Using a voxel-based krogh cylinder array to simulate microvascular contrast enhancement

The goal of this study is to better simulate microscopic and voxel-based dynamic contrast enhancement in magnetic resonance imaging. Specifically, errors imposed by the traditional two-compartment model are reduced by introducing a novel Krogh cylinder network. The two-compartment model was developed for macroscopic pharmacokinetic analysis of dynamic contrast enhancement and generalizing it to voxel dimensions, due to the significant decrease in scale, imposes physiologically unrealistic assumptions. In the project, a system of microscopic exchange between plasma and extravascular-extracellular space is built while numerically simulating the local contrast agent flow between and inside image elements. To do this, tissue parameter maps were created, contrast agent was introduced to the tissue via a flow lattice, and various data sets were simulated. The effects of sources, tissue heterogeneity, and the contribution of individual tissue parameters to an image are modeled. Further, the study attempts to demonstrate the effects of a priori flow maps on image contrast, indicating that flow data is as important as permeability data when analyzing tumor contrast enhancement. In addition, the simulations indicate that it may be possible to obtain tumor-type diagnostic information by acquiring both flow and permeability data.

The cytokinesis-block micronucleus (CBMN) assay in human populations exposed to styrene: a systematic review and meta-analysis

Styrene is a building-block of several compounds used in a wide array of materials and products. The most important human exposure to this substance occurs in industrial settings, especially among reinforced-plastics industry workers. The effect of occupational exposure to styrene on cytogenetics biomarkers has been previously reviewed with positive association observed for chromosomal aberrations, and inconclusive data for the micronucleus assay. Some limitations were noted in those studies, including inadequate exposure assessment and poor epidemiological design. Furthermore, in earlier studies micronuclei frequency was measured with protocols not as reliable as cytokinesis-block micronucleus (CBMN) assay. Aim of the present systematic review and meta-analysis is to investigate genomic instability and DNA damage as measured by the CBMN assay in lymphocytes of subjects exposed to styrene. A total of 11 studies published between 2004 and 2012 were included in the meta-analysis encompassing 479 styrene-exposed workers and 510 controls. The quality of each study was estimated by a quality scoring system which ranked studies according to the consideration of major confounders, exposure characterization, and technical parameters. An overall increase of micronuclei frequencies was found in styrene-exposure workers when compared to referents (meta-MR 1.34; 95% CI 1.18–1.52), with significant increases achieved in six individual studies. The consistency of results in individual studies, the independence of this result from major confounding factors and from the quality of the study strengthens the reliability of risk estimates and supports the use of the CBMN assay in monitoring genetic risk in styrene workers.

A study on independent component analysis over galois fields

Dissertação (mestrado)—Universidade de Brasília, Faculdade de Tecnologia, Departamento de Engenharia Elétrica, 2015.

Simulation tools for the analysis of single electronic systems

Developments in theory and experiment have raised the prospect of an electronic technology based on the discrete nature of electron tunnelling through a potential barrier. This thesis deals with novel design and analysis tools developed to study such systems. Possible devices include those constructed from ultrasmall normal tunnelling junctions. These exhibit charging effects including the Coulomb blockade and correlated electron tunnelling. They allow transistor-like control of the transfer of single carriers, and present the prospect of digital systems operating at the information theoretic limit. As such, they are often referred to as single electronic devices. Single electronic devices exhibit self quantising logic and good structural tolerance. Their speed, immunity to thermal noise, and operating voltage all scale beneficially with junction capacitance. For ultrasmall junctions the possibility of room temperature operation at sub picosecond timescales seems feasible. However, they are sensitive to external charge; whether from trapping-detrapping events, externally gated potentials, or system cross-talk. Quantum effects such as charge macroscopic quantum tunnelling may degrade performance. Finally, any practical system will be complex and spatially extended (amplifying the above problems), and prone to fabrication imperfection. This summarises why new design and analysis tools are required. Simulation tools are developed, concentrating on the basic building blocks of single electronic systems; the tunnelling junction array and gated turnstile device. Three main points are considered: the best method of estimating capacitance values from physical system geometry; the mathematical model which should represent electron tunnelling based on this data; application of this model to the investigation of single electronic systems. (DXN004909)

Chromatographic analysis of antioxidant and related compounds in Polyporus squamosus from different origins

