Boundary Integral Equation Methods for Simulation and Design of Photonic Devices

This thesis presents novel boundary integral equation (BIE) and associated optimization methodologies for photonic devices. The simulation and optimization of such structures is a vast and rapidly growing engineering area, which impacts on design of optical devices such as waveguide splitters, tapers, grating couplers, and metamaterial structures, all of which are commonly used as elements in the field of integrated photonics. The design process has been significantly facilitated in recent years on the basis of a variety of methods in computational electromagnetic (EM) simulation and design. Unfortunately, however, the expense required by previous simulation tools has limited the extent and complexity of the structures that can be treated. The methods presented in this thesis represent the results of our efforts towards accomplishing the dual goals of 1) Accurate and efficient EM simulation for general, highly-complex three-dimensional problems, and 2) Development of effective optimization methods leading to an improved state of the art in EM design. One of the main proposed elements utilizes BIE in conjunction with a modified-search algorithm to obtain the modes of uniform waveguides with arbitrary cross sections. This method avoids spurious solutions by means of a certain normalization procedure for the fields within the waveguides. In order to handle problems including nonuniform waveguide structures, we introduce the windowed Green function (WGF) method, which used in conjunction with auxiliary integral representations for bound mode excitations, has enabled accurate simulation of a wide variety of waveguide problems on the basis of highly accurate and efficient BIE, in two and three spatial dimensions. The "rectangular-polar" method provides the basic high-order singular-integration engine. Based on non-overlapping Chebyshev-discretized patches, the rectangular-polar method underlies the accuracy and efficiency of the proposed general-geometry three-dimensional BIE approach. Finally, we introduce a three-dimensional BIE framework for the efficient computation of sensitivities — i.e. gradients with respect to design parameters — via adjoint techniques. This methodology is then applied to the design of metalenses including up to a thousand parameters, where the overall optimization process takes in the order of three hours using five hundred computing cores. Forthcoming work along the lines of this effort seeks to extend and apply these methodologies to some of the most challenging and exciting design problems in electromagnetics in general, and photonics in particular.</p

GPS-MIV: The General Purpose System for Multi-display Interactive Visualization

The new age of information has created opportunities for inventions like the internet. These inventions allow us access to tremendous quantities of data. But, with the increase in information there is need to make sense of such vast quantities of information by manipulating that information to reveal hidden patterns to aid in making sense of it. Data visualization systems provide the tools to reveal patterns and filter information, aiding the processes of insight and decision making. The purpose of this thesis is to develop and test a data visualization system, The General Purpose System for Multi-display Interactive Visualization (GPS-MIV). GPS-MIV is a software system allowing the user to visualize data graphically and interact with it. At the core of the system is a graphics system that displays different computer generated scenes from multiple perspectives and with multiple views. Additionally, GSP-MIV provides interaction for the user to explore the scene

Adult Stem Cell Membrane Markers: Their Importance and Critical Role in Their Proliferation and Differentiation Potentials

The stem cells are part of the cells that belong to the stromal tissue. These cells remain in a quiescent state until they are activated by different factors, usually those generated by an alteration in the parenchymal tissue. These cells have characteristic membrane markers such as CD73, CD90, and CD105. Those are a receptor, which in response to their ligand induces strong changes in different metabolic pathways that lead to these cells, both to generate molecules with different activities and to leave their stationary phase to reproduce and even differentiate. This review describes the metabolic pathways dependent on these membrane markers and how they influence on parenchymal tissue and other stromal cells

MicroRNAs in Amyotrophic Lateral Sclerosis

miRNAs are sequences of 20–22 nucleotides that participate in the development, growth, and cell differentiation by the regulation of the mRNAs.Their possible participation in the development of degenerative diseases has been extensively investigated. Results show quantitative changes in miRNA transcription, to the pathogenesis of various neurodegenerative diseases. In this chapter, the dysregulation of microRNAs reported in the samples taken from amyotrophic lateral sclerosis (ALS) animal model or ALS patients is analyzed. Moreover,their probable participation in the pathogenesis of the disease is also analyzed

Disruptive coloration and perceptual grouping.

