Digital signal processing and artificial intelligence for the automated classification of food allergy

As a by-product of the ‘information revolution’ which is currently unfolding, lifetimes of man (and indeed computer) hours are being allocated for the automated and intelligent interpretation of data. This is particularly true in medical and clinical settings, where research into machine-assisted diagnosis of physiological conditions gains momentum daily. Of the conditions which have been addressed, however, automated classification of allergy has not been investigated, even though the numbers of allergic persons are rising, and undiagnosed allergies are most likely to elicit fatal consequences. On the basis of the observations of allergists who conduct oral food challenges (OFCs), activity-based analyses of allergy tests were performed. Algorithms were investigated and validated by a pilot study which verified that accelerometer-based inquiry of human movements is particularly well-suited for objective appraisal of activity. However, when these analyses were applied to OFCs, accelerometer-based investigations were found to provide very poor separation between allergic and non-allergic persons, and it was concluded that the avenues explored in this thesis are inadequate for the classification of allergy. Heart rate variability (HRV) analysis is known to provide very significant diagnostic information for many conditions. Owing to this, electrocardiograms (ECGs) were recorded during OFCs for the purpose of assessing the effect that allergy induces on HRV features. It was found that with appropriate analysis, excellent separation between allergic and nonallergic subjects can be obtained. These results were, however, obtained with manual QRS annotations, and these are not a viable methodology for real-time diagnostic applications. Even so, this was the first work which has categorically correlated changes in HRV features to the onset of allergic events, and manual annotations yield undeniable affirmation of this. Fostered by the successful results which were obtained with manual classifications, automatic QRS detection algorithms were investigated to facilitate the fully automated classification of allergy. The results which were obtained by this process are very promising. Most importantly, the work that is presented in this thesis did not obtain any false positive classifications. This is a most desirable result for OFC classification, as it allows complete confidence to be attributed to classifications of allergy. Furthermore, these results could be particularly advantageous in clinical settings, as machine-based classification can detect the onset of allergy which can allow for early termination of OFCs. Consequently, machine-based monitoring of OFCs has in this work been shown to possess the capacity to significantly and safely advance the current state of clinical art of allergy diagnosis

Interaction of additive and quantization noises in digital PLLs

Phase-locked loops (PLLs) are a crucial component in modern communications systems. Comprising of a phase-detector, linear filter, and controllable oscillator, they are widely used in radio receivers to retrieve the information content from remote signals. As such, they are capable of signal demodulation, phase and carrier recovery, frequency synthesis, and clock synchronization. Continuous-time PLLs are a mature area of study, and have been covered in the literature since the early classical work by Viterbi [1] in the 1950s. With the rise of computing in recent decades, discrete-time digital PLLs (DPLLs) are a more recent discipline; most of the literature published dates from the 1990s onwards. Gardner [2] is a pioneer in this area. It is our aim in this work to address the difficulties encountered by Gardner [3] in his investigation of the DPLL output phase-jitter where additive noise to the input signal is combined with frequency quantization in the local oscillator. The model we use in our novel analysis of the system is also applicable to another of the cases looked at by Gardner, that is the DPLL with a delay element integrated in the loop. This gives us the opportunity to look at this system in more detail, our analysis providing some unique insights into the variance `dip' seen by Gardner in [3]. We initially provide background on the probability theory and stochastic processes. These branches of mathematics are the basis for the study of noisy analogue and digital PLLs. We give an overview of the classical analogue PLL theory as well as the background on both the digital PLL and circle map, referencing the model proposed by Teplinsky et al. [4, 5]. For our novel work, the case of the combined frequency quantization and noisy input from [3] is investigated first numerically, and then analytically as a Markov chain via its Chapman-Kolmogorov equation. The resulting delay equation for the steady-state jitter distribution is treated using two separate asymptotic analyses to obtain approximate solutions. It is shown how the variance obtained in each case matches well to the numerical results. Other properties of the output jitter, such as the mean, are also investigated. In this way, we arrive at a more complete understanding of the interaction between quantization and input noise in the first order DPLL than is possible using simulation alone. We also do an asymptotic analysis of a particular case of the noisy first-order DPLL with delay, previously investigated by Gardner [3]. We show a unique feature of the simulation results, namely the variance `dip' seen for certain levels of input noise, is explained by this analysis. Finally, we look at the second-order DPLL with additive noise, using numerical simulations to see the effects of low levels of noise on the limit cycles. We show how these effects are similar to those seen in the noise-free loop with non-zero initial conditions.

