Low-Cost Ultra-Wide Genotyping Using Roche/454 Pyrosequencing for Surveillance of HIV Drug Resistance

Background: Great efforts have been made to increase accessibility of HIV antiretroviral therapy (ART) in low and middle-income countries. The threat of wide-scale emergence of drug resistance could severely hamper ART scale-up efforts. Population-based surveillance of transmitted HIV drug resistance ensures the use of appropriate first-line regimens to maximize efficacy of ART programs where drug options are limited. However, traditional HIV genotyping is extremely expensive, providing a cost barrier to wide-scale and frequent HIV drug resistance surveillance. Methods/Results: We have developed a low-cost laboratory-scale next-generation sequencing-based genotyping method to monitor drug resistance. We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. Using this approach, we characterized drug resistance from plasma in 81 HIV infected individuals collected in Sao Paulo, Brazil. We describe the complexities of analyzing next-generation sequencing data and present a simplified open-source workflow to analyze drug resistance data. From this data, we identified drug resistance mutations in 20% of treatment naive individuals in our cohort, which is similar to frequencies identified using traditional genotyping in Brazilian patient samples. Conclusion: The developed ultra-wide sequencing approach described here allows multiplexing of at least 48 patient samples per sequencing run, 4 times more than the current genotyping method. This method is also 4-fold more sensitive (5% minimal detection frequency vs. 20%) at a cost 3-5 x less than the traditional Sanger-based genotyping method. Lastly, by using a benchtop next-generation sequencer (Roche/454 GS Junior), this approach can be more easily implemented in low-resource settings. This data provides proof-of-concept that next-generation HIV drug resistance genotyping is a feasible and low-cost alternative to current genotyping methods and may be particularly beneficial for in-country surveillance of transmitted drug resistance.

Studio di geometrie di antenne su pcb per trasmissione wireless ultra-wideband

La presente tesi tratta la progettazione e la simulazione via software di geometrie di antenne da realizzare direttamente su Printed Circuit Board (PCB) per schede di trasmissione dati wireless Ultra Wide Band. L’obiettivo principale di questo studio è la realizzazione di un prototipo per impieghi biomedici umani (ad esempio trasmissione di dati provenienti da un ECG). Lo scopo del lavoro svolto è quello di trovare la miglior soluzione di integrazione per un’antenna il più possibile compatta da realizzare poi direttamente sul substrato dove verrà stampato il circuito del trasmettitore stesso. L’antenna verrà quindi realizzata esclusivamente attraverso microstrisce conduttrici (le medesime che formeranno i collegamenti tra i vari componenti del circuito) prendendo in considerazione le grandezze parassite di ogni conduttore, quali resistenza, induttanza, capacità ecc. In conclusione, il circuito di trasmissione wireless completo di antenna sopra descritto è attualmente in fase di realizzazione e nel prossimo futuro verrà testato in laboratorio.

Analog mitigation of out of band strong interferers in wide band acquisition for multiband HF transmissions

It is clear that in the near future much broader transmissions in the HF band will replace part of the current narrow band links. Our personal view is that a real wide band signal is infeasible in this environment because the usage is typically very intensive and may suffer interferences from all over the world. Therefore, we envision that dynamic multiband transmissions may provide better satisfactory performance. From the very beginning, we observed that real links with our broadband transceiver suffered interferences out of our multiband but within the acquisition bandwidth that degrade the expected performance. Therefore, we concluded that a mitigation structure is required that operates on severely saturated signals as the interference may be of much higher power. In this paper we address a procedure based on Higher Order Crossings (HOC) statistics that are able to extract most of the signal structure in the case where the amplitude is severely distorted and allows the estimation of the interference carrier frequency to command a variable notch filter that mitigates its effect in the analog domain.