The antioxidant potential of mushrooms is mainly attributed to their composition in polysaccharides, phenolic compounds, tocopherols and some organic acids [1]. Phenolic compounds contribute directly to the antioxidative action and play an important role in stabilizing lipid peroxidation [2]; exhibit a wide range of bioactive properties such as anti-allergenic, anti-inflammatory and antimicrobial, which have been in part related to their antioxidant activity [3]. Tocopherols are important fatsoluble antioxidants, acting in the cellular membrane; due to their role as scavenger of free radicals protecting human cells against degenerative malfunctions [4]. Some organic acids are very common in natural matrices; malic acid contributes to a pleasantly sour taste and is often used as a food additive; citric acid is known due to its antibacterial and antioxidant properties and fumaric acid is important because of its antioxidant, anti-inflammatory, antimicrobial and acidifying properties [5]. The purpose of the present study was to analyze antioxidant and related compounds (phenolic compounds, tocopherols and organic acids) of Polyporus squamosus (Huds.) Fr. samples originated from two different origins (Portugal and Serbia). Specimens of P. squamosus were collected in Bragança (Northeast Portugal) and Jabučki rit (Northern Serbia) during April 2015 and 2012, respectively. Phenolic compounds, organic acids and tocopherols were determined by high performance liquid chromatograph (HPLC) coupled to a diode array detector (DAD), in the two first cases, and a fluorescence detector in the last one. With respect to phenolic and related compounds, p-hydroxybenzoic and cinnamic acids were identified in both samples; the first one predominates in the sample from Portugal, while cinnamic acid was more abundant in the sample from Serbia. Tocopherols (α-, β and γ-isoforms) were found in the sample from Serbia, but in the sample from Portugal, γ-tocopherol was not identified. This sample showed the highest total tocopherols content, and revealed the highest level of β-tocopherol; γ- tocopherol predominated in the sample from Serbia. Among organic acids, it was possible to quantify oxalic, malic and fumaric acids in both samples. Malic acid was found in higher amounts in the sample from Serbia. Overall, the present study shows that mushroom samples from different origins have dissimilar results, but are both rich in bioactive compounds, being a valuable source for the development of natural medicines and nutraceuticals.

Performance and Robustness Analysis of Co-Prime and Nested Sampling

Coprime and nested sampling are well known deterministic sampling techniques that operate at rates significantly lower than the Nyquist rate, and yet allow perfect reconstruction of the spectra of wide sense stationary signals. However, theoretical guarantees for these samplers assume ideal conditions such as synchronous sampling, and ability to perfectly compute statistical expectations. This thesis studies the performance of coprime and nested samplers in spatial and temporal domains, when these assumptions are violated. In spatial domain, the robustness of these samplers is studied by considering arrays with perturbed sensor locations (with unknown perturbations). Simplified expressions for the Fisher Information matrix for perturbed coprime and nested arrays are derived, which explicitly highlight the role of co-array. It is shown that even in presence of perturbations, it is possible to resolve $O(M^2)$ under appropriate conditions on the size of the grid. The assumption of small perturbations leads to a novel ``bi-affine" model in terms of source powers and perturbations. The redundancies in the co-array are then exploited to eliminate the nuisance perturbation variable, and reduce the bi-affine problem to a linear underdetermined (sparse) problem in source powers. This thesis also studies the robustness of coprime sampling to finite number of samples and sampling jitter, by analyzing their effects on the quality of the estimated autocorrelation sequence. A variety of bounds on the error introduced by such non ideal sampling schemes are computed by considering a statistical model for the perturbation. They indicate that coprime sampling leads to stable estimation of the autocorrelation sequence, in presence of small perturbations. Under appropriate assumptions on the distribution of WSS signals, sharp bounds on the estimation error are established which indicate that the error decays exponentially with the number of samples. The theoretical claims are supported by extensive numerical experiments.

Microwave-assisted solvent extraction and analysis of shikimic acid from plant tissues.

