Federated architecture for biomedical data integration

The last decades have been characterized by a continuous adoption of IT solutions in the healthcare sector, which resulted in the proliferation of tremendous amounts of data over heterogeneous systems. Distinct data types are currently generated, manipulated, and stored, in the several institutions where patients are treated. The data sharing and an integrated access to this information will allow extracting relevant knowledge that can lead to better diagnostics and treatments. This thesis proposes new integration models for gathering information and extracting knowledge from multiple and heterogeneous biomedical sources. The scenario complexity led us to split the integration problem according to the data type and to the usage specificity. The first contribution is a cloud-based architecture for exchanging medical imaging services. It offers a simplified registration mechanism for providers and services, promotes remote data access, and facilitates the integration of distributed data sources. Moreover, it is compliant with international standards, ensuring the platform interoperability with current medical imaging devices. The second proposal is a sensor-based architecture for integration of electronic health records. It follows a federated integration model and aims to provide a scalable solution to search and retrieve data from multiple information systems. The last contribution is an open architecture for gathering patient-level data from disperse and heterogeneous databases. All the proposed solutions were deployed and validated in real world use cases.

Characterization of Non-linear Polymer Properties to Predict Process Induced Warpage and Residual Stress of Electronic Packages

Nonlinear thermo-mechanical properties of advanced polymers are crucial to accurate prediction of the process induced warpage and residual stress of electronics packages. The Fiber Bragg grating (FBG) sensor based method is advanced and implemented to determine temperature and time dependent nonlinear properties. The FBG sensor is embedded in the center of the cylindrical specimen, which deforms together with the specimen. The strains of the specimen at different loading conditions are monitored by the FBG sensor. Two main sources of the warpage are considered: curing induced warpage and coefficient of thermal expansion (CTE) mismatch induced warpage. The effective chemical shrinkage and the equilibrium modulus are needed for the curing induced warpage prediction. Considering various polymeric materials used in microelectronic packages, unique curing setups and procedures are developed for elastomers (extremely low modulus, medium viscosity, room temperature curing), underfill materials (medium modulus, low viscosity, high temperature curing), and epoxy molding compound (EMC: high modulus, high viscosity, high temperature pressure curing), most notably, (1) zero-constraint mold for elastomers; (2) a two-stage curing procedure for underfill materials and (3) an air-cylinder based novel setup for EMC. For the CTE mismatch induced warpage, the temperature dependent CTE and the comprehensive viscoelastic properties are measured. The cured cylindrical specimen with a FBG sensor embedded in the center is further used for viscoelastic property measurements. A uni-axial compressive loading is applied to the specimen to measure the time dependent Young’s modulus. The test is repeated from room temperature to the reflow temperature to capture the time-temperature dependent Young’s modulus. A separate high pressure system is developed for the bulk modulus measurement. The time temperature dependent bulk modulus is measured at the same temperatures as the Young’s modulus. The master curve of the Young’s modulus and bulk modulus of the EMC is created and a single set of the shift factors is determined from the time temperature superposition. The supplementary experiments are conducted to verify the validity of the assumptions associated with the linear viscoelasticity. The measured time-temperature dependent properties are further verified by a shadow moiré and Twyman/Green test.

Distal limb osteoarthritis in the horse

The aim of this thesis was to study two objective methods of osteoarthritis (OA) diagnosis in horses and use them on the assessment of new intra-articular treatments. The studied methods were a new inertial-sensor based system of lameness detection and cartilage biomarkers in serum. It was found that distal limb flexion is significantly correlated to the presence of metacarpo-phalangeal OA in hind limbs and that inertial-sensors are sensitive in detecting asymmetry in these cases. A positive and significant correlation was observed between Coll2-1 concentration in serum and the presence of joint disease in males and young horses. Fib3-2 measurement has good potential to be used since it is not influenced by sex or age. Using an experimental model of OA, adipose stem cells pre-activated with interferon-gamma decreased joint inflammation and radiographic lesions. In clinical cases, a single injection of high-concentrated and high-molecular weight hyaluronic-acid decreased joint inflammation and biomarkers’ concentration; OSTEOARTRITE DO MEMBRO DISTAL NO CAVALO Resumo: A finalidade desta tese foi estudar dois métodos de diagnóstico objetivo de osteoartrite (OA) em equinos e aplicá-los na avaliação de novas terapias intra-articulares. Utilizou-se um sistema de sensores de movimento e foi avaliada a concentração de biomarcadores de cartilagem no soro. Concluiu-se que a flexão distal positiva está correlacionada com OA na articulação metacarpofalângica nos membros posteriores e que os sensores são sensíveis na detecção de assimetria nestes casos. Existe uma correlação positiva e significativa entre as concentrações de Coll2-1 e a presença de doença articular, sobretudo em machos e jovens. A dosagem de Fib3-2 tem utilidade por não ser influenciada pelo sexo nem idade. Num modelo experimental da doença, a terapia à base de células estaminais reduziu a inflamação articular e as lesões radiográficas. Em casos clínicos, o tratamento com ácido-hialurónico de alta concentração e peso molecular provoca uma diminuição da inflamação articular e dos biomarcadores no soro.

