Nonlinear Instabilities in Chemical and Electrochemical Systems

This dissertation focuses on designing and manipulating nonlinear chemical and electrochemical reactions, with the aim of discovering new behaviors as well as gaining insights into their underlying mechanisms. In Chapter 2 the nonlinear behavior of the 4-aminophenol – bromate photoreaction was investigated from two directions. First, a second autocatalytic cycle was introduced through the incorporation of the metal catalyst cerium (IV). It was found that once the autocatalytic cycles were effectively balanced, complexity in the form of mixed mode oscillations was observed in a closed reactor. This dynamic behavior was successfully simulated using a modified model, which qualitatively reproduced the experimental results. It was also found that the precipitate which forms at the onset of the reaction of 4-aminophenol with bromate, N-bromo-1,4-benzoquinone-4-imine, could form a new bromate-based photochemical oscillator. In Chapter 3, the autocatalytic oxidation of 2-methyl-1,4-hydroquinone by acidic bromate lead to the discovery of a new photochemical oscillator. The system was found to be very sensitive to the intensity of illumination supplied, and complexity in the form of sequential oscillations was discovered using either ferroin or cerium (IV) as catalysts. Interestingly, cerium (IV) had a much more profound effect on the dynamical behavior, substantially lengthening the oscillatory period as well as being capable of inducing mixed-mode oscillations. Chapter 4 reports findings on the photosensitive 4-nitrophenol - bromate reaction. Extreme photo-inhibition was found to occur when illumination was supplied to the system whether in a stirred reactor or when being studied in a spatially extended system. Reaction diffusion experiments showed that under certain conditions long lasting complexity in the form of propagation failures took place. In Chapter 5, oscillations in both current density and potential were observed during the electro-oxidation of bromide ions. Interestingly, mechanistic findings suggest that the oscillations occurring during the oxidation of bromide ions on a platinum electrode belong to the type of oscillator referred to as Capacitance Mediated Positive Differential Resistance oscillator, and is the first solution based system to fit this class. In Chapter 6, the electro-oxidation of two sulfur compounds was seen to display nonlinear behavior. First, the oxidation of hydroxymethanesulfinate leads to oscillations in both current and potential on platinum or gold electrodes. The formation of an inhibiting layer was seen to have a substantial influence on the systems’ ability to support sustained oscillatory behavior. Electrochemical Impedance Spectroscopy showed that the oxidation of hydroxymethanesulfinate fits the class of an HN-NDR type oscillator. The oxidation of methionine only displayed nonlinear behavior on a gold surface, and only when operated under potentiostatic conditions. The oscillations were accompanied by gold dissolution and it was found that the electro-oxidation of methionine belongs to the N-NDR class. Two novel examples of utilizing nonlinear reactions towards application-based research is shown in Chapter 7. Here, the 4-nitrophenol – bromate oscillator is used to fabricate platinum nanoparticles, exploiting the dynamic bromide ion concentration to guide the growth of the noble metal nanocrystals. As an example of using an electrochemical nonlinear reaction, the gold dissolution occurring during the oxidation of methionine was found to lead to the fabrication of a Au nanoparticle modified electrode. This modified electrode was found to be capable of simultaneously detecting both hydroquinone and pyrocatechol in solutions containing both isomers, which is a significant improvement over regular Au electrodes

High-Redshift Quasars Found in Sloan Digital Sky Survey Commissioning Data IV: Luminosity Function from the Fall Equatorial Stripe Sampl