A better method for determination of shikimate in plant tissues is needed to monitor exposure of plants to the herbicide glyphosate [N-(phosphonomethyl)glycine] and to screen the plant kingdom for high levels of this valuable phytochemical precursor to the pharmaceutical oseltamivir. A simple, rapid, and efficient method using microwave-assisted extraction (MWAE) with water as the extraction solvent was developed for the determination of shikimic acid in plant tissues. High performance liquid chromatography was used for the separation of shikimic acid, and chromatographic data were acquired using photodiode array detection. This MWAE technique was successful in recovering shikimic acid from a series of fortified plant tissues at more than 90% efficiency with an interference-free chromatogram. This allowed the use of lower amounts of reagents and organic solvents, reducing the use of toxic and/or hazardous chemicals, as compared to currently used methodologies. The method was used to determine the level of endogenous shikimic acid in several species of Brachiaria and sugarcane (Saccharum officinarum) and on B. decumbens and soybean (Glycine max) after treatment with glyphosate. The method was sensitive, rapid and reliable in all cases.

MULTIMODAL PERFORMANCE AND RELIABILITY ANALYSIS OF THE PIERRE AUGER OBSERVATORY NORTH SITE

The Pierre Auger Cosmic Ray Observatory North site employs a large array of surface detector stations (tanks) to detect the secondary particle showers generated by ultra-high energy cosmic rays. Due to the rare nature of ultra-high energy cosmic rays, it is important to have a high reliability on tank communications, ensuring no valuable data is lost. The Auger North site employs a peer-to-peer paradigm, the Wireless Architecture for Hard Real-Time Embedded Networks (WAHREN), designed specifically for highly reliable message delivery over fixed networks, under hard real-time deadlines. The WAHREN design included two retransmission protocols, Micro- and Macro- retransmission. To fully understand how each retransmission protocol increased the reliability of communications, this analysis evaluated the system without using either retransmission protocol (Case-0), both Micro- and Macro-retransmission individually (Micro and Macro), and Micro- and Macro-retransmission combined. This thesis used a multimodal modeling methodology to prove that a performance and reliability analysis of WAHREN was possible, and provided the results of the analysis. A multimodal approach was necessary because these processes were driven by different mathematical models. The results from this analysis can be used as a framework for making design decisions for the Auger North communication system.

Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis

Mycobacterium avium subsp. paratuberculosis is an important animal pathogen widely disseminated in the environment that has also been associated with Crohn's disease in humans. Three M. avium subsp. paratuberculosis genomotypes are recognized, but genomic differences have not been fully described. To further investigate these potential differences, a 60-mer oligonucleotide microarray (designated the MAPAC array), based on the combined genomes of M. avium subsp. paratuberculosis (strain K-10) and Mycobacterium avium subsp. hominissuis (strain 104), was designed and validated. By use of a test panel of defined M. avium subsp. paratuberculosis strains, the MAPAC array was able to identify a set of large sequence polymorphisms (LSPs) diagnostic for each of the three major M. avium subsp. paratuberculosis types. M. avium subsp. paratuberculosis type II strains contained a smaller genomic complement than M. avium subsp. paratuberculosis type I and M. avium subsp. paratuberculosis type III genomotypes, which included a set of genomic regions also found in M. avium subsp. hominissuis 104. Specific PCRs for genes within LSPs that differentiated M. avium subsp. paratuberculosis types were devised and shown to accurately screen a panel (n = 78) of M. avium subsp. paratuberculosis strains. Analysis of insertion/deletion region INDEL12 showed deletion events causing a reduction in the complement of mycobacterial cell entry genes in M. avium subsp. paratuberculosis type II strains and significantly altering the coding of a major immunologic protein (MPT64) associated with persistence and granuloma formation. Analysis of MAPAC data also identified signal variations in several genomic regions, termed variable genomic islands (vGIs), suggestive of transient duplication/deletion events. vGIs contained significantly low GC% and were immediately flanked by insertion sequences, integrases, or short inverted repeat sequences. Quantitative PCR demonstrated that variation in vGI signals could be associated with colony growth rate and morphology.