Essays in Greenhouse/Nursery Economics

This dissertation focuses on the greenhouse and nursery industry in the United States. Two major issues are explored: irrigation and plant disease. The first two essays examine wireless soil-moisture sensor networks, an emerging technology that measures soil moisture and optimizes irrigation levels in real time. The first essay describes a study in which a nationwide survey of commercial growers was administered to generate estimates of grower demand and willingness to pay for sensor networks. We find that adoption rates for a base system and demand for expansion components are decreasing in price, as expected. The price elasticity of the probability of adoption suggests that sensor networks are likely to diffuse at a rate somewhat greater than that of drip irrigation. In the second essay, yields, time-to-harvest, and plant quality were analyzed to measure sensor network profitability. Sensor-based irrigation was found to increase revenue by 62% and profit by 65% per year. The third essay investigates greenhouse nursery growers’ response to a quarantine imposed on the west coast of the United States from 2002 to present for the plant pathogen that causes Sudden Oak Death. I investigate whether growers choose to 1) improve their sanitation practices, which reduces the underlying risk of disease without increasing the difficulty of detecting the pathogen, 2) increase fungicide use, which also prevents disease but makes existing infections much harder to detect, or 3) change their crop composition towards more resistant species. First, a theoretical model is derived to formalize hypotheses on grower responses to the quarantine, and then these predictions are empirically tested using several public data sources. I do not find evidence that growers improve their sanitation practices in response to the quarantine. I do, however, find evidence that growers heavily increase their fungicide use in response to a quarantine policy that requires visual (as opposed to laboratory) inspection for the disease before every crop shipment, suggesting that the quarantine may have the adverse effect of making the pathogen harder to identify. I also do find evidence that growers shift away from susceptible crops and towards resistant crops.

MODELING AND HARDWARE-IN-THE-LOOP SIMULATION OF POWER-SPLIT HYBRID ELECTRIC VEHICLES

Conventional vehicles are creating pollution problems, global warming and the extinction of high density fuels. To address these problems, automotive companies and universities are researching on hybrid electric vehicles where two different power devices are used to propel a vehicle. This research studies the development and testing of a dynamic model for Prius 2010 Hybrid Synergy Drive (HSD), a power-split device. The device was modeled and integrated with a hybrid vehicle model. To add an electric only mode for vehicle propulsion, the hybrid synergy drive was modified by adding a clutch to carrier 1. The performance of the integrated vehicle model was tested with UDDS drive cycle using rule-based control strategy. The dSPACE Hardware-In-the-Loop (HIL) simulator was used for HIL simulation test. The HIL simulation result shows that the integration of developed HSD dynamic model with a hybrid vehicle model was successful. The HSD model was able to split power and isolate engine speed from vehicle speed in hybrid mode.

Relationship between biomarkers of cartilage in serum and degenerative joint disease in lusitanian horses

