Multiplexed, High Density Electrophysiology with Nanofabricated Neural Probes

Extracellular electrode arrays can reveal the neuronal network correlates of behavior with single-cell, single-spike, and sub-millisecond resolution. However, implantable electrodes are inherently invasive, and efforts to scale up the number and density of recording sites must compromise on device size in order to connect the electrodes. Here, we report on silicon-based neural probes employing nanofabricated, high-density electrical leads. Furthermore, we address the challenge of reading out multichannel data with an application-specific integrated circuit (ASIC) performing signal amplification, band-pass filtering, and multiplexing functions. We demonstrate high spatial resolution extracellular measurements with a fully integrated, low noise 64-channel system weighing just 330 mg. The on-chip multiplexers make possible recordings with substantially fewer external wires than the number of input channels. By combining nanofabricated probes with ASICs we have implemented a system for performing large-scale, high-density electrophysiology in small, freely behaving animals that is both minimally invasive and highly scalable

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells

Stochastic Analysis of Some Expedited Forwarding Networks

We consider stochastic guarantees for networks with aggregate scheduling, in particular, Expedited Forwarding (EF). Our approach is based on the assumption that a node can be abstracted by a service curve, and the input flows are regulated individually at the network ingress. Both of these assumptions are inline with the current definition of EF \cite{charny-00-b,davie-01-a}. We derive bounds to the complementary distributions of the backlog, delay through a single node, and the end-to-end delay. We also give a bound on the loss-ratio. Our analysis is exact under the given assumptions. Our results should help us to understand the performance of networks with aggregate scheduling, and provide the basis for dimensioning such networks

A 16 x 16 CMOS amperometric microelectrode array for simultaneous electrochemical measurements

There is a requirement for an electrochemical sensor technology capable of making multivariate measurements in environmental, healthcare, and manufacturing applications. Here, we present a new device that is highly parallelized with an excellent bandwidth. For the first time, electrochemical cross-talk for a chip-based sensor is defined and characterized. The new CMOS electrochemical sensor chip is capable of simultaneously taking multiple, independent electroanalytical measurements. The chip is structured as an electrochemical cell microarray, comprised of a microelectrode array connected to embedded self-contained potentiostats. Speed and sensitivity are essential in dynamic variable electrochemical systems. Owing to the parallel function of the system, rapid data collection is possible while maintaining an appropriately low-scan rate. By performing multiple, simultaneous cyclic voltammetry scans in each of the electrochemical cells on the chip surface, we are able to show (with a cell-to-cell pitch of 456 μm) that the signal cross-talk is only 12% between nearest neighbors in a ferrocene rich solution. The system opens up the possibility to use multiple independently controlled electrochemical sensors on a single chip for applications in DNA sensing, medical diagnostics, environmental sensing, the food industry, neuronal sensing, and drug discovery

The effect of prewhirl on the internal aerodynamics and performance of a mixed flow research centrifugal compressor

The internal three-dimensional steady and time-varying flow through the diffusing elements of a centrifugal impeller were investigated using a moderate scale, subsonic, mixed flow research compressor facility. The characteristics of the test facility which permit the measurement of internal flow conditions throughout the entire research compressor and radial diffuser for various operating conditions are described. Results are presented in the form of graphs and charts to cover a range of mass flow rates with inlet guide vane settings varying from minus 15 degrees to plus 45 degrees. The static pressure distributions in the compressor inlet section and on the impeller and exit diffuser vanes, as well as the overall pressure and temperature rise and mass flow rate, were measured and analyzed at each operating point to determine the overall performance as well as the detailed aerodynamics throughout the compressor

Determination of Gas Emission Characteristics from Animal Wastes Using a Multiplexed Portable FTIR-Surface Chamber System

