Oscillatory stimuli differentiate adapting circuit topologies

This is the author accepted manuscript. The final version is available from Springer Nature via the DOI in this record.Biology emerges from interactions between molecules, which are challenging to elucidate with current techniques. An orthogonal approach is to probe for 'response signatures' that identify specific circuit motifs. For example, bistability, hysteresis, or irreversibility are used to detect positive feedback loops. For adapting systems, such signatures are not known. Only two circuit motifs generate adaptation: negative feedback loops (NFLs) and incoherent feed-forward loops (IFFLs). On the basis of computational testing and mathematical proofs, we propose differential signatures: in response to oscillatory stimulation, NFLs but not IFFLs show refractory-period stabilization (robustness to changes in stimulus duration) or period skipping. Applying this approach to yeast, we identified the circuit dominating cell cycle timing. In Caenorhabditis elegans AWA neurons, which are crucial for chemotaxis, we uncovered a Ca2+ NFL leading to adaptation that would be difficult to find by other means. These response signatures allow direct access to the outlines of the wiring diagrams of adapting systems.The work was supported by US National Institutes of Health grant 5RO1-GM078153-07 (F.R.C.), NRSA Training Grant CA009673-36A1 (S.J.R.), a Merck Postdoctoral Fellowship at The Rockefeller University (S.J.R.), and the Simons Foundation (S.J.R.). J.L. was supported by a fellowship from the Boehringer Ingelheim Fonds. E.D.S. was partially supported by the US Office of Naval Research (ONR N00014-13-1-0074) and the US Air Force Office of Scientific Research (AFOSR FA9550-14-1-0060)

Design and implementation of a downlink MC-CDMA receiver

Cette thèse présente une étude d'un système complet de transmission en liaison descendante utilisant la technologie multi-porteuse avec l'accès multiple par division de code (Multi-Carrier Code Division Multiple Access, MC-CDMA). L'étude inclut la synchronisation et l'estimation du canal pour un système MC-CDMA en liaison descendante ainsi que l'implémentation sur puce FPGA d'un récepteur MC-CDMA en liaison descendante en bande de base. Le MC-CDMA est une combinaison de la technique de multiplexage par fréquence orthogonale (Orthogonal Frequency Division Multiplexing, OFDM) et de l'accès multiple par répartition de code (CDMA), et ce dans le but d'intégrer les deux technologies. Le système MC-CDMA est conçu pour fonctionner à l'intérieur de la contrainte d'une bande de fréquence de 5 MHz pour les modèles de canaux intérieur/extérieur pédestre et véhiculaire tel que décrit par le "Third Genaration Partnership Project" (3GPP). La composante OFDM du système MC-CDMA a été simulée en utilisant le logiciel MATLAB dans le but d'obtenir des paramètres de base. Des codes orthogonaux à facteur d'étalement variable (OVSF) de longueur 8 ont été choisis comme codes d'étalement pour notre système MC-CDMA. Ceci permet de supporter des taux de transmission maximum jusquà 20.6 Mbps et 22.875 Mbps (données non codées, pleine charge de 8 utilisateurs) pour les canaux intérieur/extérieur pédestre et véhiculaire, respectivement. Une étude analytique des expressions de taux d'erreur binaire pour le MC-CDMA dans un canal multivoies de Rayleigh a été réalisée dans le but d'évaluer rapidement et de façon précise les performances. Des techniques d'estimation de canal basées sur les décisions antérieures ont été étudiées afin d'améliorer encore plus les performances de taux d'erreur binaire du système MC-CDMA en liaison descendante. L'estimateur de canal basé sur les décisions antérieures et utilisant le critère de l'erreur quadratique minimale linéaire avec une matrice' de corrélation du canal de taille 64 x 64 a été choisi comme étant un bon compromis entre la performance et la complexité pour une implementation sur puce FPGA. Une nouvelle séquence d'apprentissage a été conçue pour le récepteur dans la configuration intérieur/extérieur pédestre dans le but d'estimer de façon grossière le temps de synchronisation et le décalage fréquentiel fractionnaire de la porteuse dans le domaine du temps. Les estimations fines du temps de synchronisation et du décalage fréquentiel de la porteuse ont été effectués dans le domaine des fréquences à l'aide de sous-porteuses pilotes. Un récepteur en liaison descendante MC-CDMA complet pour le canal intérieur /extérieur pédestre avec les synchronisations en temps et en fréquence en boucle fermée a été simulé avant de procéder à l'implémentation matérielle. Le récepteur en liaison descendante en bande de base pour le canal intérieur/extérieur pédestre a été implémenté sur un système de développement fabriqué par la compagnie Nallatech et utilisant le circuit XtremeDSP de Xilinx. Un transmetteur compatible avec le système de réception a également été réalisé. Des tests fonctionnels du récepteur ont été effectués dans un environnement sans fil statique de laboratoire. Un environnement de test plus dynamique, incluant la mobilité du transmetteur, du récepteur ou des éléments dispersifs, aurait été souhaitable, mais n'a pu être réalisé étant donné les difficultés logistiques inhérentes. Les taux d'erreur binaire mesurés avec différents nombres d'usagers actifs et différentes modulations sont proches des simulations sur ordinateurs pour un canal avec bruit blanc gaussien additif

