Fabrication Of Integrated Optofluidic Circuits In Chalcogenide Glass Using Femtosecond Laser Direct Writing

Femtosecond laser direct writing (FLDW) is a versatile process that uses focused femtosecond pulses to modify the physical structure of a material, which can result in a shift of optical properties such as the linear and nonlinear refractive index. If the photon energy of the femtosecond pulses lies below the material bandgap, nonlinear absorption rather than linear absorption becomes the dominant mechanism of energy transfer to the material. In this manner, a focused femtosecond pulse train can be used to fabricate functional features such as optical waveguides, diffractive optical elements, or micro-fluidic elements within the volume of a transparent medium. In this dissertation, the utility of femtosecond laser processing as a fabrication technique of optical and micro-fluidic elements in chalcogenide glasses is explored. The photo-induced modifications of optical and chemical parameters of new germanium-based Chalcogenide glasses in both bulk and thin-film form are characterized for the first time and the impact of material composition and laser fabrication parameters are discussed. The glasses are found to display an increase in volume, a decrease of the linear optical refractive index, and an increase of the nonlinear refractive index when exposed to femtosecond laser pulses. A model based on avalanche ionization and multi-photon ionization is used to describe the highly nonlinear absorption of laser light in the material and correlate the photo-induced modifications to the electron density generated during irradiation. The magnitude of the induced photomodification is shown to be dependent on laser parameters such as laser dose and repetition rate. The fabrication of microfluidic elements through both direct ablation and the preferential etching of photo-modified regions is also explored. Finally, the integration of both optical elements and fluidic elements fabricated by FLDW into a single substrate is discussed. iv TABLE OF CON

Sublethal Effects of the Insecticide Pyrifluquinazon on the European Honey Bee (Hymenoptera: Apidae)

Pyrifluquinazon (PQZ) is an Insecticide Resistance Action Committee (IRAC) Group 9 insecticide that has recently been registered for use in the United States for control of soft-bodied sucking insect pests. Although it has been classified as practically nontoxic to honey bees, Apis mellifera L. (Hymenoptera: Apidae), based on acute contact bioassays, additional information on sublethal effects of this insecticide on honey bees is lacking. Using a combination of laboratory assays with video movement tracking software and near-field evaluations of colonies foraging in a high-tunnel experiment, we determined that, when fed PQZ at a concentration of 84 mg active ingredient (ai)/liter (= ppm) in sugar water, a reduction in overall movement by the foraging worker bees was observed. However, when provided with honey reserves in the hive, honey bees rejected the PQZ-treated sugar water. These results indicate that, if ingested at levels of 84 mg ai/liter, PQZ could have a negative effect on honey bee behavior; however, honey bee workers appear to be able to detect the presence of PQZ in their food and reject it

Investigation of femtosecond laser induced ripple formation on copper for varying incident angle

The hydrodynamic mechanisms associated with the formation of femtosecond laser induced ripples on copper for two angles of incidence are reported. Laser pulse length used for this work is 35 fs. A revised two-temperature model is presented that comprises transient changes of optical characteristics during the irradiation with femtosecond pulses to model relaxation processes and thermal response in bulk copper. The theoretical model takes into account the fluid flow dynamics that result in ripple periods shorter than the wavelength of the surface plasmon polaritons. Theoretical and experimental results are reported for incident angles of 0°and 45° relative to the surface normal. There is agreement between the experimentally measured and the theoretically predicted ripple periodicity for 50 pulses at 0° incidence. By contrast, for 100 pulses at 0° incidence, and 50 and 100 pulses at 45° incidence, the experimentally measured ripples have a larger period than the one predicted by the model while the trends in period with increased incident angle, and increased fluence are in agreement between the experimental and the theoretical results

Micro/nanostructures formation by femtosecond laser surface processing on amorphous and polycrystalline Ni60Nb40

Femtosecond laser surface processing is a technology that can be used to functionalize many surfaces, imparting specialized properties such as increased broadband optical absorption or superhydrophilicity/superhydrophobicity. In this study, two unique classes of surface structures, below surface growth (BSG) and above surface growth (ASG) mounds, were formed by femtosecond laser surface processing on amorphous and polycrystalline Ni60Nb40 with two different grain sizes. Cross sectional imaging of these mounds revealed thermal evidence of the unique formation processes for each class of surface structure. BSG mounds formed on all three substrates using the same laser parameters had similar surface morphology. The microstructures in the mounds were unaltered compared with the substrate before laser processing, suggesting their formation was dominated by preferential valley ablation. ASG mounds had similar morphology when formed on the polycrystalline Ni60Nb40 substrates with 100 nm and 2 [H9262]m grain size. However, the ASG mounds had significantly wider diameter and higher peak-to-valley heights when the substrate was amorphous Ni60Nb40. Hydrodynamic melting was primarily responsible for ASG mound formation. On amorphous Ni60Nb40 substrates, the ASG mounds are most likely larger due to lower thermal diffusivity. There was clear difference in growth mechanism of femtosecond laser processed BSG and ASG mounds, and grain size does not appear to be a factor

Precision Astrometry with Adaptive Optics

We investigate the limits of ground-based astrometry with adaptive optics using the core of the Galactic globular cluster M5. Adaptive optics systems provide near diffraction-limit imaging with the world's largest telescopes. The substantial improvement in both resolution and signal-to-noise ratio enables high-precision astrometry from the ground. We describe the dominant systematic errors that typically limit ground-based differential astrometry, and enumerate observational considerations for mitigating their effects. After implementing these measures, we find that the dominant limitation on astrometric performance in this experiment is caused by tilt anisoplanatism. We then present an optimal estimation technique for measuring the position of one star relative to a grid of reference stars in the face of this correlated random noise source. Our methodology has the advantage of reducing the astrometric errors as the square root of time and faster than the square root of the number of reference stars -- effectively eliminating noise caused by atmospheric tilt to the point that astrometric performance is limited by centering accuracy. Using 50 reference stars we demonstrate single-epoch astrometric precision of ~ 1 mas in 1 second, decreasing to < 100 microarcseconds in 2 minutes of integration time at the Hale 200-inch telescope. We also show that our astrometry is accurate to <~ 100 microarcseconds for observations separated by 2 months. Finally, we discuss the limits and potential of differential astrometry with current and next generation large aperture telescopes. At this level of accuracy, numerous astrometric applications become accessible, including planet detection, astrometric microlensing signatures, and kinematics of distant Galactic stellar populations.Comment: 32 pages, 12 figures; submitted to A

Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East

Background Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous taurine breeds from the Nile Delta region might provide new insights on the early spread of cattle rearing outside the Near East. Methodology Using Illumina high-throughput sequencing we characterized the mitogenomes from two cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed. Conclusions Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades

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

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

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