Paulo Lopes

Bio-microfluidic platform for gold nanoprobe based DNA detection--application to Mycobacterium tuberculosis.

We have projected and fabricated a microfluidic platform for DNA sensing that makes use of an optical colorimetric detection method based on gold nanoparticles. The platform was fabricated using replica moulding technology in PDMS patterned by high-aspect-ratio SU-8 moulds. Biochips of various geometries were tested and evaluated in order to find out the most efficient architecture, and the rational for design, microfabrication and detection performance is presented. The best biochip configuration has been successfully applied to the DNA detection of Mycobacterium tuberculosis using only 3 µl on DNA solution (i.e. 90 ng of target DNA), therefore a 20-fold reduction of reagents volume is obtained when compared with the actual state of the art.

Single nucleotide polymorphism detection using gold nanoprobes and bio‐microfluidic platform with embedded microlenses

The use of microfluidics platforms combined with the optimal optical properties of gold nanoparticles has found plenty of application in molecular biosensing. This paper describes a bio‐microfluidic platform coupled to a non‐cross‐linking colorimetric gold nanoprobe assay to detect a single nucleotide polymorphism associated with increased risk of obesity fat‐mass and obesity‐associated (FTO) rs9939609 (Carlos et al., 2014). The system enabled significant discrimination between positive and negative assays using a target DNA concentration of 5 ng/µL below the limit of detection of the conventionally used microplate reader (i.e., 15 ng/µL) with 10 times lower solution volume (i.e., 3 µL). A set of optimization of our previously reported bio‐microfluidic platform (Bernacka‐Wojcik et al., 2013) resulted in a 160% improvement of colorimetric analysis results. Incorporation of planar microlenses increased 6 times signal‐to‐loss ratio reaching the output optical fiber improving by 34% the colorimetric analysis of gold nanoparticles, while the implementation of an optoelectronic acquisition system yielded increased accuracy and reduced noise. The microfluidic chip was also integrated with a miniature fiber spectrometer to analyze the assays’ colorimetric changes and also the LEDs transmission spectra when illuminating through various solutions. Furthermore, by coupling an optical microscope to a digital camera with a long exposure time (30 s), we could visualise the different scatter intensities of gold nanoparticles within channels following salt addition. These intensities correlate well to the expected difference in aggregation between FTO positive (none to small aggregates) and negative samples (large aggregates). Biotechnol. Bioeng. 2015;112: 1210–1219.

Methodologies for Network Topology Discovery and Detection of MAC and IP Spoofing Attacks

The sustained growth and innovation of information technologies, combined with the resulting complexity in communication infrastructures, has pushed the network into an increasingly critical role within organizations of all sizes. In order to assure that operations are aligned with the business needs, monitoring and management practices are gaining importance across all network domains. As a result, network managers need the best possible tools for managing the network infrastructure and assuring that it will play its essential part in supporting the organization in a reliable, predictable, efficient and cost-effective manner. This paper proposes several algorithms that will be used on an integrated network monitoring open-source tool: an algorithm for network topology discovery and two algorithms for the detection and blocking of MAC and IP spoofing network attacks. The proposed approaches are based on the SNMP protocol, which is currently supported by most network devices, and the performance tests that were made show that they are effective, reliable and very easy to deploy in real operating scenarios.

Multifunctional microfluidic chip for optical nanoprobe based RNA detection – application to Chronic Myeloid Leukemia

Many diseases have their treatment options narrowed and end up being fatal if detected during later stages. As a consequence, point-of-care devices have an increasing importance for routine screening applications in the health sector due to their portability, fast analyses and decreased cost. For that purpose, a multifunctional chip was developed and tested using gold nanoprobes to perform RNA optical detection inside a microfluidic chip without the need of molecular amplification steps. As a proof-of-concept, this device was used for the rapid detection of chronic myeloid leukemia, a hemato-oncological disease that would benefit from early stage diagnostics and screening tests. The chip passively mixed target RNA from samples, gold nanoprobes and saline solution to infer a result from their final colorimetric properties. An optical fiber network was used to evaluate its transmitted spectra inside the chip. Trials provided accurate output results within 3 min, yielding signal-to-noise ratios up to 9 dB. When compared to actual state-of-art screening techniques of chronic myeloid leukemia, these results were, at microscale, at least 10 times faster than the reported detection methods for chronic myeloid leukemia. Concerning point-of-care applications, this work paves the way for other new and more complex versions of optical based genosensors.

Low-cost temperature measurement using LPG and total transmitted power

In this paper we present an extremely low-cost system for temperature measurement using Long Period Grating sensors (LPG) in such an unusual way that prevents experimenters and end users from utilizing OSA which are extremely expensive, thus saving tenths of thousand of euros. The basic idea is using total power measurement instead of wavelength shift for which a low-cost power meter is sufficient to precisely measure temperature. When certain fabrication conditions are met, the total transmitted power by the LPG has a monotonous behavior with temperature, making it a good and cost-effective sensor. Its sensitivity is approximately linear with 4.162 μW/°C and the uncertainty is about 1μW with a potential resolution of 0.24 °C. The results obtained so far show that this temperature sensor has a good performance and has many advantages over the standard FBG and LPG ones: exhibit short response time, portability and low cost.

Experimentations for a plastic optical pH sensor

In this paper we present the design of a transmissive pH sensor using plastic optical fiber (POF) and materials to entrap universal indicator. This sensor presents advantages over commercial ones namely lightweight, portability and low cost.

Sensitivity and reliability of LPG Temperature sensors using total transmitted Power

In this paper we present a reliable temperature sensor using total transmitted power by a specially tuned LPG fabricated in a high resolution electromechanical system.

Design and characterization of a plastic optical fiber pH sensor

In this paper are present the design and characterization of a pH sensor using plastic optical fiber (POF) technology and a material produced by the sol-gel process with TEOS (tetraethyl orthosilicate) to immobilize universal indicator of pH (comprised of Thymol Blue, Methyl Red, Bromothymol Blue and Phenolphthalein) inside the silica matrix. This matrix is positioned between two extensions of plastic optical fiber tightly positioned at each side with both fibers aligned and sharing a common optical axis. This set will work as a pH sensor since the matrix embedded with indicator and in the presence of a solution (basic or acid solution) will change the optical transmittance properties. The optical source is a superluminescent white LED and the receiver is a photodiode having a good and linear responsivity in the visible spectrum. This pH sensitive matrix has large pores which allow the diffusion of the surrounding fluid molecules into the matrix and thus the close contact of these to the indicator molecules. This contact causes the change of color of the whole matrix allowing proper colorimetric detection by the photodiode. This variation of color associated with the detector wavelength linear response is the base of operation of the proposed device. This pH sensor presents many advantages over the standard and commercial pH meters namely, lightweight, portability and a low cost.

Dual-peak wide range temperature LPG sensor fabricated with a CO2 Laser and a high resolution system

In this work we present a specially designed high resolution electromechanical system to be used with a cw CO2 Laser to fabricate high quality long period grating sensors (LPG). We also describe the experiments carried out to measure the resulting enhanced transmission spectra of the fabricated LPG and to measure their response as temperature sensors. Sharp and well pronounced spectral peaks were obtained reaching 30dB. Sensitivity values of 118 pm/°C were easily obtained without any fiber coating. Wide range temperature coverage (20 - 600 °C) was attained by making use of two distinctive peaks of the transmission spectrum.