Translational studies of molecular interactions in Parkinson's disease

Interactions between molecules are the basis of cellular function. In disease, these tightly regulated systems are often disturbed. Parkinson’s disease (PD) is recognized by protein aggregates in the brain of erroneously interacting molecules, directly linking the clinical picture to the molecular mechanisms. The currently incomplete understanding of the mechanisms behind PD pathogenesis impedes the development of disease-modifying treatment and new targets are needed since today’s dopaminergic treatment does not fully alleviate the symptoms. G protein-coupled receptors (GPCRs) are a wide group of transmembrane receptors usually targeted by drugs due to their ability to convey extracellular information into definite cellular responses. This Thesis focuses on protein interactions, from cellular models of a Parkinson-linked GPCR, GPR37, to detection of nanoaggregates in serum from PD patients as a sign of disease. The main findings relate to the interactome of GPR37 as a factor regulating cell survival. GPR37 has been suggested to accumulate and cause dopaminergic cell death in PD when improperly folded but is able to elicit cytoprotective function when correctly matured and trafficked to the cell surface. We report that GPR37 interaction with ganglioside GM1-enriched lipid rafts and a proposed ligand prosaposin affects trafficking of GPR37 to the plasma membrane. Since the role of lipids in PD pathogenesis is increasingly acknowledged and GM1 has been suggested to slow down PD progression in clinical studies, we further studied the mechanism of the GPR37-GM1 interaction. We propose that exogenous GM1 treatment increase cellular resistance to a neurotoxin partly through a GPR37-dependent mechanism. This suggests yet another molecular mechanism of GM1 cytoprotection. Moreover, GPR37 has been suggested to be a modulator of dopaminergic transmission why we investigated the proposed interaction with dopamine D2 receptor (D2R) and GPR37 in live cells. The levels of heterodimerization where generally low in our cellular system. However, it could be augmented both by chaperone treatment, inducing trafficking of GPR37, and by clinically used dopamine agonist treatment. Shifting the heterodimerization level of GPCRs is known to alter molecular response. Therefore, the physiological outcome of this interaction needs to deciphered to understand effects and side effects of dopamine agonist treatment. We also investigate improper protein interactions as a potential biomarker in serum from PD patients by detection of β-sheet enriched nanoaggregates. We report a higher detected frequency of nanoamyloids in patients compared to healthy controls and a bimodal distribution of amyloid size in serum. However, the frequency of nanoamyloids did not correlate robustly with neither disease progression or disease symptoms. Potentially this is due to heterogeneity, both clinical and molecular, in the disease. This emphasizes the need of understanding the molecular interactions in a clinical context

Wireless Sensor Networking in Challenging Environments

Recent years have witnessed growing interest in deploying wireless sensing applications in real-world environments. For example, home automation systems provide fine-grained metering and control of home appliances in residential settings. Similarly, assisted living applications employ wireless sensors to provide continuous health and wellness monitoring in homes. However, real deployments of Wireless Sensor Networks (WSNs) pose significant challenges due to their low-power radios and uncontrolled ambient environments. Our empirical study in over 15 real-world apartments shows that low-power WSNs based on the IEEE 802.15.4 standard are highly susceptible to external interference beyond user control, such as Wi-Fi access points, Bluetooth peripherals, cordless phones, and numerous other devices prevalent in residential environments that share the unlicensed 2.4 GHz ISM band with IEEE 802.15.4 radios. To address these real-world challenges, we developed two practical wireless network protocols including the Adaptive and Robust Channel Hopping (ARCH) protocol and the Adaptive Energy Detection Protocol (AEDP). ARCH enhances network reliability through opportunistically changing radio\u27s frequency to avoid interference and environmental noise and AEDP reduces false wakeups in noisy wireless environments by dynamically adjusting the wakeup threshold of low-power radios. Another major trend in WSNs is the convergence with smart phones. To deal with the dynamic wireless conditions and varying application requirements of mobile users, we developed the Self-Adapting MAC Layer (SAML) to support adaptive communication between smart phones and wireless sensors. SAML dynamically selects and switches Medium Access Control protocols to accommodate changes in ambient conditions and application requirements. Compared with the residential and personal wireless systems, industrial applications pose unique challenges due to their critical demands on reliability and real-time performance. We developed an experimental testbed by realizing key network mechanisms of industrial Wireless Sensor and Actuator Networks (WSANs) and conducted an empirical study that revealed the limitations and potential enhancements of those mechanisms. Our study shows that graph routing is more resilient to interference and its backup routes may be heavily used in noisy environments, which demonstrate the necessity of path diversity for reliable WSANs. Our study also suggests that combining channel diversity with retransmission may effectively reduce the burstiness of transmission failures and judicious allocation of multiple transmissions in a shared slot can effectively improve network capacity without significantly impacting reliability

