnation in spinach leaves. Low (300 mbar absolute pressure) and mild vacuum (150 mbar absolute pressure) impregnation protocols were used to impregnate an isotonic solution of trehalose in the leaves and CT was used to make observations of the cross section of the impregnated samples and quantify their porosity. Results revealed that the free volume in the spongy mesophyll is easier to impregnate than the spaces around the palisade mesophyll. The low vacuum impregnation protocol provoked less impregnation close to the edge of the leaf than in its centre, probably accounting for an influence of the tissue structure on impregnation. The vacuum impregnation protocols tested in this investigation drastically decreased the proportion of large pores (>100 m) and increased the proportion of small pores (<50 m). The mild vacuum impregnation protocol, which was designed on the basis of measured apparent porosity, did not achieve full impregnation of the tissue.V. Panarese acknowledges the financial support from the Portuguese Foundation of Science (FCT). F. Gomez Galindo acknowledges the financial support from European Community's Seventh Framework Program (FP7/2007-2013) under grant agreement no. 245280, also known under the acronym PRESERF. Financial support of FWO Vlaanderen (project G.0645.13), the Flemish government agency for Innovation by Science and Technology (project IWT SBO120033 TomFood) and the University of Leuven (project OT 12/055) is gratefully acknowledged. Dennis Cantre is an IRO scholar of KU Leuven. We also acknowledge the Hercules foundation for supporting the X-ray CT facility (AKUL001(HER/09/016))