Camouflage is the primary defence of many animals and includes multiple strategies that interfere with figure-ground segmentation and object recognition. While matching background colours and textures is widespread and conceptually straightforward, less well explored are the optical ‘tricks’, collectively called disruptive colouration, that exploit perceptual grouping mechanisms. Adjacent high contrast colours create false edges, but this is not sufficient for an object’s shape to be broken up; some colours must blend with the background. We test the novel hypothesis that this will be particularly effective when the colour patches on the animal appear to belong to, not merely different background colours, but different background objects. We used computer-based experiments where human participants had to find cryptic targets on artificial backgrounds. Creating what appeared to be bi-coloured foreground objects on bi-coloured backgrounds, we generated colour boundaries that had identical local contrast but either lay within or between (illusory) objects. As predicted, error rates for targets matching what appeared to be different background objects were higher than for targets which had otherwise identical local contrast to the background but appeared to belong to single background objects. This provides evidence for disruptive colouration interfering with higher-level feature integration in addition to previously demonstrated low-level effects involving contour detection. In addition, detection was impeded in treatments where targets were on or in close proximity to multiple background colour or tone boundaries. This is consistent with other studies which show a deleterious influence of visual ‘clutter’ or background complexity on search

The Interpretation of N+N and V+N Compounds by Spanish Heritage Speakers

This study investigates how Spanish heritage language speakers interpret two types of compound constructions in Spanish: head-initial [N+N] N (e.g., obra cumber ‘masterpiece,’ lit. ‘work summit’) and exocentric [V+N] N (e.g., pelagatos ‘poor man,’ lit. ‘peel+cats’). It was hypothesized that the greater the exposure of participants to English (that has right-headed compounds) the less Spanish-like their pattern of interpreting N-N compounds as left-headed. Further, it was hypothesized that Spanish heritage language speakers who acquire the V-O construction early (prior to age 12) and are thus more likely to be familiar with the conventional mechanism of word formation with the V-N configuration would be more accurate in interpreting [V+N] N than [N+N] N compounds, regardless of their degree of English-exposure. Finally, it was predicted that compounds that are higher in semantic transparency/opacity would be interpreted more accurately than those lower in opacity. Spanish-English speakers were administered a compound interpretation task in which participants were to select the correct definition for 40 compound words in Spanish. Participants were classified into three groups: late sequential bilinguals who acquired Spanish monolingually in Mexico and learned English after age 12, early sequential bilinguals who acquired Spanish monolingually in the home but came into contact with English at approximately age 6 when they started school, and simultaneous bilinguals who acquired both languages early at home and for who English has been the language of instruction and the dominant language in most social contexts. The performance of these groups was compared to that of a control group consisting of Spanish-dominant speakers. The findings showed support for the first hypothesis: individuals who acquired English late were better in interpreting the compounds that those who had more exposure to English. The second hypothesis was also supported in that all groups bilinguals interpreted [V+N] N more accurately than [N+N] N compounds regardless of their degree of English-dominance. Finally, compound transparency affected interpretation accuracy. These findings indicate that bilinguals’ performance on compound interpretation in one of their languages in affected not only by linguistic factors (headedness, transparency) but also by bilinguals’ context of acquisition and use of their two languages

Modelling and control of integrated PV-converter modules under partial shading conditions

It has been well-recognized that non-uniform solar irradiation of photovoltaic (PV) panels causes electrical mismatching of cells and may result in reduced output power and cell thermal breakdown. Bypass diodes are commonly used, but challenges exist into obtaining the maximum power point tracking in these partially shaded PV panels for each weather condition. This is due to that there are multiple peak power points present in their Power-Voltage characteristic curves which makes difficult to locate the global maximum power point. The work presented in this thesis studies in detail the converter topologies and control methods which can be used in the PV power generation systems to overcome effectively the shortcomings caused by partial shading. The proposed topology is an integrated bi-directional Cuk converter and PV-panel module. The particular example investigated includes two PV panels connected across two terminals of the Cuk converter. The features of this system in power harness are studied under partial shading conditions, its superior performance in power generation is demonstrated through simulation and practical tests. The generated power is 30% higher than that from a two PV panel system using only bypass diodes. To develop the control schemes for the above system a detailed study was performed leading to the derivation of the transfer function model describing the dynamic responses of voltages across the two PV panels corresponding to the variations of converter switch duty ratio. Experimental verification of this confirms that the model is sufficiently accurate for the application of controller design and tests. A novel maximum power point tracking scheme is developed. This consists of a switching selection scheme and a model based on an optimal control algorithm. The former determines which switch-diode pair in the bidirectional Cuk converter to be active according to measured light levels on each PV panel and the ability to predict the optimal voltage values across the individual PV panels under any practical irradiance and temperature levels. The performance of the controller is tested in simulation as well as in practice under various modes of partial shading, all giving desired results in achieving the maximum power generation. The final contribution lies in the design and construction of an experimental prototype consisting of an inner bidirectional Cuk converter across two PV panels and a terminal boost converter, controlled by DSP-based microcontroller. This setup enables further development and verification of the control schemes for this integrated converter and PV-panel system. Keywords: Photovoltaic Systems, Partial Shading, Cuk Converter, DC-DC Power Converters, Solar Power Generation, Maximum Power Point Tracking, Bypass Diode

