Model for quantitative tip-enhanced spectroscopy and the extraction of nanoscale-resolved optical constants

Near-field infrared spectroscopy by elastic scattering of light from a probe tip resolves optical contrasts in materials at dramatically sub-wavelength scales across a broad energy range, with the demonstrated capacity for chemical identification at the nanoscale. However, current models of probe-sample near-field interactions still cannot provide a sufficiently quantitatively interpretation of measured near-field contrasts, especially in the case of materials supporting strong surface phonons. We present a model of near-field spectroscopy derived from basic principles and verified by finite-element simulations, demonstrating superb predictive agreement both with tunable quantum cascade laser near-field spectroscopy of SiO$_2$ thin films and with newly presented nanoscale Fourier transform infrared (nanoFTIR) spectroscopy of crystalline SiC. We discuss the role of probe geometry, field retardation, and surface mode dispersion in shaping the measured near-field response. This treatment enables a route to quantitatively determine nano-resolved optical constants, as we demonstrate by inverting newly presented nanoFTIR spectra of an SiO$_2$ thin film into the frequency dependent dielectric function of its mid-infrared optical phonon. Our formalism further enables tip-enhanced spectroscopy as a potent diagnostic tool for quantitative nano-scale spectroscopy.Comment: 19 pages, 9 figure

Using Hubble Space Telescope Imaging of Nuclear Dust Morphology to Rule Out Bars Fueling Seyfert Nuclei

If AGN are powered by the accretion of matter onto massive black holes, how does the gas in the host galaxy lose the required angular momentum to approach the black hole? Gas easily transfers angular momentum to stars in strong bars, making them likely candidates. Although ground-based searches for bars in active galaxies using both optical and near infrared surface brightness have not found any excess of bars relative to quiescent galaxies, the searches have not been able to rule out small-scale nuclear bars. To look for these nuclear bars we use HST WFPC2-NICMOS color maps to search for the straight dust lane signature of strong bars. Of the twelve Seyfert galaxies in our sample, only three have dust lanes consistent with a strong nuclear bar. Therefore, strong nuclear bars cannot be the primary fueling mechanism for Seyfert nuclei. We do find that a majority of the galaxies show an spiral morphology in their dust lanes. These spiral arms may be a possible fueling mechanism.Comment: To be published in the Astronomical Journal, June 1999. 25 pages and 14 figures. Full resolution figures are available at ftp://www.ciw.edu/pub/mregan/fullfigs.tar.g

Bowhead whales, and not right whales, were the primary target of 16th- to 17th-century Basque whalers in the western North Atlantic

Author Posting. © Arctic Institute of North America, 2008. This article is posted here by permission of Arctic Institute of North America for personal use, not for redistribution. The definitive version was published in Arctic 61 (2008): 61-75.During the 16th and 17th centuries, Basque whalers travelled annually to the Strait of Belle Isle and Gulf of St. Lawrence to hunt whales. The hunting that occurred during this period is of primary significance for the North Atlantic right whale, Eubalaena glacialis (Müller, 1776), because it has been interpreted as the largest human-induced reduction of the western North Atlantic population, with ~12250–21 000 whales killed. It has been frequently reported that the Basques targeted two species in this region: the North Atlantic right whale and the bowhead whale, Balaena mysticetus L., 1758. To evaluate this hypothesis and the relative impact of this period of whaling on both species, we collected samples from 364 whale bones during a comprehensive search of Basque whaling ports from the 16th to the 17th century in the Strait of Belle Isle and Gulf of St. Lawrence. Bones were found and sampled at 10 of the 20 sites investigated. DNA was extracted from a subset (n = 218) of these samples. Analysis of the mitochondrial cytochrome b region identified five whale species. The identification of only a single right whale bone and 203 bowhead whale bones from at least 72 individuals indicates that the bowhead whale was likely the principal target of the hunt. These results imply that this whaling had a much greater impact (in terms of numbers of whales removed) on the bowhead whale population than on the western North Atlantic right whale population.Financial support for this work was provided by the Canadian Whale Institute, the Northern Scientific Training Program (NSTP), the Department of Fisheries and Oceans Science Subvention program, the Ocean Life Institute (Woods Hole Oceanographic Institution), and the Natural Sciences and Engineering Research Council of Canada (NSERC)