Gwas analysis for the identification of molecular basis responsible for yield related traits and disease resistance in durum wheat

The PhD thesis was developed in the framework of Innovar H2020 project. This project aimed at using genomics, transcriptomics and phenotyping techniques to update varietal registration procedure used in Europe for Value of Cultivation and Use (VCU) and Distinctiness Uniformity and Stability (DUS) protocols. The phenotypic and genotypic diversity of a durum wheat panel were assessed for different agronomic traits, connected with wheat development, disease resistance and spike fertility. A panel of 253 durum wheat varieties was characterized for VCU and DUS traits and genotyped with Illumina 90K SNP Chip array (Wang et al., 2014). GWAS analysis was performed, detecting strong QTLs confirmed also by literature review. Candidate genes were identified for each trait and molecular markers will be developed to be used for marker assisted selection in breeding programs. As for disease resistance, the panel was evaluated for resistance to Soil-Borne-Cereal-Mosaic-Virus (SBCMV). A major QTL, sbm2, was detected on chromosome 2B responsible for durum wheat resistance (Maccaferri et al., 2011). The sbm2 interval was explored by fine mapping on segregant population using KASP markers and by RNASeq analysis, detecting candidate genes involved in plant-pathogen reaction. As regards yield related traits, detailed analysis was performed on the GNI-2A QTL (Milner et al., 2016), responsible for increased number spike fertility. Fine mapping analysis was performed on durum panel identifying hox2 a strong candidate gene, codifying for transcription factor protein. The gene is paralogue of GNI-1 (Sakuma et al., 2019), and it has a 4 kbp deletion responsible for increased number of florets per spikelet. To conclude, the herein reported thesis shows a complete characterization of agronomic and disease resistance traits in modern durum wheat varieties. The results obtained will augment available information for each variety, identifying informative molecular markers for breeding purposes and QTLs/candidate genes responsible for different agronomic traits.

Real-time anomaly detection of gamma-ray bursts for the Cherenkov Telescope Array using deep learning

The Cherenkov Telescope Array (CTA) will be the next-generation ground-based observatory to study the universe in the very-high-energy domain. The observatory will rely on a Science Alert Generation (SAG) system to analyze the real-time data from the telescopes and generate science alerts. The SAG system will play a crucial role in the search and follow-up of transients from external alerts, enabling multi-wavelength and multi-messenger collaborations. It will maximize the potential for the detection of the rarest phenomena, such as gamma-ray bursts (GRBs), which are the science case for this study. This study presents an anomaly detection method based on deep learning for detecting gamma-ray burst events in real-time. The performance of the proposed method is evaluated and compared against the Li&Ma standard technique in two use cases of serendipitous discoveries and follow-up observations, using short exposure times. The method shows promising results in detecting GRBs and is flexible enough to allow real-time search for transient events on multiple time scales. The method does not assume background nor source models and doe not require a minimum number of photon counts to perform analysis, making it well-suited for real-time analysis. Future improvements involve further tests, relaxing some of the assumptions made in this study as well as post-trials correction of the detection significance. Moreover, the ability to detect other transient classes in different scenarios must be investigated for completeness. The system can be integrated within the SAG system of CTA and deployed on the onsite computing clusters. This would provide valuable insights into the method's performance in a real-world setting and be another valuable tool for discovering new transient events in real-time. Overall, this study makes a significant contribution to the field of astrophysics by demonstrating the effectiveness of deep learning-based anomaly detection techniques for real-time source detection in gamma-ray astronomy.

Analysis and design considerations of resonator arrays for inductive power transfer systems

In the frame of inductive power transfer (IPT) systems, arrays of magnetically coupled resonators have received increasing attention as they are cheap and versatile due to their simple structure. They consist of magnetically coupled coils, which resonate with their self-capacitance or lumped capacitive networks. Of great industrial interest are planar resonator arrays used to power a receiver that can be placed at any position above the array. A thorough circuit analysis has been carried out, first starting from traditional two-coil IPT devices. Then, resonator arrays have been introduced, with particular attention to the case of arrays with a receiver. To evaluate the system performance, a circuit model based on original analytical formulas has been developed and experimentally validated. The results of the analysis also led to the definition of a new doubly-fed array configuration with a receiver that can be placed above it at any position. A suitable control strategy aimed at maximising the transmitted power and the efficiency has been also proposed. The study of the array currents has been carried out resorting to the theory of magneto-inductive waves, allowing useful insight to be highlighted. The analysis has been completed with a numerical and experimental study on the magnetic field distribution originating from the array. Furthermore, an application of the resonator array as a position sensor has been investigated. The position of the receiver is estimated through the measurement of the array input impedance, for which an original analytical expression has been also obtained. The application of this sensing technique in an automotive dynamic IPT system has been discussed. The thesis concludes with an evaluation of the possible applications of two-dimensional resonator arrays in IPT systems. These devices can be used to improve system efficiency and transmitted power, as well as for magnetic field shielding.