High sporulation and overexpression of virulence factors in biofilms and reduced susceptibility to vancomycin and linezolid in recurrent Clostridium [Clostridioides] difficile infection isolates

Clostridium [Clostridioides] difficile infection (CDI) is one of the leading causes of diarrhea associated with medical care worldwide, and up to 60% of patients with CDI can develop a recurrent infection (R-CDI). A multi-species microbiota biofilm model of C. difficile was designed to evaluate the differences in the production of biofilms, sporulation, susceptibility to drugs, expression of sporulating (sigH, spo0A), quorum sensing (agrD1, and luxS), and adhesion-associated (slpA and cwp84) pathway genes between selected C. difficile isolates from R-CDI and non-recurrent patients (NR-CDI). We obtained 102 C. difficile isolates from 254 patients with confirmed CDI (66 from NR-CDI and 36 from R-CDI). Most of the isolates were biofilm producers, and most of the strains were ribotype 027 (81.374%, 83/102). Most C. difficile isolates were producers of biofilm (100/102), and most were strongly adherent. Sporulation was higher in the R-CDI than in the NR-CDI isolates (p = 0.015). The isolates from R-CDI patients more frequently demonstrated reduced susceptibility to vancomycin than isolates of NR-CDI patients (27.78% [10/36] and 9.09% [6/66], respectively, p = 0.013). The minimum inhibitory concentrations for vancomycin and linezolid against biofilms (BMIC) were up to 100 times and 20 times higher, respectively, than the corresponding planktonic MICs. Expression of sigH, spo0A, cwp84, and agrD1 was higher in R-CDI than in NR-CDI isolates. Most of the C. difficile isolates were producers of biofilms with no correlation with the ribotype. Sporulation was greater in R-CDI than in NR-CDI isolates in the biofilm model of C. difficile. The R-CDI isolates more frequently demonstrated reduced susceptibility to vancomycin and linezolid than the NR-CDI isolates in both planktonic cells and biofilm isolates. A higher expression of sporulating pathway (sigH, spo0A), quorum sensing (agrD1), and adhesion-associated (cwp84) genes was found in R-CDI than in NR-CDI isolates. All of these factors can have effect on the recurrence of the infection.Peer reviewe

Circulation of Highly Drug-Resistant Clostridium difficile Ribotypes 027 and 001 in Two Tertiary-Care Hospitals in Mexico

© 2018, Mary Ann Liebert, Inc.OBJECTIVE: To assess drug susceptibility and characterize Clostridium difficile ribotypes in isolates from two tertiary-care hospitals in Mexico. METHODS: Isolates were evaluated for genotyping, antimicrobial susceptibility testing and detection of mutations associated with drug resistance. PCR ribotyping was performed using a combination of gel-based and capillary electrophoresis-based approaches. RESULTS: MIC50 and MIC90 were ≥128 mg/L for ciprofloxacin, erythromycin, clindamycin, and rifampicin. There was no reduced susceptibility to metronidazole or tetracycline; however, reduced susceptibility to vancomycin (≥4 mg/L) and fidaxomicin (≥2 mg/L) was detected in 50 (40.3%) and 4 (3.2%) isolates, respectively. Furthermore, the rpoB Arg505Lys mutation was more frequently detected in isolates with high minimum inhibitory concentration (MIC) to rifampicin (≥32 mg/L) (OR = 52.5; 95% CI = 5.17-532.6; p < 0.000). Of the 124 C. difficile isolates recovered, 84 (66.7%) were of ribotype 027, 18 (14.5%) of ribotype 001, and the remainder were other ribotypes (353, 255, 220, 208, 176, 106, 076, 020, 019, 017, 014, 012, 003, and 002). CONCLUSION: Ribotypes 027 and 001 were the most frequent C. difficile isolates recovered in this study, and demonstrated higher MICs. Furthermore, we found four isolates with reduced susceptibility to fidaxomicin, raising a concern since this drug is currently unavailable in Mexican Hospitals.Peer reviewedFinal Accepted Versio

From a Tabula Rasa to the Governor’s Award for Historic Preservation

Prior to 2009, South Texas was essentially an archaeological tabula rasa, largely unknown in the academic, public, or grey literature due to its location far from research universities, the state historic preservation office, and cultural resource management firms. Here, we relate how a consortium of anthropologists and archaeologists, biologists, historians, geologists, and geoarchaeologists have embraced a locally focused, place-based STEAM research approach to tell the story of a largely unknown region of the United States and make it accessible to K–17 educators,1 the public, and scholars with bilingual maps, books, exhibits, films, traveling trunks, and scholarly publications. The efforts of the Community Historical Archaeology Project with Schools Program at the University of Texas Rio Grande Valley have been recognized locally, nationally, and internationally