Engineering Tools to Further Neuroscientific Investigation

Custom equipment is often necessary in the laboratory. However, costs for such equipment can be high and efficient systems with lower cost are an advantage. In this work, we showed that a cellular environment to keep cells healthy and viable for five hours on a microscope could be created using FDM printing (Chapter 3). Design criteria were that it maintained correct temperature, high humidity and proper pH to control the environment as discussed in Chapter 2. Results indicated that cells would maintain viability for up to five hours, but redesigns needed to be made for extending viability past five hours. An imaging enhancement termed PICS (Planar Imaging of Curved Surfaces) was also introduced (Chapter 5). For this project, design criteria were that the device stabilized the tissue for imaging while allowing fluid flow around the tissue and facilitate rotation of the naturally curved tissue with respect to the microscope objective lens. Three further considerations of the PICS device were: (1) that it should not add undue shear stresses to the sample tissue, (2) that there should be no unintentional translation, (3) that it should attach to a standard microscope temperature controller in such a way that it does not interfere with temperature controls and does not move unintentionally. Results indicate successful movement of tissue with respect to imaging plane to facilitate productive image capture. Finally, in Chapter 7, a microelectrochemical array was used to explore differences between glioma and normal astrocyte glutamate levels. Results showed that glioma and normal astrocyte glutamate uptake can be tracked in real-time and compared using the probe. The distinction between glioma cells and astrocytes relies on three indicators: (1) a signal more stepped like in appearance, closer to that of a calibration curve, coming to a steady baseline faster and having a shorter FDHM, is a first indication of impaired uptake; (2) a signal showing a lower k constant, indicating a slower overall clearance rate, (3) faster rise times corresponding with a slower maximum elimination rate. These corresponding factors together indicate impaired uptake in glioma cells versus normal astrocyte glutamate uptake

On the role of parvalbumin interneurons in neuronal network activity in the prefrontal cortex