Design of digital differentiators

A digital differentiator simply involves the derivation of an input signal. This work includes the presentation of first-degree and second-degree differentiators, which are designed as both infinite-impulse-response (IIR) filters and finite-impulse-response (FIR) filters. The proposed differentiators have low-pass magnitude response characteristics, thereby rejecting noise frequencies higher than the cut-off frequency. Both steady-state frequency-domain characteristics and Time-domain analyses are given for the proposed differentiators. It is shown that the proposed differentiators perform well when compared to previously proposed filters. When considering the time-domain characteristics of the differentiators, the processing of quantized signals proved especially enlightening, in terms of the filtering effects of the proposed differentiators. The coefficients of the proposed differentiators are obtained using an optimization algorithm, while the optimization objectives include magnitude and phase response. The low-pass characteristic of the proposed differentiators is achieved by minimizing the filter variance. The low-pass differentiators designed show the steep roll-off, as well as having highly accurate magnitude response in the pass-band. While having a history of over three hundred years, the design of fractional differentiator has become a ‘hot topic’ in recent decades. One challenging problem in this area is that there are many different definitions to describe the fractional model, such as the Riemann-Liouville and Caputo definitions. Through use of a feedback structure, based on the Riemann-Liouville definition. It is shown that the performance of the fractional differentiator can be improved in both the frequency-domain and time-domain. Two applications based on the proposed differentiators are described in the thesis. Specifically, the first of these involves the application of second degree differentiators in the estimation of the frequency components of a power system. The second example concerns for an image processing, edge detection application.

Error recovery in cyberphysical digital microfluidic biochips

Droplet-based digital microfluidics technology has now come of age, and software-controlled biochips for healthcare applications are starting to emerge. However, today's digital microfluidic biochips suffer from the drawback that there is no feedback to the control software from the underlying hardware platform. Due to the lack of precision inherent in biochemical experiments, errors are likely during droplet manipulation; error recovery based on the repetition of experiments leads to wastage of expensive reagents and hard-to-prepare samples. By exploiting recent advances in the integration of optical detectors (sensors) into a digital microfluidics biochip, we present a physical-aware system reconfiguration technique that uses sensor data at intermediate checkpoints to dynamically reconfigure the biochip. A cyberphysical resynthesis technique is used to recompute electrode-actuation sequences, thereby deriving new schedules, module placement, and droplet routing pathways, with minimum impact on the time-to-response. © 2012 IEEE.

Chemical and biological applications of digital-microfluidic devices

The advent of digital microfluidic lab-on-a-chip (LoC) technology offers a platform for developing diagnostic applications with the advantages of portability, reduction of the volumes of the sample and reagents, faster analysis times, increased automation, low power consumption, compatibility with mass manufacturing, and high throughput. Moreover, digital microfluidics is being applied in other areas such as airborne chemical detection, DNA sequencing by synthesis, and tissue engineering. In most diagnostic and chemical-detection applications, a key challenge is the preparation of the analyte for presentation to the on-chip detection system. Thus, in diagnostics, raw physiological samples must be introduced onto the chip and then further processed by lysing blood cells and extracting DNA. For massively parallel DNA sequencing, sample preparation can be performed off chip, but the synthesis steps must be performed in a sequential on-chip format by automated control of buffers and nucleotides to extend the read lengths of DNA fragments. In airborne particulate-sampling applications, the sample collection from an air stream must be integrated into the LoC analytical component, which requires a collection droplet to scan an exposed impacted surface after its introduction into a closed analytical section. Finally, in tissue-engineering applications, the challenge for LoC technology is to build high-resolution (less than 10 microns) 3D tissue constructs with embedded cells and growth factors by manipulating and maintaining live cells in the chip platform. This article discusses these applications and their implementation in digital-microfluidic LoC platforms. © 2007 IEEE.

Magnetophoretic circuits for digital control of single particles and cells.