Livestock production is a growing source of air pollution at regional, national, and global scales. Improved livestock manure management has the potential to reduce environmental impacts; however, there is an urgent need for cost-efficient, reliable, and easy to maintain measurement and monitoring capabilities to precisely quantify emissions from livestock manure. This research describes and evaluates a novel measurement method based on the multiplexed portable Fourier Transform Infrared (FTIR) spectroscopy analyzer - surface chamber techniques for continuous measurements and monitoring gas emissions from manure sources. The multiplexing system was designed and developed to automate the chamber network, controlling the movement of chambers and accurately managing chamber air flow distribution. The measurement accuracy of the developed system was evaluated under controlled laboratory conditions. The result of the statistical hypothesis testing showed that there is no statistically significant differences among the measurement results from each of the twelve chambers. While microbial activity is a key factor for formation of gaseous compounds in manure, the magnitude of gas exchange between manure and the atmosphere largely depends on manure physical characteristics. A series of soil science measurement and modeling techniques were applied to determine a set of fundamental physical, hydraulics, and thermal properties of cattle manure to support advanced modeling of gas emissions from manure sources. The liquid water retention characteristic for cattle manure was found to be close to that of organic peat soils. The results also suggested that Richards equation can describe the hydrodynamics taking place in cattle manure relevant to natural drying processes. However, the uncertainties of the measurement results could be due to the complexity of shrinkage, surface crust formation, and shrinkage cracks. Carbon dioxide (CO2), methane (CH4), and ammonia (NH3) emissions were estimated and characterized in field plots using the developed gas emission measurement system. The measurements included four treatments; beef manure, dairy manure, beef compost, and dairy compost. The estimated CO2, CH4, and NH3 emissions from the surface application with dairy manure were the highest among other treatments, while those from the surface application with beef compost were the lowest. Impacts of temperature and water content on gaseous emissions were found to be correlated significantly. Overall, this dissertation provides a solid foundation upon which future research can build in better understanding and modeling animal waste emission processes that impact the environment

Using Signal Processing Tools for Regulation Analysis and Implementation

Regulators often face the challenge of designing and implementing rules that both, respond to the policy objectives and that can be clearly referred to the day-to-day operations and practices in the marketplace. In many cases, the actual codes end up being a cumbersome collection of conditions that are very difficult to evaluate and re-design. This paper suggests that some of the most commonly used tools in Signal Processing could offer a convenient vehicle for tackling these difficulties. By starting from a SIMULINK(R) model of the regulation of Banco de Mexico on the foreign exchange transactions of commercial banks, this paper offers an example of how those tools could be used in this context.

Development of CRISPR-based programmable transcriptional regulators and their applications in plants