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data

Copy number variants (CNVs) are currently defined as genomic sequences that are polymorphic in copy number and range in length from 1000 to several million base pairs. Among current array-based CNV detection platforms, long-oligonucleotide arrays promise the highest resolution. However, the performance of currently available analytical tools suffers when applied to these data because of the lower signal:noise ratio inherent in oligonucleotide-based hybridization assays. We have developed wuHMM, an algorithm for mapping CNVs from array comparative genomic hybridization (aCGH) platforms comprised of 385 000 to more than 3 million probes. wuHMM is unique in that it can utilize sequence divergence information to reduce the false positive rate (FPR). We apply wuHMM to 385K-aCGH, 2.1M-aCGH and 3.1M-aCGH experiments comparing the 129X1/SvJ and C57BL/6J inbred mouse genomes. We assess wuHMM's performance on the 385K platform by comparison to the higher resolution platforms and we independently validate 10 CNVs. The method requires no training data and is robust with respect to changes in algorithm parameters. At a FPR of <10%, the algorithm can detect CNVs with five probes on the 385K platform and three on the 2.1M and 3.1M platforms, resulting in effective resolutions of 24 kb, 2–5 kb and 1 kb, respectively

Relationship between Adiponectin and apoB in individuals with diabetes in the Atlantic PATH Cohort

ContextThe increasing prevalence of obesity and diabetes greatly influences the risk for cardiovascular (CV) comorbidities and affects the quality of life of many people. However, the relationship among diabetes, obesity, and cardiovascular risk is complex and requires further investigation to understand the biological milieu connecting these conditions.ObjectiveThe aim of the current study was to explore the relationship between biological markers of adipose tissue function (adiponectin) and CV risk (apolipoprotein B) in body mass index (BMI)–matched participants with and without diabetes.DesignNested case-control study.SettingThe Atlantic Partnership for Tomorrow’s Health (PATH) cohort represents four Atlantic Canadian provinces: Newfoundland and Labrador, New Brunswick; Nova Scotia; and Prince Edward Island.ParticipantsThe study population (n = 480) was aged 35 to 69 years, 240 with diabetes and 240 without diabetes.Main Outcome MeasuresGroups with and without diabetes were matched for sex and BMI. Both measured and self-reported data were used to examine disease status, adiposity, and lifestyle factors. Immunoassays were used to measure plasma markers.ResultsIn these participants, plasma adiponectin levels were lower among those with diabetes than those without diabetes; these results were sex-specific, with a strong relationship seen in women. In contrast, in participants matched for sex and adiposity, plasma apoB levels were similar between participants with and those without diabetes.ConclusionMeasures of adiposity were higher in participants with diabetes. However, when matched for adiposity, the adipokine adiponectin exhibited a strong inverse association with diabetes

Updating quasar bolometric luminosity corrections

Bolometric corrections are used in quasar studies to quantify total energy output based on a measurement of a monochromatic luminosity. First, we enumerate and discuss the practical difficulties of determining such corrections, then we present bolometric luminosities between 1 \mu m and 8 keV rest frame and corrections derived from the detailed spectral energy distributions of 63 bright quasars of low to moderate redshift (z = 0.03-1.4). Exploring several mathematical fittings, we provide practical bolometric corrections of the forms L_iso=\zeta \lambda L_{\lambda} and log(L_iso)=A+B log(\lambda L_{\lambda}) for \lambda= 1450, 3000, and 5100 \AA, where L_iso is the bolometric luminosity calculated under the assumption of isotropy. The significant scatter in the 5100 \AA\ bolometric correction can be reduced by adding a first order correction using the optical slope, \alpha_\lambda,opt. We recommend an adjustment to the bolometric correction to account for viewing angle and the anisotropic emission expected from accretion discs. For optical/UV monochromatic luminosities, radio-loud and radio-quiet bolometric corrections are consistent within 95% confidence intervals so we do not make separate radio-loud and radio-quiet corrections. In addition, we provide several bolometric corrections to the 2-10 keV X-ray luminosity, which are shown to have very large scatter. Separate radio-loud and radio-quiet corrections are warranted by the X-ray data.Comment: 18 pages, 5 tables, 12 figures, accepted to MNRA