The ability to manipulate small fluid droplets, colloidal particles and single cells with the precision and parallelization of modern-day computer hardware has profound applications for biochemical detection, gene sequencing, chemical synthesis and highly parallel analysis of single cells. Drawing inspiration from general circuit theory and magnetic bubble technology, here we demonstrate a class of integrated circuits for executing sequential and parallel, timed operations on an ensemble of single particles and cells. The integrated circuits are constructed from lithographically defined, overlaid patterns of magnetic film and current lines. The magnetic patterns passively control particles similar to electrical conductors, diodes and capacitors. The current lines actively switch particles between different tracks similar to gated electrical transistors. When combined into arrays and driven by a rotating magnetic field clock, these integrated circuits have general multiplexing properties and enable the precise control of magnetizable objects.

A LabVIEW Platform for Preclinical Imaging Using Digital Subtraction Angiography and Micro-CT.

CT and digital subtraction angiography (DSA) are ubiquitous in the clinic. Their preclinical equivalents are valuable imaging methods for studying disease models and treatment. We have developed a dual source/detector X-ray imaging system that we have used for both micro-CT and DSA studies in rodents. The control of such a complex imaging system requires substantial software development for which we use the graphical language LabVIEW (National Instruments, Austin, TX, USA). This paper focuses on a LabVIEW platform that we have developed to enable anatomical and functional imaging with micro-CT and DSA. Our LabVIEW applications integrate and control all the elements of our system including a dual source/detector X-ray system, a mechanical ventilator, a physiological monitor, and a power microinjector for the vascular delivery of X-ray contrast agents. Various applications allow cardiac- and respiratory-gated acquisitions for both DSA and micro-CT studies. Our results illustrate the application of DSA for cardiopulmonary studies and vascular imaging of the liver and coronary arteries. We also show how DSA can be used for functional imaging of the kidney. Finally, the power of 4D micro-CT imaging using both prospective and retrospective gating is shown for cardiac imaging.

Developing Quantitative Methodologies for the Digital Humanities: A Case Study of 20th Century American Commentary on Russian Literature

Using scientific methods in the humanities is at the forefront of objective literary analysis. However, processing big data is particularly complex when the subject matter is qualitative rather than numerical. Large volumes of text require specialized tools to produce quantifiable data from ideas and sentiments. Our team researched the extent to which tools such as Weka and MALLET can test hypotheses about qualitative information. We examined the claim that literary commentary exists within political environments and used US periodical articles concerning Russian literature in the early twentieth century as a case study. These tools generated useful quantitative data that allowed us to run stepwise binary logistic regressions. These statistical tests allowed for time series experiments using sea change and emergency models of history, as well as classification experiments with regard to author characteristics, social issues, and sentiment expressed. Both types of experiments supported our claim with varying degrees, but more importantly served as a definitive demonstration that digitally enhanced quantitative forms of analysis can apply to qualitative data. Our findings set the foundation for further experiments in the emerging field of digital humanities.

Estudio del maíz blanco gigante del Cuzco (MBGC) con denominación de origen bajo la nueva economía institucional : situación actual, limitantes y estrategias

La producción mundial de maíz en general tiene carácter de ser un producto commodity, con grandes volúmenes, precios altos y homogéneos. Pero en Perú hoy en día surge la necesidad de competir globalmente, con productos especiality, con pocos volúmenes y altamente diferenciados. Dicha estrategia es aplicada por el Perú con el Maíz Blanco Gigante, presentando ventaja comparativa a nivel de otras variedades de maíz, al poseer características únicas en relación al lugar de origen y prácticas culturales que se han mantenido en su cultivo a través del tiempo. Es por ello que se da reconocimiento y certificación como DO en el año 2005, como Maíz Blanco Gigante del Cusco, presentando tendencias de exportación a partir de dicho año. La investigación se enfoca al estudio de la situación actual del MBGC como DO bajo la Nueva Economía Institucional (NEI). Los resultados del estudio indican que la conexión institucional presenta desatinos, los organismos que dieron inicio al proceso de la DO se encuentran descoordinados, con ausencia de medidas de control. Ello ha ocasionado un débil enforcement en las reglas de juego y por ende en el marco institucional, afectando la imagen, posicionamiento y falencias a nivel de la cadena del MBGC. Se recomienda definir políticas y estrategias de uso de la DO, con miras a establecer mesas de diálogo sobre la participación (promoción, normativa y/o fiscalizadora), de los entes públicos como INDECOPI, Gobierno Regional, Gobierno Local con respecto a la DO del MBGC y sus características particulares como bien público a fin de dinamizar las inversiones, comercio y mantener la ventaja competitiva.