Analysis, Design, and Hardware-in-the-Loop Validation of Multi-Active Bridge Converters

This master's thesis investigates different aspects of Dual-Active-Bridge (DAB) Converter and extends aspects further to Multi-Active-Bridges (MAB). The thesis starts with an overview of the applications of the DAB and MAB and their importance. The analytical part of the thesis includes the derivation of the peak and RMS currents, which is required for finding the losses present in the system. The power converters, considered in this thesis are DAB, Triple-Active Bridge (TAB) and Quad-Active Bridge (QAB). All the theoretical calculations are compared with the simulation results from PLECS software for identifying the correctness of the reviewed and developed theory. The Hardware-in-the-Loop (HIL) simulation is conducted for checking the control operation in real-time with the help of the RT box from the Plexim. Additionally, as in real systems digital signal processor (DSP), system-on-chip or field programmable gate array is employed for the control of the power electronic systems, and the execution of the control in the real-time simulation (RTS) conducted is performed by DSP.

Magnetic field in the outskirts of PSZ2 G096.88+24.18 from depolarization analysis of radio relics

Radio relics are one of the different types of diffuse radio sources present in a fraction of galaxy clusters. They are characterized by elongated arc-like shapes, with sizes that range between 0.5 and 2 Mpc, and highly polarized emission (up to ∼60%) at GHz frequencies The linearly polarized radiation of relics, moving through a magnetized plasma which is the ICM, is affected by the rotation of the linear polarization vector. This effect, known as “Faraday rotation”, can cause depolarization. The study of this effect allows us to constrain the magnetic field projected along the line of sight. The aim of this thesis work is to constrain the magnetic field intensity and distribution in the periphery of the cluster PSZ2 G096.88+24.18: this cluster hosts a pair of radio relics that can be used for polarization analysis. To analyse the polarization properties of the relics in PSZ2 G096.88+24.18 radio relics we used new Jansky Very Large Array (VLA) observations together with archival observations. The polarization study has been performed using the Rotation Measure Synthesis technique, which allows us to recover polarization, minimizing the bandwidth depolarization. Thanks to this technique, we recovered more polarization from the southern relic (with respect to provious works), We studied also the depolarization trend with the resolution for the southern relic, and found that the polarization fraction decreases with the beamsize. Finally, we have produced simulated magnetic fields models, varying the auto-correlation lengths of the magnetic field, in order to reproduce the observed depolarization trend in the southern relic. Comparing our observational results and model predictions, we were able to constrain the scales over which the turbulent magnetic field varies within the cluster. We conclude that the depolarization observed in the southern relic is likely due to external depolarization caused by the magnetized ICM distribution within the cluster.

Impact of convective motions on pollutant dispersion in urban canyons: an analysis through RANS simulations

Since the majority of the population of the world lives in cities and that this number is expected to increase in the next years, one of the biggest challenges of the research is the determination of the risk deriving from high temperatures experienced in urban areas, together with improving responses to climate-related disasters, for example by introducing in the urban context vegetation or built infrastructures that can improve the air quality. In this work, we will investigate how different setups of the boundary and initial conditions set on an urban canyon generate different patterns of the dispersion of a pollutant. To do so we will exploit the low computational cost of Reynolds-Averaged Navier-Stokes (RANS) simulations to reproduce the dynamics of an infinite array of two-dimensional square urban canyons. A pollutant is released at the street level to mimic the presence of traffic. RANS simulations are run using the k-ɛ closure model and vertical profiles of significant variables of the urban canyon, namely the velocity, the turbulent kinetic energy, and the concentration, are represented. This is done using the open-source software OpenFOAM and modifying the standard solver simpleFoam to include the concentration equation and the temperature by introducing a buoyancy term in the governing equations. The results of the simulation are validated with experimental results and products of Large-Eddy Simulations (LES) from previous works showing that the simulation is able to reproduce all the quantities under examination with satisfactory accuracy. Moreover, this comparison shows that despite LES are known to be more accurate albeit more expensive, RANS simulations represent a reliable tool if a smaller computational cost is needed. Overall, this work exploits the low computational cost of RANS simulations to produce multiple scenarios useful to evaluate how the dispersion of a pollutant changes by a modification of key variables, such as the temperature.