[ES] La Biología Sintética de Plantas tiene como objetivo rediseñar las plantas para que adquieran características y funcionalidades novedosas a través de circuitos reguladores ortogonales. Para lograr este objetivo, se deben desarrollar nuevas herramientas moleculares con la capacidad de interactuar con factores endógenos de manera potente y específica. CRISPR/Cas9 surgió como una herramienta prometedora que combina la capacidad personalizable de unión al DNA, a través de la versión catalíticamente inactivada de la proteína Cas9 (dCas9), con la posibilidad de anclar dominios autónomos de activación transcripcional (TADs) a su estructura para lograr una regulación específica de la expresión génica. Los activadores transcripcionales programables (PTAs) pueden actuar como procesadores específicos, ortogonales y versátiles para el desarrollo de nuevos circuitos genéticos en las plantas. En busca de dCas9-PTA optimizados, se llevó a cabo una evaluación combinatoria de diferentes arquitecturas dCas9 con un catálogo de varios TAD. La mejor herramienta resultante de esta comparación, denominada dCasEV2.1, se basa en la estrategia scRNA y la combinación de los dominios de activación EDLL y VPR con un bucle multiplexable gRNA2.1, que es una versión mutada del gRNA2.0 descrito previamente. En este trabajo, el activador programable dCasEV2.1 demostró ser una herramienta potente y específica, logrando tasas de activación más altas que otras estrategias dCas9 disponibles en plantas. Se observaron tasas de activación sin precedentes dirigidas a genes endógenos en N. benthamiana, acompañadas de una estricta especificidad en todo el genoma, lo que hace que esta herramienta sea adecuada para la regulación estricta de redes reguladoras complejas. Como prueba de concepto, se diseñaron cuatro programas de activación para distintas ramas de la ruta de los flavonoides, buscando obtener enriquecimientos metabólicos específicos en hojas de N. benthamiana. El análisis metabólico de las hojas metabólicamente reprogramadas mediante dCasEV2.1 reveló un enriquecimiento selectivo de los metabolitos diana y sus derivados glicosilados, que se correlacionaron con el programa de activación empleado. Estos resultados demuestran que dCasEV2.1 es una herramienta eficaz para la ingeniería metabólica y un componente clave en los circuitos genéticos destinados a reprogramar los flujos metabólicos. Finalmente, basándonos en dCasEV2.1, desarrollamos un sistema optimizado de regulación de genes inducidos por virus (VIGR) que utiliza un vector Potato Virus X (PVX) para el suministro de los programas de activación CRISPR codificados con gRNA. Este enfoque permite controlar el transcriptoma de la planta a través de una aplicación sistémica basada en aerosol de componentes CRISPR a plantas adultas. El nuevo sistema PVX-VIGR produjo una fuerte activación transcripcional en varios genes diana endógenos, incluidos tres factores de transcripción MYB-like seleccionados. Las activaciones específicas de MYB condujeron a perfiles metabólicos distintivos, demostrando que las aplicaciones potenciales de la herramienta dCasEV2.1 en plantas incluyen la obtención de perfiles metabólicos personalizados utilizando un suministro basado en aerosol de instrucciones de reprogramación transcripcional codificadas por gRNA. En resumen, esta tesis proporciona herramientas novedosas para la activación transcripcional fuerte, ortogonal y programable en plantas, con una caja de herramientas ampliada para el suministro de los programas de activación.[CA] La Biologia Sintètica de Plantes té com objectiu redissenyar les plantes per que obtinguen característiques i funcionalitats innovadores mitjançant circuits reguladors ortogonals. Per arribar a aquest objectiu, s'han de desenvolupar noves ferramentes moleculars amb la capacitat d'interactuar amb factor endògens d'una manera potent i específica. CRISPR/Cas9 va sorgir com una ferramenta prometedora que combina la capacitat personalitzable d'unió al DNA, mitjançant la versió catalíticament inactivada de la proteïna Cas9 (dCas9), amb la possibilitat de fixar dominis autònoms de activació transcripcional (TADs) a la seua estructura per aconseguir una regulació específica de la expressió gènica. Els activadors transcripcionals programables (PTAs) poden actuar com a processadors específics, ortogonals i versàtils per al desenvolupament de nous circuits genètics a les plantes. Buscant dCas9-PTA optimitzats, es va realitzar una avaluació combinatòria de distintes arquitectures dCas9 amb un catàleg de diversos TAD. La millor ferramenta segons aquesta comparació, anomenada dCasEV2.1, es basa en la estratègia scRNA i la combinació del dominis d'activació EDLL i VPR amb un bucle multiplexable gRNA2.1, que es una versió mutada del gRNA2.0 descrit prèviament. En aquest treball, el activador programable dCasEV2.1 es va mostrar com una ferramenta potent i específica, aconseguint nivells d'activació majors que altes estratègies dCas9 disponibles en plantes. Es van observar taxes d'activació sense precedents dirigides a gens endògens en N. benthamiana, junt a una estricta especificitat en tot el genoma, indicant que aquesta ferramenta és adequada per a la regulació estricta de xarxes reguladores complexes. Como proba de concepte, se van dissenyar quatre programes d'activació per a diferent branques de la ruta dels flavonoides, cercant obtenir enriquiments metabòlics específics en fulles de N. benthamiana. L'anàlisi metabòlic de les fulles metabòlicament reprogramades mitjançant dCasEV2.1 va revelar un enriquiment selectiu del metabòlits diana i els seus derivats glicosilats que es correlacionen amb el programa d'activació emprat. Aquests resultats demostren que dCasEV2.1 és una ferramenta eficaç per a l'enginyeria metabòlica i un component clau als circuits genètics destinats a reprogramar els fluxos metabòlics. Finalment, en base a dCasEV2.1, desenvoluparem un sistema optimitzat de regulació de gens induïts per virus (VIGR) que utilitza un vector Potato Virus X (PVX) per al subministrament dels programes d'activació CRISPR codificats amb gRNA. Aquesta aproximació permet controlar el transcriptoma de la planta mitjançant l'aplicació sistèmica basada en aerosol de components CRISPR a plantes adultes. El nou sistema PVX-VIGR va produir una gran activació transcripcional en diversos gens diana endògens, inclosos tres factors de transcripció MYB-like seleccionats prèviament. Les activacions específiques de MYB conduïren a perfils metabòlics distintius, demostrant que les aplicacions potencials de la ferramenta dCasEV2.1 en plantes inclouen la obtenció de perfils metabòlics personalitzats emprant un subministrament basat en aerosol de instruccions de reprogramació transcripcional codificades per gRNA. En resum, aquesta tesis proporciona noves ferramentes per a l'activació transcripcional forta, ortogonal i programable en plantes, amb una caixa de ferramentes eixamplada per al subministraments dels programes d'activació.[EN] Plant Synthetic Biology aims to redesign plants to acquire novel traits and functionalities through orthogonal regulatory circuits. To achieve this goal, new molecular tools with the capacity of interacting with endogenous factors in a potent and specific manner must be developed. CRISPR/Cas9 emerged as promising tools which combine a customizable DNA-binding activity through the catalytically inactivated version of Cas9 protein (dCas9) with the possibility to anchor autonomous transcriptional activation domains (TADs) to its structure to achieve a specific regulation of the gene expression. The Programmable Transcriptional Activators (PTAs) could act as specific, orthogonal and versatile processor components in the development of new genetic circuits in plants. In search for optimized dCas9-PTAs, a combinatorial evaluation of different dCas9 architectures with a catalogue of various TADs was performed. The best resulting tool of this comparison, named dCasEV2.1, is based on the scRNA strategy and the combination of EDLL and VPR activation domains with a multiplexable gRNA2.1 loop, which is a mutated version of the previously described gRNA2.0. In this work, the dCasEV2.1 programable activator was proved to be a strong and specific tool, achieving higher activation rates than other available dCas9 strategies in plants. Unprecedented activation rates were observed targeting endogenous genes in N. benthamiana, accompanied by strict genome-wide specificity that makes this tool suitable to perform a tight regulation of complex regulatory networks. As a proof of concept, a design of four activation programs to activate different branches of the flavonoid pathway and obtain specific metabolic enrichments in N. benthamiana leaves was performed. The metabolic analysis on the dCasEV2.1 metabolically reprogrammed leaves revealed a selective enrichment of the targeted metabolites and their glycosylated derivatives that correlated with the activation program employed. These results demonstrate that dCasEV2.1 is a powerful tool for metabolic engineering and a key component in genetic circuits aimed at reprogramming metabolic fluxes. Finally, based on dCasEV2.1, we developed an optimized Viral Induced Gene Regulation (VIGR) system that makes use of a Potato Virus X (PVX) vector for the delivery of the gRNA-encoded CRISPR activation programs. This approach offers a way to control the plant transcriptome through a spray-based systemic delivery of CRISPR components to adult plants. The new PVX-VIGR system led to strong transcriptional activation in several endogenous target genes, including three selected MYB-like transcription factors. Specific MYB activations lead to distinctive metabolic profiles, showing that the potential applications of the dCasEV2.1 tool in plants include the obtention of custom metabolic profiles using a spray-based delivery of gRNA-encoded transcriptional reprogramming instructions. In sum, this thesis provides novel tools for strong, orthogonal and programmable transcriptional activation in plants, with an expanded toolbox for the delivery of the activation programs.Selma García, S. (2022). Development of CRISPR-based programmable transcriptional regulators and their applications in plants [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/185046TESI