El mercado de carbono y el mecanismo de desarrollo limpio : caso Granja Tres Arroyos S.A. : un análisis desde la Nueva Economía Institucional

El calentamiento global consiste en el aumento de la temperatura de la tierra debido a la acumulación de los gases de efecto invernadero (GEI) en la atmósfera. Estos gases son producidos por actividades de generación de energía, el transporte, el uso del suelo, la industria y el manejo de los residuos. El aumento de GEI en la atmósfera provoca cambios climáticos e impactos en un sinfín de actividades humanas, en la productividad de la agricultura y ganadería, en la infraestructura y turismo, y también daños en la salud. La comunidad científica considera que el aumento de la temperatura para el fin del siglo debería ubicarse en los 2° C, para de esta forma poder limitar los impactos del cambio climático. Ello implicaría restringir las concentraciones de los GEI en valores cercanos a los 450 ppm (partes por millón). El problema económico del cambio climático subyace en que las emisiones de GEI constituyen una externalidad global. Una externalidad ocurre cuando la producción o consumo de un bien afecta a terceros que no participan directamente en su producción, venta o compra. Cuando hay presencia de externalidades, los precios de mercado no reflejan todos los costos ni beneficios sociales asociados a la producción de un bien. En el caso puntual del cambio climático, los emisores de GEI no asumen el costo de emitir gases a la atmósfera. Existen diferentes instrumentos de política ambiental que influyen en la percepción del recurso ambiental por parte del agente económico y que por ende, se reflejan en las decisiones económicas que ellos toman. Todos ellos tienen por objetivo asignar un precio/costo al recurso ambiental. El objetivo de los mercados de emisiones es asignar un precio al carbono. En ellos, se intercambian derechos a emitir cierta cantidad de GEI. El mecanismo de desarrollo limpio (MDL) es un instrumento de mercado definido en el Acuerdo de Marrakech bajo el marco institucional del Protocolo de Kyoto (PK). El MDL establece que un país Anexo I (país desarrollado), con compromisos de reducción de emisiones, invierta en proyectos de reducción o captación de emisiones en un país No Anexo I (país en desarrollo sin compromisos de reducción), mediante la compra de reducciones certificadas de emisiones (RCEs) generados a partir de la implementación de los proyectos. Argentina ratificó el PK a través de la ley nacional 25.438 en el 2001. Como el país se encuentra comprendido en las Partes No Anexo I, sólo puede participar como país anfitrión de un proyecto MDL y ser oferente de RCEs. Hasta la fecha, Argentina desarrolló 65 proyectos que se encuentran en distinta etapa de aprobación nacional o registro internacional. La mayoría corresponden a proyectos vinculados con rellenos sanitarios y energías. Bajo este marco de desarrollo en el país, resulta valiosa la exploración de un caso implementado en la Argentina. El objetivo de la investigación consiste en analizar el mercado de carbono a través del mecanismo de desarrollo limpio y su implementación en una empresa agroindustrial argentina, Granja Tres Arroyos S.A., bajo el enfoque teórico de la Nueva Economía y los Negocios Agroalimentarios.

Hierbas Aromáticas, medicinales y condimentarias en Colombia : análisis del caso C.I. Organic Aromatic S.A. desde la perspectiva de la nueva economía institucional