The prefrontal cortex (PFC) is an area important for executive functions, the initiation and temporal organization of goal-directed behavior, as well as social behaviors. Inhibitory interneurons expressing parvalbumin (PV) have a vital role in modulating PFC circuit plasticity and output, as inhibition by PV interneurons on excitatory pyramidal neurons regulates the excitability of the network. Thus, dysfunctions of prefrontal PV interneurons are implicated in the pathophysiology of a range of PFC-dependent neuropsychiatric disorders characterized by excitation and inhibition (E/I) imbalance and impaired gamma oscillations. In particular, the hypofunction of receptors important for neurotransmission and regulating cellular functions, such as the N-methyl-D-aspartate receptors (NMDARs) and the tyrosine receptor kinase B (trkB), has been implicated in PV dysfunction. Notably, this hypofunction is known to impair the normal development of PV interneurons. However, it can also affect adult brain activity. The effects of altered receptors on PV interneurons are multiple, from impaired morphological connectivity to disruption of intrinsic activity, but have not yet been fully characterized. Moreover, the effects of deficits of PV neuron-mediated inhibition on neuronal network activity are complex, involved with compensatory mechanisms, and not fully understood either. For instance, the E/I imbalance due to PV inhibition has been suggested to functionally disrupt the cortex, which can be observed through an abnormal increase in broadband gamma activity. But as the synchronous activity of cortical PV interneurons is necessary for the generation of cortical gamma oscillations, it is paradoxical that deficient PV inhibition is associated with increased broadband gamma power. This thesis aims to examine the role of PV interneurons in shaping neuronal network activity in the mouse PFC by investigating the microscopic to macroscopic functional effects of disrupting receptors necessary for the proper activity of PV interneurons. In paper I, we observed that the increase of broadband gamma power due to NMDAR hypofunction in PV neurons is associated with asynchronies of network activity, confirming that dysfunction of neuronal inhibition can cause desynchronization at multiple time scales (affecting entrainment of spikes by the LFP, as well as cross-frequency coupling and brain states fragmentation). In Paper II, we prompted and analyzed the rippling effect of PV dysfunction in the adult PFC by expressing a dominant-negative trkB receptor specifically in PV interneurons. Despite avoiding interfering with the development of the brain, we found pronounced morphological and functional alterations in the targeted PV interneurons. These changes were associated with unusual aggressive behavior coupled with gamma-band alterations and a decreased modulation of prefrontal excitatory neuronal populations by PV interneurons. Thus, the work presented in this thesis furthers our understanding of the role of PV function in PFC circuitry, particularly of two receptors that are central to the role of PV interneurons in coordinating local circuit activity. A better understanding of the potential mechanisms that could explain the neuronal changes seen in individuals with neuropsychiatric dysfunctions could lead to using gamma oscillations or BDNF-trkB levels as biomarkers in psychiatric disorders. It also presents possibilities for potential treatments designed around reestablishing E/I balance by modifying receptor levels in particular cell types