On Time Synchronization Issues in Time-Sensitive Networks with Regulators and Nonideal Clocks

Flow reshaping is used in time-sensitive networks (as in the context of IEEE TSN and IETF Detnet) in order to reduce burstiness inside the network and to support the computation of guaranteed latency bounds. This is performed using per-flow regulators (such as the Token Bucket Filter) or interleaved regulators (as with IEEE TSN Asynchronous Traffic Shaping). Both types of regulators are beneficial as they cancel the increase of burstiness due to multiplexing inside the network. It was demonstrated, by using network calculus, that they do not increase the worst-case latency. However, the properties of regulators were established assuming that time is perfect in all network nodes. In reality, nodes use local, imperfect clocks. Time-sensitive networks exist in two flavours: (1) in non-synchronized networks, local clocks run independently at every node and their deviations are not controlled and (2) in synchronized networks, the deviations of local clocks are kept within very small bounds using for example a synchronization protocol (such as PTP) or a satellite based geo-positioning system (such as GPS). We revisit the properties of regulators in both cases. In non-synchronized networks, we show that ignoring the timing inaccuracies can lead to network instability due to unbounded delay in per-flow or interleaved regulators. We propose and analyze two methods (rate and burst cascade, and asynchronous dual arrival-curve method) for avoiding this problem. In synchronized networks, we show that there is no instability with per-flow regulators but, surprisingly, interleaved regulators can lead to instability. To establish these results, we develop a new framework that captures industrial requirements on clocks in both non-synchronized and synchronized networks, and we develop a toolbox that extends network calculus to account for clock imperfections.Comment: ACM SIGMETRICS 2020 Boston, Massachusetts, USA June 8-12, 202