Cartilage degradation biomarkers are a potential tool for early diagnosis of degen- erative joint disease (DJD). In young horses, Coll2-1 and Coll2-1NO2 have been studied in serum and reported to be useful in the assessment of joint disease. Fib3-2 has been described to be higher in serum of humans with osteoarthritis but has not been assessed in horses. The aim of the current study was to evaluate biomarkers’ changes with age, sex, and exercise and correlate them with DJD. Blood collection and radiographic examination were performed in 51 Lusitanian horses. Moreover, inertial sensor-based detection of lameness was used to assess pain together with sub- jective examination. Females presented significantly higher concentrations of Coll2- 1 (P5.015) and Coll2-1NO2 (P5.014) compared to males. We found significant influence of high level of work in lower concentration of Coll2-1 (P5.001) and sig- nificant influence of sex in concentration of Coll2-1NO2 (P5.030). There was no influence of sex, age and work on Fib3-2. All biomarkers were increased in the DJD group (n535) compared to healthy controls (n516). This difference was significant for Coll2-1 (P5.015). When sorted by sex and age groups, significant difference in Coll2-1 between disease and healthy controls disappeared in old horses and females. Coll2-1 is a good marker of cartilage degradation in horses with DJD, being more specific in young horses and males. Fib3-2 may be further explored to help identify disease in particular cases.

Relationship between biomarkers of cartilage in serum and degenerative joint disease in Lusitano horses

Introduction: Cartilage degradation biomarkers are a potential tool for early diagnosis of degenerative joint disease (DJD). In young horses, Coll2-1 and Coll2-1NO2 have been studied in serum and reported to be useful in the assessment of joint disease. Fib3-2 has been described to be higher in serum of humans with osteoarthritis but was never assessed in horses. The aim of the current study was to evaluate biomarkers’ changes with age, sex and exercise and correlate them with DJD. Material and Methods: Blood collection and radiographic examination were performed in 51 Lusitanian horses. Moreover, inertial sensor-based detection of lameness was used to assess pain together with subjective examination. Results: Females presented significantly higher concentrations of Coll2-1 (p = 0.015) and Coll2-1NO2 (p = 0.014) compared to males. We have found significant influence of high level of work in lower concentration of Coll2-1 (p = 0.001) and significant influence of sex in concentration of Coll2-1NO2 (p = 0.030). There was no influence of sex, age and work on Fib3-2. All biomarkers were increased in the DJD group (n= 35) compared to healthy controls (n = 16). This difference was significant for Coll2-1 (p = 0.015). When sorted by sex and age groups, significant difference in Coll2-1 between disease and healthy controls disappeared in old horses and females. Discussion/ Conclusion: Coll2-1 is a good marker of cartilage degradation in horses with DJD, being more specific in young horses and males. Fib3-2 may be further explored to help identify disease in particular cases.

Drive up electrochemical and electrochemiluminescence signal through biosensing mechanism optimization

Biomarkers are biological indicators of human health conditions. Their ultra-sensitive quantification is of cardinal importance in clinical monitoring and early disease diagnosis. Biosensors are some worldwide simple and easy-to-use analytical devices as a matter of fact, biosensors using electrochemiluminescence (ECL) are one of the most promising biosensors that needs an ever-increasing sensitivity for improving its clinical effectiveness. The principal aspiration of this project is the investigation of the ECL generation mechanisms for enhancing the ECL intensity and the development of an ultrasensitive sensor, the use of metal-oxide materials (Mox) and the substitution of metal-free dyes. Novel dyes such as BODIPY, TADF are used to improve the sensitivity of ECL techniques thanks to their advantageous and tunable properties, enhancing the signal and also the ECL efficiency. Additionally, the use of Mox could be beneficial for the investigation of two different ECL mechanisms, which occur simultaneously. In this thesis, the investigation of size and distance effects on electrochemical (EC) mechanisms was carried out through the innovative combination of a standard detection system using different size of micromagnetic beads (MBs). That allowed the discovery of an unexpected and highly efficient mechanistic path for electrochemical generation at small distances from the electrode’s surface. The smallest MBs (0.1μm) demostrate an enhancement of electrochemical signal than the bigger one (2.8μm) until 4 times of magnitude. Finally, a novel ultrasensitive sensor, based on the coreactant-luminophores mechanism, was developed for the determination of whole viral genome specific for cardiac HBV and COVID-19 virus. In conclusion, the ECL and the use of EC techniques (such as amperometry), improved the understanding of mechanisms responsible for the ECL/EC signal led to a great enhancement in the signal.