Opportunistic communications in large uncoordinated networks

(English) The increase of wireless devices offering high data rate services limits the coexistence of wireless systems sharing the same resources in a given geographical area because of inter-system interference. Therefore, interference management plays a key role in permitting the coexistence of several heterogeneous communication services. However, classical interference management strategies require lateral information giving rise to the need for inter-system coordination and cooperation, which is not always practical. Opportunistic communications offer a potential solution to the problem of inter-system interference management. The basic principle of opportunistic communications is to efficiently and robustly exploit the resources available in a wireless network and adapt the transmitted signals to the state of the network to avoid inter-system interference. Therefore, opportunistic communications depend on inferring the available network resources that can be safely exploited without inducing interference in coexisting communication nodes. Once the available network resources are identified, the most prominent opportunistic communication techniques consist in designing scenario-adapted precoding/decoding strategies to exploit the so-called null space. Despite this, classical solutions in the literature suffer from two main drawbacks: the lack of robustness to detection errors and the need for intra-system cooperation. This thesis focuses on the design of a null space-based opportunistic communication scheme that addresses the drawbacks exhibited by existing methodologies under the assumption that opportunistic nodes do not cooperate. For this purpose, a generalized detection error model independent of the null-space identification mechanism is introduced that allows the design of solutions that exhibit minimal inter-system interference in the worst case. These solutions respond to a maximum signal-to-interference ratio (SIR) criterion, which is optimal under non-cooperative conditions. The proposed methodology allows the design of a family of orthonormal waveforms that perform a spreading of the modulated symbols within the detected null space, which is key to minimizing the induced interference density. The proposed solutions are invariant within the inferred null space, allowing the removal of the feedback link without giving up coherent waveform detection. In the absence of coordination, the waveform design relies solely on locally sensed network state information, inducing a mismatch between the null spaces identified by the transmitter and receiver that may worsen system performance. Although the proposed solution is robust to this mismatch, the design of enhanced receivers using active subspace detection schemes is also studied. When the total number of network resources increases arbitrarily, the proposed solutions tend to be linear combinations of complex exponentials, providing an interpretation in the frequency domain. This asymptotic behavior allows us to adapt the proposed solution to frequency-selective channels by means of a cyclic prefix and to study an efficient modulation similar to the time division multiplexing scheme but using circulant waveforms. Finally, the impact of the use of multiple antennas in opportunistic null space-based communications is studied. The performed analysis reveals that, in any case, the structure of the antenna clusters affects the opportunistic communication, since the proposed waveform mimics the behavior of a single-antenna transmitter. On the other hand, the number of sensors employed translates into an improvement in terms of SIR.(Català) El creixement incremental dels dispositius sense fils que requereixen serveis d'alta velocitat de dades limita la coexistència de sistemes sense fils que comparteixen els mateixos recursos en una àrea geogràfica donada a causa de la interferència entre sistemes. Conseqüentment, la gestió d'interferència juga un paper fonamental per a facilitar la coexistència de diversos serveis de comunicació heterogenis. No obstant això, les estratègies clàssiques de gestió d'interferència requereixen informació lateral originant la necessitat de coordinació i cooperació entre sistemes, que no sempre és pràctica. Les comunicacions oportunistes ofereixen una solució potencial al problema de la gestió de les interferències entre sistemes. El principi bàsic de les comunicacions oportunistes és explotar de manera eficient i robusta els recursos disponibles en una xarxa sense fils i adaptar els senyals transmesos a l'estat de la xarxa per evitar interferències entre sistemes. Per tant, les comunicacions oportunistes depenen de la inferència dels recursos de xarxa disponibles que poden ser explotats de manera segura sense induir interferència en els nodes de comunicació coexistents. Una vegada que s'han identificat els recursos de xarxa disponibles, les tècniques de comunicació oportunistes més prominents consisteixen en el disseny d'estratègies de precodificació/descodificació adaptades a l'escenari per explotar l'anomenat espai nul. Malgrat això, les solucions clàssiques en la literatura sofreixen dos inconvenients principals: la falta de robustesa als errors de detecció i la necessitat de cooperació intra-sistema. Aquesta tesi tracta el disseny d'un esquema de comunicació oportunista basat en l'espai nul que afronta els inconvenients exposats per les metodologies existents assumint que els nodes oportunistes no cooperen. Per a aquest propòsit, s'introdueix un model generalitzat d'error de detecció independent del mecanisme d'identificació de l'espai nul que permet el disseny de solucions que exhibeixen interferències mínimes entre sistemes en el cas pitjor. Aquestes solucions responen a un criteri de