Photoconductivity and Electro-Optical Properties of Wide Band Gap Metal Oxides

The PhD activity described in this Thesis was focused on the study of metal-oxide wide-bandgap materials, aiming at fabricating new optoelectronic devices such as solar-blind UV photodetectors, high power electronics, and gas sensors. Photocurrent spectroscopy and DC photocurrent time evolution were used to investigate the performance of prototypes under different atmospheres, temperatures and excitation wavelengths (or dark conditions). Cathodoluminescence, absorption spectroscopy, XRD and SEM were used to assess structural, morphologic, electrical and optical properties of materials. This thesis is divided into two main sections, each describing the work done on a different metal-oxide semiconductor. 1) MOVPE-grown Ga2O3 thin films for UV solar-blind photodetectors and high power devices The semiconducting oxides, among them Ga2O3, have been employed for several decades as transparent conducting oxide (TCO) electrodes for fabrication of solar cells, displays, electronic, and opto-electronic devices. The interest was mainly confined to such applications, as these materials tend to grow intrinsically n-type, and attempts to get an effective p-type doping has consistently failed. The key requirements of TCO electrodes are indeed high electrical conductivity and good transparency, while crystallographic perfection is a minor issue. Furthermore, for a long period no high-quality substrates and epi-layers were available, which in turn impeded the development of a truly full-oxide electronics. Recently, Ga2O3 has attracted renewed interest, as large single crystals and high-quality homo- and hetero-epitaxial layers became available, which paved the way to novel application areas. Our research group spent the last two years in developing a low temperature (500-700°C) MOVPE growth procedure to obtain thin films of Ga2O3 on different substrates (Dept. of Physics and IMEM-CNR at UNIPR). We obtained a significant result growing on oriented sapphire epitaxial films of high crystalline, undoped, pure phase -Ga2O3 (hexagonal). The crystallographic properties of this phase were investigated by XRD, in order to clarify the lattice parameters of the hexagonal cell. First design and development of solar blind UV photodetectors based on -phase was carried out and the optoelectronic performance is evaluated by means of photocurrent spectroscopy. The UV-response is adequately fast and reliable to render this unusual phase a subject of great interest for future applications. The availability of a hexagonal phase of Ga2O3 stable up to 700°C, belonging to the same space group of gallium nitride, with high crystallinity and tunable electrical properties, is intriguing in view of the development of nitride-based devices, by taking advantage of the more favorable symmetry and epitaxial relationships with respect to the monoclinic β-phase. In addition, annealing at temperatures higher than 700°C demonstrate that the hexagonal phase converts totally in the monoclinic one. 2) ZnO nano-tetrapods: charge transport mechanisms and time-response in optoelectronic devices and sensors Size and morphology of ZnO at the nanometer scale play a key role in tailoring its physical and chemical properties. Thanks to the possibility of growing zinc oxide in a variety of different nanostructures, there is a great variety of applications, among which gas sensors, light emitting diodes, transparent conducting oxides, solar cells. Even if the operation of ZnO nanostructure-based devices has been recently demonstrated, the mechanisms of charge transport in these assembly is still under debate. The candidate performed an accurate investigation by photocurrent spectroscopy and DC-photocurrent time evolution of electrical response of both single-tetrapod and tetrapod-assembly devices. During the research done for this thesis, a thermal activation energy enables the performance of samples at high temperatures (above about 300°C). The energy barrier is related to the leg-to-leg interconnection in the assembly of nanotetrapods. Percolation mechanisms are responsible for both the very slow photo-response (minutes to hours or days) and the significant persistent photocurrent. Below the bandgap energy, electronic states were investigated but their contribution to the photocurrent are two-three order of magnitude lower than the band edge. Such devices are suitable for employ in photodetectors as well as in gas sensors, provided that the mechanism by which the photo-current is generated and gas adsorption on the surface modify the conductivity of the material are known.

Radio astronomy report; propagation through a disturbed ionosphere: effect upon range and angular resolution, Project Wide Band.

"RADC contract no. AF 30(602)-2077."

SAR imaging of buried objects from MoM modelled scattered field

Synthetic aperture radar (SAR) images of resonant buried objects are modelled in the presence of ground surface clutter. The method of moments (MoM) is used to model scattered fields from a resonant buried conductor and clutter is modelled as a bivariant Gaussian distribution. A diffraction stack SAR imaging technique is applied to the ultra-wideband waveforms to give a bipolar signal image. A number of examples have been computed to illustrate the combined effects of SAR processing with resonant targets and clutter. SAR images of different targets show differences which may facilitate target identification. To maximise the peak signal-to-clutter ratio, an image correlation technique is applied and the results are shown.

Estudo de viabilidade de utilização de VLC em infra-estruturas ITS baseadas em semáforos rodoviários a LEDs

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia de Electrónica e Telecomunicações

Transreceptor de faixa larga baseado em impulso de rádio para sensor sem fios de curta distância implementado em tecnologia CMOS

Dissertação para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores

Diseño de filtros transversales mediante el híbrido de 90º

Los filtros de microondas son uno de los elementos clave en el diseño de la mayoría de sistemas de RF que soportan servicios de telecomunicaciones modernos. Algunas de las aplicaciones actuales son, por ejemplo, los nuevos sistemas radar de banda ultra ancha (UWB – Ultra Wide Band) y sistemas de transmisión de servicios multimedia, donde se requieren dimensiones pequeñas del circuito, bajas pérdidas de inserción y una alta selectividad. Una de las tendencias que ha surgido como alternativa a las teorías clásicas de diseño de filtros, es el diseño de filtros basados en técnicas de señales interferentes, conocidos como filtros transversales. En esta memoria es muestra como diseñar un filtro transversal mediante el Híbrido de 90º y mediante el Híbrido de 90º con líneas acopladas, planteando 3 posibles soluciones de la ubicación de las líneas acopladas.