An alternative method for the simultaneous determination of copper and lead for quality control of sugar cane spirit using a nanotube-based sensor

The development of an electroanalytical method for simultaneous determination of copper and lead ions in sugar cane spirit (cachaça) using carbon paste electrode modified with ascorbic acid and carbon nanotubes (CPE-AaCNT) is described. Squarewave voltammetry (SWV) with anodic stripping was employed, and this technique was optimized with respect to the following parameters: frequency (50 Hz), amplitude (100 mV) and scan increment (9 mV). The analytical curves were linear in the range from 0.0900 to 7.00 mg L - 1 for lead and copper. The limits of detection were 48.5 and 23.9 µg L - 1 for lead and copper, respectively. The developed method was applied to the simultaneous determination of copper and lead in five commercial samples of sugar cane spirit. The results were in good agreement with those obtained by F AAS/GF AAS (flame atomic absorption spectrometry/graphite furnace atomic absorption spectrometry) and showed that CPE-AaCNT can be successfully employed in the simultaneous determination of these metals in real sugar cane spirit samples.

An Alternative Method for the Simultaneous Determination of Copper and Lead for Quality Control of Sugar Cane Spirit using a Nanotube-Based Sensor

The development of an electroanalytical method for simultaneous determination of copper and lead ions in sugar cane spirit (cachaca) using carbon paste electrode modified with ascorbic acid and carbon nanotubes (CPE-AaCNT) is described. Squarewave voltammetry (SWV) with anodic stripping was employed, and this technique was optimized with respect to the following parameters: frequency (50 Hz), amplitude (100 mV) and scan increment (9 mV). The analytical curves were linear in the range from 0.0900 to 7.00 mg L-1 for lead and copper. The limits of detection were 48.5 and 23.9 mu g L-1 for lead and copper, respectively. The developed method was applied to the simultaneous determination of copper and lead in five commercial samples of sugar cane spirit. The results were in good agreement with those obtained by F AAS/GF AAS (flame atomic absorption spectrometry/graphite furnace atomic absorption spectrometry) and showed that CPE-AaCNT can be successfully employed in the simultaneous determination of these metals in real sugar cane spirit samples.

An alternative method for the simultaneous determination of copper and lead for quality control of sugar cane spirit using a nanotube-based sensor

The development of an electroanalytical method for simultaneous determination of copper and lead ions in sugar cane spirit (cachaça) using carbon paste electrode modified with ascorbic acid and carbon nanotubes (CPE-AaCNT) is described. Squarewave voltammetry (SWV) with anodic stripping was employed, and this technique was optimized with respect to the following parameters: frequency (50 Hz), amplitude (100 mV) and scan increment (9 mV). The analytical curves were linear in the range from 0.0900 to 7.00 mg L- 1 for lead and copper. The limits of detection were 48.5 and 23.9 µg L- 1 for lead and copper, respectively. The developed method was applied to the simultaneous determination of copper and lead in five commercial samples of sugar cane spirit. The results were in good agreement with those obtained by F AAS/GF AAS (flame atomic absorption spectrometry/graphite furnace atomic absorption spectrometry) and showed that CPE-AaCNT can be successfully employed in the simultaneous determination of these metals in real sugar cane spirit samples.

A Survey on FPGA-Based Sensor Systems: Towards Intelligent and Reconfigurable Low-Power Sensors for Computer Vision, Control and Signal Processing

The current trend in the evolution of sensor systems seeks ways to provide more accuracy and resolution, while at the same time decreasing the size and power consumption. The use of Field Programmable Gate Arrays (FPGAs) provides specific reprogrammable hardware technology that can be properly exploited to obtain a reconfigurable sensor system. This adaptation capability enables the implementation of complex applications using the partial reconfigurability at a very low-power consumption. For highly demanding tasks FPGAs have been favored due to the high efficiency provided by their architectural flexibility (parallelism, on-chip memory, etc.), reconfigurability and superb performance in the development of algorithms. FPGAs have improved the performance of sensor systems and have triggered a clear increase in their use in new fields of application. A new generation of smarter, reconfigurable and lower power consumption sensors is being developed in Spain based on FPGAs. In this paper, a review of these developments is presented, describing as well the FPGA technologies employed by the different research groups and providing an overview of future research within this field.

Architecture for machining process and production monitoring based in open computer numerical control

This paper proposes an architecture for machining process and production monitoring to be applied in machine tools with open Computer numerical control (CNC). A brief description of the advantages of using open CNC for machining process and production monitoring is presented with an emphasis on the CNC architecture using a personal computer (PC)-based human-machine interface. The proposed architecture uses the CNC data and sensors to gather information about the machining process and production. It allows the development of different levels of monitoring systems with mininium investment, minimum need for sensor installation, and low intrusiveness to the process. Successful examples of the utilization of this architecture in a laboratory environment are briefly described. As a Conclusion, it is shown that a wide range of monitoring solutions can be implemented in production processes using the proposed architecture.