màxima relació de senyal a interferència (SIR), que és òptim en condicions de no cooperació. La metodologia proposada permet dissenyar una família de formes d'ona ortonormals que realitzen un spreading dels símbols modulats dins de l'espai nul detectat, que és clau per minimitzar la densitat d’interferència induïda. Les solucions proposades són invariants dins de l'espai nul inferit, permetent suprimir l'enllaç de retroalimentació i, tot i així, realitzar una detecció coherent de forma d'ona. Sota l’absència de coordinació, el disseny de la forma d'ona es basa únicament en la informació de l'estat de la xarxa detectada localment, induint un desajust entre els espais nuls identificats pel transmissor i receptor que pot empitjorar el rendiment del sistema. Tot i que la solució proposada és robusta a aquest desajust, també s'estudia el disseny de receptors millorats fent ús de tècniques de detecció de subespai actiu. Quan el nombre total de recursos de xarxa augmenta arbitràriament, les solucions proposades tendeixen a ser combinacions lineals d'exponencials complexes, proporcionant una interpretació en el domini freqüencial. Aquest comportament asimptòtic permet adaptar la solució proposada a entorns selectius en freqüència fent ús d'un prefix cíclic i estudiar una modulació eficient derivada de l'esquema de multiplexat per divisió de temps emprant formes d'ona circulant. Finalment, s’estudia l'impacte de l'ús de múltiples antenes en comunicacions oportunistes basades en l'espai nul. L'anàlisi realitzada permet concloure que, en cap cas, l'estructura de les agrupacions d'antenes tenen un impacte sobre la comunicació oportunista, ja que la forma d'ona proposada imita el comportament d'un transmissor mono-antena. D'altra banda, el nombre de sensors emprat es tradueix en una millora en termes de SIR.(Español) El incremento de los dispositivos inalámbricos que ofrecen servicios de alta velocidad de datos limita la coexistencia de sistemas inalámbricos que comparten los mismos recursos en un área geográfica dada a causa de la interferencia inter-sistema. Por tanto, la gestión de interferencia juega un papel fundamental para facilitar la coexistencia de varios servicios de comunicación heterogéneos. Sin embargo, las estrategias clásicas de gestión de interferencia requieren información lateral originando la necesidad de coordinación y cooperación entre sistemas, que no siempre es práctica. Las comunicaciones oportunistas ofrecen una solución potencial al problema de la gestión de las interferencias entre sistemas. El principio básico de las comunicaciones oportunistas es explotar de manera eficiente y robusta los recursos disponibles en una red inalámbricas y adaptar las señales transmitidas al estado de la red para evitar interferencias entre sistemas. Por lo tanto, las comunicaciones oportunistas dependen de la inferencia de los recursos de red disponibles que pueden ser explotados de manera segura sin inducir interferencia en los nodos de comunicación coexistentes. Una vez identificados los recursos disponibles, las técnicas de comunicación oportunistas más prominentes consisten en el diseño de estrategias de precodificación/descodificación adaptadas al escenario para explotar el llamado espacio nulo. A pesar de esto, las soluciones clásicas en la literatura sufren dos inconvenientes principales: la falta de robustez a los errores de detección y la necesidad de cooperación intra-sistema. Esta tesis propone diseñar un esquema de comunicación oportunista basado en el espacio nulo que afronta los inconvenientes expuestos por las metodologías existentes asumiendo que los nodos oportunistas no cooperan. Para este propósito, se introduce un modelo generalizado de error de detección independiente del mecanismo de identificación del espacio nulo que permite el diseño de soluciones que exhiben interferencias mínimas entre sistemas en el caso peor. Estas soluciones responden a un criterio de máxima relación de señal a interferencia (SIR), que es óptimo en condiciones de no cooperación. La metodología propuesta permite diseñar una familia de formas de onda ortonormales que realizan un spreading de los símbolos modulados dentro del espacio nulo detectado, que es clave para minimizar la densidad de interferencia inducida. Las soluciones propuestas son invariantes dentro del espacio nulo inferido, permitiendo suprimir el enlace de retroalimentación sin renunciar a la detección coherente de forma de onda. En ausencia de coordinación, el diseño de la forma de onda se basa únicamente en la información del estado de la red detectada localmente, induciendo un desajuste entre los espacios nulos identificados por el transmisor y receptor que puede empeorar el rendimiento del sistema. A pesar de que la solución propuesta es robusta a este desajuste, también se estudia el diseño de receptores mejorados usando técnicas de detección de subespacio activo. Cuando el número total de recursos de red aumenta arbitrariamente, las soluciones propuestas tienden a ser combinaciones lineales de exponenciales complejas, proporcionando una interpretación en el dominio frecuencial. Este comportamiento asintótico permite adaptar la solución propuesta a canales selectivos en frecuencia mediante un prefijo cíclico y estudiar una modulación eficiente derivada del esquema de multiplexado por división de tiempo empleando formas de onda circulante. Finalmente, se estudia el impacto del uso de múltiples antenas en comunicaciones oportunistas basadas en el espacio nulo. El análisis realizado revela que la estructura de las agrupaciones de antenas no afecta la comunicación oportunista, ya que la forma de onda propuesta imita el comportamiento de un transmisor mono-antena. Por otro lado, el número de sensores empleado se traduce en una mejora en términos de SIR.Postprint (published version