The New Generation Atlas of Quasar Spectral Energy Distributions from Radio to X-rays

We have produced the next generation of quasar spectral energy distributions (SEDs), essentially updating the work of Elvis et al. (1994) by using high-quality data obtained with several space and ground-based telescopes, including NASA's Great Observatories. We present an atlas of SEDs of 85 optically bright, non-blazar quasars over the electromagnetic spectrum from radio to X-rays. The heterogeneous sample includes 27 radio-quiet and 58 radio-loud quasars. Most objects have quasi-simultaneous ultraviolet-optical spectroscopic data, supplemented with some far-ultraviolet spectra, and more than half also have Spitzer mid-infrared IRS spectra. The X-ray spectral parameters are collected from the literature where available. The radio, far-infrared, and near-infrared photometric data are also obtained from either the literature or new observations. We construct composite spectral energy distributions for radio-loud and radio-quiet objects and compare these to those of Elvis et al., finding that ours have similar overall shapes, but our improved spectral resolution reveals more detailed features, especially in the mid and near-infrared.Comment: 46 pages, 10 figures, 10 tables, Accepted by ApJS. Composite SED data files for radio-loud and radio-quiet quasars (rlmsedMR.txt, rqmsedMR.txt) are included in the source (Other formats -> Source). Supplemental figures are not include

Climate and plant controls on soil organic matter in coastal wetlands

Coastal wetlands are among the most productive and carbon‐rich ecosystems on Earth. Long‐term carbon storage in coastal wetlands occurs primarily belowground as soil organic matter (SOM). In addition to serving as a carbon sink, SOM influences wetland ecosystem structure, function, and stability. To anticipate and mitigate the effects of climate change, there is a need to advance understanding of environmental controls on wetland SOM. Here, we investigated the influence of four soil formation factors: climate, biota, parent materials, and topography. Along the northern Gulf of Mexico, we collected wetland plant and soil data across elevation and zonation gradients within 10 estuaries that span broad temperature and precipitation gradients. Our results highlight the importance of climate–plant controls and indicate that the influence of elevation is scale and location dependent. Coastal wetland plants are sensitive to climate change; small changes in temperature or precipitation can transform coastal wetland plant communities. Across the region, SOM was greatest in mangrove forests and in salt marshes dominated by graminoid plants. SOM was lower in salt flats that lacked vascular plants and in salt marshes dominated by succulent plants. We quantified strong relationships between precipitation, salinity, plant productivity, and SOM. Low precipitation leads to high salinity, which limits plant productivity and appears to constrain SOM accumulation. Our analyses use data from the Gulf of Mexico, but our results can be related to coastal wetlands across the globe and provide a foundation for predicting the ecological effects of future reductions in precipitation and freshwater availability. Coastal wetlands provide many ecosystem services that are SOM dependent and highly vulnerable to climate change. Collectively, our results indicate that future changes in SOM and plant productivity, regulated by cascading effects of precipitation on freshwater availability and salinity, could impact wetland stability and affect the supply of some wetland ecosystem services

Infrared nanoscopy of Dirac plasmons at the graphene-SiO2 interface

We report on infrared (IR) nanoscopy of 2D plasmon excitations of Dirac fermions in graphene. This is achieved by confining mid-IR radiation at the apex of a nanoscale tip: an approach yielding two orders of magnitude increase in the value of in-plane component of incident wavevector q compared to free space propagation. At these high wavevectors, the Dirac plasmon is found to dramatically enhance the near-field interaction with mid-IR surface phonons of SiO2 substrate. Our data augmented by detailed modeling establish graphene as a new medium supporting plasmonic effects that can be controlled by gate voltage.Comment: 12 pages, 4 figure