SSTRED: A data-processing and metadata-generating pipeline for CHROMIS and CRISP

We present a data pipeline for the newly installed SST/CHROMIS imaging spectrometer, as well as for the older SST/CRISP spectropolarimeter. The aim is to provide observers with a user-friendly data pipeline, that delivers science-ready data with the metadata needed for archival. We generalized the CRISPRED data pipeline for multiple instruments and added metadata according to recommendations worked out as part of the SOLARNET project. We made improvements to several steps in the pipeline, including the MOMFBD image restoration. A part of that is a new fork of the MOMFBD program called REDUX, with several new features that are needed in the new pipeline. The CRISPEX data viewer has been updated to accommodate data cubes stored in this format. The pipeline code, as well as REDUX and CRISPEX are all freely available through git repositories or web download. We derive expressions for combining statistics of individual frames into statistics for a set of frames. We define a new extension to the World Coordinate System, that allow us to specify cavity errors as distortions to the spectral coordinate.Comment: Draf

Design and implementation of a modular controller for robotic machines

This research focused on the design and implementation of an Intelligent Modular Controller (IMC) architecture designed to be reconfigurable over a robust network. The design incorporates novel communication, hardware, and software architectures. This was motivated by current industrial needs for distributed control systems due to growing demand for less complexity, more processing power, flexibility, and greater fault tolerance. To this end, three main contributions were made. Most distributed control architectures depend on multi-tier heterogeneous communication networks requiring linking devices and/or complex middleware. In this study, first, a communication architecture was proposed and implemented with a homogenous network employing the ubiquitous Ethernet for both real-time and non real-time communication. This was achieved by a producer-consumer coordination model for real-time data communication over a segmented network, and a client-server model for point-to-point transactions. The protocols deployed use a Time-Triggered (TT) approach to schedule real-time tasks on the network. Unlike other TT approaches, the scheduling mechanism does not need to be configured explicitly when controller nodes are added or removed. An implicit clock synchronization technique was also developed to complement the architecture. Second, a reconfigurable mechanism based on an auto-configuration protocol was developed. Modules on the network use this protocol to automatically detect themselves, establish communication, and negotiate for a desired configuration. Third, the research demonstrated hardware/software co-design as a contribution to the growing discipline of mechatronics. The IMC consists of a motion controller board designed and prototyped in-house, and a Java microcontroller. An IMC is mapped to each machine/robot axis, and an additional IMC can be configured to serve as a real-time coordinator. The entire architecture was implemented in Java, thus reinforcing uniformity, simplicity, modularity, and openness. Evaluation results showed the potential of the flexible controller to meet medium to high performance machining requirements

MEASUREMENT AND MODELING OF HUMIDITY SENSORS

Humidity measurement has been increasingly important in many industries and process control applications. This thesis research focus mainly on humidity sensor calibration and characterization. The humidity sensor instrumentation is briefly described. The testing infrastructure was designed for sensor data acquisition, in order to compensate the humidity sensor’s temperature coefficient, temperature chambers using Peltier elements are used to achieve easy-controllable stable temperatures. The sensor characterization falls into a multivariate interpolation problem. Neuron networks is tried for non-linear data fitting, but in the circumstance of limited training data, an innovative algorithm was developed to utilize shape preserving polynomials in multiple planes in this kind of multivariate interpolation problems

Myocardial tagging by Cardiovascular Magnetic Resonance: evolution of techniques--pulse sequences, analysis algorithms, and applications

Cardiovascular magnetic resonance (CMR) tagging has been established as an essential technique for measuring regional myocardial function. It allows quantification of local intramyocardial motion measures, e.g. strain and strain rate. The invention of CMR tagging came in the late eighties, where the technique allowed for the first time for visualizing transmural myocardial movement without having to implant physical markers. This new idea opened the door for a series of developments and improvements that continue up to the present time. Different tagging techniques are currently available that are more extensive, improved, and sophisticated than they were twenty years ago. Each of these techniques has different versions for improved resolution, signal-to-noise ratio (SNR), scan time, anatomical coverage, three-dimensional capability, and image quality. The tagging techniques covered in this article can be broadly divided into two main categories: 1) Basic techniques, which include magnetization saturation, spatial modulation of magnetization (SPAMM), delay alternating with nutations for tailored excitation (DANTE), and complementary SPAMM (CSPAMM); and 2) Advanced techniques, which include harmonic phase (HARP), displacement encoding with stimulated echoes (DENSE), and strain encoding (SENC). Although most of these techniques were developed by separate groups and evolved from different backgrounds, they are in fact closely related to each other, and they can be interpreted from more than one perspective. Some of these techniques even followed parallel paths of developments, as illustrated in the article. As each technique has its own advantages, some efforts have been made to combine different techniques together for improved image quality or composite information acquisition. In this review, different developments in pulse sequences and related image processing techniques are described along with the necessities that led to their invention, which makes this article easy to read and the covered techniques easy to follow. Major studies that applied CMR tagging for studying myocardial mechanics are also summarized. Finally, the current article includes a plethora of ideas and techniques with over 300 references that motivate the reader to think about the future of CMR tagging