A wireless sensor network platform for structural health monitoring: enabling accurate and synchronized measurements through COTS+custom-based design

Structural health monitoring has long been identified as a prominent application of Wireless Sensor Networks (WSNs), as traditional wired-based solutions present some inherent limitations such as installation/maintenance cost, scalability and visual impact. Nevertheless, there is a lack of ready-to-use and off-the-shelf WSN technologies that are able to fulfill some most demanding requirements of these applications, which can span from critical physical infrastructures (e.g. bridges, tunnels, mines, energy grid) to historical buildings or even industrial machinery and vehicles. Low-power and low-cost yet extremely sensitive and accurate accelerometer and signal acquisition hardware and stringent time synchronization of all sensors data are just examples of the requirements imposed by most of these applications. This paper presents a prototype system for health monitoring of civil engineering structures that has been jointly conceived by a team of civil, and electrical and computer engineers. It merges the benefits of standard and off-the-shelf (COTS) hardware and communication technologies with a minimum set of custom-designed signal acquisition hardware that is mandatory to fulfill all application requirements.

Electrospun Polyaniline-Reduced Graphene Oxide Composite Nanofibers Based High Sensitive Ammonia Gas Sensor

Ammonia is an important gas in many power plants and industrial processes so its detection is of extreme importance in environmental monitoring and process control due to its high toxicity. Ammonia’s threshold limit is 25 ppm and the exposure time limit is 8 h, however exposure to 35 ppm is only secure for 10 min. In this work a brief introduction to ammonia aspects are presented, like its physical and chemical properties, the dangers in its manipulation, its ways of production and its sources. The application areas in which ammonia gas detection is important and needed are also referred: environmental gas analysis (e.g. intense farming), automotive-, chemical- and medical industries. In order to monitor ammonia gas in these different areas there are some requirements that must be attended. These requirements determine the choice of sensor and, therefore, several types of sensors with different characteristics were developed, like metal oxides, surface acoustic wave-, catalytic-, and optical sensors, indirect gas analyzers, and conducting polymers. All the sensors types are described, but more attention will be given to polyaniline (PANI), particularly to its characteristics, syntheses, chemical doping processes, deposition methods, transduction modes, and its adhesion to inorganic materials. Besides this, short descriptions of PANI nanostructures, the use of electrospinning in the formation of nanofibers/microfibers, and graphene and its characteristics are included. The created sensor is an instrument that tries to achieve a goal of the medical community in the control of the breath’s ammonia levels being an easy and non-invasive method for diagnostic of kidney malfunction and/or gastric ulcers. For that the device should be capable to detect different levels of ammonia gas concentrations. So, in the present work an ammonia gas sensor was developed using a conductive polymer composite which was immobilized on a carbon transducer surface. The experiments were targeted to ammonia measurements at ppb level. Ammonia gas measurements were carried out in the concentration range from 1 ppb to 500 ppb. A commercial substrate was used; screen-printed carbon electrodes. After adequate surface pre-treatment of the substrate, its electrodes were covered by a nanofibrous polymeric composite. The conducting polyaniline doped with sulfuric acid (H2SO4) was blended with reduced graphene oxide (RGO) obtained by wet chemical synthesis. This composite formed the basis for the formation of nanofibers by electrospinning. Nanofibers will increase the sensitivity of the sensing material. The electrospun PANI-RGO fibers were placed on the substrate and then dried at ambient temperature. Amperometric measurements were performed at different ammonia gas concentrations (1 to 500 ppb). The I-V characteristics were registered and some interfering gases were studied (NO2, ethanol, and acetone). The gas samples were prepared in a custom setup and were diluted with dry nitrogen gas. Electrospun nanofibers of PANI-RGO composite demonstrated an enhancement in NH3 gas detection when comparing with only electrospun PANI nanofibers. Was visible higher range of resistance at concentrations from 1 to 500 ppb. It was also observed that the sensor had stable, reproducible and recoverable properties. Moreover, it had better response and recovery times. The new sensing material of the developed sensor demonstrated to be a good candidate for ammonia gas determination.