Dual carrier modulation demapping methods and performances for wireless USB

Dual Carrier Modulation (DCM) was chosen as the higher data rate modulation scheme for MB-OFDM (Multiband Orthogonal Frequency Division Multiplexing) in the UWB (Ultra-Wide Band) radio platform ECMA-368. ECMA-368 has been chosen as the physical implementation for high data rate Wireless USB (W-USB) and Bluetooth 3.0. In this paper, different demapping methods for the DCM demapper are presented, being Soft Bit, Maximum Likely (ML) Soft Bit and Log Likelihood Ratio (LLR). Frequency diversity and Channel State Information (CSI) are further techniques to enhance demapping methods. The system performance for those DCM demapping methods simulated in realistic multi-path environments are provided and compared.

A complete CMOS UWB timed-array transmitter with a 3D Vivaldi antenna array for electronic high-resolution beam spatial scanning

We present a new Ultra Wide Band (UWB) Timed- Array Transmitter System with Beamforming capability for high-resolution remote acquisition of vital signals. The system consists of four identical channels, where each is formed of a serial topology with three modules: programmable delay circuit (PDC or τ), a novel UWB 5th Gaussian Derivative order pulse generator circuit (PG), and a planar Vivaldi antenna. The circuit was designed using 0.18μm CMOS standard process and the planar antenna array was designed with filmconductor on Rogers RO3206 substrate. Spice simulations results showed the pulse generation with 104 mVpp amplitude and 500 ps width. The power consumption is 543 μW, and energy consumption 0.27 pJ per pulse using a 2V power supply at a pulse repetition rate (PRR) of 100 MHz. Electromagnetic simulations results, using CST Microwave (MW) Studio 2011, showed the main lobe radiation with a gain maximum of 13.2 dB, 35.5º x 36.7º angular width, and a beam steering between 17º and -11º for azimuthal (θ) angles and 17º and -18º for elevation (φ) angles at the center frequency of 6 GHz

Tracking di target multipli in reti di sensori radar

Viene proposta una possibile soluzione al problema del tracking multitarget, tramite una rete di sensori radar basata su tecnoligia ultra wide-band. L'area sorvegliata ha una superficie pari a 100 metri quadri e all'interno di essa si vuole tracciare la traiettoria di più persone.

Analisi di algoritmi per reti di sensori radar uwb basati su misure sperimentali

In un sistema radar è fondamentale rilevare, riconoscere e cercare di seguire il percorso di un eventuale intruso presente in un’area di osservazione al fine ultimo della sicurezza, sia che si consideri l’ambito militare, che anche quello civile. A questo proposito sono stati fatti passi avanti notevoli nella creazione e sviluppo di sistemi di localizzazione passiva che possano rilevare un target (il quale ha come unica proprietà quella di riflettere un segnale inviato dal trasmettitore), in modo che esso sia nettamente distinto rispetto al caso di assenza dell’intruso stesso dall’area di sorveglianza. In particolare l’ultilizzo di Radar Multistatico (ossia un trasmettitore e più ricevitori) permette una maggior precisione nel controllo dell’area d’osservazione. Tra le migliori tecnologie a supporto di questa analisi vi è l’UWB (Ultra Wide-Band), che permette di sfruttare una banda molto grande con il riscontro di una precisione che può arrivare anche al centimetro per scenari in-door. L’UWB utilizza segnali ad impulso molto brevi, a banda larga e che quindi permettono una risoluzione elevata, tanto da consentire, in alcune applicazioni, di superare i muri, rimuovendo facilmente gli elementi presenti nell’ambiente, ossia il clutter. Quindi è fondamentale conoscere algoritmi che permettano la detection ed il tracking del percorso compiuto dal target nell’area. In particolare in questa tesi vengono elaborati nuovi algoritmi di Clustering del segnale ricevuto dalla riflessione sull’intruso, utilizzati al fine di migliorare la visualizzazione dello stesso in post-processing. Infine questi algoritmi sono stati anche implementati su misure sperimentali attuate tramite nodi PulsOn 410 Time Domain, al fine ultimo della rilevazione della presenza di un target nell’area di osservazione dei nodi.

UWB radar sensor networks: Detection algorithms design and experimental analysis

In the last years radar sensor networks for localization and tracking in indoor environment have generated more and more interest, especially for anti-intrusion security systems. These networks often use Ultra Wide Band (UWB) technology, which consists in sending very short (few nanoseconds) impulse signals. This approach guarantees high resolution and accuracy and also other advantages such as low price, low power consumption and narrow-band interference (jamming) robustness. In this thesis the overall data processing (done in MATLAB environment) is discussed, starting from experimental measures from sensor devices, ending with the 2D visualization of targets movements over time and focusing mainly on detection and localization algorithms. Moreover, two different scenarios and both single and multiple target tracking are analyzed.

Sviluppo di una applicazione di test per un sistema di localizzazione

La tesi consiste nella descrizione di una applicazione in Java atta a eseguire test e simulazioni di un sistema di localizzazione in radiofrequenza. Viene descritta l'interfaccia e le funzionalità.