Development and certification of mixed-criticality embedded systems based on probabilistic timing analysis

An increasing variety of emerging systems relentlessly replaces or augments the functionality of mechanical subsystems with embedded electronics. For quantity, complexity, and use, the safety of such subsystems is an increasingly important matter. Accordingly, those systems are subject to safety certification to demonstrate system's safety by rigorous development processes and hardware/software constraints. The massive augment in embedded processors' complexity renders the arduous certification task significantly harder to achieve. The focus of this thesis is to address the certification challenges in multicore architectures: despite their potential to integrate several applications on a single platform, their inherent complexity imperils their timing predictability and certification. Recently, the Measurement-Based Probabilistic Timing Analysis (MBPTA) technique emerged as an alternative to deal with hardware/software complexity. The innovation that MBPTA brings about is, however, a major step from current certification procedures and standards. The particular contributions of this Thesis include: (i) the definition of certification arguments for mixed-criticality integration upon multicore processors. In particular we propose a set of safety mechanisms and procedures as required to comply with functional safety standards. For timing predictability, (ii) we present a quantitative approach to assess the likelihood of execution-time exceedance events with respect to the risk reduction requirements on safety standards. To this end, we build upon the MBPTA approach and we present the design of a safety-related source of randomization (SoR), that plays a key role in the platform-level randomization needed by MBPTA. And (iii) we evaluate current certification guidance with respect to emerging high performance design trends like caches. Overall, this Thesis pushes the certification limits in the use of multicore and MBPTA technology in Critical Real-Time Embedded Systems (CRTES) and paves the way towards their adoption in industry.Una creciente variedad de sistemas emergentes reemplazan o aumentan la funcionalidad de subsistemas mecánicos con componentes electrónicos embebidos. El aumento en la cantidad y complejidad de dichos subsistemas electrónicos así como su cometido, hacen de su seguridad una cuestión de creciente importancia. Tanto es así que la comercialización de estos sistemas críticos está sujeta a rigurosos procesos de certificación donde se garantiza la seguridad del sistema mediante estrictas restricciones en el proceso de desarrollo y diseño de su hardware y software. Esta tesis trata de abordar los nuevos retos y dificultades dadas por la introducción de procesadores multi-núcleo en dichos sistemas críticos: aunque su mayor rendimiento despierta el interés de la industria para integrar múltiples aplicaciones en una sola plataforma, suponen una mayor complejidad. Su arquitectura desafía su análisis temporal mediante los métodos tradicionales y, asimismo, su certificación es cada vez más compleja y costosa. Con el fin de lidiar con estas limitaciones, recientemente se ha desarrollado una novedosa técnica de análisis temporal probabilístico basado en medidas (MBPTA). La innovación de esta técnica, sin embargo, supone un gran cambio cultural respecto a los estándares y procedimientos tradicionales de certificación. En esta línea, las contribuciones de esta tesis están agrupadas en tres ejes principales: (i) definición de argumentos de seguridad para la certificación de aplicaciones de criticidad-mixta sobre plataformas multi-núcleo. Se definen, en particular, mecanismos de seguridad, técnicas de diagnóstico y reacción de faltas acorde con el estándar IEC 61508 sobre una arquitectura multi-núcleo de referencia. Respecto al análisis temporal, (ii) presentamos la cuantificación de la probabilidad de exceder un límite temporal y su relación con los requisitos de reducción de riesgos derivados de los estándares de seguridad funcional. Con este fin, nos basamos en la técnica MBPTA y presentamos el diseño de una fuente de números aleatorios segura; un componente clave para conseguir las propiedades aleatorias requeridas por MBPTA a nivel de plataforma. Por último, (iii) extrapolamos las guías actuales para la certificación de arquitecturas multi-núcleo a una solución comercial de 8 núcleos y las evaluamos con respecto a las tendencias emergentes de diseño de alto rendimiento (caches). Con estas contribuciones, esta tesis trata de abordar los retos que el uso de procesadores multi-núcleo y MBPTA implican en el proceso de certificación de sistemas críticos de tiempo real y facilita, de esta forma, su adopción por la industria.Postprint (published version

Proceedings of the Second International Mobile Satellite Conference (IMSC 1990)

Presented here are the proceedings of the Second International Mobile Satellite Conference (IMSC), held June 17-20, 1990 in Ottawa, Canada. Topics covered include future mobile satellite communications concepts, aeronautical applications, modulation and coding, propagation and experimental systems, mobile terminal equipment, network architecture and control, regulatory and policy considerations, vehicle antennas, and speech compression