Las hierbas aromáticas han tenido en la última década un auge mundial y su demanda cada vez se incrementa más. En Colombia la producción y exportación de estas hierbas viene en aumento. En los últimos 4 años la exportación colombiana creció en 142 por ciento y el principal país de destino fue Estados Unidos a donde se exporto el 74 por ciento de las hierbas aromáticas. En este momento la tendencia del mercado mundial, es hacia los productos orgánicos o limpios, así que algunos productores se han dedicado a buscar los mecanismos para generar producciones y procesos con certificados orgánicos, para acceder a los mercados demandantes. Estas certificaciones son bastante exigentes y requieren un cambio y adaptación de las organizaciones, además de una fuerte inversión económica. El objetivo general de este trabajo es estudiar por medio del caso de la empresa colombiana C.I. Organic Aromatic S.A. la forma de adaptación a la demanda creciente del nuevo mercado internacional de hierbas aromáticas. Se realiza un análisis estructural discreto para el sector y de estar forma comprender el marco general donde se mueve la empresa. Al igual, se describe la empresa y su funcionamiento, los puntos críticos de la misma y de las transacciones que realiza. La cadena del sector esta descrita en el trabajo, los principales actores son: los proveedores, los productores donde se diferencian los pequeños de los medianos y grandes (los grandes productores son los exportadores de la cadena), los importadores o mayoristas, los transformadores, los minoristas, supermercados o tiendas especializadas y por último el cliente final, que cada vez más busca este tipo de productos por salud. C.I. Organic Aromatic S.A., es una empresa dedicada a la producción 100 por ciento orgánica y exportación de hierbas aromáticas y culinarias. La empresa tiene certificación de producto 100 por orgánico, buenas prácticas de manejo y certificación ISO entre otros. Llevan 7 años de funcionamiento, pero con esta razón social trabajan desde 2012 cuando decidieron exportar directamente a Estados Unidos y convertirse en C.I. (comercializadora internacional). Para disminuir la incertidumbre se integran verticalmente hacia adelante, bajo la marca Exotic Organic Herbs, quienes están ubicados en Miami, para manejar la logística de la importación en Estados Unidos.

El mercado de carbono y el mecanismo de desarrollo limpio : caso Granja Tres Arroyos S.A. : un análisis desde la Nueva Economía Institucional

El calentamiento global consiste en el aumento de la temperatura de la tierra debido a la acumulación de los gases de efecto invernadero (GEI) en la atmósfera. Estos gases son producidos por actividades de generación de energía, el transporte, el uso del suelo, la industria y el manejo de los residuos. El aumento de GEI en la atmósfera provoca cambios climáticos e impactos en un sinfín de actividades humanas, en la productividad de la agricultura y ganadería, en la infraestructura y turismo, y también daños en la salud. La comunidad científica considera que el aumento de la temperatura para el fin del siglo debería ubicarse en los 2° C, para de esta forma poder limitar los impactos del cambio climático. Ello implicaría restringir las concentraciones de los GEI en valores cercanos a los 450 ppm (partes por millón). El problema económico del cambio climático subyace en que las emisiones de GEI constituyen una externalidad global. Una externalidad ocurre cuando la producción o consumo de un bien afecta a terceros que no participan directamente en su producción, venta o compra. Cuando hay presencia de externalidades, los precios de mercado no reflejan todos los costos ni beneficios sociales asociados a la producción de un bien. En el caso puntual del cambio climático, los emisores de GEI no asumen el costo de emitir gases a la atmósfera. Existen diferentes instrumentos de política ambiental que influyen en la percepción del recurso ambiental por parte del agente económico y que por ende, se reflejan en las decisiones económicas que ellos toman. Todos ellos tienen por objetivo asignar un precio/costo al recurso ambiental. El objetivo de los mercados de emisiones es asignar un precio al carbono. En ellos, se intercambian derechos a emitir cierta cantidad de GEI. El mecanismo de desarrollo limpio (MDL) es un instrumento de mercado definido en el Acuerdo de Marrakech bajo el marco institucional del Protocolo de Kyoto (PK). El MDL establece que un país Anexo I (país desarrollado), con compromisos de reducción de emisiones, invierta en proyectos de reducción o captación de emisiones en un país No Anexo I (país en desarrollo sin compromisos de reducción), mediante la compra de reducciones certificadas de emisiones (RCEs) generados a partir de la implementación de los proyectos. Argentina ratificó el PK a través de la ley nacional 25.438 en el 2001. Como el país se encuentra comprendido en las Partes No Anexo I, sólo puede participar como país anfitrión de un proyecto MDL y ser oferente de RCEs. Hasta la fecha, Argentina desarrolló 65 proyectos que se encuentran en distinta etapa de aprobación nacional o registro internacional. La mayoría corresponden a proyectos vinculados con rellenos sanitarios y energías. Bajo este marco de desarrollo en el país, resulta valiosa la exploración de un caso implementado en la Argentina. El objetivo de la investigación consiste en analizar el mercado de carbono a través del mecanismo de desarrollo limpio y su implementación en una empresa agroindustrial argentina, Granja Tres Arroyos S.A., bajo el enfoque teórico de la Nueva Economía y los Negocios Agroalimentarios.