This is the fourth paper in a series aimed at finding high-redshift quasars from five-color imaging data taken along the Celestial Equator by the SDSS. during its commissioning phase. In this paper, we use the color-selected sample of 39 luminous high-redshift quasars presented in Paper III to derive the evolution of the quasar luminosity function over the range of 3.6<z<5.0, and -27.5<M_1450<-25.5 (Omega=1, H_0=50 km s^-1 Mpc^-1). We use the selection function derived in Paper III to correct for sample incompleteness. The luminosity function is estimated using three different methods: (1) the 1/V_a estimator; (2) a maximum likelihood solution, assuming that the density of quasars depends exponentially on redshift and as a power law in luminosity and (3) Lynden-Bell's non-parametric C^- estimator. All three methods give consistent results. The luminous quasar density decreases by a factor of ~ 6 from z=3.5 to z=5.0, consistent with the decline seen from several previous optical surveys at z<4.5. The luminosity function follows psi(L) ~ L^{-2.5} for z~4 at the bright end, significantly flatter than the bright end luminosity function psi(L) \propto L^{-3.5} found in previous studies for z<3, suggesting that the shape of the quasar luminosity function evolves with redshift as well, and that the quasar evolution from z=2 to 5 cannot be described as pure luminosity evolution. Possible selection biases and the effect of dust extinction on the redshift evolution of the quasar density are also discussed.Comment: AJ accepted, with minor change

SNP genotyping to screen for a common deletion in CHARGE Syndrome

BACKGROUND: CHARGE syndrome is a complex of birth defects including coloboma, choanal atresia, ear malformations and deafness, cardiac defects, and growth delay. We have previously hypothesized that CHARGE syndrome could be caused by unidentified genomic microdeletion, but no such deletion was detected using short tandem repeat (STR) markers spaced an average of 5 cM apart. Recently, microdeletion at 8q12 locus was reported in two patients with CHARGE, although point mutation in CHD7 on chromosome 8 was the underlying etiology in most of the affected patients. METHODS: We have extended our previous study by employing a much higher density of SNP markers (3258) with an average spacing of approximately 800 kb. These SNP markers are diallelic and, therefore, have much different properties for detection of deletions than STRs. RESULTS: A global error rate estimate was produced based on Mendelian inconsistency. One marker, rs431722 exceeded the expected frequency of inconsistencies, but no deletion could be demonstrated after retesting the 4 inconsistent pedigrees with local flanking markers or by FISH with the corresponding BAC clone. Expected deletion detection (EDD) was used to assess the coverage of specific intervals over the genome by deriving the probability of detecting a common loss of heterozygosity event over each genomic interval. This analysis estimated the fraction of unobserved deletions, taking into account the allele frequencies at the SNPs, the known marker spacing and sample size. CONCLUSIONS: The results of our genotyping indicate that more than 35% of the genome is included in regions with very low probability of a deletion of at least 2 Mb

The Seventh Data Release of the Sloan Digital Sky Survey

This paper describes the Seventh Data Release of the Sloan Digital Sky Survey (SDSS), marking the completion of the original goals of the SDSS and the end of the phase known as SDSS-II. It includes 11663 deg^2 of imaging data, with most of the roughly 2000 deg^2 increment over the previous data release lying in regions of low Galactic latitude. The catalog contains five-band photometry for 357 million distinct objects. The survey also includes repeat photometry over 250 deg^2 along the Celestial Equator in the Southern Galactic Cap. A coaddition of these data goes roughly two magnitudes fainter than the main survey. The spectroscopy is now complete over a contiguous area of 7500 deg^2 in the Northern Galactic Cap, closing the gap that was present in previous data releases. There are over 1.6 million spectra in total, including 930,000 galaxies, 120,000 quasars, and 460,000 stars. The data release includes improved stellar photometry at low Galactic latitude. The astrometry has all been recalibrated with the second version of the USNO CCD Astrograph Catalog (UCAC-2), reducing the rms statistical errors at the bright end to 45 milli-arcseconds per coordinate. A systematic error in bright galaxy photometr is less severe than previously reported for the majority of galaxies. Finally, we describe a series of improvements to the spectroscopic reductions, including better flat-fielding and improved wavelength calibration at the blue end, better processing of objects with extremely strong narrow emission lines, and an improved determination of stellar metallicities. (Abridged)Comment: 20 pages, 10 embedded figures. Accepted to ApJS after minor correction

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment