Time-of-flight secondary ion mass spectrometry studies of cluster ion analysis for semiconductors and diffusion of manganese in gallium arsenide at low temperatures

NASA Astrophysics Data System (ADS)

Goacher, Robyn Elizabeth

Secondary Ion Mass Spectrometry (SIMS) is an established method for the quantitative analysis of dopants in semiconductors. The quasi-parallel mass acquisition of Time-of-Flight SIMS, along with the development of polyatomic primary ions, have rapidly increased the use of SIMS for analysis of organic and biological specimens. However, the advantages and disadvantages of using cluster primary ions for quantitative analysis of inorganic materials are not clear. The research described in this dissertation investigates the consequences of using polyatomic primary ions for the analysis of inorganic compounds in ToF-SIMS. Furthermore, the diffusion of Mn in GaAs, which is important in Spintronic material applications such as spin injection, is also studied by quantitative ToF-SIMS depth profiling. In the first portion of this work, it was discovered that primary ion bombardment of pre-sputtered compound semiconductors GaAs and InP for the purpose of spectral analysis resulted in the formation of cluster secondary ions, as well as atomic secondary ions (Chapter 2). In particular, bombardment using a cluster primary ion such as Bi3q + or C60q+ resulted in higher yields of high-mass cluster secondary ions. These cluster secondary ions did not have bulk stoichiometry, "non-stoichiometric", in contrast to the paradigm of stoichiometric cluster ions generated from salts. This is attributed to the covalent bonding of the compound semiconductors, as well as to preferential sputtering. The utility of high-mass cluster secondary ions in depth profiling is also discussed. Relative sensitivity factors (RSFs) calculated for ion-implanted Fe and Mn samples in GaAs also exhibit differences based on whether monatomic or polyatomic primary ions are utilized (Chapter 3). These RSFs are important for the quantitative conversion of intensity to concentration. When Bi 32+ primary ions are used for analysis instead of Bi + primary ions, there is a significantly higher proportion of Mn and Fe ions present in the spectra, as referenced to the matrix species. The magnitude of this effect differs depending on the sputtering ion, Cs or C60. The use of C60cluster primary ions for depth profiling of GaAs is also investigated (Chapter 4). In particular, for quantitative depth profiling, parameters such as depth resolution, ion and sputter yields, and relative sensitivity factors are pertinent to profiling thin layered structures quantitatively and quickly. C60 sputtering is compared to Cs sputtering in all of these aspects. It is found that 10 keV C60+ is advantageous for the analysis of metals (such as Au contacts on Si) but that previously reported roughness problems prohibit successful analysis in Si. For Al delta layers and quantum wells in GaAs, C60 q+ sputtering induced very little roughness in the sample, and resulted in high ion yields and excellent signal-to-noise as compared to Cs+ sputtering. However, the depth resolution of C60 is at best equivalent to 1 keV Cs+ and does not extend into the sub 2-nm range. Furthermore, C60 sputtering results in significant carbon implantation. In the second portion of this work, quantitative ToF-SIMS depth profiling was used to evaluate the diffusion of Mn into GaAs. Samples were prepared by Molecular Beam Epitaxy in the department of Physics. Mn diffusion from MnAs was investigated first, and Mn diffusion from layered epitaxial structures of GaAs / Ga1-xMnxAs / GaAs was investigated second. Diffusion experiments were conducted by annealing portions of the samples in sealed glass ampoules at low temperatures (200-400°C). Different sputtering rates were measured for MnAs and GaAs and the measured depth profiles were corrected for these effects. RSFs measured for Mn ion-implanted standards were used to calibrate the intensity scale. For diffusion from MnAs, thin MnAs layers resulted in no measurable changes except in the surface transient. For thick MnAs layers, it was determined that substantial loss of As occurred at 400°C, resulting in severe sample roughening, which inhibited proper SIMS analysis. Results for the diffusion of Mn out of a thick buried layer of Ga1-xMnxAs show that annealing induces diffusion of Mn species from the Ga1-xMnxAs layer into the neighboring GaAs with an activation energy of 0.69+/-0.09 eV. This results in doping of the GaAs layer, which is detrimental to spin injection for Spintronics devices.

Quantitative SIMS depth profiling of diffusion barrier gate-oxynitride structures in TFT-LCDs.

PubMed

Dreer, Sabine; Wilhartitz, Peter; Piplits, Kurt; Mayerhofer, Karl; Foisner, Johann; Hutter, Herbert

2004-06-01

Gate oxynitride structures of TFT-LCDs were investigated by SIMS, and successful solutions are demonstrated to overcome difficulties arising due to the charging effects of the multilayer systems, the matrix effect of the method, and the small pattern sizes of the samples. Because of the excellent reproducibility achieved by applying exponential relative sensitivity functions for quantitative analysis, minor differences in the barrier gate-oxynitride composition deposited on molybdenum capped aluminium-neodymium metallisation electrodes were determined between the centre and the edge of the TFT-LCD substrates. No differences were found for molybdenum-tungsten metallisations. Furthermore, at the edge of the glass substrates, aluminium, neodymium, and molybdenum SIMS depth profiles show an exponential trend. With TEM micrographs an inhomogeneous thickness of the molybdenum capping is revealed as the source of this effect, which influences the electrical behaviour of the device. The production process was improved after these results and the aging behaviour of TFT-LCDs was investigated in order to explain the change in control voltage occurring during the lifetime of the displays. SIMS and TEM show an enrichment of neodymium at the interface to the molybdenum layer, confirming good diffusion protection of the molybdenum barrier during accelerated aging. The reason for the shift of the control voltage was finally located by semi-quantitative depth profiling of the sodium diffusion originating from the glass substrate. Molybdenum-tungsten was a much better buffer for the highly-mobile charge carriers than aluminium-neodymium. Best results were achieved with PVD silicon oxynitride as diffusion barrier and gate insulator deposited on aluminium-neodymium metallisation layers.

Quantitative estimation of carbonation and chloride penetration in reinforced concrete by laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Eto, Shuzo; Matsuo, Toyofumi; Matsumura, Takuro; Fujii, Takashi; Tanaka, Masayoshi Y.

2014-11-01

The penetration profile of chlorine in a reinforced concrete (RC) specimen was determined by laser-induced breakdown spectroscopy (LIBS). The concrete core was prepared from RC beams with cracking damage induced by bending load and salt water spraying. LIBS was performed using a specimen that was obtained by splitting the concrete core, and the line scan of laser pulses gave the two-dimensional emission intensity profiles of 100 × 80 mm2 within one hour. The two-dimensional profile of the emission intensity suggests that the presence of the crack had less effect on the emission intensity when the measurement interval was larger than the crack width. The chlorine emission spectrum was measured without using the buffer gas, which is usually used for chlorine measurement, by collinear double-pulse LIBS. The apparent diffusion coefficient, which is one of the most important parameters for chloride penetration in concrete, was estimated using the depth profile of chlorine emission intensity and Fick's law. The carbonation depth was estimated on the basis of the relationship between carbon and calcium emission intensities. When the carbon emission intensity was statistically higher than the calcium emission intensity at the measurement point, we determined that the point was carbonated. The estimation results were consistent with the spraying test results using phenolphthalein solution. These results suggest that the quantitative estimation by LIBS of carbonation depth and chloride penetration can be performed simultaneously.

Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gritsenko, Marina A.; Xu, Zhe; Liu, Tao

Comprehensive, quantitative information on abundances of proteins and their post-translational modifications (PTMs) can potentially provide novel biological insights into diseases pathogenesis and therapeutic intervention. Herein, we introduce a quantitative strategy utilizing isobaric stable isotope-labelling techniques combined with two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) for large-scale, deep quantitative proteome profiling of biological samples or clinical specimens such as tumor tissues. The workflow includes isobaric labeling of tryptic peptides for multiplexed and accurate quantitative analysis, basic reversed-phase LC fractionation and concatenation for reduced sample complexity, and nano-LC coupled to high resolution and high mass accuracy MS analysis for high confidence identification andmore » quantification of proteins. This proteomic analysis strategy has been successfully applied for in-depth quantitative proteomic analysis of tumor samples, and can also be used for integrated proteome and PTM characterization, as well as comprehensive quantitative proteomic analysis across samples from large clinical cohorts.« less

Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS.

PubMed

Gritsenko, Marina A; Xu, Zhe; Liu, Tao; Smith, Richard D

2016-01-01

Comprehensive, quantitative information on abundances of proteins and their posttranslational modifications (PTMs) can potentially provide novel biological insights into diseases pathogenesis and therapeutic intervention. Herein, we introduce a quantitative strategy utilizing isobaric stable isotope-labeling techniques combined with two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) for large-scale, deep quantitative proteome profiling of biological samples or clinical specimens such as tumor tissues. The workflow includes isobaric labeling of tryptic peptides for multiplexed and accurate quantitative analysis, basic reversed-phase LC fractionation and concatenation for reduced sample complexity, and nano-LC coupled to high resolution and high mass accuracy MS analysis for high confidence identification and quantification of proteins. This proteomic analysis strategy has been successfully applied for in-depth quantitative proteomic analysis of tumor samples and can also be used for integrated proteome and PTM characterization, as well as comprehensive quantitative proteomic analysis across samples from large clinical cohorts.

Quantitative depth profiling of Ce(3+) in Pt/CeO2 by in situ high-energy XPS in a hydrogen atmosphere.

PubMed

Kato, Shunsuke; Ammann, Markus; Huthwelker, Thomas; Paun, Cristina; Lampimäki, Markus; Lee, Ming-Tao; Rothensteiner, Matthäus; van Bokhoven, Jeroen A

2015-02-21

The redox property of ceria is a key factor in the catalytic activity of ceria-based catalysts. The oxidation state of well-defined ceria nanocubes in gas environments was analysed in situ by a novel combination of near-ambient pressure X-ray Photoelectron Spectroscopy (XPS) and high-energy XPS at a synchrotron X-ray source. In situ high-energy XPS is a promising new tool to determine the electronic structure of matter under defined conditions. The aim was to quantitatively determine the degree of cerium reduction in a nano-structured ceria-supported platinum catalyst as a function of the gas environment. To obtain a non-destructive depth profile at near-ambient pressure, in situ high-energy XPS analysis was performed by varying the kinetic energy of photoelectrons from 1 to 5 keV, and, thus, the probing depth. In ceria nanocubes doped with platinum, oxygen vacancies formed only in the uppermost layers of ceria in an atmosphere of 1 mbar hydrogen and 403 K. For pristine ceria nanocubes, no change in the cerium oxidation state in various hydrogen or oxygen atmospheres was observed as a function of probing depth. In the absence of platinum, hydrogen does not dissociate and, thus, does not lead to reduction of ceria.

Radial widths, optical depths, and eccentricities of the Uranian rings

NASA Technical Reports Server (NTRS)

Nicholson, P. D.; Matthews, K.; Goldreich, P.

1982-01-01

Observations of the stellar occultation by the Uranian rings of 15/16 August 1980 are used to estimate radial widths and normal optical depths for segments of rings 6, 5, 4, alpha, beta, eta, gamma, and delta. Synthetic occultation profiles are generated to match the observed light curves. A review of published data confirms the existence of width-radius relations for rings alpha and beta, and indicates that the optical depths of these two rings vary inversely with their radial widths. Masses are obtained for rings alpha and beta, on the assumption that differential precession is prevented by their self-gravity. A quantitative comparison of seven epsilon-ring occultation profiles obtained over a period of 3.4 yr reveals a consistent structure, which may reflect the presence of unresolved gaps and subrings.

Depth-time interpolation of feature trends extracted from mobile microelectrode data with kernel functions.

PubMed

Wong, Stephen; Hargreaves, Eric L; Baltuch, Gordon H; Jaggi, Jurg L; Danish, Shabbar F

2012-01-01

Microelectrode recording (MER) is necessary for precision localization of target structures such as the subthalamic nucleus during deep brain stimulation (DBS) surgery. Attempts to automate this process have produced quantitative temporal trends (feature activity vs. time) extracted from mobile MER data. Our goal was to evaluate computational methods of generating spatial profiles (feature activity vs. depth) from temporal trends that would decouple automated MER localization from the clinical procedure and enhance functional localization in DBS surgery. We evaluated two methods of interpolation (standard vs. kernel) that generated spatial profiles from temporal trends. We compared interpolated spatial profiles to true spatial profiles that were calculated with depth windows, using correlation coefficient analysis. Excellent approximation of true spatial profiles is achieved by interpolation. Kernel-interpolated spatial profiles produced superior correlation coefficient values at optimal kernel widths (r = 0.932-0.940) compared to standard interpolation (r = 0.891). The choice of kernel function and kernel width resulted in trade-offs in smoothing and resolution. Interpolation of feature activity to create spatial profiles from temporal trends is accurate and can standardize and facilitate MER functional localization of subcortical structures. The methods are computationally efficient, enhancing localization without imposing additional constraints on the MER clinical procedure during DBS surgery. Copyright © 2012 S. Karger AG, Basel.

Insights into biodegradation through depth-resolved microbial community functional and structural profiling of a crude-oil contaminant plume

USGS Publications Warehouse

Fahrenfeld, Nicole; Cozzarelli, Isabelle M.; Bailey, Zach; Pruden, Amy

2014-01-01

Small-scale geochemical gradients are a key feature of aquifer contaminant plumes, highlighting the need for functional and structural profiling of corresponding microbial communities on a similar scale. The purpose of this study was to characterize the microbial functional and structural diversity with depth across representative redox zones of a hydrocarbon plume and an adjacent wetland, at the Bemidji Oil Spill site. A combination of quantitative PCR, denaturing gradient gel electrophoresis, and pyrosequencing were applied to vertically sampled sediment cores. Levels of the methanogenic marker gene, methyl coenzyme-M reductase A (mcrA), increased with depth near the oil body center, but were variable with depth further downgradient. Benzoate degradation N (bzdN) hydrocarbon-degradation gene, common to facultatively anaerobic Azoarcus spp., was found at all locations, but was highest near the oil body center. Microbial community structural differences were observed across sediment cores, and bacterial classes containing known hydrocarbon degraders were found to be low in relative abundance. Depth-resolved functional and structural profiling revealed the strongest gradients in the iron-reducing zone, displaying the greatest variability with depth. This study provides important insight into biogeochemical characteristics in different regions of contaminant plumes, which will aid in improving models of contaminant fate and natural attenuation rates.

Secondary Ion Mass Spectrometry SIMS XI

NASA Astrophysics Data System (ADS)

Gillen, G.; Lareau, R.; Bennett, J.; Stevie, F.

2003-05-01

This volume contains 252 contributions presented as plenary, invited and contributed poster and oral presentations at the 11th International Conference on Secondary Ion Mass Spectrometry (SIMS XI) held at the Hilton Hotel, Walt Disney World Village, Orlando, Florida, 7 12 September, 1997. The book covers a diverse range of research, reflecting the rapid growth in advanced semiconductor characterization, ultra shallow depth profiling, TOF-SIMS and the new areas in which SIMS techniques are being used, for example in biological sciences and organic surface characterization. Papers are presented under the following categories: Isotopic SIMS Biological SIMS Semiconductor Characterization Techniques and Applications Ultra Shallow Depth Profiling Depth Profiling Fundamental/Modelling and Diffusion Sputter-Induced Topography Fundamentals of Molecular Desorption Organic Materials Practical TOF-SIMS Polyatomic Primary Ions Materials/Surface Analysis Postionization Instrumentation Geological SIMS Imaging Fundamentals of Sputtering Ion Formation and Cluster Formation Quantitative Analysis Environmental/Particle Characterization Related Techniques These proceedings provide an invaluable source of reference for both newcomers to the field and experienced SIMS users.

Depth profiling of mechanical degradation of PV backsheets after UV exposure

NASA Astrophysics Data System (ADS)

Gu, Xiaohong; Krommenhoek, Peter J.; Lin, Chiao-Chi; Yu, Li-Chieh; Nguyen, Tinh; Watson, Stephanie S.

2015-09-01

Polymeric multilayer backsheets protect the photovoltaic modules from damage of moisture and ultraviolet (UV) while providing electrical insulation. Due to the multilayer structures, the properties of the inner layers of the backsheets, including their interfaces, during weathering are not well known. In this study, a commercial type of PPE (polyethylene terephthalate (PET)/PET/ethylene vinyl acetate (EVA)) backsheet films was selected as a model system for a depth profiling study of mechanical properties of a backsheet film during UV exposure. The NIST SPHERE (Simulated Photodegradation via High Energy Radiant Exposure) was used for the accelerated laboratory exposure of the materials with UV at 85°C and two relative humidities (RH) of 5 % (dry) and 60 % (humid). Cryomicrotomy was used to obtain cross-sectional PPE samples. Mechanical depth profiling of the cross-sections of aged and unaged samples was conducted by nanoindentation, and a peak-force based quantitative nanomechanical atomic force microscopy (QNM-AFM) mapping techniquewas used to investigate the microstructure and adhesion properties of the adhesive tie layers. The nanoindentation results show the stiffening of the elastic modulus in the PET outer and pigmented EVA layers. From QNM-AFM, the microstructures and adhesion properties of the adhesive layers between PET outer and core layers and between PET core and EVA inner layers are revealed and found to degrade significantly after aging under humidity environment. The results from mechanical depth profiling of the PPE backsheet are further related to the previous chemical depth profiling of the same material, providing new insights into the effects of accelerated UV and humidity on the degradation of multilayer backsheet.

Quantification of Hydrogen Concentrations in Surface and Interface Layers and Bulk Materials through Depth Profiling with Nuclear Reaction Analysis.

PubMed

Wilde, Markus; Ohno, Satoshi; Ogura, Shohei; Fukutani, Katsuyuki; Matsuzaki, Hiroyuki

2016-03-29

Nuclear reaction analysis (NRA) via the resonant (1)H((15)N,αγ)(12)C reaction is a highly effective method of depth profiling that quantitatively and non-destructively reveals the hydrogen density distribution at surfaces, at interfaces, and in the volume of solid materials with high depth resolution. The technique applies a (15)N ion beam of 6.385 MeV provided by an electrostatic accelerator and specifically detects the (1)H isotope in depths up to about 2 μm from the target surface. Surface H coverages are measured with a sensitivity in the order of ~10(13) cm(-2) (~1% of a typical atomic monolayer density) and H volume concentrations with a detection limit of ~10(18) cm(-3) (~100 at. ppm). The near-surface depth resolution is 2-5 nm for surface-normal (15)N ion incidence onto the target and can be enhanced to values below 1 nm for very flat targets by adopting a surface-grazing incidence geometry. The method is versatile and readily applied to any high vacuum compatible homogeneous material with a smooth surface (no pores). Electrically conductive targets usually tolerate the ion beam irradiation with negligible degradation. Hydrogen quantitation and correct depth analysis require knowledge of the elementary composition (besides hydrogen) and mass density of the target material. Especially in combination with ultra-high vacuum methods for in-situ target preparation and characterization, (1)H((15)N,αγ)(12)C NRA is ideally suited for hydrogen analysis at atomically controlled surfaces and nanostructured interfaces. We exemplarily demonstrate here the application of (15)N NRA at the MALT Tandem accelerator facility of the University of Tokyo to (1) quantitatively measure the surface coverage and the bulk concentration of hydrogen in the near-surface region of a H2 exposed Pd(110) single crystal, and (2) to determine the depth location and layer density of hydrogen near the interfaces of thin SiO2 films on Si(100).

Quantification of Hydrogen Concentrations in Surface and Interface Layers and Bulk Materials through Depth Profiling with Nuclear Reaction Analysis

PubMed Central

Wilde, Markus; Ohno, Satoshi; Ogura, Shohei; Fukutani, Katsuyuki; Matsuzaki, Hiroyuki

2016-01-01

Nuclear reaction analysis (NRA) via the resonant 1H(15N,αγ)12C reaction is a highly effective method of depth profiling that quantitatively and non-destructively reveals the hydrogen density distribution at surfaces, at interfaces, and in the volume of solid materials with high depth resolution. The technique applies a 15N ion beam of 6.385 MeV provided by an electrostatic accelerator and specifically detects the 1H isotope in depths up to about 2 μm from the target surface. Surface H coverages are measured with a sensitivity in the order of ~1013 cm-2 (~1% of a typical atomic monolayer density) and H volume concentrations with a detection limit of ~1018 cm-3 (~100 at. ppm). The near-surface depth resolution is 2-5 nm for surface-normal 15N ion incidence onto the target and can be enhanced to values below 1 nm for very flat targets by adopting a surface-grazing incidence geometry. The method is versatile and readily applied to any high vacuum compatible homogeneous material with a smooth surface (no pores). Electrically conductive targets usually tolerate the ion beam irradiation with negligible degradation. Hydrogen quantitation and correct depth analysis require knowledge of the elementary composition (besides hydrogen) and mass density of the target material. Especially in combination with ultra-high vacuum methods for in-situ target preparation and characterization, 1H(15N,αγ)12C NRA is ideally suited for hydrogen analysis at atomically controlled surfaces and nanostructured interfaces. We exemplarily demonstrate here the application of 15N NRA at the MALT Tandem accelerator facility of the University of Tokyo to (1) quantitatively measure the surface coverage and the bulk concentration of hydrogen in the near-surface region of a H2 exposed Pd(110) single crystal, and (2) to determine the depth location and layer density of hydrogen near the interfaces of thin SiO2 films on Si(100). PMID:27077920

Basalt weathering rates on Earth and the duration of liquid water on the plains of Gusev Crater, Mars

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steefel, Carl; Hausrath, E.M.; Navarre-Sitchler, A.K.

2008-03-15

Where Martian rocks have been exposed to liquid water, chemistry versus depth profiles could elucidate both Martian climate history and potential for life. The persistence of primary minerals in weathered profiles constrains the exposure time to liquid water: on Earth, mineral persistence times range from {approx}10 ka (olivine) to {approx}250 ka (glass) to {approx}1Ma (pyroxene) to {approx}5Ma (plagioclase). Such persistence times suggest mineral persistence minima on Mars. However, Martian solutions may have been more acidic than on Earth. Relative mineral weathering rates observed for basalt in Svalbard (Norway) and Costa Rica demonstrate that laboratory pH trends can be used tomore » estimate exposure to liquid water both qualitatively (mineral absence or presence) and quantitatively (using reactive transport models). Qualitatively, if the Martian solution pH > {approx}2, glass should persist longer than olivine; therefore, persistence of glass may be a pH-indicator. With evidence for the pH of weathering, the reactive transport code CrunchFlow can quantitatively calculate the minimum duration of exposure to liquid water consistent with a chemical profile. For the profile measured on the surface of Humphrey in Gusev Crater, the minimum exposure time is 22 ka. If correct, this estimate is consistent with short-term, episodic alteration accompanied by ongoing surface erosion. More of these depth profiles should be measured to illuminate the weathering history of Mars.« less

Interfacial mixing in as-deposited Si/Ni/Si layers analyzed by x-ray and polarized neutron reflectometry

NASA Astrophysics Data System (ADS)

Bhattacharya, Debarati; Basu, Saibal; Singh, Surendra; Roy, Sumalay; Dev, Bhupendra Nath

2012-12-01

Interdiffusion occurring across the interfaces in a Si/Ni/Si layered system during deposition at room temperature was probed using x-ray reflectivity (XRR) and polarized neutron reflectivity (PNR). Exploiting the complementarity of these techniques, both structural and magnetic characterization with nanometer depth resolution could be achieved. Suitable model fitting of the reflectivity profiles identified the formation of Ni-Si mixed alloy layers at the Si/Ni and Ni/Si interfaces. The physical parameters of the layered structure, including quantitative assessment of the stoichiometry of interfacial alloys, were obtained from the analyses of XRR and PNR patterns. In addition, PNR provided magnetic moment density profile as a function of depth in the stratified medium.

Objective characterization of bruise evolution using photothermal depth profiling and Monte Carlo modeling

NASA Astrophysics Data System (ADS)

Vidovič, Luka; Milanič, Matija; Majaron, Boris

2015-01-01

Pulsed photothermal radiometry (PPTR) allows noninvasive determination of laser-induced temperature depth profiles in optically scattering layered structures. The obtained profiles provide information on spatial distribution of selected chromophores such as melanin and hemoglobin in human skin. We apply the described approach to study time evolution of incidental bruises (hematomas) in human subjects. By combining numerical simulations of laser energy deposition in bruised skin with objective fitting of the predicted and measured PPTR signals, we can quantitatively characterize the key processes involved in bruise evolution (i.e., hemoglobin mass diffusion and biochemical decomposition). Simultaneous analysis of PPTR signals obtained at various times post injury provides an insight into the variations of these parameters during the bruise healing process. The presented methodology and results advance our understanding of the bruise evolution and represent an important step toward development of an objective technique for age determination of traumatic bruises in forensic medicine.

3-D Surface Depression Profiling Using High Frequency Focused Air-Coupled Ultrasonic Pulses

NASA Technical Reports Server (NTRS)

Roth, Don J.; Kautz, Harold E.; Abel, Phillip B.; Whalen, Mike F.; Hendricks, J. Lynne; Bodis, James R.

1999-01-01

Surface topography is an important variable in the performance of many industrial components and is normally measured with diamond-tip profilometry over a small area or using optical scattering methods for larger area measurement. This article shows quantitative surface topography profiles as obtained using only high-frequency focused air-coupled ultrasonic pulses. The profiles were obtained using a profiling system developed by NASA Glenn Research Center and Sonix, Inc (via a formal cooperative agreement). (The air transducers are available as off-the-shelf items from several companies.) The method is simple and reproducible because it relies mainly on knowledge and constancy of the sound velocity through the air. The air transducer is scanned across the surface and sends pulses to the sample surface where they are reflected back from the surface along the same path as the incident wave. Time-of-flight images of the sample surface are acquired and converted to depth/surface profile images using the simple relation (d = V*t/2) between distance (d), time-of-flight (t), and the velocity of sound in air (V). The system has the ability to resolve surface depression variations as small as 25 microns, is useable over a 1.4 mm vertical depth range, and can profile large areas only limited by the scan limits of the particular ultrasonic system. (Best-case depth resolution is 0.25 microns which may be achievable with improved isolation from vibration and air currents.) The method using an optimized configuration is reasonably rapid and has all quantitative analysis facilities on-line including 2-D and 3-D visualization capability, extreme value filtering (for faulty data), and leveling capability. Air-coupled surface profilometry is applicable to plate-like and curved samples. In this article, results are shown for several proof-of-concept samples, plastic samples burned in microgravity on the STS-54 space shuttle mission, and a partially-coated cylindrical ceramic composite sample. Impressive results were obtained for all samples when compared with diamond-tip profiles and measurements from micrometers. The method is completely nondestructive, noninvasive, non-contact and does not require light-reflective surfaces.

Determination of defect content and defect profile in semiconductor heterostructures

NASA Astrophysics Data System (ADS)

Zubiaga, A.; Garcia, J. A.; Plazaola, F.; Zúñiga-Pérez, J.; Muñoz-Sanjosé, V.

2011-01-01

In this article we present an overview of the technique to obtain the defects depth profile and width of a deposited layer and multilayer based on positron annihilation spectroscopy. In particular we apply the method to ZnO and ZnO/ZnCdO layers deposited on sapphire substrates. After introducing some terminology we first calculate the trend that the W/S parameters of the Doppler broadening measurements must follow, both in a qualitative and quantitative way. From this point we extend the results to calculate the width and defect profiles in deposited layer samples.

Background of SAM atom-fraction profiles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ernst, Frank

Atom-fraction profiles acquired by SAM (scanning Auger microprobe) have important applications, e.g. in the context of alloy surface engineering by infusion of carbon or nitrogen through the alloy surface. However, such profiles often exhibit an artifact in form of a background with a level that anti-correlates with the local atom fraction. This article presents a theory explaining this phenomenon as a consequence of the way in which random noise in the spectrum propagates into the discretized differentiated spectrum that is used for quantification. The resulting model of “energy channel statistics” leads to a useful semi-quantitative background reduction procedure, which ismore » validated by applying it to simulated data. Subsequently, the procedure is applied to an example of experimental SAM data. The analysis leads to conclusions regarding optimum experimental acquisition conditions. The proposed method of background reduction is based on general principles and should be useful for a broad variety of applications. - Highlights: • Atom-fraction–depth profiles of carbon measured by scanning Auger microprobe • Strong background, varies with local carbon concentration. • Needs correction e.g. for quantitative comparison with simulations • Quantitative theory explains background. • Provides background removal strategy and practical advice for acquisition.« less

Non-perturbational surface-wave inversion: A Dix-type relation for surface waves

USGS Publications Warehouse

Haney, Matt; Tsai, Victor C.

2015-01-01

We extend the approach underlying the well-known Dix equation in reflection seismology to surface waves. Within the context of surface wave inversion, the Dix-type relation we derive for surface waves allows accurate depth profiles of shear-wave velocity to be constructed directly from phase velocity data, in contrast to perturbational methods. The depth profiles can subsequently be used as an initial model for nonlinear inversion. We provide examples of the Dix-type relation for under-parameterized and over-parameterized cases. In the under-parameterized case, we use the theory to estimate crustal thickness, crustal shear-wave velocity, and mantle shear-wave velocity across the Western U.S. from phase velocity maps measured at 8-, 20-, and 40-s periods. By adopting a thin-layer formalism and an over-parameterized model, we show how a regularized inversion based on the Dix-type relation yields smooth depth profiles of shear-wave velocity. In the process, we quantitatively demonstrate the depth sensitivity of surface-wave phase velocity as a function of frequency and the accuracy of the Dix-type relation. We apply the over-parameterized approach to a near-surface data set within the frequency band from 5 to 40 Hz and find overall agreement between the inverted model and the result of full nonlinear inversion.

Ti diffusion in ion prebombarded MgO(100). I. A model for quantitative analysis

NASA Astrophysics Data System (ADS)

Lu, M.; Lupu, C.; Styve, V. J.; Lee, S. M.; Rabalais, J. W.

2002-01-01

Enhancement of Ti diffusion in MgO(100) prebombarded with 7 keV Ar+ has been observed. Diffusion was induced by annealing to 1000 °C following the prebombardment and Ti evaporation. Such a sample geometry and experimental procedure alleviates the continuous provision of freely mobile defects introduced by ion irradiation during annealing for diffusion, making diffusion proceed in a non-steady-state condition. Diffusion penetration profiles were obtained by using secondary ion mass spectrometry depth profiling techniques. A model that includes a depth-dependent diffusion coefficient was proposed, which successfully explains the observed non-steady-state radiation enhanced diffusion. The diffusion coefficients are of the order of 10-20 m2/s and are enhanced due to the defect structure inflected by the Ar+ prebombardment.

Weathering profiles in soils and rocks on Earth and Mars

NASA Astrophysics Data System (ADS)

Hausrath, E.; Adcock, C. T.; Bamisile, T.; Baumeister, J. L.; Gainey, S.; Ralston, S. J.; Steiner, M.; Tu, V.

2017-12-01

Interactions of liquid water with rock, soil, or sediments can result in significant chemical and mineralogical changes with depth. These changes can include transformation from one phase to another as well as translocation, addition, and loss of material. The resulting chemical and mineralogical depth profiles can record characteristics of the interacting liquid water such as pH, temperature, duration, and abundance. We use a combined field, laboratory, and modeling approach to interpret the environmental conditions preserved in soils and rocks. We study depth profiles in terrestrial field environments; perform dissolution experiments of primary and secondary phases important in soil environments; and perform numerical modeling to quantitatively interpret weathering environments. In our field studies we have measured time-integrated basaltic mineral dissolution rates, and interpreted the impact of pH and temperature on weathering in basaltic and serpentine-containing rocks and soils. These results help us interpret fundamental processes occurring in soils on Earth and on Mars, and can also be used to inform numerical modeling and laboratory experiments. Our laboratory experiments provide fundamental kinetic data to interpret processes occurring in soils. We have measured dissolution rates of Mars-relevant phosphate minerals, clay minerals, and amorphous phases, as well as dissolution rates under specific Mars-relevant conditions such as in concentrated brines. Finally, reactive transport modeling allows a quantitative interpretation of the kinetic, thermodynamic, and transport processes occurring in soil environments. Such modeling allows the testing of conditions under longer time frames and under different conditions than might be possible under either terrestrial field or laboratory conditions. We have used modeling to examine the weathering of basalt, olivine, carbonate, phosphate, and clay minerals, and placed constraints on the duration, pH, and solution chemistry of past aqueous alteration occurring on Mars.

Characterization of free-standing InAs quantum membranes by standing wave hard x-ray photoemission spectroscopy

NASA Astrophysics Data System (ADS)

Conti, G.; Nemšák, S.; Kuo, C.-T.; Gehlmann, M.; Conlon, C.; Keqi, A.; Rattanachata, A.; Karslıoǧlu, O.; Mueller, J.; Sethian, J.; Bluhm, H.; Rault, J. E.; Rueff, J. P.; Fang, H.; Javey, A.; Fadley, C. S.

2018-05-01

Free-standing nanoribbons of InAs quantum membranes (QMs) transferred onto a (Si/Mo) multilayer mirror substrate are characterized by hard x-ray photoemission spectroscopy (HXPS) and by standing-wave HXPS (SW-HXPS). Information on the chemical composition and on the chemical states of the elements within the nanoribbons was obtained by HXPS and on the quantitative depth profiles by SW-HXPS. By comparing the experimental SW-HXPS rocking curves to x-ray optical calculations, the chemical depth profile of the InAs(QM) and its interfaces were quantitatively derived with ångström precision. We determined that (i) the exposure to air induced the formation of an InAsO4 layer on top of the stoichiometric InAs(QM); (ii) the top interface between the air-side InAsO4 and the InAs(QM) is not sharp, indicating that interdiffusion occurs between these two layers; (iii) the bottom interface between the InAs(QM) and the native oxide SiO2 on top of the (Si/Mo) substrate is abrupt. In addition, the valence band offset (VBO) between the InAs(QM) and the SiO2/(Si/Mo) substrate was determined by HXPS. The value of VBO = 0.2 ± 0.04 eV is in good agreement with literature results obtained by electrical characterization, giving a clear indication of the formation of a well-defined and abrupt InAs/SiO2 heterojunction. We have demonstrated that HXPS and SW-HXPS are non-destructive, powerful methods for characterizing interfaces and for providing chemical depth profiles of nanostructures, quantum membranes, and 2D layered materials.

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

PubMed Central

Turner, Stephanie; Mikutta, Robert; Meyer-Stüve, Sandra; Guggenberger, Georg; Schaarschmidt, Frank; Lazar, Cassandre S.; Dohrmann, Reiner; Schippers, Axel

2017-01-01

Along a long-term ecosystem development gradient, soil nutrient contents and mineralogical properties change, therefore probably altering soil microbial communities. However, knowledge about the dynamics of soil microbial communities during long-term ecosystem development including progressive and retrogressive stages is limited, especially in mineral soils. Therefore, microbial abundances (quantitative PCR) and community composition (pyrosequencing) as well as their controlling soil properties were investigated in soil depth profiles along the 120,000 years old Franz Josef chronosequence (New Zealand). Additionally, in a microcosm incubation experiment the effects of particular soil properties, i.e., soil age, soil organic matter fraction (mineral-associated vs. particulate), O2 status, and carbon and phosphorus additions, on microbial abundances (quantitative PCR) and community patterns (T-RFLP) were analyzed. The archaeal to bacterial abundance ratio not only increased with soil depth but also with soil age along the chronosequence, coinciding with mineralogical changes and increasing phosphorus limitation. Results of the incubation experiment indicated that archaeal abundances were less impacted by the tested soil parameters compared to Bacteria suggesting that Archaea may better cope with mineral-induced substrate restrictions in subsoils and older soils. Instead, archaeal communities showed a soil age-related compositional shift with the Bathyarchaeota, that were frequently detected in nutrient-poor, low-energy environments, being dominant at the oldest site. However, bacterial communities remained stable with ongoing soil development. In contrast to the abundances, the archaeal compositional shift was associated with the mineralogical gradient. Our study revealed, that archaeal and bacterial communities in whole soil profiles are differently affected by long-term soil development with archaeal communities probably being better adapted to subsoil conditions, especially in nutrient-depleted old soils. PMID:28579976

Detection of Matrix Elements and Trace Impurities in Cu(In, Ga)Se2 Photovoltaic Absorbers Using Surface Analytical Techniques.

PubMed

Kim, Min Jung; Lee, Jihye; Kim, Seon Hee; Kim, Haidong; Lee, Kang-Bong; Lee, Yeonhee

2015-10-01

Chalcopyrite Cu(In, Ga)Se2 (CIGS) thin films are well known as the next-generation solar cell materials notable for their high absorption coefficient for solar radiation, suitable band gap, and ability for deposition on flexible substrate materials, allowing the production of highly flexible and lightweight solar panels. To improve solar cell performances, a quantitative and depth-resolved elemental analysis of photovoltaic thin films is much needed. In this study, Cu(In, Ga)Se2 thin films were prepared on molybdenum back contacts deposited on soda-lime glass substrates via three-stage evaporation. Surface analyses via AES and SIMS were used to characterize the CIGS thin films and compare their depth profiles. We determined the average concentration of the matrix elements, Cu, In, Ga, and Se, using ICP-AES, XRF, and EPMA. We also obtained depth profiling results using TOF-SIMS, magnetic sector SIMS and AES, and APT, a sub-nanometer resolution characterization technique that enables three-dimensional elemental mapping. The SIMS technique, with its high detection limit and ability to obtain the profiles of elements in parallel, is a powerful tool for monitoring trace elements in CIGS thin films. To identify impurities in a CIGS layer, the distribution of trace elements was also observed according to depth by SIMS and APT.

Pulsed photothermal depth profiling of tattoos undergoing laser removal treatment

NASA Astrophysics Data System (ADS)

Milanic, Matija; Majaron, Boris

2012-02-01

Pulsed photothermal radiometry (PPTR) allows noninvasive determination of temperature depth profiles induced by pulsed laser irradiation of strongly scattering biological tissues and organs, including human skin. In present study, we evaluate the potential of this technique for investigational characterization and possibly quantitative evaluation of laser tattoo removal. The study involved 5 healthy volunteers (3 males, 2 females), age 20-30 years, undergoing tattoo removal treatment using a Q-switched Nd:YAG laser. There were four measurement and treatment sessions in total, separated by 2-3 months. Prior to each treatment, PPTR measurements were performed on several tattoo sites and one nearby healthy site in each patient, using a 5 ms Nd:YAG laser at low radiant exposure values and a dedicated radiometric setup. The laser-induced temperature profiles were then reconstructed by applying a custom numerical code. In addition, each tatoo site was documented with a digital camera and measured with a custom colorimetric system (in tristimulus color space), providing an objective evaluation of the therapeutic efficacy to be correlated with our PPTR results. The results show that the laser-induced temperature profile in untreated tattoos is invariably located at a subsurface depth of 300 μm. In tattoo sites that responded well to laser therapy, a significant drop of the temperature peak was observed in the profiles obtained from PPTR record. In several sites that appeared less responsive, as evidenced by colorimetric data, a progressive shift of the temperature profile deeper into the dermis was observed over the course of consecutive laser treatments, indicating that the laser tattoo removal was efficient.

New Technology-Large-Area Three- Dimensional Surface Profiling Using Only Focused Air-Coupled Ultrasound-Given 1999 R&D 100 Award

NASA Technical Reports Server (NTRS)

Roth, Don J.; Kautz, Harold E.; Abel, Phillip B.; Whalen, Mike F.; Hendricks, J. Lynne; Bodis, James R.

2000-01-01

Surface topography, which significantly affects the performance of many industrial components, is normally measured with diamond-tip profilometry over small areas or with optical scattering methods over larger areas. To develop air-coupled surface profilometry, the NASA Glenn Research Center at Lewis Field initiated a Space Act Agreement with Sonix, Inc., through two Glenn programs, the Advanced High Temperature Engine Materials Program (HITEMP) and COMMTECH. The work resulted in quantitative surface topography profiles obtained using only high-frequency, focused ultrasonic pulses in air. The method is nondestructive, noninvasive, and noncontact, and it does not require light-reflective surfaces. Air surface profiling may be desirable when diamond-tip or laserbased methods are impractical, such as over large areas, when a significant depth range is required, or for curved surfaces. When the configuration is optimized, the method is reasonably rapid and all the quantitative analysis facilities are online, including two- and three-dimensional visualization, extreme value filtering (for faulty data), and leveling.

Acclimation to different depths by the marine angiosperm Posidonia oceanica: transcriptomic and proteomic profiles

PubMed Central

Dattolo, Emanuela; Gu, Jenny; Bayer, Philipp E.; Mazzuca, Silvia; Serra, Ilia A.; Spadafora, Antonia; Bernardo, Letizia; Natali, Lucia; Cavallini, Andrea; Procaccini, Gabriele

2013-01-01

For seagrasses, seasonal and daily variations in light and temperature represent the mains factors driving their distribution along the bathymetric cline. Changes in these environmental factors, due to climatic and anthropogenic effects, can compromise their survival. In a framework of conservation and restoration, it becomes crucial to improve our knowledge about the physiological plasticity of seagrass species along environmental gradients. Here, we aimed to identify differences in transcriptomic and proteomic profiles, involved in the acclimation along the depth gradient in the seagrass Posidonia oceanica, and to improve the available molecular resources in this species, which is an important requisite for the application of eco-genomic approaches. To do that, from plant growing in shallow (−5 m) and deep (−25 m) portions of a single meadow, (i) we generated two reciprocal Expressed Sequences Tags (EST) libraries using a Suppressive Subtractive Hybridization (SSH) approach, to obtain depth/specific transcriptional profiles, and (ii) we identified proteins differentially expressed, using the highly innovative USIS mass spectrometry methodology, coupled with 1D-SDS electrophoresis and labeling free approach. Mass spectra were searched in the open source Global Proteome Machine (GPM) engine against plant databases and with the X!Tandem algorithm against a local database. Transcriptional analysis showed both quantitative and qualitative differences between depths. EST libraries had only the 3% of transcripts in common. A total of 315 peptides belonging to 64 proteins were identified by mass spectrometry. ATP synthase subunits were among the most abundant proteins in both conditions. Both approaches identified genes and proteins in pathways related to energy metabolism, transport and genetic information processing, that appear to be the most involved in depth acclimation in P. oceanica. Their putative rules in acclimation to depth were discussed. PMID:23785376

Acclimation to different depths by the marine angiosperm Posidonia oceanica: transcriptomic and proteomic profiles.

PubMed

Dattolo, Emanuela; Gu, Jenny; Bayer, Philipp E; Mazzuca, Silvia; Serra, Ilia A; Spadafora, Antonia; Bernardo, Letizia; Natali, Lucia; Cavallini, Andrea; Procaccini, Gabriele

2013-01-01

For seagrasses, seasonal and daily variations in light and temperature represent the mains factors driving their distribution along the bathymetric cline. Changes in these environmental factors, due to climatic and anthropogenic effects, can compromise their survival. In a framework of conservation and restoration, it becomes crucial to improve our knowledge about the physiological plasticity of seagrass species along environmental gradients. Here, we aimed to identify differences in transcriptomic and proteomic profiles, involved in the acclimation along the depth gradient in the seagrass Posidonia oceanica, and to improve the available molecular resources in this species, which is an important requisite for the application of eco-genomic approaches. To do that, from plant growing in shallow (-5 m) and deep (-25 m) portions of a single meadow, (i) we generated two reciprocal Expressed Sequences Tags (EST) libraries using a Suppressive Subtractive Hybridization (SSH) approach, to obtain depth/specific transcriptional profiles, and (ii) we identified proteins differentially expressed, using the highly innovative USIS mass spectrometry methodology, coupled with 1D-SDS electrophoresis and labeling free approach. Mass spectra were searched in the open source Global Proteome Machine (GPM) engine against plant databases and with the X!Tandem algorithm against a local database. Transcriptional analysis showed both quantitative and qualitative differences between depths. EST libraries had only the 3% of transcripts in common. A total of 315 peptides belonging to 64 proteins were identified by mass spectrometry. ATP synthase subunits were among the most abundant proteins in both conditions. Both approaches identified genes and proteins in pathways related to energy metabolism, transport and genetic information processing, that appear to be the most involved in depth acclimation in P. oceanica. Their putative rules in acclimation to depth were discussed.

Assessment of biofilm changes and concentration-depth profiles during arsenopyrite oxidation by Acidithiobacillus thiooxidans.

PubMed

Ramírez-Aldaba, Hugo; Vazquez-Arenas, Jorge; Sosa-Rodríguez, Fabiola S; Valdez-Pérez, Donato; Ruiz-Baca, Estela; García-Meza, Jessica Viridiana; Trejo-Córdova, Gabriel; Lara, René H

2017-08-01

Biofilm formation and evolution are key factors to consider to better understand the kinetics of arsenopyrite biooxidation. Chemical and surface analyses were carried out using Raman spectroscopy, scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), glow discharge spectroscopy (GDS), and protein analysis (i.e., quantification) in order to evaluate the formation of intermediate secondary compounds and any significant changes arising in the biofilm structure of Acidithiobacillus thiooxidans during a 120-h period of biooxidation. Results show that the biofilm first evolves from a low cell density structure (1 to 12 h) into a formation of microcolonies (24 to 120 h) and then finally becomes enclosed by a secondary compound matrix that includes pyrite (FeS 2 )-like, S n 2- /S 0 , and As 2 S 3 compounds, as shown by Raman and SEM-EDS. GDS analyses (concentration-depth profiles, i.e., 12 h) indicate significant differences for depth speciation between abiotic control and biooxidized surfaces, thus providing a quantitative assessment of surface-bulk changes across samples (i.e. reactivity and /or structure-activity relationship). Respectively, quantitative protein analyses and CLSM analyses suggest variations in the type of extracellular protein expressed and changes in the biofilm structure from hydrophilic (i.e., exopolysaccharides) to hydrophobic (i.e., lipids) due to arsenopyrite and cell interactions during the 120-h period of biooxidation. We suggest feasible environmental and industrial implications for arsenopyrite biooxidation based on the findings of this study.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wulff, J; Huggins, A

Purpose: The shape of a single beam in proton PBS influences the resulting dose distribution. Spot profiles are modelled as two-dimensional Gaussian (single/ double) distributions in treatment planning systems (TPS). Impact of slight deviations from an ideal Gaussian on resulting dose distributions is typically assumed to be small due to alleviation by multiple Coulomb scattering (MCS) in tissue and superposition of many spots. Quantitative limits are however not clear per se. Methods: A set of 1250 deliberately deformed profiles with sigma=4 mm for a Gaussian fit were constructed. Profiles and fit were normalized to the same area, resembling output calibrationmore » in the TPS. Depth-dependent MCS was considered. The deviation between deformed and ideal profiles was characterized by root-mean-squared deviation (RMSD), skewness/ kurtosis (SK) and full-width at different percentage of maximum (FWxM). The profiles were convolved with different fluence patterns (regular/ random) resulting in hypothetical dose distributions. The resulting deviations were analyzed by applying a gamma-test. Results were compared to measured spot profiles. Results: A clear correlation between pass-rate and profile metrics could be determined. The largest impact occurred for a regular fluence-pattern with increasing distance between single spots, followed by a random distribution of spot weights. The results are strongly dependent on gamma-analysis dose and distance levels. Pass-rates of >95% at 2%/2 mm and 40 mm depth (=70 MeV) could only be achieved for RMSD<10%, deviation in FWxM at 20% and root of quadratic sum of SK <0.8. As expected the results improve for larger depths. The trends were well resembled for measured spot profiles. Conclusion: All measured profiles from ProBeam sites passed the criteria. Given the fact, that beam-line tuning can result shape distortions, the derived criteria represent a useful QA tool for commissioning and design of future beam-line optics.« less

Quantitative Analysis of Human Pluripotency and Neural Specification by In-Depth (Phospho)Proteomic Profiling.

PubMed

Singec, Ilyas; Crain, Andrew M; Hou, Junjie; Tobe, Brian T D; Talantova, Maria; Winquist, Alicia A; Doctor, Kutbuddin S; Choy, Jennifer; Huang, Xiayu; La Monaca, Esther; Horn, David M; Wolf, Dieter A; Lipton, Stuart A; Gutierrez, Gustavo J; Brill, Laurence M; Snyder, Evan Y

2016-09-13

Controlled differentiation of human embryonic stem cells (hESCs) can be utilized for precise analysis of cell type identities during early development. We established a highly efficient neural induction strategy and an improved analytical platform, and determined proteomic and phosphoproteomic profiles of hESCs and their specified multipotent neural stem cell derivatives (hNSCs). This quantitative dataset (nearly 13,000 proteins and 60,000 phosphorylation sites) provides unique molecular insights into pluripotency and neural lineage entry. Systems-level comparative analysis of proteins (e.g., transcription factors, epigenetic regulators, kinase families), phosphorylation sites, and numerous biological pathways allowed the identification of distinct signatures in pluripotent and multipotent cells. Furthermore, as predicted by the dataset, we functionally validated an autocrine/paracrine mechanism by demonstrating that the secreted protein midkine is a regulator of neural specification. This resource is freely available to the scientific community, including a searchable website, PluriProt. Published by Elsevier Inc.

Complex EUV imaging reflectometry: spatially resolved 3D composition determination and dopant profiling with a tabletop 13nm source

NASA Astrophysics Data System (ADS)

Porter, Christina L.; Tanksalvala, Michael; Gerrity, Michael; Miley, Galen P.; Esashi, Yuka; Horiguchi, Naoto; Zhang, Xiaoshi; Bevis, Charles S.; Karl, Robert; Johnsen, Peter; Adams, Daniel E.; Kapteyn, Henry C.; Murnane, Margaret M.

2018-03-01

With increasingly 3D devices becoming the norm, there is a growing need in the semiconductor industry and in materials science for high spatial resolution, non-destructive metrology techniques capable of determining depth-dependent composition information on devices. We present a solution to this problem using ptychographic coherent diffractive imaging (CDI) implemented using a commercially available, tabletop 13 nm source. We present the design, simulations, and preliminary results from our new complex EUV imaging reflectometer, which uses coherent 13 nm light produced by tabletop high harmonic generation. This tool is capable of determining spatially-resolved composition vs. depth profiles for samples by recording ptychographic images at multiple incidence angles. By harnessing phase measurements, we can locally and nondestructively determine quantities such as device and thin film layer thicknesses, surface roughness, interface quality, and dopant concentration profiles. Using this advanced imaging reflectometer, we can quantitatively characterize materials-sciencerelevant and industry-relevant nanostructures for a wide variety of applications, spanning from defect and overlay metrology to the development and optimization of nano-enhanced thermoelectric or spintronic devices.

Depth dependence of defect evolution and TED during annealing

NASA Astrophysics Data System (ADS)

Colombeau, B.; Cowern, N. E. B.; Cristiano, F.; Calvo, P.; Lamrani, Y.; Cherkashin, N.; Lampin, E.; Claverie, A.

2004-02-01

A quantitative transmission electron microscopy (TEM) study on the depth profile of extended defects, formed after Si implantation, has been carried out. Two different Si + implant conditions have been considered. TEM analysis for the highest energy/dose shows that {1 1 3} defects evolve into dislocation loops whilst the defect depth distribution remains unchanged as a function of annealing time. For the lowest energy/dose, {1 1 3} defects grow and dissolve while the defect band shrinks preferentially on the surface side. At the same time, extraction of boron transient enhanced diffusion (TED) as a function of depth shows a decrease of the supersaturation towards the surface, starting at the location of the defect band. The study clearly shows that in these systems the silicon surface is the principal sink for interstitials. The results provide a critical test of the ability of physical models to simulate defect evolution and TED.

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium.

PubMed

Pereira, Arthur Prudêncio de Araujo; Andrade, Pedro Avelino Maia de; Bini, Daniel; Durrer, Ademir; Robin, Agnès; Bouillet, Jean Pierre; Andreote, Fernando Dini; Cardoso, Elke Jurandy Bran Nogueira

2017-01-01

Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil.

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium

PubMed Central

de Andrade, Pedro Avelino Maia; Bini, Daniel; Durrer, Ademir; Robin, Agnès; Bouillet, Jean Pierre; Andreote, Fernando Dini; Cardoso, Elke Jurandy Bran Nogueira

2017-01-01

Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil. PMID:28686690

The A-Like Faker Assay for Measuring Yeast Chromosome III Stability.

PubMed

Novoa, Carolina A; Ang, J Sidney; Stirling, Peter C

2018-01-01

The ability to rapidly assess chromosome instability (CIN) has enabled profiling of most yeast genes for potential effects on genome stability. The A-like faker (ALF) assay is one of several qualitative and quantitative marker loss assays that indirectly measure loss or conversion of genetic material using a counterselection step. The ALF assay relies on the ability to count spurious mating events that occur upon loss of the MATα locus of haploid Saccharomyces cerevisiae strains. Here, we describe the deployment of the ALF assay for both rapid and simple qualitative, and more in-depth quantitative analysis allowing determination of absolute ALF frequencies.

Integrated work-flow for quantitative metabolome profiling of plants, Peucedani Radix as a case.

PubMed

Song, Yuelin; Song, Qingqing; Liu, Yao; Li, Jun; Wan, Jian-Bo; Wang, Yitao; Jiang, Yong; Tu, Pengfei

2017-02-08

Universal acquisition of reliable information regarding the qualitative and quantitative properties of complicated matrices is the premise for the success of metabolomics study. Liquid chromatography-mass spectrometry (LC-MS) is now serving as a workhorse for metabolomics; however, LC-MS-based non-targeted metabolomics is suffering from some shortcomings, even some cutting-edge techniques have been introduced. Aiming to tackle, to some extent, the drawbacks of the conventional approaches, such as redundant information, detector saturation, low sensitivity, and inconstant signal number among different runs, herein, a novel and flexible work-flow consisting of three progressive steps was proposed to profile in depth the quantitative metabolome of plants. The roots of Peucedanum praeruptorum Dunn (Peucedani Radix, PR) that are rich in various coumarin isomers, were employed as a case study to verify the applicability. First, offline two dimensional LC-MS was utilized for in-depth detection of metabolites in a pooled PR extract namely universal metabolome standard (UMS). Second, mass fragmentation rules, notably concerning angular-type pyranocoumarins that are the primary chemical homologues in PR, and available databases were integrated for signal assignment and structural annotation. Third, optimum collision energy (OCE) as well as ion transition for multiple monitoring reaction measurement was online optimized with a reference compound-free strategy for each annotated component and large-scale relative quantification of all annotated components was accomplished by plotting calibration curves via serially diluting UMS. It is worthwhile to highlight that the potential of OCE for isomer discrimination was described and the linearity ranges of those primary ingredients were extended by suppressing their responses. The integrated workflow is expected to be qualified as a promising pipeline to clarify the quantitative metabolome of plants because it could not only holistically provide qualitative information, but also straightforwardly generate accurate quantitative dataset. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative measurement of marginal disintegration of ceramic inlays.

PubMed

Hayashi, Mikako; Tsubakimoto, Yuko; Takeshige, Fumio; Ebisu, Shigeyuki

2004-01-01

The objectives of this study include establishing a method for quantitative measurement of marginal change in ceramic inlays and clarifying their marginal disintegration in vivo. An accurate CCD optical laser scanner system was used for morphological measurement of the marginal change of ceramic inlays. The accuracy of the CCD measurement was assessed by comparing it with microscopic measurement. Replicas of 15 premolars restored with Class II ceramic inlays at the time of placement and eight years after restoration were used for morphological measurement by means of the CCD laser scanner system. Occlusal surfaces of the restored teeth were scanned and cross-sections of marginal areas were computed with software. Marginal change was defined as the area enclosed by two profiles obtained by superimposing two cross-sections of the same location at two different times and expressing the maximum depth and mean area of the area enclosed. The accuracy of this method of measurement was 4.3 +/- 3.2 microm in distance and 2.0 +/- 0.6% in area. Quantitative marginal changes for the eight-year period were 10 x 10 microm in depth and 50 x 10(3) microm2 in area at the functional cusp area and 7 x 10 microm in depth and 28 x 10(3) microm2 in area at the non-functional cusp area. Marginal disintegration at the functional cusp area was significantly greater than at the non-functional cusp area (Wilcoxon signed-ranks test, p < 0.05). This study constitutes a quantitative measurement of in vivo deterioration in marginal adaptation of ceramic inlays and indicates that occlusal force may accelerate marginal disintegration.

Measuring depth profiles of residual stress with Raman spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Enloe, W.S.; Sparks, R.G.; Paesler, M.A.

Knowledge of the variation of residual stress is a very important factor in understanding the properties of machined surfaces. The nature of the residual stress can determine a part`s susceptibility to wear deformation, and cracking. Raman spectroscopy is known to be a very useful technique for measuring residual stress in many materials. These measurements are routinely made with a lateral resolution of 1{mu}m and an accuracy of 0.1 kbar. The variation of stress with depth; however, has not received much attention in the past. A novel technique has been developed that allows quantitative measurement of the variation of the residualmore » stress with depth with an accuracy of 10nm in the z direction. Qualitative techniques for determining whether the stress is varying with depth are presented. It is also demonstrated that when the stress is changing over the volume sampled, errors can be introduced if the variation of the stress with depth is ignored. Computer aided data analysis is used to determine the depth dependence of the residual stress.« less

Structure and Optical Properties of the Atmospheric Boundary Layer over Dusty Hot Deserts

NASA Astrophysics Data System (ADS)

Chalermthai, B.; Al Marzooqi, M.; Basha, G.; Ouarda, T.; Armstrong, P.; Molini, A.

2014-12-01

Strong sensible heat fluxes and deep turbulent mixing - together with marked dustiness and a low substrate water content - represent a characteristic signature of the atmospheric boundary layer (ABL) over hot deserts, resulting in "thicker" mixing layers and peculiar optical properties. Beside these main common features however, desert boundary layers present extremely complex local structures that have been scarcely addressed in the literature, and whose understanding is essential in modeling processes such as transport and deposition of dust and pollutants, local wind fields, turbulent fluxes and their impacts on the sustainable development, human health and solar energy harvesting in these regions. In this study, we explore the potential of the joint usage of Lidar Ceilometer backscattering profiles and sun-photometer optical depth retrievals to quantitatively determine the vertical aerosol profile over dusty hot desert regions. Toward this goal, we analyze a continuous record of observations of the atmospheric boundary layer height from a single lens LiDAR ceilometer operated at Masdar Institute Field Station (24.4425N 54.6163E, Abu Dhabi, United Arab Emirates), starting March 2013, and the concurrent measurements of aerosol optical depth derived independently from the Masdar Institute AERONET sun-photometer. The main features of the desert ABL are obtained from the ceilometer range corrected backscattering profiles through bi-dimensional clustering technique we developed as a modification of the recently proposed single-profile clustering method, and therefore "directly" and "indirectly" calibrated to obtain a full diurnal cycle climatology of the aerosol optical depth and aerosol profiles. The challenges and the advantages of applying a similar methodology to the monitoring of aerosols and dust over hyper-arid regions are also discussed, together with the issues related to the sensitivity of commercial ceilometers to changes in the solar background.

XANES analyses of silicon crystalline irradiated by nitrogen/oxygen ions.

PubMed

Yoshida, T; Hara, T; Li, T; Yoshida, H; Tanabe, T

2001-03-01

X-ray absorption techniques have been applied to the characterization of 5 keV nitrogen / oxygen ions implanted silicon samples. The depth selective measurement of XANES by recording in PEY mode and the quantitative analysis by superposition of XANES spectra were carried out to elucidate the depth profile of implanted ions. It has been revealed that the silicon nitride phase were formed in silicon after prolonged N+ irradiation and it extended over the deep part of the damaged region from the surface. On the other hand, for the O+ irradiation, silicon dioxide phase were produced only in the shallow part of the damaged region, i.e., the silicon dioxide phase likely broke off during the irradiation.

Coexistence of colossal stress and texture gradients in sputter deposited nanocrystalline ultra-thin metal films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuru, Yener; Welzel, Udo; Mittemeijer, Eric J.

2014-12-01

This paper demonstrates experimentally that ultra-thin, nanocrystalline films can exhibit coexisting colossal stress and texture depth gradients. Their quantitative determination is possible by X-ray diffraction experiments. Whereas a uniform texture by itself is known to generally cause curvature in so-called sin{sup 2}ψ plots, it is shown that the combined action of texture and stress gradients provides a separate source of curvature in sin{sup 2}ψ plots (i.e., even in cases where a uniform texture does not induce such curvature). On this basis, the texture and stress depth profiles of a nanocrystalline, ultra-thin (50 nm) tungsten film could be determined.

Coherent diffraction surface imaging in reflection geometry.

PubMed

Marathe, Shashidhara; Kim, S S; Kim, S N; Kim, Chan; Kang, H C; Nickles, P V; Noh, D Y

2010-03-29

We present a reflection based coherent diffraction imaging method which can be used to reconstruct a non periodic surface image from a diffraction amplitude measured in reflection geometry. Using a He-Ne laser, we demonstrated that a surface image can be reconstructed solely from the reflected intensity from a surface without relying on any prior knowledge of the sample object or the object support. The reconstructed phase image of the exit wave is particularly interesting since it can be used to obtain quantitative information of the surface depth profile or the phase change during the reflection process. We believe that this work will broaden the application areas of coherent diffraction imaging techniques using light sources with limited penetration depth.

Fourier phase in Fourier-domain optical coherence tomography.

PubMed

Uttam, Shikhar; Liu, Yang

2015-12-01

Phase of an electromagnetic wave propagating through a sample-of-interest is well understood in the context of quantitative phase imaging in transmission-mode microscopy. In the past decade, Fourier-domain optical coherence tomography has been used to extend quantitative phase imaging to the reflection-mode. Unlike transmission-mode electromagnetic phase, however, the origin and characteristics of reflection-mode Fourier phase are poorly understood, especially in samples with a slowly varying refractive index. In this paper, the general theory of Fourier phase from first principles is presented, and it is shown that Fourier phase is a joint estimate of subresolution offset and mean spatial frequency of the coherence-gated sample refractive index. It is also shown that both spectral-domain phase microscopy and depth-resolved spatial-domain low-coherence quantitative phase microscopy are special cases of this general theory. Analytical expressions are provided for both, and simulations are presented to explain and support the theoretical results. These results are further used to show how Fourier phase allows the estimation of an axial mean spatial frequency profile of the sample, along with depth-resolved characterization of localized optical density change and sample heterogeneity. Finally, a Fourier phase-based explanation of Doppler optical coherence tomography is also provided.

Effect of water on solid electrolyte interphase formation in Li-ion batteries

NASA Astrophysics Data System (ADS)

Saito, M.; Fujita, M.; Aoki, Y.; Yoshikawa, M.; Yasuda, K.; Ishigami, R.; Nakata, Y.

2016-03-01

Time-of-flight-elastic recoil detection analysis (TOF-ERDA) with 20 MeV Cu ions has been applied to measure the depth profiles of solid electrolyte interphase (SEI) layers on the negative electrode of lithium ion batteries (LIB). In order to obtain quantitative depth profiles, the detector efficiency was first assessed, and the test highlighted a strong mass and energy dependence of the recoiled particles, especially H and He. Subsequently, we prepared LIB cells with different water contents in the electrolyte, and subjected them to different charge-discharge cycle tests. TOF-ERDA, X-ray photoelectron spectrometry (XPS), gas chromatography (GC), ion chromatography (IC), and 1H nuclear magnetic resonance (1H NMR) were applied to characterize the SEI region of the negative electrode. The results showed that the SEI layer is formed after 300 cycle tests, and a 500 ppm water concentration in the electrolyte does not appear to cause significant differences in the elemental and organic content of the SEI.

Experimental Verification of Modeled Thermal Distribution Produced by a Piston Source in Physiotherapy Ultrasound

PubMed Central

Lopez-Haro, S. A.; Leija, L.

2016-01-01

Objectives. To present a quantitative comparison of thermal patterns produced by the piston-in-a-baffle approach with those generated by a physiotherapy ultrasonic device and to show the dependency among thermal patterns and acoustic intensity distributions. Methods. The finite element (FE) method was used to model an ideal acoustic field and the produced thermal pattern to be compared with the experimental acoustic and temperature distributions produced by a real ultrasonic applicator. A thermal model using the measured acoustic profile as input is also presented for comparison. Temperature measurements were carried out with thermocouples inserted in muscle phantom. The insertion place of thermocouples was monitored with ultrasound imaging. Results. Modeled and measured thermal profiles were compared within the first 10 cm of depth. The ideal acoustic field did not adequately represent the measured field having different temperature profiles (errors 10% to 20%). Experimental field was concentrated near the transducer producing a region with higher temperatures, while the modeled ideal temperature was linearly distributed along the depth. The error was reduced to 7% when introducing the measured acoustic field as the input variable in the FE temperature modeling. Conclusions. Temperature distributions are strongly related to the acoustic field distributions. PMID:27999801

A TPS kernel for calculating survival vs. depth: distributions in a carbon radiotherapy beam, based on Katz's cellular Track Structure Theory.

PubMed

Waligórski, M P R; Grzanka, L; Korcyl, M; Olko, P

2015-09-01

An algorithm was developed of a treatment planning system (TPS) kernel for carbon radiotherapy in which Katz's Track Structure Theory of cellular survival (TST) is applied as its radiobiology component. The physical beam model is based on available tabularised data, prepared by Monte Carlo simulations of a set of pristine carbon beams of different input energies. An optimisation tool developed for this purpose is used to find the composition of pristine carbon beams of input energies and fluences which delivers a pre-selected depth-dose distribution profile over the spread-out Bragg peak (SOBP) region. Using an extrapolation algorithm, energy-fluence spectra of the primary carbon ions and of all their secondary fragments are obtained over regular steps of beam depths. To obtain survival vs. depth distributions, the TST calculation is applied to the energy-fluence spectra of the mixed field of primary ions and of their secondary products at the given beam depths. Katz's TST offers a unique analytical and quantitative prediction of cell survival in such mixed ion fields. By optimising the pristine beam composition to a published depth-dose profile over the SOBP region of a carbon beam and using TST model parameters representing the survival of CHO (Chinese Hamster Ovary) cells in vitro, it was possible to satisfactorily reproduce a published data set of CHO cell survival vs. depth measurements after carbon ion irradiation. The authors also show by a TST calculation that 'biological dose' is neither linear nor additive. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Seismic profile analysis of the Kangra and Dehradun re-entrant of NW Himalayan Foreland thrust belt, India: A new approach to delineate subsurface geometry

NASA Astrophysics Data System (ADS)

Dey, Joyjit; Perumal, R. Jayangonda; Sarkar, Subham; Bhowmik, Anamitra

2017-08-01

In the NW Sub-Himalayan frontal thrust belt in India, seismic interpretation of subsurface geometry of the Kangra and Dehradun re-entrant mismatch with the previously proposed models. These procedures lack direct quantitative measurement on the seismic profile required for subsurface structural architecture. Here we use a predictive angular function for establishing quantitative geometric relationships between fault and fold shapes with `Distance-displacement method' (D-d method). It is a prognostic straightforward mechanism to probe the possible structural network from a seismic profile. Two seismic profiles Kangra-2 and Kangra-4 of Kangra re-entrant, Himachal Pradesh (India), are investigated for the fault-related folds associated with the Balh and Paror anticlines. For Paror anticline, the final cut-off angle β =35{°} was obtained by transforming the seismic time profile into depth profile to corroborate the interpreted structures. Also, the estimated shortening along the Jawalamukhi Thrust and Jhor Fault, lying between the Himalayan Frontal Thrust (HFT) and the Main Boundary Thrust (MBT) in the frontal fold-thrust belt, were found to be 6.06 and 0.25 km, respectively. Lastly, the geometric method of fold-fault relationship has been exercised to document the existence of a fault-bend fold above the Himalayan Frontal Thrust (HFT). Measurement of shortening along the fault plane is employed as an ancillary tool to prove the multi-bending geometry of the blind thrust of the Dehradun re-entrant.

Quantitative analysis of the Ge concentration in a SiGe quantum well: comparison of low-energy RBS and SIMS measurements.

PubMed

Krecar, D; Rosner, M; Draxler, M; Bauer, P; Hutter, H

2006-01-01

The germanium concentration and the position and thickness of the quantum well in molecular beam epitaxy (MBE)-grown SiGe were quantitatively analyzed via low-energy Rutherford backscattering (RBS) and secondary ion mass spectrometry (SIMS). In these samples, the concentrations of Si and Ge were assumed to be constant, except for the quantum well, where the germanium concentration was lower. The thickness of the analyzed quantum well was about 12 nm and it was situated at a depth of about 60 nm below the surface. A dip showed up in the RBS spectra due to the lower germanium concentration in the quantum well, and this was evaluated. Good depth resolution was required in order to obtain quantitative results, and this was obtained by choosing a primary energy of 500 keV and a tilt angle of 51 degrees with respect to the surface normal. Quantitative information was deduced from the raw data by comparing it with SIMNRA simulated spectra. The SIMS measurements were performed with oxygen primary ions. Given the response function of the SIMS instrument (the SIMS depth profile of the germanium delta (delta) layer), and using the forward convolution (point-to-point convolution) model, it is possible to determine the germanium concentration and the thickness of the analyzed quantum well from the raw SIMS data. The aim of this work was to compare the results obtained via RBS and SIMS and to show their potential for use in the semiconductor and microelectronics industry. The detection of trace elements (here the doping element antimony) that could not be evaluated with RBS in low-energy mode is also demonstrated using SIMS instead.

SILAC-based proteomics of human primary endothelial cell morphogenesis unveils tumor angiogenic markers.

PubMed

Zanivan, Sara; Maione, Federica; Hein, Marco Y; Hernández-Fernaud, Juan Ramon; Ostasiewicz, Pawel; Giraudo, Enrico; Mann, Matthias

2013-12-01

Proteomics has been successfully used for cell culture on dishes, but more complex cellular systems have proven to be challenging and so far poorly approached with proteomics. Because of the complexity of the angiogenic program, we still do not have a complete understanding of the molecular mechanisms involved in this process, and there have been no in depth quantitative proteomic studies. Plating endothelial cells on matrigel recapitulates aspects of vessel growth, and here we investigate this mechanism by using a spike-in SILAC quantitative proteomic approach. By comparing proteomic changes in primary human endothelial cells morphogenesis on matrigel to general adhesion mechanisms in cells spreading on culture dish, we pinpoint pathways and proteins modulated by endothelial cells. The cell-extracellular matrix adhesion proteome depends on the adhesion substrate, and a detailed proteomic profile of the extracellular matrix secreted by endothelial cells identified CLEC14A as a matrix component, which binds to MMRN2. We verify deregulated levels of these proteins during tumor angiogenesis in models of multistage carcinogenesis. This is the most in depth quantitative proteomic study of endothelial cell morphogenesis, which shows the potential of applying high accuracy quantitative proteomics to in vitro models of vessel growth to shed new light on mechanisms that accompany pathological angiogenesis. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000359.

Quantitative X-ray photoelectron spectroscopy-based depth profiling of bioleached arsenopyrite surface by Acidithiobacillus ferrooxidans

NASA Astrophysics Data System (ADS)

Zhu, Tingting; Lu, Xiancai; Liu, Huan; Li, Juan; Zhu, Xiangyu; Lu, Jianjun; Wang, Rucheng

2014-02-01

In supergene environments, microbial activities significantly enhance sulfide oxidation and result in the release of heavy metals, causing serious contamination of soils and waters. As the most commonly encountered arsenic mineral in nature, arsenopyrite (FeAsS) accounts for arsenic contaminants in various environments. In order to investigate the geochemical behavior of arsenic during microbial oxidation of arsenopyrite, (2 3 0) surfaces of arsenopyrite slices were characterized after acidic (pH 2.00) and oxidative decomposition with or without an acidophilic microorganism Acidithiobacillus ferrooxidans. The morphology as well as chemical and elemental depth profiles of the oxidized arsenopyrite surface were investigated by scanning electron microscopy and X-ray photoelectron spectroscopy. With the mediation of bacteria, cell-shaped and acicular pits were observed on the reacted arsenopyrite surface, and the concentration of released arsenic species in solution was 50 times as high as that of the abiotic reaction after 10 days reaction. Fine-scale XPS depth profiles of the reacted arsenopyrite surfaces after both microbial and abiotic oxidation provided insights into the changes in chemical states of the elements in arsenopyrite surface layers. Within the 450 nm surface layer of abiotically oxidized arsenopyrite, Fe(III)-oxides appeared and gradually increased towards the surface, and detectable sulfite and monovalent arsenic appeared above 50 nm. In comparison, higher contents of ferric sulfate, sulfite, and arsenite were found in the surface layer of approximately 3 μm of the microbially oxidized arsenopyrite. Intermediates, such as Fe(III)-AsS and S0, were detectable in the presence of bacteria. Changes of oxidative species derived from XPS depth profiles show the oxidation sequence is Fe > As = S in abiotic oxidation, and Fe > S > As in microbial oxidation. Based on these results, a possible reaction path of microbial oxidation was proposed in a concept model.

X-ray Photoelectron Spectroscopy of High-κ Dielectrics

NASA Astrophysics Data System (ADS)

Mathew, A.; Demirkan, K.; Wang, C.-G.; Wilk, G. D.; Watson, D. G.; Opila, R. L.

2005-09-01

Photoelectron spectroscopy is a powerful technique for the analysis of gate dielectrics because it can determine the elemental composition, the chemical states, and the compositional depth profiles non-destructively. The sampling depth, determined by the escape depth of the photoelectrons, is comparable to the thickness of current gate oxides. A maximum entropy algorithm was used to convert photoelectron collection angle dependence of the spectra to compositional depth profiles. A nitrided hafnium silicate film is used to demonstrate the utility of the technique. The algorithm balances deviations from a simple assumed depth profile against a calculated depth profile that best fits the angular dependence of the photoelectron spectra. A flow chart of the program is included in this paper. The development of the profile is also shown as the program is iterated. Limitations of the technique include the electron escape depths and elemental sensitivity factors used to calculate the profile. The technique is also limited to profiles that extend to the depth of approximately twice the escape depth. These limitations restrict conclusions to comparison among a family of similar samples. Absolute conclusions about depths and concentrations must be used cautiously. Current work to improve the algorithm is also described.

Minimalistic models of the vertical distribution of roots under stochastic hydrological forcing

NASA Astrophysics Data System (ADS)

Laio, Francesco

2014-05-01

The assessment of the vertical root profile can be useful for multiple purposes: the partition of water fluxes between evaporation and transpiration, the evaluation of root soil reinforcement for bioengineering applications, the influence of roots on biogeochemical and microbial processes in the soil, etc. In water-controlled ecosystems the shape of the root profile is mainly determined by the soil moisture availability at different depths. The long term soil water balance in the root zone can be assessed by modeling the stochastic incoming and outgoing water fluxes, influenced by the stochastic rainfall pulses and/or by the water table fluctuations. Through an ecohydrological analysis one obtains that in water-controlled ecosystems the vertical root distribution is a decreasing function with depth, whose parameters depend on pedologic and climatic factors. The model can be extended to suitably account for the influence of the water table fluctuations, when the water table is shallow enough to exert an influence on root development, in which case the vertical root distribution tends to assume a non-monotonic form. In order to evaluate the validity of the ecohydrological estimation of the root profile we have tested it on a case study in the north of Tuscany (Italy). We have analyzed data from 17 landslide-prone sites: in each of these sites we have assessed the pedologic and climatic descriptors necessary to apply the model, and we have measured the mean rooting depth. The results show a quite good matching between observed and modeled mean root depths. The merit of this minimalistic approach to the modeling of the vertical root distribution relies on the fact that it allows a quantitative estimation of the main features of the vertical root distribution without resorting to time- and money-demanding measuring surveys.

Quantitative subsurface analysis using frequency modulated thermal wave imaging

NASA Astrophysics Data System (ADS)

Subhani, S. K.; Suresh, B.; Ghali, V. S.

2018-01-01

Quantitative depth analysis of the anomaly with an enhanced depth resolution is a challenging task towards the estimation of depth of the subsurface anomaly using thermography. Frequency modulated thermal wave imaging introduced earlier provides a complete depth scanning of the object by stimulating it with a suitable band of frequencies and further analyzing the subsequent thermal response using a suitable post processing approach to resolve subsurface details. But conventional Fourier transform based methods used for post processing unscramble the frequencies with a limited frequency resolution and contribute for a finite depth resolution. Spectral zooming provided by chirp z transform facilitates enhanced frequency resolution which can further improves the depth resolution to axially explore finest subsurface features. Quantitative depth analysis with this augmented depth resolution is proposed to provide a closest estimate to the actual depth of subsurface anomaly. This manuscript experimentally validates this enhanced depth resolution using non stationary thermal wave imaging and offers an ever first and unique solution for quantitative depth estimation in frequency modulated thermal wave imaging.

Fourier phase in Fourier-domain optical coherence tomography

PubMed Central

Uttam, Shikhar; Liu, Yang

2015-01-01

Phase of an electromagnetic wave propagating through a sample-of-interest is well understood in the context of quantitative phase imaging in transmission-mode microscopy. In the past decade, Fourier-domain optical coherence tomography has been used to extend quantitative phase imaging to the reflection-mode. Unlike transmission-mode electromagnetic phase, however, the origin and characteristics of reflection-mode Fourier phase are poorly understood, especially in samples with a slowly varying refractive index. In this paper, the general theory of Fourier phase from first principles is presented, and it is shown that Fourier phase is a joint estimate of subresolution offset and mean spatial frequency of the coherence-gated sample refractive index. It is also shown that both spectral-domain phase microscopy and depth-resolved spatial-domain low-coherence quantitative phase microscopy are special cases of this general theory. Analytical expressions are provided for both, and simulations are presented to explain and support the theoretical results. These results are further used to show how Fourier phase allows the estimation of an axial mean spatial frequency profile of the sample, along with depth-resolved characterization of localized optical density change and sample heterogeneity. Finally, a Fourier phase-based explanation of Doppler optical coherence tomography is also provided. PMID:26831383

Characterisation of case depth in induction-hardened medium carbon steels based on magnetic minor hysteresis loop measurement technique

NASA Astrophysics Data System (ADS)

He, Cunfu; Yang, Meng; Liu, Xiucheng; Wang, Xueqian; Wu, Bin

2017-11-01

The magnetic hysteresis behaviours of ferromagnetic materials vary with the heat treatment-induced micro-structural changes. In the study, the minor hysteresis loop measurement technique was used to quantitatively characterise the case depth in two types of medium carbon steels. Firstly, high-frequency induction quenching was applied in rod samples to increase the volume fraction of hard martensite to the soft ferrite/pearlite (or sorbite) in the sample surface. In order to determine the effective and total case depth, a complementary error function was employed to fit the measured hardness-depth profiles of induction-hardened samples. The cluster of minor hysteresis loops together with the tangential magnetic field (TMF) were recorded from all the samples and the comparative study was conducted among three kinds of magnetic parameters, which were sensitive to the variation of case depth. Compared to the parameters extracted from an individual minor loop and the distortion factor of the TMF, the magnitude of three-order harmonic of TMF was more suitable to indicate the variation in case depth. Two new minor-loop coefficients were introduced by combining two magnetic parameters with cumulative statistics of the cluster of minor-loops. The experimental results showed that the two coefficients monotonically linearly varied with the case depth within the carefully selected magnetisation region.

In-depth Qualitative and Quantitative Profiling of Tyrosine Phosphorylation Using a Combination of Phosphopeptide Immunoaffinity Purification and Stable Isotope Dimethyl Labeling*

PubMed Central

Boersema, Paul J.; Foong, Leong Yan; Ding, Vanessa M. Y.; Lemeer, Simone; van Breukelen, Bas; Philp, Robin; Boekhorst, Jos; Snel, Berend; den Hertog, Jeroen; Choo, Andre B. H.; Heck, Albert J. R.

2010-01-01

Several mass spectrometry-based assays have emerged for the quantitative profiling of cellular tyrosine phosphorylation. Ideally, these methods should reveal the exact sites of tyrosine phosphorylation, be quantitative, and not be cost-prohibitive. The latter is often an issue as typically several milligrams of (stable isotope-labeled) starting protein material are required to enable the detection of low abundance phosphotyrosine peptides. Here, we adopted and refined a peptidecentric immunoaffinity purification approach for the quantitative analysis of tyrosine phosphorylation by combining it with a cost-effective stable isotope dimethyl labeling method. We were able to identify by mass spectrometry, using just two LC-MS/MS runs, more than 1100 unique non-redundant phosphopeptides in HeLa cells from about 4 mg of starting material without requiring any further affinity enrichment as close to 80% of the identified peptides were tyrosine phosphorylated peptides. Stable isotope dimethyl labeling could be incorporated prior to the immunoaffinity purification, even for the large quantities (mg) of peptide material used, enabling the quantification of differences in tyrosine phosphorylation upon pervanadate treatment or epidermal growth factor stimulation. Analysis of the epidermal growth factor-stimulated HeLa cells, a frequently used model system for tyrosine phosphorylation, resulted in the quantification of 73 regulated unique phosphotyrosine peptides. The quantitative data were found to be exceptionally consistent with the literature, evidencing that such a targeted quantitative phosphoproteomics approach can provide reproducible results. In general, the combination of immunoaffinity purification of tyrosine phosphorylated peptides with large scale stable isotope dimethyl labeling provides a cost-effective approach that can alleviate variation in sample preparation and analysis as samples can be combined early on. Using this approach, a rather complete qualitative and quantitative picture of tyrosine phosphorylation signaling events can be generated. PMID:19770167

Comprehensive and quantitative profiling of lipid species in human milk, cow milk and a phospholipid-enriched milk formula by GC and MS/MSALL.

PubMed

Sokol, Elena; Ulven, Trond; Færgeman, Nils J; Ejsing, Christer S

2015-06-01

Here we present a workflow for in-depth analysis of milk lipids that combines gas chromatography (GC) for fatty acid (FA) profiling and a shotgun lipidomics routine termed MS/MS ALL for structural characterization of molecular lipid species. To evaluate the performance of the workflow we performed a comparative lipid analysis of human milk, cow milk, and Lacprodan® PL-20, a phospholipid-enriched milk protein concentrate for infant formula. The GC analysis showed that human milk and Lacprodan have a similar FA profile with higher levels of unsaturated FAs as compared to cow milk. In-depth lipidomic analysis by MS/MS ALL revealed that each type of milk sample comprised distinct composition of molecular lipid species. Lipid class composition showed that the human and cow milk contain a higher proportion of triacylglycerols (TAGs) as compared to Lacprodan. Notably, the MS/MS ALL analysis demonstrated that the similar FA profile of human milk and Lacprodan determined by GC analysis is attributed to the composition of individual TAG species in human milk and glycerophospholipid species in Lacprodan. Moreover, the analysis of TAG molecules in Lacprodan and cow milk showed a high proportion of short-chain FAs that could not be monitored by GC analysis. The results presented here show that complementary GC and MS/MS ALL analysis is a powerful approach for characterization of molecular lipid species in milk and milk products. : Milk lipid analysis is routinely performed using gas chromatography. This method reports the total fatty acid composition of all milk lipids, but provides no structural or quantitative information about individual lipid molecules in milk or milk products. Here we present a workflow that integrates gas chromatography for fatty acid profiling and a shotgun lipidomics routine termed MS/MS ALL for structural analysis and quantification of molecular lipid species. We demonstrate the efficacy of this complementary workflow by a comparative analysis of molecular lipid species in human milk, cow milk, and a milk-based supplement used for infant formula.

Comprehensive and quantitative profiling of lipid species in human milk, cow milk and a phospholipid-enriched milk formula by GC and MS/MSALL

PubMed Central

Sokol, Elena; Ulven, Trond; Færgeman, Nils J; Ejsing, Christer S

2015-01-01

Here we present a workflow for in-depth analysis of milk lipids that combines gas chromatography (GC) for fatty acid (FA) profiling and a shotgun lipidomics routine termed MS/MSALL for structural characterization of molecular lipid species. To evaluate the performance of the workflow we performed a comparative lipid analysis of human milk, cow milk, and Lacprodan® PL-20, a phospholipid-enriched milk protein concentrate for infant formula. The GC analysis showed that human milk and Lacprodan have a similar FA profile with higher levels of unsaturated FAs as compared to cow milk. In-depth lipidomic analysis by MS/MSALL revealed that each type of milk sample comprised distinct composition of molecular lipid species. Lipid class composition showed that the human and cow milk contain a higher proportion of triacylglycerols (TAGs) as compared to Lacprodan. Notably, the MS/MSALL analysis demonstrated that the similar FA profile of human milk and Lacprodan determined by GC analysis is attributed to the composition of individual TAG species in human milk and glycerophospholipid species in Lacprodan. Moreover, the analysis of TAG molecules in Lacprodan and cow milk showed a high proportion of short-chain FAs that could not be monitored by GC analysis. The results presented here show that complementary GC and MS/MSALL analysis is a powerful approach for characterization of molecular lipid species in milk and milk products. Practical applications : Milk lipid analysis is routinely performed using gas chromatography. This method reports the total fatty acid composition of all milk lipids, but provides no structural or quantitative information about individual lipid molecules in milk or milk products. Here we present a workflow that integrates gas chromatography for fatty acid profiling and a shotgun lipidomics routine termed MS/MSALL for structural analysis and quantification of molecular lipid species. We demonstrate the efficacy of this complementary workflow by a comparative analysis of molecular lipid species in human milk, cow milk, and a milk-based supplement used for infant formula. PMID:26089741

M.S.L.A.P. Modular Spectral Line Analysis Program documentation

NASA Technical Reports Server (NTRS)

Joseph, Charles L.; Jenkins, Edward B.

1991-01-01

MSLAP is a software for analyzing spectra, providing the basic structure to identify spectral features, to make quantitative measurements of this features, and to store the measurements for convenient access. MSLAP can be used to measure not only the zeroth moment (equivalent width) of a profile, but also the first and second moments. Optical depths and the corresponding column densities across the profile can be measured as well for sufficiently high resolution data. The software was developed for an interactive, graphical analysis where the computer carries most of the computational and data organizational burden and the investigator is responsible only for all judgement decisions. It employs sophisticated statistical techniques for determining the best polynomial fit to the continuum and for calculating the uncertainties.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smentkowski, Vincent S., E-mail: smentkow@ge.com

Changes in the oxidation state of an element can result in significant changes in the ionization efficiency and hence signal intensity during secondary ion mass spectrometry (SIMS) analysis; this is referred to as the SIMS matrix effect [Secondary Ion Mass Spectrometry: A Practical Handbook for Depth Profiling and Bulk Impurity Analysis, edited by R. G. Wilson, F. A. Stevie, and C. W. Magee (Wiley, New York, 1990)]. The SIMS matrix effect complicates quantitative analysis. Quantification of SIMS data requires the determination of relative sensitivity factors (RSFs), which can be used to convert the as measured intensity into concentration units [Secondarymore » Ion Mass Spectrometry: A Practical Handbook for Depth Profiling and Bulk Impurity Analysis, edited by R. G. Wilson, F. A. Stevie, and C. W. Magee (Wiley, New York, 1990)]. In this manuscript, the authors report both: RSFs which were determined for quantification of B in Si and SiO{sub 2} matrices using a dual beam time of flight secondary ion mass spectrometry (ToF-SIMS) instrument and the protocol they are using to provide quantitative ToF-SIMS images and line scan traces. The authors also compare RSF values that were determined using oxygen and Ar ion beams for erosion, discuss the problems that can be encountered when bulk calibration samples are used to determine RSFs, and remind the reader that errors in molecular details of the matrix (density, volume, etc.) that are used to convert from atoms/cm{sup 3} to other concentration units will propagate into errors in the determined concentrations.« less

Use of XPS to clarify the Hall coefficient sign variation in thin niobium layers buried in silicon

NASA Astrophysics Data System (ADS)

Demchenko, Iraida N.; Lisowski, Wojciech; Syryanyy, Yevgen; Melikhov, Yevgen; Zaytseva, Iryna; Konstantynov, Pavlo; Chernyshova, Maryna; Cieplak, Marta Z.

2017-03-01

Si/Nb/Si trilayers formed with 9.5 and 1.3 nm thick niobium layer buried in amorphous silicon were prepared by magnetron sputtering and studied using XPS depth-profile techniques in order to investigate the change of Hall coefficient sign with thickness. The analysis of high-resolution (HR) XPS spectra revealed that the thicker layer sample has sharp top interface and metallic phase of niobium, thus holes dominate the transport. In contrast, the analysis indicates that the thinner layer sample has a Nb-rich mixed alloy formation at the top interface. The authors suggest that the main effect leading to a change of sign of the Hall coefficient for the thinner layer sample (which is negative contrary to the positive sign for the thicker layer sample) may be related to strong boundary scattering enhanced by the presence of silicon ions in the layer close to the interface/s. The depth-profile reconstruction was performed by SESSA software tool confirming that it can be reliably used for quantitative analysis/interpretation of experimental XPS data.

Structural and magnetic depth profiles of magneto-ionic heterostructures beyond the interface limit

DOE PAGES

Gilbert, Dustin A.; Grutter, Alexander J.; Arenholz, Elke; ...

2016-07-22

Electric field control of magnetism provides a promising route towards ultralow power information storage and sensor technologies. The effects of magneto-ionic motion have been prominently featured in the modification of interface characteristics. Here, we demonstrate magnetoelectric coupling moderated by voltage-driven oxygen migration beyond the interface in relatively thick AlO x/GdO x/Co(15 nm) films. Oxygen migration and Co magnetization are quantitatively mapped with polarized neutron reflectometry under electro-thermal conditioning. The depth-resolved profiles uniquely identify interfacial and bulk behaviours and a semi-reversible control of the magnetization. Magnetometry measurements suggest changes in the microstructure which disrupt long-range ferromagnetic ordering, resulting in an additionalmore » magnetically soft phase. X-ray spectroscopy confirms changes in the Co oxidation state, but not in the Gd, suggesting that the GdO x transmits oxygen but does not source or sink it. These results together provide crucial insight into controlling magnetism via magneto-ionic motion, both at interfaces and throughout the bulk of the films.« less

Field Measurements of the 1983 Royal Gardens Lava Flows, Kilauea Volcano, and 1984 Mauna Loa Lava Flow, Hawaii

NASA Technical Reports Server (NTRS)

Fink, J.; Zimbelman, J.

1985-01-01

Theoretical models used in the remote determination of lava flow rheology and compositions rely on estimates of such geometric and flow parameters as volume flow rates, levee heights, and channel dimensions, as well as morphologic and structural patterns on the flow surfaces. Quantitative measures of these variables are difficult to obtain, even under optimum conditions. Detailed topographic profiles across several Hawaiian lava flows that were carefully monitored by the U.S. Geological Survey during their emplacement in 1983 were surveyed in order to test various flow emplacement models. Twenty two accurate channel cross sections were constructed by combining these profiles with digitized pre-flow topographic measurements. Levee heights, shear zone widths, and flow depths could then be read directly from the cross sections and input into the models. The profiles were also compared with ones constructed for some Martian lava flows.

Analysis of DGGE profiles to explore the relationship between prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin.

PubMed

Fry, John C; Webster, Gordon; Cragg, Barry A; Weightman, Andrew J; Parkes, R John

2006-10-01

The aim of this work was to relate depth profiles of prokaryotic community composition with geochemical processes in the deep subseafloor biosphere at two shallow-water sites on the Peru Margin in the Pacific Ocean (ODP Leg 201, sites 1228 and 1229). Principal component analysis of denaturing gradient gel electrophoresis banding patterns of deep-sediment Bacteria, Archaea, Euryarchaeota and the novel candidate division JS1, followed by multiple regression, showed strong relationships with prokaryotic activity and geochemistry (R(2)=55-100%). Further correlation analysis, at one site, between the principal components from the community composition profiles for Bacteria and 12 other variables quantitatively confirmed their relationship with activity and geochemistry, which had previously only been implied. Comparison with previously published cell counts enumerated by fluorescent in situ hybridization with rRNA-targeted probes confirmed that these denaturing gradient gel electrophoresis profiles described an active prokaryotic community.

Depth profile measurement with lenslet images of the plenoptic camera

NASA Astrophysics Data System (ADS)

Yang, Peng; Wang, Zhaomin; Zhang, Wei; Zhao, Hongying; Qu, Weijuan; Zhao, Haimeng; Asundi, Anand; Yan, Lei

2018-03-01

An approach for carrying out depth profile measurement of an object with the plenoptic camera is proposed. A single plenoptic image consists of multiple lenslet images. To begin with, these images are processed directly with a refocusing technique to obtain the depth map, which does not need to align and decode the plenoptic image. Then, a linear depth calibration is applied based on the optical structure of the plenoptic camera for depth profile reconstruction. One significant improvement of the proposed method concerns the resolution of the depth map. Unlike the traditional method, our resolution is not limited by the number of microlenses inside the camera, and the depth map can be globally optimized. We validated the method with experiments on depth map reconstruction, depth calibration, and depth profile measurement, with the results indicating that the proposed approach is both efficient and accurate.

Interpreting Repeated Temperature-Depth Profiles for Groundwater Flow

NASA Astrophysics Data System (ADS)

Bense, Victor F.; Kurylyk, Barret L.; van Daal, Jonathan; van der Ploeg, Martine J.; Carey, Sean K.

2017-10-01

Temperature can be used to trace groundwater flows due to thermal disturbances of subsurface advection. Prior hydrogeological studies that have used temperature-depth profiles to estimate vertical groundwater fluxes have either ignored the influence of climate change by employing steady-state analytical solutions or applied transient techniques to study temperature-depth profiles recorded at only a single point in time. Transient analyses of a single profile are predicated on the accurate determination of an unknown profile at some time in the past to form the initial condition. In this study, we use both analytical solutions and a numerical model to demonstrate that boreholes with temperature-depth profiles recorded at multiple times can be analyzed to either overcome the uncertainty associated with estimating unknown initial conditions or to form an additional check for the profile fitting. We further illustrate that the common approach of assuming a linear initial temperature-depth profile can result in significant errors for groundwater flux estimates. Profiles obtained from a borehole in the Veluwe area, Netherlands in both 1978 and 2016 are analyzed for an illustrative example. Since many temperature-depth profiles were collected in the late 1970s and 1980s, these previously profiled boreholes represent a significant and underexploited opportunity to obtain repeat measurements that can be used for similar analyses at other sites around the world.

Multilayered phantoms with tunable optical properties for a better understanding of light/tissue interactions

NASA Astrophysics Data System (ADS)

Roig, Blandine; Koenig, Anne; Perraut, François; Piot, Olivier; Vignoud, Séverine; Lavaud, Jonathan; Manfait, Michel; Dinten, Jean-Marc

2015-03-01

Light/tissue interactions, like diffuse reflectance, endogenous fluorescence and Raman scattering, are a powerful means for providing skin diagnosis. Instrument calibration is an important step. We thus developed multilayered phantoms for calibration of optical systems. These phantoms mimic the optical properties of biological tissues such as skin. Our final objective is to better understand light/tissue interactions especially in the case of confocal Raman spectroscopy. The phantom preparation procedure is described, including the employed method to obtain a stratified object. PDMS was chosen as the bulk material. TiO2 was used as light scattering agent. Dye and ink were adopted to mimic, respectively, oxy-hemoglobin and melanin absorption spectra. By varying the amount of the incorporated components, we created a material with tunable optical properties. Monolayer and multilayered phantoms were designed to allow several characterization methods. Among them, we can name: X-ray tomography for structural information; Diffuse Reflectance Spectroscopy (DRS) with a homemade fibered bundle system for optical characterization; and Raman depth profiling with a commercial confocal Raman microscope for structural information and for our final objective. For each technique, the obtained results are presented and correlated when possible. A few words are said on our final objective. Raman depth profiles of the multilayered phantoms are distorted by elastic scattering. The signal attenuation through each single layer is directly dependent on its own scattering property. Therefore, determining the optical properties, obtained here with DRS, is crucial to properly correct Raman depth profiles. Thus, it would be permitted to consider quantitative studies on skin for drug permeation follow-up or hydration assessment, for instance.

Patterns and drivers of fungal community depth stratification in Sphagnum peat.

PubMed

Lamit, Louis J; Romanowicz, Karl J; Potvin, Lynette R; Rivers, Adam R; Singh, Kanwar; Lennon, Jay T; Tringe, Susannah G; Kane, Evan S; Lilleskov, Erik A

2017-07-01

Peatlands store an immense pool of soil carbon vulnerable to microbial oxidation due to drought and intentional draining. We used amplicon sequencing and quantitative PCR to (i) examine how fungi are influenced by depth in the peat profile, water table and plant functional group at the onset of a multiyear mesocosm experiment, and (ii) test if fungi are correlated with abiotic variables of peat and pore water. We hypothesized that each factor influenced fungi, but that depth would have the strongest effect early in the experiment. We found that (i) communities were strongly depth stratified; fungi were four times more abundant in the upper (10-20 cm) than the lower (30-40 cm) depth, and dominance shifted from ericoid mycorrhizal fungi to saprotrophs and endophytes with increasing depth; (ii) the influence of plant functional group was depth dependent, with Ericaceae structuring the community in the upper peat only; (iii) water table had minor influences; and (iv) communities strongly covaried with abiotic variables, including indices of peat and pore water carbon quality. Our results highlight the importance of vertical stratification to peatland fungi, and the depth dependency of plant functional group effects, which must be considered when elucidating the role of fungi in peatland carbon dynamics. Published by Oxford University Press on behalf of FEMS 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Preliminary research on eddy current bobbin quantitative test for heat exchange tube in nuclear power plant

NASA Astrophysics Data System (ADS)

Qi, Pan; Shao, Wenbin; Liao, Shusheng

2016-02-01

For quantitative defects detection research on heat transfer tube in nuclear power plants (NPP), two parts of work are carried out based on the crack as the main research objects. (1) Production optimization of calibration tube. Firstly, ASME, RSEM and homemade crack calibration tubes are applied to quantitatively analyze the defects depth on other designed crack test tubes, and then the judgment with quantitative results under crack calibration tube with more accuracy is given. Base on that, weight analysis of influence factors for crack depth quantitative test such as crack orientation, length, volume and so on can be undertaken, which will optimize manufacture technology of calibration tubes. (2) Quantitative optimization of crack depth. Neural network model with multi-calibration curve adopted to optimize natural crack test depth generated in in-service tubes shows preliminary ability to improve quantitative accuracy.

Shear-wave seismic reflection imaging and impedance inversion for a near-surface point-bar

NASA Astrophysics Data System (ADS)

Benton, N. W.; Morrison, M.; Lorenzo, J. M.; Odom, B.; Clift, P. D.; Olson, E.; Gostic, A.

2017-12-01

Imaging and inversion of SH-waves are useful to detect, map, and quantitatively characterize near-surface point-bar strata. We conduct a horizontally-polarized (SH) reflection survey across and along a near-surface (9 - 40 m) downstream point-bar. We invert for shear-impedance profiles and correlate our interpretation to electrical conductivity (EC) logs in adjacent wells to study the internal architecture and lithology of point-bars. We acquire two common-midpoint (CMP) SH-wave seismic reflection lines at False River (Point Coupee Parish, Louisiana). A 104 m long seismic line (L1) is oriented orthogonal (NW - SE) to point-bar strike. A second line (L2) is 48 m long and set parallel to point-bar strike (NE - SW). Two EC wells lie 33 m apart. Both wells are parallel with respect to the L1 survey and offset from it by 15 m. EC log measurements range from 1 - 25 m depth. Interference of Love-waves prevents seismic imaging at depths less than 9 m. The L1 and L2 data sets are inverted for shear-impedance using a model-based band-limited impedance (BLIMP) algorithm that incorporates a low-frequency velocity model. This model is also used for the depthing processing. The L1 cross-section shows coherent dipping reflection events ( 4 - 7º) from 0.15 - 0.35 s (10 - 40 m). The corresponding shear-impedance profile also reveals coherent and dipping impedance contrasts that grow in magnitude with increasing depth. The L2 cross-section shows comparatively less dip ( 1º) as well as sharper and shallower continuity of reflection events (0.1 - 0.28 s TWT or 9 - 25 m). Depth-converted (TVD) seismic amplitudes and impedance values correlate to near-surface point-bar geology via superposition of log data. The first well (W5) shows distinct EC local maxima (+50 - 70 mS/m) at 14.5 and 15.5 m depth that correlate well with the seismic amplitudes and impedance values from both L1 and L2 data sets. The second well (W7) shows comparatively lower local maxima (+40 - 60 mS/m) but at greater depths (15.5 and 16.5 m). W5 correlates better with the seismic cross-section and impedance profile from L2 at 10, 12.5, 14.5, 15.5, and 19 m depth. EC maxima align with distinct shear-impedance values for L1 and L2 profiles. Our results provide a new and useful perspective of remotely analyzing the architecture and lithological properties of near-surface point-bars.

Hybrid Organic/Inorganic Materials Depth Profiling Using Low Energy Cesium Ions

NASA Astrophysics Data System (ADS)

Noël, Céline; Houssiau, Laurent

2016-05-01

The structures developed in organic electronics, such as organic light emitting diodes (OLEDs) or organic photovoltaics (OPVs) devices always involve hybrid interfaces, joining metal or oxide layers with organic layers. No satisfactory method to probe these hybrid interfaces physical chemistry currently exists. One promising way to analyze such interfaces is to use in situ ion beam etching, but this requires ion beams able to depth profile both inorganic and organic layers. Mono- or diatomic ion beams commonly used to depth profile inorganic materials usually perform badly on organics, while cluster ion beams perform excellently on organics but yield poor results when organics and inorganics are mixed. Conversely, low energy Cs+ beams (<500 eV) allow organic and inorganic materials depth profiling with comparable erosion rates. This paper shows a successful depth profiling of a model hybrid system made of metallic (Au, Cr) and organic (tyrosine) layers, sputtered with 500 eV Cs+ ions. Tyrosine layers capped with metallic overlayers are depth profiled easily, with high intensities for the characteristic molecular ions and other specific fragments. Metallic Au or Cr atoms are recoiled into the organic layer where they cause some damage near the hybrid interface as well as changes in the erosion rate. However, these recoil implanted metallic atoms do not appear to severely degrade the depth profile overall quality. This first successful hybrid depth profiling report opens new possibilities for the study of OLEDs, organic solar cells, or other hybrid devices.

Depth profile by Total IBA in perovskite active layers for solar cells

NASA Astrophysics Data System (ADS)

Barreiros, M. A.; Alves, L. C.; Brites, M. J.; Corregidor, V.

2017-08-01

In recent years the record efficiency of perovskite solar cells (PSCs) has been updated exceeding now 20%. However, it is difficult to make PSCs consistently. Definite correlation has been established between the PSC performance and the perovskite film quality which involves mainly morphology, crystallinity and composition. The manufacturing development of these devices is dependent on the characterisation methodologies, on the availability of suitable and reliable analytical techniques to assess the materials composition and quality and on the relationship of these results with the cell performance. Ion beam analytical (IBA) techniques jointly with a micro-ion beam are powerful tools for materials characterisation and can provide a valuable input for the knowledge of perovskite films. Perovskite films based on CH3NH3PbI3 were prepared (from CH3NH3I and PbI2 precursors) in a planar architecture and in a mesoporous TiO2 scaffold. Proton and helium micro-beams at different energies were used in the analysis of PSC active layers, previously characterised by SEM-FEG (Scanning Electron Microscopy with a field emission gun) and XRD (X-ray diffraction). Self-consistent fit of all the obtained PIXE (Particle Induced X-ray Emission) and RBS (Rutherford Backscattering Spectrometry) spectra through Total IBA approach provided depth profiling of perovskite, its precursors and TiO2 and assess their distribution in the films. PbI2 presence and location on the active layer may hinder the charge transport and highly affect the cell performance. IBA techniques allowed to identify regions of non-uniform surface coverage and homogeneous areas and it was possible to establish the undesired presence of PbI2 and its quantitative depth profile in the planar architecture film. In the mesostructured perovskite film it was verified a non-homogeneous distribution with a decreasing of perovskite concentration down to the thin blocking layer. The good agreement between the best fits obtained in a Total IBA approach and the experimental data granted reliability to depth profile results for the studied perovskite films.

Using spin-label W-band EPR to study membrane fluidity profiles in samples of small volume

NASA Astrophysics Data System (ADS)

Mainali, Laxman; Hyde, James S.; Subczynski, Witold K.

2013-01-01

Conventional and saturation-recovery (SR) EPR at W-band (94 GHz) using phosphatidylcholine spin labels (labeled at the alkyl chain [n-PC] and headgroup [T-PC]) to obtain profiles of membrane fluidity has been demonstrated. Dimyristoylphosphatidylcholine (DMPC) membranes with and without 50 mol% cholesterol have been studied, and the results have been compared with similar studies at X-band (9.4 GHz) (L. Mainali, J.B. Feix, J.S. Hyde, W.K. Subczynski, J. Magn. Reson. 212 (2011) 418-425). Profiles of the spin-lattice relaxation rate (T1-1) obtained from SR EPR measurements for n-PCs and T-PC were used as a convenient quantitative measure of membrane fluidity. Additionally, spectral analysis using Freed's MOMD (microscopic-order macroscopic-disorder) model (E. Meirovitch, J.H. Freed J. Phys. Chem. 88 (1984) 4995-5004) provided rotational diffusion coefficients (R⊥ and R||) and order parameters (S0). Spectral analysis at X-band provided one rotational diffusion coefficient, R⊥. T1-1, R⊥, and R|| profiles reflect local membrane dynamics of the lipid alkyl chain, while the order parameter shows only the amplitude of the wobbling motion of the lipid alkyl chain. Using these dynamic parameters, namely T1-1, R⊥, and R||, one can discriminate the different effects of cholesterol at different depths, showing that cholesterol has a rigidifying effect on alkyl chains to the depth occupied by the rigid steroid ring structure and a fluidizing effect at deeper locations. The nondynamic parameter, S0, shows that cholesterol has an ordering effect on alkyl chains at all depths. Conventional and SR EPR measurements with T-PC indicate that cholesterol has a fluidizing effect on phospholipid headgroups. EPR at W-band provides more detailed information about the depth-dependent dynamic organization of the membrane compared with information obtained at X-band. EPR at W-band has the potential to be a powerful tool for studying membrane fluidity in samples of small volume, ˜30 nL, compared with a representative sample volume of ˜3 μL at X-band.

High-definition optical coherence tomography intrinsic skin ageing assessment in women: a pilot study.

PubMed

Boone, M A L M; Suppa, M; Marneffe, A; Miyamoto, M; Jemec, G B E; Del Marmol, V

2015-10-01

Several non-invasive two-dimensional techniques with different lateral resolution and measurable depth range have proved to be useful in assessing and quantifying morphological changes in skin ageing. Among these, only in vivo microscopy techniques permit histometric measurements in vivo. Qualitative and quantitative assessment of chronological (intrinsic) age-related (IAR) morphological changes of epidermis, dermo-epidermal junction (DEJ), papillary dermis (PD), papillary-reticular dermis junction and reticular dermis (RD) have been performed by high-definition optical coherence tomography in real time 3-D. HD-OCT images were taken at the internal site of the right upper arm. Qualitative HD-OCT IAR descriptors were reported at skin surface, at epidermal layer, DEJ, PD and upper RD. Quantitative evaluation of age-related compaction and backscattered intensity or brightness of different skin layers was performed by using the plugin plot z-axis profile of ImageJ(®) software permitting intensity assessment of HD-OCT (DICOM) images (3-D images). Analysis was in blind from all clinical information. Sixty, fair-skinned (Fitzpatrick types I-III) healthy females were analysed retrospectively in this study. The subjects belonged to three age groups: twenty in group I aged 20-39, twenty in group II aged 40-59 and twenty in group III aged 60-79. Only intrinsic ageing in women has been studied. Significant age-related qualitative and quantitative differences could be noticed. IAR changes in dermal matrix fibers morphology/organisation and in microvasculature were observed. The brightness and compaction of the different skin layers increased significantly with intrinsic skin ageing. The depth of visibility of fibers in RD increased significantly in the older age group. In conclusion, HD-OCT allows 3-D in vivo and real time qualitative and quantitative assessment of chronological (intrinsic) age-related morphological skin changes at high resolution from skin surface to a depth of the superficial reticular dermis.

eSIP: A Novel Solution-Based Sectioned Image Property Approach for Microscope Calibration

PubMed Central

Butzlaff, Malte; Weigel, Arwed; Ponimaskin, Evgeni; Zeug, Andre

2015-01-01

Fluorescence confocal microscopy represents one of the central tools in modern sciences. Correspondingly, a growing amount of research relies on the development of novel microscopic methods. During the last decade numerous microscopic approaches were developed for the investigation of various scientific questions. Thereby, the former qualitative imaging methods became replaced by advanced quantitative methods to gain more and more information from a given sample. However, modern microscope systems being as complex as they are, require very precise and appropriate calibration routines, in particular when quantitative measurements should be compared over longer time scales or between different setups. Multispectral beads with sub-resolution size are often used to describe the point spread function and thus the optical properties of the microscope. More recently, a fluorescent layer was utilized to describe the axial profile for each pixel, which allows a spatially resolved characterization. However, fabrication of a thin fluorescent layer with matching refractive index is technically not solved yet. Therefore, we propose a novel type of calibration concept for sectioned image property (SIP) measurements which is based on fluorescent solution and makes the calibration concept available for a broader number of users. Compared to the previous approach, additional information can be obtained by application of this extended SIP chart approach, including penetration depth, detected number of photons, and illumination profile shape. Furthermore, due to the fit of the complete profile, our method is less susceptible to noise. Generally, the extended SIP approach represents a simple and highly reproducible method, allowing setup independent calibration and alignment procedures, which is mandatory for advanced quantitative microscopy. PMID:26244982

Oxy-nitrides characterization with a new ERD-TOF system

NASA Astrophysics Data System (ADS)

Chicoine, M.; Schiettekatte, F.; Laitinen, M. I.; Sajavaara, T.

2017-09-01

A new time-of-flight (TOF) camera was installed on Elastic Recoil Detection (ERD) measurement setup on the Tandem Accelerator at Université de Montréal. The camera consists of two timing detectors, developed and built by the Jyvaskyla group, that use a thin carbon foil and microchannel plates (MCP) to produce the start and stop signals. The position of the first detector is fixed at 18 cm from the target, while the position of the second detector can be varied between 50 and 90 cm from the first detector. This allows to increase time resolution by increasing the distance between the time-of-flight detectors or to increase solid angle by decreasing the distance. Moving the detector also helps determining the parameters such as the effective distance between detector foils and the delay time. Compared to the original system, which had only one timing detector and relied on a surface barrier energy detector to measure both the energy and the stop signal, in the new system the energy is now obtained from the timing signal with much better resolution, reaching ∼4 nm near the surface. There is also no more need to keep track of the surface barrier detector calibration for each element, including the pulse height defect. We show examples of quantitative depth profiles of oxy-nitride layers that has been characterized with this new system. It allows quantitative depth profiling of targets that would be difficult to analyze with other techniques, especially when light elements such as hydrogen, carbon, or nitrogen are mixed in various proportions in a heavy element matrix.

Gene Expression Analysis of Early Stage Endometrial Cancers Reveals Unique Transcripts Associated with Grade and Histology but Not Depth of Invasion

PubMed Central

Risinger, John I.; Allard, Jay; Chandran, Uma; Day, Roger; Chandramouli, Gadisetti V. R.; Miller, Caela; Zahn, Christopher; Oliver, Julie; Litzi, Tracy; Marcus, Charlotte; Dubil, Elizabeth; Byrd, Kevin; Cassablanca, Yovanni; Becich, Michael; Berchuck, Andrew; Darcy, Kathleen M.; Hamilton, Chad A.; Conrads, Thomas P.; Maxwell, G. Larry

2013-01-01

Endometrial cancer is the most common gynecologic malignancy in the United States but it remains poorly understood at the molecular level. This investigation was conducted to specifically assess whether gene expression changes underlie the clinical and pathologic factors traditionally used for determining treatment regimens in women with stage I endometrial cancer. These include the effect of tumor grade, depth of myometrial invasion and histotype. We utilized oligonucleotide microarrays to assess the transcript expression profile in epithelial glandular cells laser microdissected from 79 endometrioid and 12 serous stage I endometrial cancers with a heterogeneous distribution of grade and depth of myometrial invasion, along with 12 normal post-menopausal endometrial samples. Unsupervised multidimensional scaling analyses revealed that serous and endometrioid stage I cancers have similar transcript expression patterns when compared to normal controls where 900 transcripts were identified to be differentially expressed by at least fourfold (univariate t-test, p < 0.001) between the cancers and normal endometrium. This analysis also identified transcript expression differences between serous and endometrioid cancers and tumor grade, but no apparent differences were identified as a function of depth of myometrial invasion. Four genes were validated by quantitative PCR on an independent set of cancer and normal endometrium samples. These findings indicate that unique gene expression profiles are associated with histologic type and grade, but not myometrial invasion among early stage endometrial cancers. These data provide a comprehensive perspective on the molecular alterations associated with stage I endometrial cancer, particularly those subtypes that have the worst prognosis. PMID:23785665

Quantitative phase imaging of cell division in yeast cells and E.coli using digital holographic microscopy

NASA Astrophysics Data System (ADS)

Pandiyan, Vimal Prabhu; John, Renu

2015-12-01

Digital holographic microscope (DHM) is an emerging quantitative phase imaging technique with unique imaging scales and resolutions leading to multitude of applications. DHM is promising as a novel investigational and applied tool for cell imaging, studying the morphology and real time dynamics of cells and a number of related applications. The use of numerical propagation and computational digital optics offer unique flexibility to tune the depth of focus, and compensate for image aberrations. In this work, we report imaging the dynamics of cell division in E.coli and yeast cells using a DHM platform. We demonstrate 3-D and depth imaging as well as reconstruction of phase profiles of E.coli and yeast cells using the system. We record a digital hologram of E.coli and yeast cells and reconstruct the image using Fresnel propagation algorithm. We also use aberration compensation algorithms for correcting the aberrations that are introduced by the microscope objective in the object path using linear least square fitting techniques. This work demonstrates the strong potential of a DHM platform in 3-D live cell imaging, fast clinical quantifications and pathological applications.

Two-dimensional numerical simulation of boron diffusion for pyramidally textured silicon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Fa-Jun, E-mail: Fajun.Ma@nus.edu.sg; Duttagupta, Shubham; Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, 117576

2014-11-14

Multidimensional numerical simulation of boron diffusion is of great relevance for the improvement of industrial n-type crystalline silicon wafer solar cells. However, surface passivation of boron diffused area is typically studied in one dimension on planar lifetime samples. This approach neglects the effects of the solar cell pyramidal texture on the boron doping process and resulting doping profile. In this work, we present a theoretical study using a two-dimensional surface morphology for pyramidally textured samples. The boron diffusivity and segregation coefficient between oxide and silicon in simulation are determined by reproducing measured one-dimensional boron depth profiles prepared using different boronmore » diffusion recipes on planar samples. The established parameters are subsequently used to simulate the boron diffusion process on textured samples. The simulated junction depth is found to agree quantitatively well with electron beam induced current measurements. Finally, chemical passivation on planar and textured samples is compared in device simulation. Particularly, a two-dimensional approach is adopted for textured samples to evaluate chemical passivation. The intrinsic emitter saturation current density, which is only related to Auger and radiative recombination, is also simulated for both planar and textured samples. The differences between planar and textured samples are discussed.« less

A deep structural ridge beneath central India

NASA Astrophysics Data System (ADS)

Agrawal, P. K.; Thakur, N. K.; Negi, J. G.

A joint-inversion of magnetic satellite (MAGSAT) and free air gravity data has been conducted to quantitatively investigate the cause for Bouguer gravity anomaly over Central Indian plateaus and possible fold consequences beside Himalayan zone in the Indian sub-continent due to collision between Indian and Eurasian plates. The appropriate inversion with 40 km crustal depth model has delineated after discriminating high density and magnetisation models, for the first time, about 1500 km long hidden ridge structure trending NW-SE. The structure is parallel to Himalayan fold axis and the Indian Ocean ridge in the Arabian Sea. A quantitative relief model across a representative anomaly profile confirms the ridge structure with its highest point nearly 6 km higher than the surrounding crustal level in peninsular India. The ridge structure finds visible support from the astro-geoidal contours.

A quantitative index of soil development from field descriptions: Examples from a chronosequence in central California

USGS Publications Warehouse

Harden, J.W.

1982-01-01

A soil development index has been developed in order to quantitatively measure the degree of soil profile development. This index, which combines eight soil field properties with soil thickness, is designed from field descriptions of the Merced River chronosequence in central California. These eight properties are: clay films, texture plus wet consistence, rubification (color hue and chroma), structure, dry consistence, moist consistence, color value, and pH. Other properties described in the field can be added when more soils are studied. Most of the properties change systematically within the 3 m.y. age span of the Merced River chronosequence. The absence of properties on occasion does not significantly affect the index. Individual quantified field properties, as well as the integrated index, are examined and compared as functions of soil depth and age. ?? 1982.

Vertical Structure of Shadow Zone Arrivals: Comparison of Parabolic Equation Simulations and Acoustic Data

DTIC Science & Technology

2011-01-01

676 677 Travel Time (sec) 678 45 95 £ 85 ? 75 £ 65 3 55 *§ 85 75 65 55 85 75 65 55 45’— 673 dB re 1 uPa A :,. 1.. i b , u . k , AL...1. u * .1 t., J. .1. 674 675 676 677 Travel Time (sec) 678 673 674 675 676 677 Travel Time (sec) 678 Range...hydrophone data at the 3892 -meter depth (Figure 2(d)). A more quantitative measure of the vertical extension of the cusp is the energy profile of the cusp

Direct band gap measurement of Cu(In,Ga)(Se,S){sub 2} thin films using high-resolution reflection electron energy loss spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heo, Sung; College of Information and Communication Engineering, Sungkyunkwan University, Cheoncheon-dong 300, Jangan-gu, Suwon 440-746; Lee, Hyung-Ik

2015-06-29

To investigate the band gap profile of Cu(In{sub 1−x},Ga{sub x})(Se{sub 1−y}S{sub y}){sub 2} of various compositions, we measured the band gap profile directly as a function of in-depth using high-resolution reflection energy loss spectroscopy (HR-REELS), which was compared with the band gap profile calculated based on the auger depth profile. The band gap profile is a double-graded band gap as a function of in-depth. The calculated band gap obtained from the auger depth profile seems to be larger than that by HR-REELS. Calculated band gaps are to measure the average band gap of the spatially different varying compositions with respectmore » to considering its void fraction. But, the results obtained using HR-REELS are to be affected by the low band gap (i.e., out of void) rather than large one (i.e., near void). Our findings suggest an analytical method to directly determine the band gap profile as function of in-depth.« less

Water Plume Temperature Measurements by an Unmanned Aerial System (UAS)

PubMed Central

DeMario, Anthony; Lopez, Pete; Plewka, Eli; Wix, Ryan; Xia, Hai; Zamora, Emily; Gessler, Dan; Yalin, Azer P.

2017-01-01

We report on the development and testing of a proof of principle water temperature measurement system deployed on an unmanned aerial system (UAS), for field measurements of thermal discharges into water. The primary elements of the system include a quad-copter UAS to which has been integrated, for the first time, both a thermal imaging infrared (IR) camera and an immersible probe that can be dipped below the water surface to obtain vertical water temperature profiles. The IR camera is used to take images of the overall water surface to geo-locate the plume, while the immersible probe provides quantitative temperature depth profiles at specific locations. The full system has been tested including the navigation of the UAS, its ability to safely carry the sensor payload, and the performance of both the IR camera and the temperature probe. Finally, the UAS sensor system was successfully deployed in a pilot field study at a coal burning power plant, and obtained images and temperature profiles of the thermal effluent. PMID:28178215

Water Plume Temperature Measurements by an Unmanned Aerial System (UAS).

PubMed

DeMario, Anthony; Lopez, Pete; Plewka, Eli; Wix, Ryan; Xia, Hai; Zamora, Emily; Gessler, Dan; Yalin, Azer P

2017-02-07

We report on the development and testing of a proof of principle water temperature measurement system deployed on an unmanned aerial system (UAS), for field measurements of thermal discharges into water. The primary elements of the system include a quad-copter UAS to which has been integrated, for the first time, both a thermal imaging infrared (IR) camera and an immersible probe that can be dipped below the water surface to obtain vertical water temperature profiles. The IR camera is used to take images of the overall water surface to geo-locate the plume, while the immersible probe provides quantitative temperature depth profiles at specific locations. The full system has been tested including the navigation of the UAS, its ability to safely carry the sensor payload, and the performance of both the IR camera and the temperature probe. Finally, the UAS sensor system was successfully deployed in a pilot field study at a coal burning power plant, and obtained images and temperature profiles of the thermal effluent.

Compositional depth profiles of the type 316 stainless steel undergone the corrosion in liquid lithium using laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Li, Ying; Ke, Chuan; Liu, Xiang; Gou, Fujun; Duan, Xuru; Zhao, Yong

2017-12-01

Liquid metal lithium cause severe corrosion on the surface of metal structure material that used in the blanket and first wall of fusion device. Fast and accurate compositional depth profile measurement for the boundary layer of the corroded specimen will reveal the clues for the understanding and evaluation of the liquid lithium corrosion process as well as the involved corrosion mechanism. In this work, the feasibility of laser-induced breakdown spectroscopy for the compositional depth profile analysis of type 316 stainless steel which was corroded by liquid lithium in certain conditions was demonstrated. High sensitivity of LIBS was revealed especially for the corrosion medium Li in addition to the matrix elements of Fe, Cr, Ni and Mn by the spectral analysis of the plasma emission. Compositional depth profile analysis for the concerned elements which related to corrosion was carried out on the surface of the corroded specimen. Based on the verified local thermodynamic equilibrium shot-by-shot along the depth profile, the matrix effect was evaluated as negligible by the extracted physical parameter of the plasmas generated by each laser pulse in the longitudinal depth profile. In addition, the emission line intensity ratios were introduced to further reduce the impact on the emission line intensity variations arise from the strong inhomogeneities on the corroded surface. Compositional depth profiles for the matrix elements of Fe, Cr, Ni, Mn and the corrosion medium Li were constructed with their measured relative emission line intensities. The distribution and correlations of the concerned elements in depth profile may indicate the clues to the complicated process of composition diffusion and mass transfer. The results obtained demonstrate the potentiality of LIBS as an effective technique to perform spectrochemical measurement in the research fields of liquid metal lithium corrosion.

Nitric oxide assisted C60 secondary ion mass spectrometry for molecular depth profiling of polyelectrolyte multilayers.

PubMed

Zappalà, G; Motta, V; Tuccitto, N; Vitale, S; Torrisi, A; Licciardello, A

2015-12-15

Secondary ion mass spectrometry (SIMS) with polyatomic primary ions provides a successful tool for molecular depth profiling of polymer systems, relevant in many technological applications. Widespread C60 sources, however, cause in some polymers extensive damage with loss of molecular information along depth. We study a method, based on the use of a radical scavenger, for inhibiting ion-beam-induced reactions causing sample damage. Layered polystyrene sulfonate and polyacrylic acid based polyelectrolyte films, behaving differently towards C60 beam-induced damage, were selected and prepared as model systems. They were depth profiled by means of time-of-flight (TOF)-SIMS in dual beam mode, using fullerene ions for sputtering. Nitric oxide was introduced into the analysis chamber as a radical scavenger. The effect of sample cooling combined with NO-dosing on the quality of depth profiles was explored. NO-dosing during C60-SIMS depth profiling of >1 micrometer-thick multilayered polyelectrolytes allows detection, along depth, of characteristic fragments from systems otherwise damaged by C60 bombardment, and increases sputtering yield by more than one order of magnitude. By contrast, NO has little influence on those layers that are well profiled with C60 alone. Such leveling effect, more pronounced at low temperature, leads to a dramatic improvement of profile quality, with a clear definition of interfaces. NO-dosing provides a tool for extending the applicability, in SIMS depth profiling, of the widely spread fullerene ion sources. In view of the acceptable erosion rates on inorganics, obtainable with C60, the method could be of relevance also in connection with the 3D-imaging of hybrid polymer/inorganic systems. Copyright © 2015 John Wiley & Sons, Ltd.

An Orbital "Virtual Radar" from TRMM Passive Microwave and Lightning Observations

NASA Technical Reports Server (NTRS)

Boccippio, Dennis J.

2004-01-01

The retrieval of vertical structure from joint passive microwave and lightning observations is demonstrated. Three years of data from the TRMM (Tropical Rainfall Measuring Mission) are used as a training dataset for regression and classification neural networks; the TMI (TRMM Microwave Imager) and LIS (Lightning Imaging Sensor) provide the inputs, the PR (Precipitation Radar) provides the training targets. Both vertical reflectivity profile categorization (into 9 convective, 7 stratiform, 2 mixed and 6 anvil types) and geophysical parameters (surface rainfall, vertically integrated liquid (VIL), ice water content (IWC) and echo tops) are retrieved. Retrievals are successful over both land and ocean surfaces. The benefit of using lightning observations as inputs to these retrievals is quantitatively demonstrated; lightning essentially provides an additional convective/stratiform discriminator, and is most important for isolation of midlevel (tops in the mixed phase region) convective profile types (this is because high frequency passive microwave observations already provide good convective/stratiform discrimination for deep convective profiles). This is highly relevant as midlevel convective profiles account for an extremely large fraction of tropical rainfall, and yet are most difficult to discriminate from comparable-depth stratiform profile types using passive microwave observations alone.

A numerical model for the movement of H 2O, H 218O, and 2HHO in the unsaturated zone

NASA Astrophysics Data System (ADS)

Shurbaji, Abdel-Rahman M.; Phillips, Fred M.

1995-09-01

Vertical profiles of H 218O and 2HHO concentrations have yielded useful information on evaporation and infiltration processes in soils. However, in the field, quantitative interpretation of such profiles has been limited by the restrictions inherent in the quasi-steady-state and transient analytical models available to describe the physical processes. This study presents a flexible numerical model that simulates transient fluxes of heat, liquid water, water vapor, and isotopic species. The model can simulate both infiltration and evaporation under fluctuating meteorological conditions and thus should be useful in reproducing changes in field isotope profiles. A transition factor is introduced in the isotope transport equation. This factor combines hydrologic and isotopic parameters and changes slowly with depth in the soil profile but strongly in the evaporation zone, owing to the rapid change in the dominant phase of water from liquid to vapor. Using the transition factor in the isotope transport equation facilitates obtaining the typical shape of the isotope profile (bulge at the evaporation zone). This factor also facilitates producing broad isotope enrichment peaks that may be seen in very dry soils.

Measurement and inference of profile soil-water dynamics at different hillslope positions in a semiarid agricultural watershed

NASA Astrophysics Data System (ADS)

Green, Timothy R.; Erskine, Robert H.

2011-12-01

Dynamics of profile soil water vary with terrain, soil, and plant characteristics. The objectives addressed here are to quantify dynamic soil water content over a range of slope positions, infer soil profile water fluxes, and identify locations most likely influenced by multidimensional flow. The instrumented 56 ha watershed lies mostly within a dryland (rainfed) wheat field in semiarid eastern Colorado. Dielectric capacitance sensors were used to infer hourly soil water content for approximately 8 years (minus missing data) at 18 hillslope positions and four or more depths. Based on previous research and a new algorithm, sensor measurements (resonant frequency) were rescaled to estimate soil permittivity, then corrected for temperature effects on bulk electrical conductivity before inferring soil water content. Using a mass-conservation method, we analyzed multitemporal changes in soil water content at each sensor to infer the dynamics of water flux at different depths and landscape positions. At summit positions vertical processes appear to control profile soil water dynamics. At downslope positions infrequent overland flow and unsaturated subsurface lateral flow appear to influence soil water dynamics. Crop water use accounts for much of the variability in soil water between transects that are either cropped or fallow in alternating years, while soil hydraulic properties and near-surface hydrology affect soil water variability across landscape positions within each management zone. The observed spatiotemporal patterns exhibit the joint effects of short-term hydrology and long-term soil development. Quantitative methods of analyzing soil water patterns in space and time improve our understanding of dominant soil hydrological processes and provide alternative measures of model performance.

Laser microprobe and resonant laser ablation for depth profile measurements of hydrogen isotope atoms contained in graphite.

PubMed

Yorozu, M; Yanagida, T; Nakajyo, T; Okada, Y; Endo, A

2001-04-20

We measured the depth profile of hydrogen atoms in graphite by laser microprobing combined with resonant laser ablation. Deuterium-implanted graphite was employed for the measurements. The sample was ablated by a tunable laser with a wavelength corresponding to the resonant wavelength of 1S-2S of deuterium with two-photon excitation. The ablated deuterium was ionized by a 2 + 1 resonant ionization process. The ions were analyzed by a time-of-flight mass spectrometer. The deuterium ions were detected clearly with the resonant ablation. The detection limit was estimated to be less than 10(16) atoms/cm(3) in our experiments. We determined the depth profile by considering the etching profile and the etching rate. The depth profile agreed well with Monte Carlo simulations to within a precision of 23 mum for the center position and 4-mum precision for distributions for three different implantation depths.

Dynamic Vertical Profiles of Peat Porewater Chemistry in a Northern Peatland

DOE Office of Scientific and Technical Information (OSTI.GOV)

Griffiths, Natalie A.; Sebestyen, Stephen D.

We measured pH, cations, nutrients, and total organic carbon (TOC) over 3 years to examine weekly to monthly variability in porewater chemistry depth profiles (0–3.0 m) in an ombrotrophic bog in Minnesota, USA. We also compared temporal variation at one location to spatial variation in depth profiles at 16 locations across the bog. Most solutes exhibited large gradients with depth. pH increased by two units and calcium concentrations increased over 20 fold with depth, and may reflect peatland development from minerotrophic to ombrotrophic conditions. Ammonium concentrations increased almost 20 fold and TOC concentrations decreased by half with depth, and thesemore » patterns likely reflect mineralization of peat or decomposition of TOC. There was also considerable temporal variation in the porewater chemistry depth profiles. Ammonium, soluble reactive phosphorus, and potassium showed greater temporal variation in near-surface porewater, while pH, calcium, and TOC varied more at depth. This variation demonstrates that deep peat porewater chemistry is not static. Lastly, temporal variation in solute chemistry depth profiles was greater than spatial variation in several instances, especially in shallow porewaters. In conclusion, characterizing both temporal and spatial variability is necessary to ensure representative sampling in peatlands, especially when calculating solute pools and fluxes and parameterizing process-based models.« less

Dynamic Vertical Profiles of Peat Porewater Chemistry in a Northern Peatland

DOE PAGES

Griffiths, Natalie A.; Sebestyen, Stephen D.

2016-10-14

We measured pH, cations, nutrients, and total organic carbon (TOC) over 3 years to examine weekly to monthly variability in porewater chemistry depth profiles (0–3.0 m) in an ombrotrophic bog in Minnesota, USA. We also compared temporal variation at one location to spatial variation in depth profiles at 16 locations across the bog. Most solutes exhibited large gradients with depth. pH increased by two units and calcium concentrations increased over 20 fold with depth, and may reflect peatland development from minerotrophic to ombrotrophic conditions. Ammonium concentrations increased almost 20 fold and TOC concentrations decreased by half with depth, and thesemore » patterns likely reflect mineralization of peat or decomposition of TOC. There was also considerable temporal variation in the porewater chemistry depth profiles. Ammonium, soluble reactive phosphorus, and potassium showed greater temporal variation in near-surface porewater, while pH, calcium, and TOC varied more at depth. This variation demonstrates that deep peat porewater chemistry is not static. Lastly, temporal variation in solute chemistry depth profiles was greater than spatial variation in several instances, especially in shallow porewaters. In conclusion, characterizing both temporal and spatial variability is necessary to ensure representative sampling in peatlands, especially when calculating solute pools and fluxes and parameterizing process-based models.« less

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.

PubMed

Łabaj, Paweł P; Leparc, Germán G; Linggi, Bryan E; Markillie, Lye Meng; Wiley, H Steven; Kreil, David P

2011-07-01

Measurement precision determines the power of any analysis to reliably identify significant signals, such as in screens for differential expression, independent of whether the experimental design incorporates replicates or not. With the compilation of large-scale RNA-Seq datasets with technical replicate samples, however, we can now, for the first time, perform a systematic analysis of the precision of expression level estimates from massively parallel sequencing technology. This then allows considerations for its improvement by computational or experimental means. We report on a comprehensive study of target identification and measurement precision, including their dependence on transcript expression levels, read depth and other parameters. In particular, an impressive recall of 84% of the estimated true transcript population could be achieved with 331 million 50 bp reads, with diminishing returns from longer read lengths and even less gains from increased sequencing depths. Most of the measurement power (75%) is spent on only 7% of the known transcriptome, however, making less strongly expressed transcripts harder to measure. Consequently, <30% of all transcripts could be quantified reliably with a relative error<20%. Based on established tools, we then introduce a new approach for mapping and analysing sequencing reads that yields substantially improved performance in gene expression profiling, increasing the number of transcripts that can reliably be quantified to over 40%. Extrapolations to higher sequencing depths highlight the need for efficient complementary steps. In discussion we outline possible experimental and computational strategies for further improvements in quantification precision. rnaseq10@boku.ac.at

Spatial distribution of microbial biomass, activity, community structure, and the biodegradation of linear alkylbenzene sulfonate (LAS) and linear alcohol ethoxylate (LAE) in the subsurface.

PubMed

Federle, T W; Ventullo, R M; White, D C

1990-12-01

The vertical distribution of microbial biomass, activity, community structure and the mineralization of xenobiotic chemicals was examined in two soil profiles in northern Wisconsin. One profile was impacted by infiltrating wastewater from a laundromat, while the other served as a control. An unconfined aquifer was present 14 meters below the surface at both sites. Biomass and community structure were determined by acridine orange direct counts and measuring concentrations of phospholipid-derived fatty acids (PLFA). Microbial activity was estimated by measuring fluorescein diacetate (FDA) hydrolysis, thymidine incorporation into DNA, and mixed amino acid (MAA) mineralization. Mineralization kinetics of linear alkylbenzene sulfonate (LAS) and linear alcohol ethoxylate (LAE) were determined at each depth. Except for MAA mineralization rates, measures of microbial biomass and activity exhibited similar patterns with depth. PLFA concentration and rates of FDA hydrolysis and thymidine incorporation decreased 10-100 fold below 3 m and then exhibited little variation with depth. Fungal fatty acid markers were found at all depths and represented from 1 to 15% of the total PLFAs. The relative proportion of tuberculostearic acid (TBS), an actinomycete marker, declined with depth and was not detected in the saturated zone. The profile impacted by wastewater exhibited higher levels of PLFA but a lower proportion of TBS than the control profile. This profile also exhibited faster rates of FDA hydrolysis and amino acid mineralization at most depths. LAS was mineralized in the upper 2 m of the vadose zone and in the saturated zone of both profiles. Little or no LAS biodegradation occurred at depths between 2 and 14 m. LAE was mineralized at all depths in both profiles, and the mineralization rate exhibited a similar pattern with depth as biomass and activity measurements. In general, biomass and biodegradative activities were much lower in groundwater than in soil samples obtained from the same depth.

Refractive microlensarray made of silver-halide sensitized gelatin (SHSG) etched by enzyme with SLM-based lithography

NASA Astrophysics Data System (ADS)

Guo, Xiaowei; Chen, Mingyong; Zhu, Jianhua; Ma, Yanqin; Du, Jinglei; Guo, Yongkang; Du, Chunlei

2006-01-01

A novel method for the fabrication of continuous micro-optical components is presented in this paper. It employs a computer controlled digital-micromirror-device(DMD TM) as a switchable projection mask and silver-halide sensitized gelatin (SHSG) as recording material. By etching SHSG with enzyme solution, the micro-optical components with relief modulation can be generated through special processing procedures. The principles of etching SHSG with enzyme and theoretical analysis for deep etching are also discussed in detail, and the detailed quantitative experiments on the processing procedures are conducted to determine optimum technique parameters. A good linear relationship within a depth range of 4μm was experimentally obtained between exposure dose and relief depth. At last, the microlensarray with 256.8μm radius and 2.572μm depth was achieved. This method is simple, cheap and the aberration in processing procedures can be corrected in the step of designing mask, so it is a practical method to fabricate good continuous profile for low-volume production.

Neutron Depth Profiling: Overview and Description of NIST Facilities

PubMed Central

Downing, R. G.; Lamaze, G. P.; Langland, J. K.; Hwang, S. T.

1993-01-01

The Cold Neutron Depth Profiling (CNDP) instrument at the NIST Cold Neutron Research Facility (CNRF) is now operational. The neutron beam originates from a 16 L D2O ice cold source and passes through a filter of 135 mm of single crystal sapphire. The neutron energy spectrum may be described by a 65 K Maxwellian distribution. The sample chamber configuration allows for remote controlled scanning of 150 × 150 mm sample areas including the varying of both sample and detector angle. The improved sensitivity over the current thermal depth profiling instrument has permitted the first nondestructive measurements of 17O profiles. This paper describes the CNDP instrument, illustrates the neutron depth profiling (NDP) technique with examples, and gives a separate bibliography of NDP publications. PMID:28053461

Depth resolution and preferential sputtering in depth profiling of sharp interfaces

NASA Astrophysics Data System (ADS)

Hofmann, S.; Han, Y. S.; Wang, J. Y.

2017-07-01

The influence of preferential sputtering on depth resolution of sputter depth profiles is studied for different sputtering rates of the two components at an A/B interface. Surface concentration and intensity depth profiles on both the sputtering time scale (as measured) and the depth scale are obtained by calculations with an extended Mixing-Roughness-Information depth (MRI)-model. The results show a clear difference for the two extreme cases (a) preponderant roughness and (b) preponderant atomic mixing. In case (a), the interface width on the time scale (Δt(16-84%)) increases with preferential sputtering if the faster sputtering component is on top of the slower sputtering component, but the true resolution on the depth scale (Δz(16-84%)) stays constant. In case (b), the interface width on the time scale stays constant but the true resolution on the depth scale varies with preferential sputtering. For similar order of magnitude of the atomic mixing and the roughness parameters, a transition state between the two extremes is obtained. While the normalized intensity profile of SIMS represents that of the surface concentration, an additional broadening effect is encountered in XPS or AES by the influence of the mean electron escape depth which may even cause an additional matrix effect at the interface.

SU-E-T-635: Quantitative Study On Beam Flatness Variation with Beam Energy Change

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, J S; Eldib, A; Ma, C

2014-06-15

Purpose: Beam flatness check has been proposed for beam energy check for photon beams with flattering filters. In this work, beam flatness change with beam energy was investigated quantitatively using the Monte Carlo method and its significance was compared with depth dose curve change. Methods: Monte Carlo simulations for a linear accelerator with flattering filter were performed with different initial electron energies for photon beams of 6MV and 10MV. Dose calculations in a water phantom were then perform with the phase space files obtained from the simulations. The beam flatness was calculated based on the dose profile at 10 cmmore » depth for all the beams with different initial electron energies. The percentage depth dose (PDD) curves were also analyzed. The dose at 10cm depth (D10) and the ratio of the dose at 10cm and 20cm depth (D10/D20) and their change with the beam energy were calculated and compared with the beam flatness variation. Results: It was found that the beam flatness variation with beam energy change was more significant than the change of D10 and the ratio between D10 and D20 for both 6MV and 10MV beams. Half MeV difference on the initial electron beam energy brought in at least 20% variation on the beam flatness but only half percent change on the ratio of D10 and D20. The change of D10 or D20 alone is even less significant. Conclusion: The beam energy impact on PDD is less significant than that on the beam flatness. If the PDD is used for checking the beam energy, uncertainties of the measurement could possibly disguise its change. Beam flatness changes more significantly with beam energy and therefore it can be used for monitoring the energy change for photon beams with flattering filters. However, other factors which may affect the beam flatness should be watched as well.« less

Estimating sub-surface dispersed oil concentration using acoustic backscatter response.

PubMed

Fuller, Christopher B; Bonner, James S; Islam, Mohammad S; Page, Cheryl; Ojo, Temitope; Kirkey, William

2013-05-15

The recent Deepwater Horizon disaster resulted in a dispersed oil plume at an approximate depth of 1000 m. Several methods were used to characterize this plume with respect to concentration and spatial extent including surface supported sampling and autonomous underwater vehicles with in situ instrument payloads. Additionally, echo sounders were used to track the plume location, demonstrating the potential for remote detection using acoustic backscatter (ABS). This study evaluated use of an Acoustic Doppler Current Profiler (ADCP) to quantitatively detect oil-droplet suspensions from the ABS response in a controlled laboratory setting. Results from this study showed log-linear ABS responses to oil-droplet volume concentration. However, the inability to reproduce ABS response factors suggests the difficultly in developing meaningful calibration factors for quantitative field analysis. Evaluation of theoretical ABS intensity derived from the particle size distribution provided insight regarding method sensitivity in the presence of interfering ambient particles. Copyright © 2013 Elsevier Ltd. All rights reserved.

Profilometric characterization of DOEs with continuous microrelief

NASA Astrophysics Data System (ADS)

Korolkov, V. P.; Ostapenko, S. V.; Shimansky, R. V.

2008-09-01

Methodology of local characterization of continuous-relief diffractive optical elements has been discussed. The local profile depth can be evaluated using "approximated depth" defined without taking a profile near diffractive zone boundaries into account. Several methods to estimate the approximated depth have been offered.

The impact of aerosol vertical distribution on aerosol optical depth retrieval using CALIPSO and MODIS data: Case study over dust and smoke regions

NASA Astrophysics Data System (ADS)

Wu, Yerong; de Graaf, Martin; Menenti, Massimo

2017-08-01

Global quantitative aerosol information has been derived from MODerate Resolution Imaging SpectroRadiometer (MODIS) observations for decades since early 2000 and widely used for air quality and climate change research. However, the operational MODIS Aerosol Optical Depth (AOD) products Collection 6 (C6) can still be biased, because of uncertainty in assumed aerosol optical properties and aerosol vertical distribution. This study investigates the impact of aerosol vertical distribution on the AOD retrieval. We developed a new algorithm by considering dynamic vertical profiles, which is an adaptation of MODIS C6 Dark Target (C6_DT) algorithm over land. The new algorithm makes use of the aerosol vertical profile extracted from Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) measurements to generate an accurate top of the atmosphere (TOA) reflectance for the AOD retrieval, where the profile is assumed to be a single layer and represented as a Gaussian function with the mean height as single variable. To test the impact, a comparison was made between MODIS DT and Aerosol Robotic Network (AERONET) AOD, over dust and smoke regions. The results show that the aerosol vertical distribution has a strong impact on the AOD retrieval. The assumed aerosol layers close to the ground can negatively bias the retrievals in C6_DT. Regarding the evaluated smoke and dust layers, the new algorithm can improve the retrieval by reducing the negative biases by 3-5%.

Utilizing of magnetic parameters for evaluation of soil erosion rates on two different agricultural sites

NASA Astrophysics Data System (ADS)

Kapicka, A.; Grison, H.; Petrovsky, E.; Jaksik, O.; Kodesova, R.

2015-12-01

Field measurements of magnetic susceptibility were carried out on regular grid, resulting in 101 data points at Brumovice and 65 at Vidim locality. Mass specific magnetic susceptibility χ and its frequency dependence χFD was used to estimate the significance of SP ferrimagnetic particles of pedogenic origin in topsoil horizons. The lowest magnetic susceptibility was obtained on the steep valley sides. Here the original topsoil was eroded and mixed by tillage with the soil substrate (loess). Soil profiles unaffected by erosion were investigated in detail. The vertical distribution of magnetic susceptibility along these "virgin" profiles was measured in laboratory on samples collected with 2-cm spacing. The differences between the distribution of susceptibility in the undisturbed soil profiles and the magnetic signal after uniform mixing of the soil material as a result of erosion and tillage are fundamental for the estimation of soil loss in the studied test fields. Maximum cumulative soil erosion depth in Brumovice and Vidim is around 100 cm and 50 cm respectively. The magnetic method is suitable for mapping at the chernozem localities and measurement of soil magnetic susceptibility is in this case useful and fast technique for quantitative estimation of soil loss caused by erosion. However, it is less suitable (due to lower magnetic differentiation with depth) in areas with luvisol as dominant soil unit. Acknowledgement: This study was supported by NAZV Agency of the Ministry of Agriculture of the Czech Republic through grant No QJ1230319.

Comparison of Air Fluorescence and Ionization Measurements of E.M. Shower Depth Profiles: Test of a UHECR Detector Technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belz, J.; Cao, Z.; Huentemeyer, P.

Measurements are reported on the fluorescence of air as a function of depth in electromagnetic showers initiated by bunches of 28.5 GeV electrons. The light yield is compared with the expected and observed depth profiles of ionization in the showers. It validates the use of atmospheric fluorescence profiles in measuring ultra high energy cosmic rays.

Profiling defect depth in composite materials using thermal imaging NDE

NASA Astrophysics Data System (ADS)

Obeidat, Omar; Yu, Qiuye; Han, Xiaoyan

2018-04-01

Sonic Infrared (IR) NDE, is a relatively new NDE technology; it has been demonstrated as a reliable and sensitive method to detect defects. SIR uses ultrasonic excitation with IR imaging to detect defects and flaws in the structures being inspected. An IR camera captures infrared radiation from the target for a period of time covering the ultrasound pulse. This period of time may be much longer than the pulse depending on the defect depth and the thermal properties of the materials. With the increasing deployment of composites in modern aerospace and automobile structures, fast, wide-area and reliable NDE methods are necessary. Impact damage is one of the major concerns in modern composites. Damage can occur at a certain depth without any visual indication on the surface. Defect depth information can influence maintenance decisions. Depth profiling relies on the time delays in the captured image sequence. We'll present our work on the defect depth profiling by using the temporal information of IR images. An analytical model is introduced to describe heat diffusion from subsurface defects in composite materials. Depth profiling using peak time is introduced as well.

Magnetic Nonuniformity and Thermal Hysteresis of Magnetism in a Manganite Thin Film [Depth profiling of magnetization and coupling of strain with magnetization in (La 0.4Pr 0.6) 0.67Ca 0.33MnO 3 films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Surendra; Fitzsimmons, M. R.; Lookman, T.

We measured the chemical and magnetic depth profiles of a single crystalline film grown on a NdGaO 3 substrate using x-ray reflectometry, electron microscopy, electron energy-loss spectroscopy and polarized neutron reflectometry. Our data indicate that the film exhibits coexistence of different magnetic phases as a function of depth. The magnetic depth profile is correlated with a variation of chemical composition with depth. The thermal hysteresis of ferromagnetic order in the film suggests a first order ferromagnetic transition at low temperatures

Microstructural analysis in the depth direction of a heteroepitaxial AlN thick film grown on a trench-patterned template by nanobeam X-ray diffraction

NASA Astrophysics Data System (ADS)

Shida, K.; Takeuchi, S.; Tohei, T.; Miyake, H.; Hiramatsu, K.; Sumitani, K.; Imai, Y.; Kimura, S.; Sakai, A.

2018-04-01

This work quantitatively assessed the three-dimensional distribution of crystal lattice distortions in an epitaxial AlN thick film grown on a trench-patterned template, using nanobeam X-ray diffraction. Position-dependent ω-2θ-φ mapping clearly demonstrated local tilting, spacing and twisting of lattice planes as well as fluctuations in these phenomena on a sub-micrometer scale comparable to the pitch of the trench-and-terrace patterning. Analysis of the crystal lattice distortion in the depth direction was performed using a newly developed method in which the X-ray nanobeam diffracted from the sample surface to specific depths can be selectively detected by employing a Pt wire profiler. This technique generated depth-resolved ω-2θ-φ maps confirming that fluctuations in lattice plane tilting and spacing greatly depend on the dislocation distribution and the history of the AlN epitaxial growth on the trench-patterned structure. It was also found that both fluctuations were reduced on approaching the AlN surface and, in particular, were sharply reduced at specific depths in the terrace regions. These sharp reductions are attributed to the formation of sacrificial zones with degraded crystal quality around the trenches and possibly lead to raising the crystal quality near the surface of the AlN film.

Maine Geological Survey Borehole Temperature Profiles

DOE Data Explorer

Marvinney, Robert

2013-11-06

This dataset includes temperature profiles from 30 boreholes throughout Maine that were selected for their depth, location, and lithologies encountered. Depths range from about 300 feet to 2,200 feet. Most of the boreholes selected for measurement were completed in granite because this lithology can be assumed to be nearly homogeneous over the depth of the borehole. Boreholes were also selected to address gaps in existing geothermal datasets. Temperature profiles were collected in October and November, 2012.

Nondestructive strain depth profiling with high energy X-ray diffraction: System capabilities and limitations

NASA Astrophysics Data System (ADS)

Zhang, Zhan; Wendt, Scott; Cosentino, Nicholas; Bond, Leonard J.

2018-04-01

Limited by photon energy, and penetration capability, traditional X-ray diffraction (XRD) strain measurements are only capable of achieving a few microns depth due to the use of copper (Cu Kα1) or molybdenum (Mo Kα1) characteristic radiation. For deeper strain depth profiling, destructive methods are commonly necessary to access layers of interest by removing material. To investigate deeper depth profiles nondestructively, a laboratory bench-top high-energy X-ray diffraction (HEXRD) system was previously developed. This HEXRD method uses an industrial 320 kVp X-Ray tube and the Kα1 characteristic peak of tungsten, to produces a higher intensity X-ray beam which enables depth profiling measurement of lattice strain. An aluminum sample was investigated with deformation/load provided using a bending rig. It was shown that the HEXRD method is capable of strain depth profiling to 2.5 mm. The method was validated using an aluminum sample where both the HEXRD method and the traditional X-ray diffraction method gave data compared with that obtained using destructive etching layer removal, performed by a commercial provider. The results demonstrate comparable accuracy up to 0.8 mm depth. Nevertheless, higher attenuation capabilities in heavier metals limit the applications in other materials. Simulations predict that HEXRD works for steel and nickel in material up to 200 µm, but experiment results indicate that the HEXRD strain profile is not practical for steel and nickel material, and the measured diffraction signals are undetectable when compared to the noise.

Submicron mapping of strained silicon-on-insulator features induced

NASA Astrophysics Data System (ADS)

Murray, Conal E.; Sankarapandian, M.; Polvino, S. M.; Noyan, I. C.; Lai, B.; Cai, Z.

2007-04-01

Real-space maps of strain within silicon-on-insulator (SOI) features induced by adjacent, embedded shallow-trench-isolation (STI) SiO2 regions were obtained using x-ray microbeam diffraction. The quantitative strain mapping indicated that the SOI strain was largest at the SOI/STI interface and decreased as a function of distance from this interface. An out-of-plane residual strain of approximately -31μɛ was observed in the blanket regions of the SOI. A comparison of the depth-averaged strain distributions to the strain profiles calculated from an Eshelby inclusion model indicated an equivalent eigenstrain of -0.55% in the STI regions acting on the SOI features.

Upper mantle electrical conductivity for seven subcontinental regions of the Earth

USGS Publications Warehouse

Campbell, W.H.; Schiffmacher, E.R.

1988-01-01

Spherical harmonic analysis coefficients of the external and internal parts of the quiet-day geomagnetic field variations (Sq) separated for the 7 continental regions of the observatories have been used to determine conductivity profiles to depths of about 600 km by the Schmucker equivalent substitute conductor method. The profiles give evidence of increases in conductivity between about 150 and 350 km depth, then a general increase in conductivity thereafter. For South America we found a high conductivity at shallow depths. The European profile showed a highly conducting layer near 125 km. At the greater depths, Europe, Australia and South America had the lowest values of conductivity. North America and east Asia had intermediate values whereas the African and central Asian profiles both showed the conductivities rising rapidly beyond 450 km depth. The regional differences indicate that there may be considerable lateral heterogeneity of electrical conductivity in the Earth's upper mantle. -Authors

Impact of inflammation on iron stores in involved and non-involved psoriatic skin

NASA Astrophysics Data System (ADS)

Pinheiro, T.; Ynsa, M. D.; Alves, L. C.; Teixeira, P.; Ferreira, J.; Filipe, P.

2015-04-01

Accumulating evidence supports a role for cellular Fe in cell proliferation, inflammation, and disease tolerance. Psoriasis is a severe inflammatory and hyper proliferative condition of human skin whose aetiology remains poorly understood. Herein, we performed nuclear microscopy techniques to quantify with cellular resolution and high sensitivity the concentration of Fe in lesional (psoriatic plaques) and non-lesional adjacent skin of psoriatic patients. Fe contents were measured across skin depth and along epidermal strata either by quantitatively imaging Fe distribution in regions of interest, or by determining Fe profiles through analysis of sequential points along selected transepts. Both procedures require deconvolution of spectra to project quantitative elemental data through the application of different software codes. Using these approaches a detailed quantitative distribution of Fe was resolved. We show that in both lesional and non-lesional skin, the epidermal profiles of Fe contents showed a peak at the basal layer and that Fe concentration along the basal layer was not uniformly distributed. Typically, Fe levels were significantly higher in epidermal ridges relative to regions above dermal papillae. Lesional skin displayed excess Fe over extended regions above basal layer. In conclusion, we found significantly increased Fe deposits in the epidermis of psoriatic patients, particularly in areas of epidermal hyper proliferation. These findings suggest an important role for Fe in the pathogenesis of psoriasis. They also raise the possibility that manipulation of Fe levels in the skin may become relevant for the clinical management of psoriasis.

Methane, Carbon Dioxide and Nitrous Oxide Fluxes in Soil Profile under a Winter Wheat-Summer Maize Rotation in the North China Plain

PubMed Central

Wang, Yuying; Hu, Chunsheng; Ming, Hua; Oenema, Oene; Schaefer, Douglas A.; Dong, Wenxu; Zhang, Yuming; Li, Xiaoxin

2014-01-01

The production and consumption of the greenhouse gases (GHGs) methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O) in soil profile are poorly understood. This work sought to quantify the GHG production and consumption at seven depths (0–30, 30–60, 60–90, 90–150, 150–200, 200–250 and 250–300 cm) in a long-term field experiment with a winter wheat-summer maize rotation system, and four N application rates (0; 200; 400 and 600 kg N ha−1 year−1) in the North China Plain. The gas samples were taken twice a week and analyzed by gas chromatography. GHG production and consumption in soil layers were inferred using Fick’s law. Results showed nitrogen application significantly increased N2O fluxes in soil down to 90 cm but did not affect CH4 and CO2 fluxes. Soil moisture played an important role in soil profile GHG fluxes; both CH4 consumption and CO2 fluxes in and from soil tended to decrease with increasing soil water filled pore space (WFPS). The top 0–60 cm of soil was a sink of atmospheric CH4, and a source of both CO2 and N2O, more than 90% of the annual cumulative GHG fluxes originated at depths shallower than 90 cm; the subsoil (>90 cm) was not a major source or sink of GHG, rather it acted as a ‘reservoir’. This study provides quantitative evidence for the production and consumption of CH4, CO2 and N2O in the soil profile. PMID:24892931

Noncontact quantitative biomechanical characterization of cardiac muscle using shear wave imaging optical coherence tomography

PubMed Central

Wang, Shang; Lopez, Andrew L.; Morikawa, Yuka; Tao, Ge; Li, Jiasong; Larina, Irina V.; Martin, James F.; Larin, Kirill V.

2014-01-01

We report on a quantitative optical elastographic method based on shear wave imaging optical coherence tomography (SWI-OCT) for biomechanical characterization of cardiac muscle through noncontact elasticity measurement. The SWI-OCT system employs a focused air-puff device for localized loading of the cardiac muscle and utilizes phase-sensitive OCT to monitor the induced tissue deformation. Phase information from the optical interferometry is used to reconstruct 2-D depth-resolved shear wave propagation inside the muscle tissue. Cross-correlation of the displacement profiles at various spatial locations in the propagation direction is applied to measure the group velocity of the shear waves, based on which the Young’s modulus of tissue is quantified. The quantitative feature and measurement accuracy of this method is demonstrated from the experiments on tissue-mimicking phantoms with the verification using uniaxial compression test. The experiments are performed on ex vivo cardiac muscle tissue from mice with normal and genetically altered myocardium. Our results indicate this optical elastographic technique is useful as a noncontact tool to assist the cardiac muscle studies. PMID:25071943

The Presence and Distribution of Salts as a Palaeoprecipitation Proxy in Atacama Soils

NASA Astrophysics Data System (ADS)

McKay, Lucy; Claire, Mark

2016-04-01

The Atacama Desert in northern Chile (17 to 27° S) is the driest and oldest warm desert on Earth and contains unique abundances of atmospherically-derived salts such as nitrate and perchlorate (Ewing et al., 2006; Jackson et al., 2015). Near-surface accumulation of extremely soluble salts indicates a scarcity of long-term precipitation-driven leaching from Atacama soils. The prolonged absence of substantial precipitation has enabled nitrate and perchlorate to accumulate for millions of years to measurable levels, while interacting with occasional rainfall to move vertically through the soil profile. We investigate the near-surface presence and distribution of atmospherically-generated soluble salts at Earth's most arid extreme, aiming to quantify Atacama palaeoprecipitation during the Quaternary. Previous field and modelling studies have revealed a strong correlation between the depth of peak nitrate and past precipitation events in the U.S. desert southwest (Walvoord et al., 2003; Marion et al., 2008). We extend these studies to regions of much lower rainfall, and report the largest ever near-surface concentrations of nitrate and perchlorate in Earth's soils. We present salt distribution profiles from soil pits in six localities, spanning ~1000 km of the south-to-north (27° to 24° S) natural rainfall and ecosystem function gradient that spans the arid to hyperarid transition (from 20 to <1 mm rainfall y-1). Localities include the well-characterised Yungay desert research station, initially declared as the driest place on Earth beyond the limit for microbial life (McKay et al., 2003). Importantly, our nitrate and perchlorate data confirm and extend suspicions that drier localities than Yungay exist (Azua-Bustos et al., 2015). For example, our "km40" site reveals 10 mg/kg of perchlorate at the surface, with a peak of 35 mg/kg at 10 cm depth. At "PONR", perchlorate peaks at >100 mg/kg at 120 cm depth, with an astonishing 22 mg/kg at the surface. In comparison, perchlorate peaks at ~4 mg/kg at 90 cm depth in our Yungay soil profile. Given that perchlorate is the most soluble naturally-existing salt, "km40" and "PONR" indicate a complete lack of recent precipitation and are candidates for the driest place on Earth. We use the numerical model of Marion et al. (2008) to quantitatively constrain the maximum rainfall distributions and event frequencies that are permitted by our measured profiles. Our Atacama soil profiles exhibit vertical variation in their geochemistry, suggesting considerable climatic and precipitation variability in recent years, enabling constraints on both maximum rainfall events and their temporal occurrence. Through geochemistry and modelling, this research identifies a unique quantitative palaeoprecipitation proxy for Earth's driest desert, with significant consequences for understanding and predicting the future ecohydrological cycle in desert ecosystems, as well as for the planet-wide desert on Mars. References Azua-Bustos A., et al., 2015. Environmental Microbiology Reports, 7, pp.388-394 Ewing S.A., et al., 2006. Geochimica et Cosmochimica Acta, 70, pp.5293-5322 Jackson W.A., et al., 2015. Geochimica et Cosmochimica Acta, 164, pp.502-522 Marion G.M., et al., 2008. Journal of Arid Environments, 72, pp.1012-1033 McKay C.P., et al., 2003. Astrobiology, 3, pp.393-406 Walvoord M.A., et al., 2003. Science, 302, pp.1021-1024

Hardness depth profile of lattice strained cemented carbide modified by high-energy boron ion implantation

NASA Astrophysics Data System (ADS)

Yoshida, Y.; Matsumura, A.; Higeta, K.; Inoue, T.; Shimizu, S.; Motonami, Y.; Sato, M.; Sadahiro, T.; Fujii, K.

1991-07-01

The hardness depth profiles of cemented carbides which were implanted with high-energy B + ions have been estimated using a dynamic microhardness tester. The B + implantations into (16% Co)-cemented WC alloys were carried out under conditions where the implantation energies were 1-3 MeV and the fluences 1 × 10 17-1 × 10 18ions/cm 2. The profiles show that the implanted layer becomes harder as fluences are chosen at higher values and there is a peak at a certain depth which depends on the implantation energy. In X-ray diffraction (XRD) studies of the implanted surface the broadened refraction peaks of only WC and Co are detected and the increments of lattice strain and of residual stress in the near-surface region are observed. It is supposed that the hardening effect should be induced by an increase in residual stress produced by lattice strain. The hardness depth profile in successive implantation of ions with different energies agrees with the compounded profile of each one of the implantations. It is concluded that the hardness depth profile can be controlled under adequate conditions of implantation.

Computer simulation of backscattering spectra from paint

NASA Astrophysics Data System (ADS)

Mayer, M.; Silva, T. F.

2017-09-01

To study the role of lateral non-homogeneity on backscattering analysis of paintings, a simplified model of paint consisting of randomly distributed spherical pigment particles embedded in oil/binder has been developed. Backscattering spectra for lead white pigment particles in linseed oil have been calculated for 3 MeV H+ at a scattering angle of 165° for pigment volume concentrations ranging from 30 vol.% to 70 vol.% using the program STRUCTNRA. For identical pigment volume concentrations the heights and shapes of the backscattering spectra depend on the diameter of the pigment particles: This is a structural ambiguity for identical mean atomic concentrations but different lateral arrangement of materials. Only for very small pigment particles the resulting spectra are close to spectra calculated supposing atomic mixing and assuming identical concentrations of all elements. Generally, a good fit can be achieved when evaluating spectra from structured materials assuming atomic mixing of all elements and laterally homogeneous depth distributions. However, the derived depth profiles are inaccurate by a factor of up to 3. The depth range affected by this structural ambiguity ranges from the surface to a depth of roughly 0.5-1 pigment particle diameters. Accurate quantitative evaluation of backscattering spectra from paintings therefore requires taking the correct microstructure of the paint layer into account.

Establishing the suitability of quantitative optical CT microscopy of PRESAGE® radiochromic dosimeters for the verification of synchrotron microbeam therapy

NASA Astrophysics Data System (ADS)

Doran, Simon J.; Rahman, A. T. Abdul; Bräuer-Krisch, Elke; Brochard, Thierry; Adamovics, John; Nisbet, Andrew; Bradley, David

2013-09-01

Previous research on optical computed tomography (CT) microscopy in the context of the synchrotron microbeam has shown the potential of the technique and demonstrated high quality images, but has left two questions unanswered: (i) are the images suitably quantitative for 3D dosimetry? and (ii) what is the impact on the spatial resolution of the system of the limited depth-of-field of the microscope optics? Cuvette and imaging studies are reported here that address these issues. Two sets of cuvettes containing the radiochromic plastic PRESAGE® were irradiated at the ID17 biomedical beamline of the European Synchrotron Radiation facility over the ranges 0-20 and 0-35 Gy and a third set of cuvettes was irradiated over the range 0-20 Gy using a standard medical linac. In parallel, three cylindrical PRESAGE® samples of diameter 9.7 mm were irradiated with test patterns that allowed the quantitative capabilities of the optical CT microscope to be verified, and independent measurements of the imaging modulation transfer function (MTF) to be made via two different methods. Both spectrophotometric analysis and imaging gave a linear dose response, with gradients ranging from 0.036-0.041 cm-1 Gy-1 in the three sets of cuvettes and 0.037 (optical CT units) Gy-1 for the imaging. High-quality, quantitative imaging results were obtained throughout the 3D volume, as illustrated by depth-dose profiles. These profiles are shown to be monoexponential, and the linear attention coefficient of PRESAGE® for the synchrotron-generated x-ray beam is measured to be (0.185 ± 0.02) cm-1 in excellent agreement with expectations. Low-level (<5%) residual image artefacts are discussed in detail. It was possible to resolve easily slit patterns of width 37 µm (which are smaller than many of the microbeams used on ID-17), but some uncertainty remains as to whether the low values of MTF for the higher spatial frequencies are scanner related or a result of genuine (but non-ideal) dose distributions. We conclude that microscopy images from our scanner do indeed have intensities that are proportional to spectrophotometric optical density and can thus be used as the basis for accurate dosimetry. However, further investigations are necessary before the microscopy images can be used to make the quantitative measures of peak-to-valley ratios for small-diameter microbeams. We suggest various strategies for moving forward and are optimistic about the future potential of this system.

ToF-SIMS Depth Profiling Of Insulating Samples, Interlaced Mode Or Non-interlaced Mode?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Zhaoying; Jin, Ke; Zhang, Yanwen

2014-11-01

Dual beam depth profiling strategy has been widely adopted in ToF-SIMS depth profiling, in which two basic operation modes, interlaced mode and non-interlaced mode, are commonly used. Generally, interlaced mode is recommended for conductive or semi-conductive samples, whereas non-interlaced mode is recommended for insulating samples, where charge compensation can be an issue. Recent publications, however, show that the interlaced mode can be used effectively for glass depth profiling, despite the fact that glass is an insulator. In this study, we provide a simple guide for choosing between interlaced mode and non-interlaced mode for insulator depth profiling. Two representative cases aremore » presented: (1) depth profiling of a leached glass sample, and (2) depth profiling of a single crystal MgO sample. In brief, the interlaced mode should be attempted first, because (1) it may provide reasonable-quality data, and (2) it is time-saving for most cases, and (3) it introduces low H/C/O background. If data quality is the top priority and measurement time is flexible, non-interlaced mode is recommended because interlaced mode may suffer from low signal intensity and poor mass resolution. A big challenge is tracking trace H/C/O in a highly insulating sample (e.g., MgO), because non-interlaced mode may introduce strong H/C/O background but interlaced mode may suffer from low signal intensity. Meanwhile, a C or Au coating is found to be very effective to improve the signal intensity. Surprisingly, the best analyzing location is not on the C or Au coating, but at the edge (outside) of the coating.« less

Target-depth estimation in active sonar: Cramer-Rao bounds for a bilinear sound-speed profile.

PubMed

Mours, Alexis; Ioana, Cornel; Mars, Jérôme I; Josso, Nicolas F; Doisy, Yves

2016-09-01

This paper develops a localization method to estimate the depth of a target in the context of active sonar, at long ranges. The target depth is tactical information for both strategy and classification purposes. The Cramer-Rao lower bounds for the target position as range and depth are derived for a bilinear profile. The influence of sonar parameters on the standard deviations of the target range and depth are studied. A localization method based on ray back-propagation with a probabilistic approach is then investigated. Monte-Carlo simulations applied to a summer Mediterranean sound-speed profile are performed to evaluate the efficiency of the estimator. This method is finally validated on data in an experimental tank.

Depth elemental characterization of 1D self-aligned TiO2 nanotubes using calibrated radio frequency glow discharge optical emission spectroscopy (GDOES)

NASA Astrophysics Data System (ADS)

Mohajernia, Shiva; Mazare, Anca; Hwang, Imgon; Gaiaschi, Sofia; Chapon, Patrick; Hildebrand, Helga; Schmuki, Patrik

2018-06-01

In this work we study the depth composition of anodic TiO2 nanotube layers. We use elemental depth profiling with Glow Discharge Optical Emission Spectroscopy and calibrate the results of this technique with X-ray photoelectron spectroscopy (XPS) and energy dispersive spectroscopy (EDS). We establish optimized sputtering conditions for nanotubular structures using the pulsed RF mode, which causes minimized structural damage during the depth profiling of the nanotubular structures. This allows to obtain calibrated sputter rates that account for the nanotubular "porous" morphology. Most importantly, sputter-artifact free compositional profiles of these high aspect ratio 3D structures are obtained, as well as, in combination with SEM, elegant depth sectional imaging.

Carotenoids and carotenoid esters of orange- and yellow-fleshed mamey sapote (Pouteria sapota (Jacq.) H.E. Moore & Stearn) fruit and their post-prandial absorption in humans.

PubMed

Chacón-Ordóñez, Tania; Schweiggert, Ralf M; Bosy-Westphal, Anja; Jiménez, Víctor M; Carle, Reinhold; Esquivel, Patricia

2017-04-15

Although different genotypes of mamey sapote with distinct pulp colors are consumed in countries from Central to South America, in-depth knowledge on genotype-related differences of their carotenoid profile is lacking. Since the fruit was found to contain the potentially vitamin A-active keto-carotenoids sapotexanthin and cryptocapsin, we sought to qualitatively and quantitatively describe the carotenoid profile of different genotypes by HPLC-DAD-MS n . Sapotexanthin and cryptocapsin were present in all genotypes. Keto-carotenoids such as cryptocapsin, capsoneoxanthin, and their esters were most abundant in orange-fleshed fruit, whereas several carotenoid epoxides prevailed in yellow-fleshed fruit. Differing carotenoid profiles were associated with different color hues of the fruit pulp, while the widely variable carotenoid content (3.7-8.0mg/100gFW) was mainly reflected by differences in color intensity (chroma C ∗ ). Furthermore, the post-prandial absorption of sapotexanthin to human plasma was proven for the first time. Besides sapotexanthin, cryptocapsin was found to be resorbed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Scalable and Cost-Effective Assignment of Mobile Crowdsensing Tasks Based on Profiling Trends and Prediction: The ParticipAct Living Lab Experience

PubMed Central

Bellavista, Paolo; Corradi, Antonio; Foschini, Luca; Ianniello, Raffaele

2015-01-01

Nowadays, sensor-rich smartphones potentially enable the harvesting of huge amounts of valuable sensing data in urban environments, by opportunistically involving citizens to play the role of mobile virtual sensors to cover Smart City areas of interest. This paper proposes an in-depth study of the challenging technical issues related to the efficient assignment of Mobile Crowd Sensing (MCS) data collection tasks to volunteers in a crowdsensing campaign. In particular, the paper originally describes how to increase the effectiveness of the proposed sensing campaigns through the inclusion of several new facilities, including accurate participant selection algorithms able to profile and predict user mobility patterns, gaming techniques, and timely geo-notification. The reported results show the feasibility of exploiting profiling trends/prediction techniques from volunteers’ behavior; moreover, they quantitatively compare different MCS task assignment strategies based on large-scale and real MCS data campaigns run in the ParticipAct living lab, an ongoing MCS real-world experiment that involved more than 170 students of the University of Bologna for more than one year. PMID:26263985

Lateral femoral notch depth is not associated with increased rotatory instability in ACL-injured knees: a quantitative pivot shift analysis.

PubMed

Kanakamedala, Ajay C; Burnham, Jeremy M; Pfeiffer, Thomas R; Herbst, Elmar; Kowalczuk, Marcin; Popchak, Adam; Irrgang, James; Fu, Freddie H; Musahl, Volker

2018-05-01

A deep lateral femoral notch (LFN) on lateral radiographs is indicative of ACL injury. Prior studies have suggested that a deep LFN may also be a sign of persistent rotatory instability and a concomitant lateral meniscus tear. Therefore, the purpose of this study was to evaluate the relationship between LFN depth and both quantitative measures of rotatory knee instability and the incidence of lateral meniscus tears. It was hypothesized that greater LFN depth would be correlated with increased rotatory instability, quantified by lateral compartment translation and tibial acceleration during a quantitative pivot shift test, and incidence of lateral meniscus tears. ACL-injured patients enrolled in a prospective ACL registry from 2014 to 2016 were analyzed. To limit confounders, patients were only included if they had primary ACL tears, no concurrent ligamentous or bony injuries requiring operative treatment, and no previous knee injuries or surgeries to either knee. Eighty-four patients were included in the final analysis. A standardized quantitative pivot shift test was performed pre-operatively under anesthesia in both knees, and rotatory instability, specifically lateral compartment translation and tibial acceleration, was quantified using tablet image analysis software and accelerometer sensors. Standard lateral radiographs and sagittal magnetic resonance images (MRI) of the injured knee were evaluated for LFN depth. There were no significant correlations between LFN depth on either imaging modality and ipsilateral lateral compartment translation or tibial acceleration during a quantitative pivot shift test or side-to-side differences in these measurements. Patients with lateral meniscus tears were found to have significantly greater LFN depths than those without on conventional radiograph and MRI (1.0 vs. 0.6 mm, p < 0.05; 1.2 vs. 0.8 mm, p < 0.05, respectively). There was no correlation between lateral femoral notch depth on conventional radiographs or MRI and quantitative measures of rotatory instability. Concomitant lateral meniscus injury was associated with significantly greater LFN depth. Based on these findings, LFN depth should not be used as an indicator of excessive rotatory instability, but may be an indicator of lateral meniscus injury in ACL-injured patients. Prognostic level IV.

Depth Profilometry via Multiplexed Optical High-Coherence Interferometry

PubMed Central

Kazemzadeh, Farnoud; Wong, Alexander; Behr, Bradford B.; Hajian, Arsen R.

2015-01-01

Depth Profilometry involves the measurement of the depth profile of objects, and has significant potential for various industrial applications that benefit from non-destructive sub-surface profiling such as defect detection, corrosion assessment, and dental assessment to name a few. In this study, we investigate the feasibility of depth profilometry using an Multiplexed Optical High-coherence Interferometry MOHI instrument. The MOHI instrument utilizes the spatial coherence of a laser and the interferometric properties of light to probe the reflectivity as a function of depth of a sample. The axial and lateral resolutions, as well as imaging depth, are decoupled in the MOHI instrument. The MOHI instrument is capable of multiplexing interferometric measurements into 480 one-dimensional interferograms at a location on the sample and is built with axial and lateral resolutions of 40 μm at a maximum imaging depth of 700 μm. Preliminary results, where a piece of sand-blasted aluminum, an NBK7 glass piece, and an optical phantom were successfully probed using the MOHI instrument to produce depth profiles, demonstrate the feasibility of such an instrument for performing depth profilometry. PMID:25803289

Depth profilometry via multiplexed optical high-coherence interferometry.

PubMed

Kazemzadeh, Farnoud; Wong, Alexander; Behr, Bradford B; Hajian, Arsen R

2015-01-01

Depth Profilometry involves the measurement of the depth profile of objects, and has significant potential for various industrial applications that benefit from non-destructive sub-surface profiling such as defect detection, corrosion assessment, and dental assessment to name a few. In this study, we investigate the feasibility of depth profilometry using an Multiplexed Optical High-coherence Interferometry MOHI instrument. The MOHI instrument utilizes the spatial coherence of a laser and the interferometric properties of light to probe the reflectivity as a function of depth of a sample. The axial and lateral resolutions, as well as imaging depth, are decoupled in the MOHI instrument. The MOHI instrument is capable of multiplexing interferometric measurements into 480 one-dimensional interferograms at a location on the sample and is built with axial and lateral resolutions of 40 μm at a maximum imaging depth of 700 μm. Preliminary results, where a piece of sand-blasted aluminum, an NBK7 glass piece, and an optical phantom were successfully probed using the MOHI instrument to produce depth profiles, demonstrate the feasibility of such an instrument for performing depth profilometry.

High Spectral Resolution Lidar Data

DOE Data Explorer

Eloranta, Ed

2004-12-01

The HSRL provided calibrated vertical profiles of optical depth, backscatter cross section and depoloarization at a wavelength of 532 nm. Profiles were acquired at 2.5 second intervals with 7.5 meter resolution. Profiles extended from an altitude of 100 m to 30 km in clear air. The lidar penetrated to a maximum optical depth of ~ 4 under cloudy conditions. Our data contributed directly to the aims of the M-PACE experiment, providing calibrated optical depth and optical backscatter measurements which were not available from any other instrument.

Spectral analysis of aeromagnetic profiles for depth estimation principles, software, and practical application

USGS Publications Warehouse

Sadek, H.S.; Rashad, S.M.; Blank, H.R.

1984-01-01

If proper account is taken of the constraints of the method, it is capable of providing depth estimates to within an accuracy of about 10 percent under suitable circumstances. The estimates are unaffected by source magnetization and are relatively insensitive to assumptions as to source shape or distribution. The validity of the method is demonstrated by analyses of synthetic profiles and profiles recorded over Harrat Rahat, Saudi Arabia, and Diyur, Egypt, where source depths have been proved by drilling.

Evaluation of Variable-Depth Liner Configurations for Increased Broadband Noise Reduction

NASA Technical Reports Server (NTRS)

Jones, M. G.; Watson, W. R.; Nark, D. M.; Howerton, B. M.

2015-01-01

This paper explores the effects of variable-depth geometry on the amount of noise reduction that can be achieved with acoustic liners. Results for two variable-depth liners tested in the NASA Langley Grazing Flow Impedance Tube demonstrate significant broadband noise reduction. An impedance prediction model is combined with two propagation codes to predict corresponding sound pressure level profiles over the length of the Grazing Flow Impedance Tube. The comparison of measured and predicted sound pressure level profiles is sufficiently favorable to support use of these tools for investigation of a number of proposed variable-depth liner configurations. Predicted sound pressure level profiles for these proposed configurations reveal a number of interesting features. Liner orientation clearly affects the sound pressure level profile over the length of the liner, but the effect on the total attenuation is less pronounced. The axial extent of attenuation at an individual frequency continues well beyond the location where the liner depth is optimally tuned to the quarter-wavelength of that frequency. The sound pressure level profile is significantly affected by the way in which variable-depth segments are distributed over the length of the liner. Given the broadband noise reduction capability for these liner configurations, further development of impedance prediction models and propagation codes specifically tuned for this application is warranted.

Direct depth distribution measurement of deuterium in bulk tungsten exposed to high-flux plasma

DOE PAGES

Taylor, Chase N.; Shimada, M.

2017-05-08

Understanding tritium retention and permeation in plasma-facing components is critical for fusion safety and fuel cycle control. Glow discharge optical emission spectroscopy (GD-OES) is shown to be an effective tool to reveal the depth profile of deuterium in tungsten. Results confirm the detection of deuterium. Furthermore, a ~46 µm depth profile revealed that the deuterium content decreased precipitously in the first 7 µm, and detectable amounts were observed to depths in excess of 20 µm. The large probing depth of GD-OES (up to 100s of µm) enables studies not previously accessible to the more conventional techniques for investigating deuterium retention.more » Of particular applicability is the use of GD-OES to measure the depth profile for experiments where high diffusion is expected: deuterium retention in neutron irradiated materials, and ultra-high deuterium fluences in burning plasma environment.« less

Direct depth distribution measurement of deuterium in bulk tungsten exposed to high-flux plasma

NASA Astrophysics Data System (ADS)

Taylor, C. N.; Shimada, M.

2017-05-01

Understanding tritium retention and permeation in plasma-facing components is critical for fusion safety and fuel cycle control. Glow discharge optical emission spectroscopy (GD-OES) is shown to be an effective tool to reveal the depth profile of deuterium in tungsten. Results confirm the detection of deuterium. A ˜46 μm depth profile revealed that the deuterium content decreased precipitously in the first 7 μm, and detectable amounts were observed to depths in excess of 20 μm. The large probing depth of GD-OES (up to 100s of μm) enables studies not previously accessible to the more conventional techniques for investigating deuterium retention. Of particular applicability is the use of GD-OES to measure the depth profile for experiments where high deuterium concentration in the bulk material is expected: deuterium retention in neutron irradiated materials, and ultra-high deuterium fluences in burning plasma environment.

Depth profiling of ion-induced damage in D9 alloy using X-ray diffraction

NASA Astrophysics Data System (ADS)

Dey, S.; Gayathri, N.; Mukherjee, P.

2018-04-01

The ion-induced depthwise damage profile in 35 MeV α-irradiated D9 alloy samples with doses of 5 × 1015 He2+/cm2, 6.4 × 1016 He2+/cm2 and 2 × 1017 He2+/cm2 has been assessed using X-ray diffraction technique. The microstructural characterisation has been done along the depth from beyond the stopping region (peak damage region) to the homogeneous damage region (surface) as simulated from SRIM. The parameters such as domain size and microstrain have been evaluated using two different X-ray diffraction line profile analysis techniques. The results indicate that at low dose the damage profile shows a prominent variation as a function of depth but, with increasing dose, it becomes more homogeneous along the depth. This suggests that enhanced defect diffusion and their annihilation in pre-existing and newly formed sinks play a significant role in deciding the final microstructure of the irradiated sample as a function of depth.

Revealing sub-μm and μm-scale textures in H2O ice at megabar pressures by time-domain Brillouin scattering

PubMed Central

Nikitin, Sergey M.; Chigarev, Nikolay; Tournat, Vincent; Bulou, Alain; Gasteau, Damien; Castagnede, Bernard; Zerr, Andreas; Gusev, Vitalyi E.

2015-01-01

The time-domain Brillouin scattering technique, also known as picosecond ultrasonic interferometry, allows monitoring of the propagation of coherent acoustic pulses, having lengths ranging from nanometres to fractions of a micrometre, in samples with dimension of less than a micrometre to tens of micrometres. In this study, we applied this technique to depth-profiling of a polycrystalline aggregate of ice compressed in a diamond anvil cell to megabar pressures. The method allowed examination of the characteristic dimensions of ice texturing in the direction normal to the diamond anvil surfaces with sub-micrometre spatial resolution via time-resolved measurements of the propagation velocity of the acoustic pulses travelling in the compressed sample. The achieved imaging of ice in depth and in one of the lateral directions indicates the feasibility of three-dimensional imaging and quantitative characterisation of the acoustical, optical and acousto-optical properties of transparent polycrystalline aggregates in a diamond anvil cell with tens of nanometres in-depth resolution and a lateral spatial resolution controlled by pump laser pulses focusing, which could approach hundreds of nanometres. PMID:25790808

Novel dental dynamic depth profilometric imaging using simultaneous frequency-domain infrared photothermal radiometry and laser luminescence

NASA Astrophysics Data System (ADS)

Nicolaides, Lena; Mandelis, Andreas

2000-01-01

A high-spatial-resolution dynamic experimental imaging setup, which can provide simultaneous measurements of laser- induced frequency-domain infrared photothermal radiometric and luminescence signals from defects in teeth, has been developed for the first time. The major findings of this work are: (1) radiometric images are complementary to (anticorrelated with) luminescence images, as a result of the nature of the two physical signal generation processes; (2) the radiometric amplitude exhibits much superior dynamic (signal resolution) range to luminescence in distinguishing between intact and cracked sub-surface structures in the enamel; (3) the radiometric signal (amplitude and phase) produces dental images with much better defect localization, delineation, and resolution; (4) radiometric images (amplitude and phase) at a fixed modulation frequency are depth profilometric, whereas luminescence images are not; and (5) luminescence frequency responses from enamel and hydroxyapatite exhibit two relaxation lifetimes, the longer of which (approximately ms) is common to all and is not sensitive to the defect state and overall quality of the enamel. Simultaneous radiometric and luminescence frequency scans for the purpose of depth profiling were performed and a quantitative theoretical two-lifetime rate model of dental luminescence was advanced.

Infiltration and Selective Interactions at the Interface in Polymer-Oxide Hybrid Solar Cells

NASA Astrophysics Data System (ADS)

Ferragut, R.; Aghion, S.; Moia, F.; Binda, M.; Canesi, E. V.; Lanzani, G.; Petrozza, A.

2013-06-01

Positron annihilation spectroscopy was used to characterize polymer-based hybrid solar cells formed by poly(3-hexylthiophene) (P3HT) finely infiltrated in a porous TiO2 skeleton. A step-change improvement in the device performance is enabled by engineering the hybrid interface by the insertion of a proper molecular interlayer namely 4-mercaptopyridine (4-MP). In order to obtain depth-resolved data, positrons were implanted in the sample using a variable-energy positron beam. The characteristics of the partially filled nanoporous structures were evaluated in terms of the depth profile of the positronium yield and the S-parameter. A quantitative evaluation of the pore filling in the deep region is given from the analysis of Coincidence Doppler Broadening taken at fixed implantation energy. We note a remarkable difference in terms of the positronium yield when the 4-MP interlayer is introduced, which means a better covering of P3HT on the porous surface.

Genetic Algorithm for Opto-thermal Skin Hydration Depth Profiling Measurements

NASA Astrophysics Data System (ADS)

Cui, Y.; Xiao, Perry; Imhof, R. E.

2013-09-01

Stratum corneum is the outermost skin layer, and the water content in stratum corneum plays a key role in skin cosmetic properties as well as skin barrier functions. However, to measure the water content, especially the water concentration depth profile, within stratum corneum is very difficult. Opto-thermal emission radiometry, or OTTER, is a promising technique that can be used for such measurements. In this paper, a study on stratum corneum hydration depth profiling by using a genetic algorithm (GA) is presented. The pros and cons of a GA compared against other inverse algorithms such as neural networks, maximum entropy, conjugate gradient, and singular value decomposition will be discussed first. Then, it will be shown how to use existing knowledge to optimize a GA for analyzing the opto-thermal signals. Finally, these latest GA results on hydration depth profiling of stratum corneum under different conditions, as well as on the penetration profiles of externally applied solvents, will be shown.

He, U, and Th Depth Profiling of Apatite and Zircon Using Laser Ablation Noble Gas Mass Spectrometry and SIMS

NASA Astrophysics Data System (ADS)

Monteleone, B. D.; van Soest, M. C.; Hodges, K. V.; Hervig, R.; Boyce, J. W.

2008-12-01

Conventional (U-Th)/He thermochronology utilizes single or multiple grain analyses of U- and Th-bearing minerals such as apatite and zircon and does not allow for assessment of spatial variation in concentration of He, U, or Th within individual crystals. As such, age calculation and interpretation require assumptions regarding 4He loss through alpha ejection, diffusive redistribution of 4He, and U and Th distribution as an initial condition for these processes. Although models have been developed to predict 4He diffusion parameters, correct for the effect of alpha ejection on calculated cooling ages, and account for the effect of U and Th zonation within apatite and zircon, measurements of 4He, U, and Th distribution have not been combined within a single crystal. We apply ArF excimer laser ablation, combined with noble gas mass spectrometry, to obtain depth profiles within apatite and zircon crystals in order to assess variations in 4He concentration with depth. Our initial results from pre-cut, pre-heated slabs of Durango apatite, each subjected to different T-t schedules, suggest a general agreement of 4He profiles with those predicted by theoretical diffusion models (Farley, 2000). Depth profiles through unpolished grains give reproducible alpha ejection profiles in Durango apatite that deviate from alpha ejection profiles predicted for ideal, homogenous crystals. SIMS depth profiling utilizes an O2 primary beam capable of sputtering tens of microns and measuring sub-micron resolution variation in [U], [Th], and [Sm]. Preliminary results suggest that sufficient [U] and [Th] zonation is present in Durango apatite to influence the form of the 4He alpha ejection profile. Future work will assess the influence of measured [U] and [Th] zonation on previously measured 4He depth profiles. Farley, K.A., 2000. Helium diffusion from apatite; general behavior as illustrated by Durango fluorapatite. J. Geophys. Res., B Solid Earth Planets 105 (2), 2903-2914.

Phase calibration target for quantitative phase imaging with ptychography.

PubMed

Godden, T M; Muñiz-Piniella, A; Claverley, J D; Yacoot, A; Humphry, M J

2016-04-04

Quantitative phase imaging (QPI) utilizes refractive index and thickness variations that lead to optical phase shifts. This gives contrast to images of transparent objects. In quantitative biology, phase images are used to accurately segment cells and calculate properties such as dry mass, volume and proliferation rate. The fidelity of the measured phase shifts is of critical importance in this field. However to date, there has been no standardized method for characterizing the performance of phase imaging systems. Consequently, there is an increasing need for protocols to test the performance of phase imaging systems using well-defined phase calibration and resolution targets. In this work, we present a candidate for a standardized phase resolution target, and measurement protocol for the determination of the transfer of spatial frequencies, and sensitivity of a phase imaging system. The target has been carefully designed to contain well-defined depth variations over a broadband range of spatial frequencies. In order to demonstrate the utility of the target, we measure quantitative phase images on a ptychographic microscope, and compare the measured optical phase shifts with Atomic Force Microscopy (AFM) topography maps and surface profile measurements from coherence scanning interferometry. The results show that ptychography has fully quantitative nanometer sensitivity in optical path differences over a broadband range of spatial frequencies for feature sizes ranging from micrometers to hundreds of micrometers.

Interpretation of TOF SIMS depth profiles from ultrashallow high-k dielectric stacks assisted by hybrid collisional computer simulation

NASA Astrophysics Data System (ADS)

Ignatova, V. A.; Möller, W.; Conard, T.; Vandervorst, W.; Gijbels, R.

2005-06-01

The TRIDYN collisional computer simulation has been modified to account for emission of ionic species and molecules during sputter depth profiling, by introducing a power law dependence of the ion yield as a function of the oxygen surface concentration and by modelling the sputtering of monoxide molecules. The results are compared to experimental data obtained with dual beam TOF SIMS depth profiling of ZrO2/SiO2/Si high-k dielectric stacks with thicknesses of the SiO2 interlayer of 0.5, 1, and 1.5 nm. Reasonable agreement between the experiment and the computer simulation is obtained for most of the experimental features, demonstrating the effects of ion-induced atomic relocation, i.e., atomic mixing and recoil implantation, and preferential sputtering. The depth scale of the obtained profiles is significantly distorted by recoil implantation and the depth-dependent ionization factor. A pronounced double-peak structure in the experimental profiles related to Zr is not explained by the computer simulation, and is attributed to ion-induced bond breaking and diffusion, followed by a decoration of the interfaces by either mobile Zr or O.

Comparison of two laboratory-based systems for evaluation of halos in intraocular lenses

PubMed Central

Alexander, Elsinore; Wei, Xin; Lee, Shinwook

2018-01-01

Purpose Multifocal intraocular lenses (IOLs) can be associated with unwanted visual phenomena, including halos. Predicting potential for halos is desirable when designing new multifocal IOLs. Halo images from 6 IOL models were compared using the Optikos modulation transfer function bench system and a new high dynamic range (HDR) system. Materials and methods One monofocal, 1 extended depth of focus, and 4 multifocal IOLs were evaluated. An off-the-shelf optical bench was used to simulate a distant (>50 m) car headlight and record images. A custom HDR system was constructed using an imaging photometer to simulate headlight images and to measure quantitative halo luminance data. A metric was developed to characterize halo luminance properties. Clinical relevance was investigated by correlating halo measurements to visual outcomes questionnaire data. Results The Optikos system produced halo images useful for visual comparisons; however, measurements were relative and not quantitative. The HDR halo system provided objective and quantitative measurements used to create a metric from the area under the curve (AUC) of the logarithmic normalized halo profile. This proposed metric differentiated between IOL models, and linear regression analysis found strong correlations between AUC and subjective clinical ratings of halos. Conclusion The HDR system produced quantitative, preclinical metrics that correlated to patients’ subjective perception of halos. PMID:29503526

Advanced body composition assessment: from body mass index to body composition profiling.

PubMed

Borga, Magnus; West, Janne; Bell, Jimmy D; Harvey, Nicholas C; Romu, Thobias; Heymsfield, Steven B; Dahlqvist Leinhard, Olof

2018-06-01

This paper gives a brief overview of common non-invasive techniques for body composition analysis and a more in-depth review of a body composition assessment method based on fat-referenced quantitative MRI. Earlier published studies of this method are summarized, and a previously unpublished validation study, based on 4753 subjects from the UK Biobank imaging cohort, comparing the quantitative MRI method with dual-energy X-ray absorptiometry (DXA) is presented. For whole-body measurements of adipose tissue (AT) or fat and lean tissue (LT), DXA and quantitative MRIs show excellent agreement with linear correlation of 0.99 and 0.97, and coefficient of variation (CV) of 4.5 and 4.6 per cent for fat (computed from AT) and LT, respectively, but the agreement was found significantly lower for visceral adipose tissue, with a CV of >20 per cent. The additional ability of MRI to also measure muscle volumes, muscle AT infiltration and ectopic fat, in combination with rapid scanning protocols and efficient image analysis tools, makes quantitative MRI a powerful tool for advanced body composition assessment. © American Federation for Medical Research (unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Modulated Electron Emission by Scattering-Interference of Primary Electrons

NASA Astrophysics Data System (ADS)

Valeri, Sergio; di Bona, Alessandro

We review the effects of scattering-interference of the primary, exciting beam on the electron emission from ordered atomic arrays. The yield of elastically and inelastically backscattered electrons, Auger electrons and secondary electrons shows a marked dependence on the incidence angle of primary electrons. Both the similarity and the relative importance of processes experienced by incident and excident electrons are discussed. We also present recent studies of electron focusing and defocusing along atomic chains. The interplay between these two processes determines the in-depth profile of the primary electron intensity anisotropy. Finally, the potential for surface-structural studies and limits for quantitative analysis are discussed, in comparison with the Auger electron diffraction (AED) and photoelectron diffraction (PD) techniques.

Fast analysis of wood preservers using laser induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Uhl, A.; Loebe, K.; Kreuchwig, L.

2001-06-01

Laser-induced breakdown spectroscopy (LIBS) is used for the investigation of wood preservers in timber and in furniture. Both experiments in laboratory and practical applications in recycling facilities and on a building site prove the new possibilities for the fast detection of harmful agents in wood. A commercial system was developed for mobile laser-plasma-analysis as well as for industrial use in sorting plants. The universal measuring principle in combination with an Echelle optics permits real simultaneous multi-element-analysis in the range of 200-780 nm with a resolution of a few picometers. It enables the user to detect main and trace elements in wood within a few seconds, nearly independent of the matrix, knowing that different kinds of wood show an equal elemental composition. Sample preparation is not required. The quantitative analysis of inorganic wood preservers (containing, e.g. Cu, Cr, B, As, Pb, Hg) has been performed exactly using carbon as reference element. It can be shown that the detection limits for heavy metals in wood are in the ppm-range. Additional information is given concerning the quantitative analysis. Statistical data, e.g. the standard deviation (S.D.), were determined and calibration curves were used for each particular element. A comparison between ICP-AES and LIBS is given using depth profile correction factors regarding the different penetration depths with respect to the different volumes in wood analyzed by both analytical methods.

A perspective on two chemometrics tools: PCA and MCR, and introduction of a new one: Pattern recognition entropy (PRE), as applied to XPS and ToF-SIMS depth profiles of organic and inorganic materials

NASA Astrophysics Data System (ADS)

Chatterjee, Shiladitya; Singh, Bhupinder; Diwan, Anubhav; Lee, Zheng Rong; Engelhard, Mark H.; Terry, Jeff; Tolley, H. Dennis; Gallagher, Neal B.; Linford, Matthew R.

2018-03-01

X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) are much used analytical techniques that provide information about the outermost atomic and molecular layers of materials. In this work, we discuss the application of multivariate spectral techniques, including principal component analysis (PCA) and multivariate curve resolution (MCR), to the analysis of XPS and ToF-SIMS depth profiles. Multivariate analyses often provide insight into data sets that is not easily obtained in a univariate fashion. Pattern recognition entropy (PRE), which has its roots in Shannon's information theory, is also introduced. This approach is not the same as the mutual information/entropy approaches sometimes used in data processing. A discussion of the theory of each technique is presented. PCA, MCR, and PRE are applied to four different data sets obtained from: a ToF-SIMS depth profile through ca. 100 nm of plasma polymerized C3F6 on Si, a ToF-SIMS depth profile through ca. 100 nm of plasma polymerized PNIPAM (poly (N-isopropylacrylamide)) on Si, an XPS depth profile through a film of SiO2 on Si, and an XPS depth profile through a film of Ta2O5 on Ta. PCA, MCR, and PRE reveal the presence of interfaces in the films, and often indicate that the first few scans in the depth profiles are different from those that follow. PRE and backward difference PRE provide this information in a straightforward fashion. Rises in the PRE signals at interfaces suggest greater complexity to the corresponding spectra. Results from PCA, especially for the higher principal components, were sometimes difficult to understand. MCR analyses were generally more interpretable.

Meteoric 10Be in soil profiles - A global meta-analysis

USGS Publications Warehouse

Graly, Joseph A.; Bierman, Paul R.; Reusser, Lucas J.; Pavich, Milan J.

2010-01-01

In order to assess current understanding of meteoric 10Be dynamics and distribution in terrestrial soils, we assembled a database of all published meteoric 10Be soil depth profiles, including 104 profiles from 27 studies in globally diverse locations, collectively containing 679 individual measurements. This allows for the systematic comparison of meteoric 10Be concentration to other soil characteristics and the comparison of profile depth distributions between geologic settings. Percent clay, 9Be, and dithionite-citrate extracted Al positively correlate to meteoric 10Be in more than half of the soils where they were measured, but the lack of significant correlation in other soils suggests that no one soil factor controls meteoric 10Be distribution with depth. Dithionite-citrate extracted Fe and cation exchange capacity are only weakly correlated to meteoric 10Be. Percent organic carbon and pH are not significantly related to meteoric 10Be concentration when all data are complied.The compilation shows that meteoric 10Be concentration is seldom uniform with depth in a soil profile. In young or rapidly eroding soils, maximum meteoric 10Be concentrations are typically found in the uppermost 20 cm. In older, more slowly eroding soils, the highest meteoric 10Be concentrations are found at depth, usually between 50 and 200 cm. We find that the highest measured meteoric 10Be concentration in a soil profile is an important metric, as both the value and the depth of the maximum meteoric 10Be concentration correlate with the total measured meteoric 10Be inventory of the soil profile.In order to refine the use of meteoric 10Be as an estimator of soil erosion rate, we compare near-surface meteoric 10Be concentrations to total meteoric 10Be soil inventories. These trends are used to calibrate models of meteoric 10Be loss by soil erosion. Erosion rates calculated using this method vary based on the assumed depth and timing of erosional events and on the reference data selected.

Breadth and Depth of Vocabulary Knowledge and Their Effects on L2 Vocabulary Profiles

ERIC Educational Resources Information Center

Bardakçi, Mehmet

2016-01-01

Breadth and depth of vocabulary knowledge have been studied from many different perspectives, but the related literature lacks serious studies dealing with their effects on vocabulary profiles of EFL learners. In this paper, with an aim to fill this gap, the relative effects of breadth and depth of vocabulary knowledge on L2 vocabulary profiles…

Estimating the Soil Temperature Profile from a Single Depth Observation: A Simple Empirical Heatflow Solution

NASA Technical Reports Server (NTRS)

Holmes, Thomas; Owe, Manfred; deJeu, Richard

2007-01-01

Two data sets of experimental field observations with a range of meteorological conditions are used to investigate the possibility of modeling near-surface soil temperature profiles in a bare soil. It is shown that commonly used heat flow methods that assume a constant ground heat flux can not be used to model the extreme variations in temperature that occur near the surface. This paper proposes a simple approach for modeling the surface soil temperature profiles from a single depth observation. This approach consists of two parts: 1) modeling an instantaneous ground flux profile based on net radiation and the ground heat flux at 5cm depth; 2) using this ground heat flux profile to extrapolate a single temperature observation to a continuous near surface temperature profile. The new model is validated with an independent data set from a different soil and under a range of meteorological conditions.

XPS investigation of depth profiling induced chemistry

NASA Astrophysics Data System (ADS)

Pratt, Quinn; Skinner, Charles; Koel, Bruce; Chen, Zhu

2017-10-01

Surface analysis is an important tool for understanding plasma-material interactions. Depth profiles are typically generated by etching with a monatomic argon ion beam, however this can induce unintended chemical changes in the sample. Tantalum pentoxide, a sputtering standard, and PEDOT:PSS, a polymer that was used to mimic the response of amorphous carbon-hydrogen co-deposits, were studied. We compare depth profiles generated with monatomic and gas cluster argon ion beams (GCIB) using X-ray photoelectron spectroscopy (XPS) to quantify chemical changes. In both samples, monatomic ion bombardment led to beam-induced chemical changes. Tantalum pentoxide exhibited preferential sputtering of oxygen and the polymer experienced significant bond modification. Depth profiling with clusters is shown to mitigate these effects. We present sputtering rates for Ta2O5 and PEDOT:PSS as a function of incident energy and flux. Support was provided through DOE Contract Number DE-AC02-09CH11466.

Influence of surface topography on depth profiles obtained with secondary-ion mass spectrometry

NASA Astrophysics Data System (ADS)

Walker, A. J.; Borchert, M. T.; Vriezema, C. J.; Zalm, P. C.

1990-11-01

Lithographically generated well-defined surface topography of submicron dimensions has been etched into silicon (100) previously implanted with 25 keV 11B to a fluence of 2×1014 atoms/cm2. The thus-obtained samples were depth profiled via secondary-ion mass spectrometry (SIMS). The boron concentration distributions measured were contrasted against those found on undisturbed flat parts of the target. From this intercomparison the otherwise trivial observation that surface topography causes profile distortion becomes suddenly alarming as an apparent improvement of depth resolution occurs. Scanning electron microscope images enable identification of the origin of this remarkable phenomenon. The present results imply that (i) the hitherto commonly accepted assumption in the interpretation of SIMS depth profiles that perceived gradients are never steeper than actual ones is subject to revision; (ii) it may prove very difficult, if not impossible, to construct SIMS equipment for reliable on-chip analysis of submicron details.

An optical fiber expendable seawater temperature/depth profile sensor

NASA Astrophysics Data System (ADS)

Zhao, Qiang; Chen, Shizhe; Zhang, Keke; Yan, Xingkui; Yang, Xianglong; Bai, Xuejiao; Liu, Shixuan

2017-10-01

Marine expendable temperature/depth profiler (XBT) is a disposable measuring instrument which can obtain temperature/depth profile data quickly in large area waters and mainly used for marine surveys, scientific research, military application. The temperature measuring device is a thermistor in the conventional XBT probe (CXBT)and the depth data is only a calculated value by speed and time depth calculation formula which is not an accurate measurement result. Firstly, an optical fiber expendable temperature/depth sensor based on the FBG-LPG cascaded structure is proposed to solve the problems of the CXBT, namely the use of LPG and FBG were used to detect the water temperature and depth, respectively. Secondly, the fiber end reflective mirror is used to simplify optical cascade structure and optimize the system performance. Finally, the optical path is designed and optimized using the reflective optical fiber end mirror. The experimental results show that the sensitivity of temperature and depth sensing based on FBG-LPG cascade structure is about 0.0030C and 0.1%F.S. respectively, which can meet the requirements of the sea water temperature/depth observation. The reflectivity of reflection mirror is in the range from 48.8% to 72.5%, the resonant peak of FBG and LPG are reasonable and the whole spectrum are suitable for demodulation. Through research on the optical fiber XBT (FXBT), the direct measurement of deep-sea temperature/depth profile data can be obtained simultaneously, quickly and accurately. The FXBT is a new all-optical seawater temperature/depth sensor, which has important academic value and broad application prospect and is expected to replace the CXBT in the future.

Depth-Related Changes in Community Structure of Culturable Mineral Weathering Bacteria and in Weathering Patterns Caused by Them along Two Contrasting Soil Profiles

PubMed Central

Huang, Jing; Xi, Jun; Huang, Zhi; Wang, Qi; Zhang, Zhen-Dong

2014-01-01

Bacteria play important roles in mineral weathering and soil formation. However, few reports of mineral weathering bacteria inhabiting subsurfaces of soil profiles have been published, raising the question of whether the subsurface weathering bacteria are fundamentally distinct from those in surface communities. To address this question, we isolated and characterized mineral weathering bacteria from two contrasting soil profiles with respect to their role in the weathering pattern evolution, their place in the community structure, and their depth-related changes in these two soil profiles. The effectiveness and pattern of bacterial mineral weathering were different in the two profiles and among the horizons within the respective profiles. The abundance of highly effective mineral weathering bacteria in the Changshu profile was significantly greater in the deepest horizon than in the upper horizons, whereas in the Yanting profile it was significantly greater in the upper horizons than in the deeper horizons. Most of the mineral weathering bacteria from the upper horizons of the Changshu profile and from the deeper horizons of the Yanting profile significantly acidified the culture media in the mineral weathering process. The proportion of siderophore-producing bacteria in the Changshu profile was similar in all horizons except in the Bg2 horizon, whereas the proportion of siderophore-producing bacteria in the Yanting profile was higher in the upper horizons than in the deeper horizons. Both profiles existed in different highly depth-specific culturable mineral weathering community structures. The depth-related changes in culturable weathering communities were primarily attributable to minor bacterial groups rather than to a change in the major population structure. PMID:24077700

Geophysical investigations of the Umm ar Rummf copper prospect, Al Qunfudhah Quadrangle, Kingdom of Saudi Arabia

USGS Publications Warehouse

Sadek, Hamdy S.; Blank, H. Richard

1983-01-01

The Umm ar Rummf copper prospect, located about 30 km east of Al Qunfudhah, Kingdom of Saudi Arabia, consists of zones of malachite disseminations and fracture fillings in outcrops of north-trending impure quartzite of the Bahah group. Systematic Crone electromagnetic and self-potential surveys indicate that weakly conductive tabular bodies having a weak to moderate self-potential effect extend downdip from two discontinuously exposed, parallel ridges of mineralized quartzite. Crone electromagnetic data were quantitatively interpreted using characteristic parameter lines adapted for use at 1830 and 5010 Hz, the frequencies employed at Umm ar Rummf. Depths to the top of the conductors were computed to be from 20 to 40 m or about the thickness of the oxidized zone, which behaves as a variably conductive overburden. Both tabular conductors can also be traced geophysically to the north and south of the copper-bearing outcrops. The association of the geophysical anomalies with copper-mineralized rocks has been proved by drilling. Reconnaissance MAXMIN electromagnetic profiles across the target using a wide coil separation show broad, low-amplitude anomalies that may indicate mineralized rocks at depth, and reconnaissance ground-magnetic profiles show strong total-field intensity anomalies associated with basaltic dikes of probable Tertiary age. In the central part of the area of investigation, these dikes produce large disturbances of the electrical fields.

Membrane fluidity profiles as deduced by saturation-recovery EPR measurements of spin-lattice relaxation times of spin labels

NASA Astrophysics Data System (ADS)

Mainali, Laxman; Feix, Jimmy B.; Hyde, James S.; Subczynski, Witold K.

2011-10-01

There are no easily obtainable EPR spectral parameters for lipid spin labels that describe profiles of membrane fluidity. The order parameter, which is most often used as a measure of membrane fluidity, describes the amplitude of wobbling motion of alkyl chains relative to the membrane normal and does not contain explicitly time or velocity. Thus, this parameter can be considered as nondynamic. The spin-lattice relaxation rate ( T1-1) obtained from saturation-recovery EPR measurements of lipid spin labels in deoxygenated samples depends primarily on the rotational correlation time of the nitroxide moiety within the lipid bilayer. Thus, T1-1 can be used as a convenient quantitative measure of membrane fluidity that reflects local membrane dynamics. T1-1 profiles obtained for 1-palmitoyl-2-( n-doxylstearoyl)phosphatidylcholine ( n-PC) spin labels in dimyristoylphosphatidylcholine (DMPC) membranes with and without 50 mol% cholesterol are presented in parallel with profiles of the rotational diffusion coefficient, R⊥, obtained from simulation of EPR spectra using Freed's model. These profiles are compared with profiles of the order parameter obtained directly from EPR spectra and with profiles of the order parameter obtained from simulation of EPR spectra. It is shown that T1-1 and R⊥ profiles reveal changes in membrane fluidity that depend on the motional properties of the lipid alkyl chain. We find that cholesterol has a rigidifying effect only to the depth occupied by the rigid steroid ring structure and a fluidizing effect at deeper locations. These effects cannot be differentiated by profiles of the order parameter. All profiles in this study were obtained at X-band (9.5 GHz).

Upper Ocean Profiles Measurements with ASIP

NASA Astrophysics Data System (ADS)

Ward, B.; Callaghan, A. H.; Fristedt, T.; Vialard, J.; Cuypers, Y.; Weller, R. A.; Grosch, C. E.

2009-04-01

This presentation describes results from the Air-Sea Interaction Profiler (ASIP), an autonomous profiling instrument for upper ocean measurements. The measurements from ASIP are well suited to enhancing research on air-sea interfacial and near surface processes. Autonomous profiling is accomplished with a thruster, which submerges ASIP to a programmed depth. Once this depth is reached the positively buoyant instrument will ascend to the surface acquiring data. ASIP can profile from a maximum depth of 100 m to the surface, allowing both mixed layer and near-surface measurements to be conducted. The sensor payload on ASIP include microstructure sensors (two shear probes and a thermistor); a slow response accurate thermometer; a pair of conductivity sensors; pressure for a record of depth; PAR for measurements of light absorption in the water column. Other non-environmental sensors are acceleration, rate, and heading for determination of vehicle motion. Power is provided with rechargable lithium-ion batteries, supplying 1000 Whr, allowing approximately 300 profiles. ASIP also contains an iridium/GPS system, which allows realtime reporting of its position. ASIP was deployed extensively during the Cirene Indian Ocean campaign and our results focus on the data from the temperature, salinity, light, and shear sensors.

Geophysical techniques for reconnaissance investigations of soils and surficial deposits in mountainous terrain

USGS Publications Warehouse

Olson, C.G.; Doolittle, J.A.

1985-01-01

Two techniques were assessed for their capabilities in reconnaissance studies of soil characteristics: depth to the water table and depth to bedrock beneath surficial deposits in mountainous terrain. Ground-penetrating radar had the best near-surface resolution in the upper 2 m of the profile and provided continuous interpretable imagery of soil profiles and bedrock surfaces. Where thick colluvium blankets side slopes, the GPR could not consistently define the bedrock interface. In areas with clayey or shaley sediments, the GPR is also more limited in defining depth and is less reliable. Seismic refraction proved useful in determining the elevation of the water table and depth to bedrock, regardless of thickness of overlying material, but could not distinguish soil-profile characteristics.-from Authors

The effects of wavelength on photodegradation depth profiles in Japanese cedar (Cryptomeria japonica D. Don) earlywood

Treesearch

Yutaka Kataoka; Makoto Kiguchi; R. Sam Williams; Philip D. Evans

2006-01-01

FT-IR microscopy was used to depth profile the photodegradation of Japanese cedar earlywood exposed to monochromatic light in the UV and visible ranges (band pass: 20nm). Parallel experiments assessed the transmission of the light through thin sections of Japanese cedar. The depth of photodegradation increased with wavelength up to and including the violet region of...

Quantitative bioimaging of trace elements in the human lens by LA-ICP-MS.

PubMed

Konz, Ioana; Fernández, Beatriz; Fernández, M Luisa; Pereiro, Rosario; González-Iglesias, Héctor; Coca-Prados, Miguel; Sanz-Medel, Alfredo

2014-04-01

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) was used for the quantitative imaging of Fe, Cu and Zn in cryostat sections of human eye lenses and for depth profiling analysis in bovine lenses. To ensure a tight temperature control throughout the experiments, a new Peltier-cooled laser ablation cell was employed. For quantification purposes, matrix-matched laboratory standards were prepared from a pool of human lenses from eye donors and spiked with standard solutions containing different concentrations of natural abundance Fe, Cu and Zn. A normalisation strategy was also carried out to correct matrix effects, lack of tissue homogeneity and/or instrumental drifts using a thin gold film deposited on the sample surface. Quantitative images of cryo-sections of human eye lenses analysed by LA-ICP-MS revealed a homogeneous distribution of Fe, Cu and Zn in the nuclear region and a slight increase in Fe concentration in the outer cell layer (i.e. lens epithelium) at the anterior pole. These results were assessed also by isotope dilution mass spectrometry, and Fe, Cu and Zn concentrations determined by ID-ICP-MS in digested samples of lenses and lens capsules.

A measurement system for vertical seawater profiles close to the air-sea interface

NASA Astrophysics Data System (ADS)

Sims, Richard P.; Schuster, Ute; Watson, Andrew J.; Yang, Ming Xi; Hopkins, Frances E.; Stephens, John; Bell, Thomas G.

2017-09-01

This paper describes a near-surface ocean profiler, which has been designed to precisely measure vertical gradients in the top 10 m of the ocean. Variations in the depth of seawater collection are minimized when using the profiler compared to conventional CTD/rosette deployments. The profiler consists of a remotely operated winch mounted on a tethered yet free-floating buoy, which is used to raise and lower a small frame housing sensors and inlet tubing. Seawater at the inlet depth is pumped back to the ship for analysis. The profiler can be used to make continuous vertical profiles or to target a series of discrete depths. The profiler has been successfully deployed during wind speeds up to 10 m s-1 and significant wave heights up to 2 m. We demonstrate the potential of the profiler by presenting measured vertical profiles of the trace gases carbon dioxide and dimethylsulfide. Trace gas measurements use an efficient microporous membrane equilibrator to minimize the system response time. The example profiles show vertical gradients in the upper 5 m for temperature, carbon dioxide and dimethylsulfide of 0.15 °C, 4 µatm and 0.4 nM respectively.

Lithium diffusion in polyether ether ketone and polyimide stimulated by in situ electron irradiation and studied by the neutron depth profiling method

NASA Astrophysics Data System (ADS)

Vacik, J.; Hnatowicz, V.; Attar, F. M. D.; Mathakari, N. L.; Dahiwale, S. S.; Dhole, S. D.; Bhoraskar, V. N.

2014-10-01

Diffusion of lithium from a LiCl aqueous solution into polyether ether ketone (PEEK) and polyimide (PI) assisted by in situ irradiation with 6.5 MeV electrons was studied by the neutron depth profiling method. The number of the Li atoms was found to be roughly proportional to the diffusion time. Regardless of the diffusion time, the measured depth profiles in PEEK exhibit a nearly exponential form, indicating achievement of a steady-state phase of a diffusion-reaction process specified in the text. The form of the profiles in PI is more complex and it depends strongly on the diffusion time. For the longer diffusion time, the profile consists of near-surface bell-shaped part due to Fickian-like diffusion and deeper exponential part.

Surface topography of 1€ coin measured by stereo-PIXE

NASA Astrophysics Data System (ADS)

Gholami-Hatam, E.; Lamehi-Rachti, M.; Vavpetič, P.; Grlj, N.; Pelicon, P.

2013-07-01

We demonstrate the stereo-PIXE method by measurement of surface topography of the relief details on 1€ coin. Two X-ray elemental maps were simultaneously recorded by two X-ray detectors positioned at the left and the right side of the proton microbeam. The asymmetry of the yields in the pixels of the two X-ray maps occurs due to different photon attenuation on the exit travel path of the characteristic X-rays from the point of emission through the sample into the X-ray detectors. In order to calibrate the inclination angle with respect to the X-ray asymmetry, a flat inclined surface model was at first applied for the sample in which the matrix composition and the depth elemental concentration profile is known. After that, the yield asymmetry in each image pixel was transferred into corresponding local inclination angle using calculated dependence of the asymmetry on the surface inclination. Finally, the quantitative topography profile was revealed by integrating the local inclination angle over the lateral displacement of the probing beam.

Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells.

PubMed

Zhu, Ying; Piehowski, Paul D; Zhao, Rui; Chen, Jing; Shen, Yufeng; Moore, Ronald J; Shukla, Anil K; Petyuk, Vladislav A; Campbell-Thompson, Martha; Mathews, Clayton E; Smith, Richard D; Qian, Wei-Jun; Kelly, Ryan T

2018-02-28

Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Ying; Piehowski, Paul D.; Zhao, Rui

Nanoscale or single cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here, we report the development of a nanoPOTS (Nanodroplet Processing in One pot for Trace Samples) platform as a major advance in overall sensitivity. NanoPOTS dramatically enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive LC-MS, nanoPOTS allows identification of ~1500 to ~3,000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runsmore » algorithm of MaxQuant, >3000 proteins were consistently identified from as few as 10 cells. Furthermore, we demonstrate robust quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.« less

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Ying; Piehowski, Paul D.; Zhao, Rui

Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here in this paper, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Betweenmore » Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.« less

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

DOE PAGES

Zhu, Ying; Piehowski, Paul D.; Zhao, Rui; ...

2018-02-28

Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here in this paper, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Betweenmore » Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.« less

Towards nanometric resolution in multilayer depth profiling: a comparative study of RBS, SIMS, XPS and GDOES.

PubMed

Escobar Galindo, Ramón; Gago, Raul; Duday, David; Palacio, Carlos

2010-04-01

An increasing amount of effort is currently being directed towards the development of new functionalized nanostructured materials (i.e., multilayers and nanocomposites). Using an appropriate combination of composition and microstructure, it is possible to optimize and tailor the final properties of the material to its final application. The analytical characterization of these new complex nanostructures requires high-resolution analytical techniques that are able to provide information about surface and depth composition at the nanometric level. In this work, we comparatively review the state of the art in four different depth-profiling characterization techniques: Rutherford backscattering spectroscopy (RBS), secondary ion mass spectrometry (SIMS), X-ray photoelectron spectroscopy (XPS) and glow discharge optical emission spectroscopy (GDOES). In addition, we predict future trends in these techniques regarding improvements in their depth resolutions. Subnanometric resolution can now be achieved in RBS using magnetic spectrometry systems. In SIMS, the use of rotating sample holders and oxygen flooding during analysis as well as the optimization of floating low-energy ion guns to lower the impact energy of the primary ions improves the depth resolution of the technique. Angle-resolved XPS provides a very powerful and nondestructive technique for obtaining depth profiling and chemical information within the range of a few monolayers. Finally, the application of mathematical tools (deconvolution algorithms and a depth-profiling model), pulsed sources and surface plasma cleaning procedures is expected to greatly improve GDOES depth resolution.

High-resolution depth profiling using a range-gated CMOS SPAD quanta image sensor.

PubMed

Ren, Ximing; Connolly, Peter W R; Halimi, Abderrahim; Altmann, Yoann; McLaughlin, Stephen; Gyongy, Istvan; Henderson, Robert K; Buller, Gerald S

2018-03-05

A CMOS single-photon avalanche diode (SPAD) quanta image sensor is used to reconstruct depth and intensity profiles when operating in a range-gated mode used in conjunction with pulsed laser illumination. By designing the CMOS SPAD array to acquire photons within a pre-determined temporal gate, the need for timing circuitry was avoided and it was therefore possible to have an enhanced fill factor (61% in this case) and a frame rate (100,000 frames per second) that is more difficult to achieve in a SPAD array which uses time-correlated single-photon counting. When coupled with appropriate image reconstruction algorithms, millimeter resolution depth profiles were achieved by iterating through a sequence of temporal delay steps in synchronization with laser illumination pulses. For photon data with high signal-to-noise ratios, depth images with millimeter scale depth uncertainty can be estimated using a standard cross-correlation approach. To enhance the estimation of depth and intensity images in the sparse photon regime, we used a bespoke clustering-based image restoration strategy, taking into account the binomial statistics of the photon data and non-local spatial correlations within the scene. For sparse photon data with total exposure times of 75 ms or less, the bespoke algorithm can reconstruct depth images with millimeter scale depth uncertainty at a stand-off distance of approximately 2 meters. We demonstrate a new approach to single-photon depth and intensity profiling using different target scenes, taking full advantage of the high fill-factor, high frame rate and large array format of this range-gated CMOS SPAD array.

Auger analysis of a fiber/matrix interface in a ceramic matrix composite

NASA Technical Reports Server (NTRS)

Honecy, Frank S.; Pepper, Stephen V.

1988-01-01

Auger electron spectroscopy (AES) depth profiling was used to characterize the fiber/matrix interface of an SiC fiber, reaction bonded Si3N4 matrix composite. Depth profiles of the as received double coated fiber revealed concentration oscillations which disappeared after annealing the fiber in the environment used to fabricate the composite. After the composite was fractured, the Auger depth profiles showed that failure occurred in neither the Beta-SiC fiber body nor in the Si3N4 matrix but, concurrently, at the fiber coating/matrix interface and within the fiber coating itself.

Boron depth profiles and residual damage following rapid thermal annealing of low-temperature BSi molecular ion implantation in silicon

NASA Astrophysics Data System (ADS)

Liang, J. H.; Wang, S. C.

2007-08-01

The influence of substrate temperature on both the implantation and post-annealing characteristics of molecular-ion-implanted 5 × 1014 cm-2 77 keV BSi in silicon was investigated in terms of boron depth profiles and damage microstructures. The substrate temperatures under investigation consisted of room temperature (RT) and liquid nitrogen temperature (LT). Post-annealing treatments were performed using rapid thermal annealing (RTA) at 1050 °C for 25 s. Boron depth profiles and damage microstructures in both the as-implanted and as-annealed specimens were determined using secondary ion mass spectrometry (SIMS) and transmission electron microscopy (TEM), respectively. The as-implanted results revealed that, compared to the RT specimen, the LT specimen yields a shallower boron depth profile with a reduced tail into the bulk. An amorphous layer containing a smooth amorphous-to-crystalline (a/c) interface is evident in the LT specimen while just the opposite is true in the as-implanted RT one. The as-annealed results illustrated that the extension of the boron depth profile into the bulk via transient-enhanced diffusion (TED) in the LT specimen is less than it is in the RT one. Only residual defects are visible in the LT specimen while two clear bands of dislocation loops appear in the RT one.

Quantitative assessment of the presence of a single leg separation in Björk-Shiley convexoconcave prosthetic heart valves.

PubMed

Vrooman, H A; Maliepaard, C; van der Linden, L P; Jessurun, E R; Ludwig, J W; Plokker, H W; Schalij, M J; Weeda, H W; Laufer, J L; Huysmans, H A; Reiber, J H

1997-09-01

The authors developed an analytic software package for the objective and reproducible assessment of a single leg separation (SLS) in the outlet strut of Björk-Shiley convexoconcave (BSCC) prosthetic heart valves. The radiographic cinefilm recordings of 18 phantom valves (12 intact and 6 SLS) and of 43 patient valves were acquired. After digitization of regions of interest in a cineframe, several processing steps were carried out to obtain a one-dimensional corrected and averaged density profile along the central axis of each strut leg. To characterize the degree of possible separation, two quantitative measures were introduced: the normalized pit depth (NPD) and the depth-sigma ratio (DSR). The group of 43 patient studies was divided into a learning set (25 patients) and a test set (18 patients). All phantom valves with an SLS were detected (sensitivity, 100%) at a specificity of 100%. The threshold values for the NPD and the DSR to decide whether a fracture was present or not were 3.6 and 2.5, respectively. On the basis of the visual interpretations of the 25 patient studies (learning set) by an expert panel, it was concluded that none of the patients had an SLS. To achieve a 100% specificity by quantitative analysis, the threshold values for the NPD and the DSR were set at 5.8 and 2.5, respectively, for the patient data. Based on these threshold values, the analysis of patient data from the test set resulted in one false-negative detection and three false-positive detections. An analytic software package for the detection of an SLS was developed. Phantom data showed excellent sensitivity (100%) and specificity (100%). Further research and software development is needed to increase the sensitivity and specificity for patient data.

Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan

PubMed Central

Yoshida, Mitsuhiro; Mochizuki, Tomohiro; Urayama, Syun-Ichi; Yoshida-Takashima, Yukari; Nishi, Shinro; Hirai, Miho; Nomaki, Hidetaka; Takaki, Yoshihiro; Nunoura, Takuro; Takai, Ken

2018-01-01

Previous studies on marine environmental virology have primarily focused on double-stranded DNA (dsDNA) viruses; however, it has recently been suggested that single-stranded DNA (ssDNA) viruses are more abundant in marine ecosystems. In this study, we performed a quantitative viral community DNA analysis to estimate the relative abundance and composition of both ssDNA and dsDNA viruses in offshore upper bathyal sediment from Tohoku, Japan (water depth = 500 m). The estimated dsDNA viral abundance ranged from 3 × 106 to 5 × 106 genome copies per cm3 sediment, showing values similar to the range of fluorescence-based direct virus counts. In contrast, the estimated ssDNA viral abundance ranged from 1 × 108 to 3 × 109 genome copies per cm3 sediment, thus providing an estimation that the ssDNA viral populations represent 96.3–99.8% of the benthic total DNA viral assemblages. In the ssDNA viral metagenome, most of the identified viral sequences were associated with ssDNA viral families such as Circoviridae and Microviridae. The principle components analysis of the ssDNA viral sequence components from the sedimentary ssDNA viral metagenomic libraries found that the different depth viral communities at the study site all exhibited similar profiles compared with deep-sea sediment ones at other reference sites. Our results suggested that deep-sea benthic ssDNA viruses have been significantly underestimated by conventional direct virus counts and that their contributions to deep-sea benthic microbial mortality and geochemical cycles should be further addressed by such a new quantitative approach. PMID:29467725

Sulfide-Induced Dissimilatory Nitrate Reduction to Ammonium Supports Anaerobic Ammonium Oxidation (Anammox) in an Open-Water Unit Process Wetland

PubMed Central

Jones, Zackary L.; Jasper, Justin T.; Sedlak, David L.

2017-01-01

ABSTRACT Open-water unit process wetlands host a benthic diatomaceous and bacterial assemblage capable of nitrate removal from treated municipal wastewater with unexpected contributions from anammox processes. In exploring mechanistic drivers of anammox, 16S rRNA gene sequencing profiles of the biomat revealed significant microbial community shifts along the flow path and with depth. Notably, there was an increasing abundance of sulfate reducers (Desulfococcus and other Deltaproteobacteria) and anammox microorganisms (Brocadiaceae) with depth. Pore water profiles demonstrated that nitrate and sulfate concentrations exhibited a commensurate decrease with biomat depth accompanied by the accumulation of ammonium. Quantitative PCR targeting the anammox hydrazine synthase gene, hzsA, revealed a 3-fold increase in abundance with biomat depth as well as a 2-fold increase in the sulfate reductase gene, dsrA. These microbial and geochemical trends were most pronounced in proximity to the influent region of the wetland where the biomat was thickest and influent nitrate concentrations were highest. While direct genetic queries for dissimilatory nitrate reduction to ammonium (DNRA) microorganisms proved unsuccessful, an increasing depth-dependent dominance of Gammaproteobacteria and diatoms that have previously been functionally linked to DNRA was observed. To further explore this potential, a series of microcosms containing field-derived biomat material confirmed the ability of the community to produce sulfide and reduce nitrate; however, significant ammonium production was observed only in the presence of hydrogen sulfide. Collectively, these results suggest that biogenic sulfide induces DNRA, which in turn can explain the requisite coproduction of ammonium and nitrite from nitrified effluent necessary to sustain the anammox community. IMPORTANCE This study aims to increase understanding of why and how anammox is occurring in an engineered wetland with limited exogenous contributions of ammonium and nitrite. In doing so, the study has implications for how geochemical parameters could potentially be leveraged to impact nutrient cycling and attenuation during the operation of treatment wetlands. The work also contributes to ongoing discussions about biogeochemical signatures surrounding anammox processes and enhances our understanding of the contributions of anammox processes in freshwater environments. PMID:28526796

Spatial analysis for susceptibility of second-time karst sinkholes: A case study of Jili Village in Guangxi, China

NASA Astrophysics Data System (ADS)

Zhou, Guoqing; Yan, Hongbo; Chen, Kunhua; Zhang, Rongting

2016-04-01

After a big karst sinkhole happened in Jili Village of Guangxi, China, the local government was eager to quantitatively analyze and map susceptible areas of the potential second-time karst sinkholes in order to make timely decisions whether the residents living in the first-time sinkhole areas should move. For this reason, karst sinkholes susceptibility geospatial analysis is investigated using multivariate spatial data, logistic regression model (LRM) and Geographical Information System (GIS). Ten major karst sinkholes related factors, including (1) formation lithology, (2) soil structure, (3) profile curvature, (4) groundwater depth, (5) fluctuation of groundwater level, (6) percolation rate of soil, (7) degree of karst development, (8) distance from fault, (9) distance from the traffic route, and (10) overburden thickness were selected, and then each of factors was classified and quantitated with the three or four levels. The LRM was applied to evaluate which factor makes significant contributions to sinkhole. The results demonstrated that formation lithology, soil structure, profile curvature, groundwater depth, ground water level, percolation rate of soil, and degree of karst development, the distance from fault, and overburden thickness are positive, while one factor, the distance from traffic routes is negative, which is deleted from LRM model. The susceptibility of the potential sinkholes in the study area is estimated and mapped using the solved impact factors. The susceptible degrees of the study area are classified into five levels, very high, high, moderate, low, and ignore susceptibility. It has been found that that both very high and high susceptibility areas are along Datou Hill and the foothills of the study area. This finding is verified by field observations. With the investigations conducted in this paper, it can be concluded that the susceptibility maps produced in this paper are reliable and accurate, and useful as a reference for local governments to make decisions regarding whether or not residents living within sinkhole areas should move.

Aggregating available soil water holding capacity data for crop yield models

NASA Technical Reports Server (NTRS)

Seubert, C. E.; Daughtry, C. S. T.; Holt, D. A.; Baumgardner, M. F.

1984-01-01

The total amount of water available to plants that is held against gravity in a soil is usually estimated as the amount present at -0.03 MPa average water potential minus the amount present at -1.5 MPa water potential. This value, designated available water-holding capacity (AWHC), is a very important soil characteristic that is strongly and positively correlated to the inherent productivity of soils. In various applications, including assessing soil moisture status over large areas, it is necessary to group soil types or series as to their productivity. Current methods to classify AWHC of soils consider only total capacity of soil profiles and thus may group together soils which differ greatly in AWHC as a function of depth in the profile. A general approach for evaluating quantitatively the multidimensional nature of AWHC in soils is described. Data for 902 soil profiles, representing 184 soil series, in Indiana were obtained from the Soil Characterization Laboratory at Purdue University. The AWHC for each of ten 150-mm layers in each soil was established, based on soil texture and parent material. A multivariate clustering procedure was used to classify each soil profile into one of 4, 8, or 12 classes based upon ten-dimensional AWHC values. The optimum number of classes depends on the range of AWHC in the population of oil profiles analyzed and on the sensitivity of a crop to differences in distribution of water within the soil profile.

Scattering attenuation profile of the Moon: Implications for shallow moonquakes and the structure of the megaregolith

NASA Astrophysics Data System (ADS)

Gillet, K.; Margerin, L.; Calvet, M.; Monnereau, M.

2017-01-01

We report measurements of the attenuation of short period seismic waves in the Moon based on the quantitative analysis of envelope records of lunar quakes. Our dataset consists of waveforms corresponding to 62 events, including artificial and natural impacts, shallow moonquakes and deep moonquakes, recorded by the four seismometers deployed during Apollo missions 12, 14, 15 and 16. To quantify attenuation and distinguish between elastic (scattering) and inelastic (absorption) mechanisms we measure the time of arrival of the maximum of energy tmax and the coda quality factor Qc . The former is controlled by both scattering and absorption, while the latter is an excellent proxy for absorption. Consistent with the strong broadening of seismogram envelopes in the Moon, we employ diffusion theory in spherical geometry to model the propagation of seismic energy in depth-dependent scattering and absorbing media. To minimize the misfit between predicted and observed tmax for deep moonquakes and impacts, we employ a genetic algorithm and explore a large number of depth-dependent attenuation models quantified by the scattering quality factor Qsc or equivalently the wave diffusivity D, and the absorption quality factor Qi . The scattering and absorption profiles that best fit the data display very strong scattering attenuation (Qsc ≤ 10) or equivalently very low wave diffusivity (D ≈ 2 km2/s) in the first 10 km of the Moon. These values correspond to the most heterogeneous regions on Earth, namely volcanic areas. Below this surficial layer, the diffusivity rises very slowly up to a depth of approximately 80 km where Qsc and D exhibit an abrupt increase of about one order of magnitude. Below 100 km depth, Qsc increases rapidly up to approximately 2000 at a depth of about 150 km, a value similar to the one found in the Earth's mantle. By contrast, the absorption quality factor on the Moon Qi ≈ 2400 is about one order or magnitude larger than on Earth. Our results suggest the existence of an approximately 100 km thick megaregolith, which is much larger than what was previously thought. The rapid decrease of scattering attenuation below this depth is compatible with crack healing through viscoelastic mechanisms. Using our best attenuation model, we invert for the depth of shallow moonquakes based on the observed variation of tmax with epicentral distance. On average, they are found to originate from a depth of about 50 km ± 20 km, which suggests that these earthquakes are caused by the failure of deep faults in the brittle part of the Moon.

Determination of rare earth elements concentration at different depth profile of Precambrian pegmatites using instrumental neutron activation analysis.

PubMed

Sadiq Aliyu, Abubakar; Musa, Yahaya; Liman, M S; Abba, Habu T; Chaanda, Mohammed S; Ngene, Nnamani C; Garba, N N

2018-01-01

The Keffi area hosts abundant pegmatite bodies as a result of the surrounding granitic intrusions. Keffi is part of areas that are geologically classified as North Central Basement Complex. Data on the mineralogy and mineralogical zonation of the Keffi pegmatite are scanty. Hence the need to understand the geology and mineralogical zonation of Keffi pegmatites especially at different depth profiles is relevant as a study of the elemental composition of the pegmatite is essential for the estimation of its economic viability. Here, the relative standardization method of instrumental neutron activation analysis (INAA) has been used to investigate the vertical deviations of the elemental concentrations of rare earth elements (REEs) at different depth profile of Keffi pegmatite. This study adopted the following metrics in investigating the vertical variations of REEs concentrations. Namely, the total contents of rare earth elements (∑REE); ratio of light to heavy rare earth elements (LREE/HREE), which defines the enrichment or depletion of REEs; europium anomaly (Eu/Sm); La/Lu ratio relative to chondritic meteorites. The study showed no significant variations in the total content of rare elements between the vertical depth profiles (100-250m). However, higher total concentrations of REEs (~ 92.65ppm) were recorded at the upper depth of the pegmatite and the europium anomaly was consistently negative at all the depth profiles suggesting that the Keffi pegmatite is enriched with light REEs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dynamic vertical profiles of peat porewater chemistry in a northern peatland

Treesearch

Natalie A. Griffiths; Stephen D. Sebestyen

2016-01-01

We measured pH, cations, nutrients, and total organic carbon (TOC) over 3 years to examine weekly to monthly variability in porewater chemistry depth profiles (0–3.0 m) in an ombrotrophic bog in Minnesota, USA. We also compared temporal variation at one location to spatial variation in depth profiles at 16 locations across the bog. Most solutes exhibited large...

Microbial Ecological Niche Partitioning Affects N2 gas Production in the Largest Marine Oxygen Minimum Zone

NASA Astrophysics Data System (ADS)

Fuchsman, C. A.; Penn, J. L.; Devol, A.; Palevsky, H. I.; Deutsch, C. A.; Keil, R.; Ward, B. B.; Rocap, G.

2016-02-01

Up to half of oceanic N2 production occurs in oxygen minimum zones (OMZs). In the Eastern Tropical North Pacific OMZ in April 2012, we measured a nine station coast to open ocean transect of N2 gas in the heart of the ETNP OMZ. Depth profiles of excess N2 gas had dual maxima located at the top of the OMZ and at 300m. An ecosystem biogeochemical model of the ETNP was also found to produce dual maxima at stations with a shallow OMZ. The model indicated that high N2 production rates caused the upper N2 maxima while long water residence time caused the deeper maxima. At a low productivity open ocean station where dual N2 maxima were observed, we obtained a depth profile of metagenomic sequences from both free living and >30 μm fractions to determine which N2 producing microbes were living in these three ecological niches. We use a phylogenetically-aware approach to identify metagenomic sequences by placing them on reference trees, which allows us to utilize them in a semi-quantitative manner. Overall, genes for denitrification (napA, nirS, nirK, qnor, nosZ) were enriched on particles while anammox was free-living. However, separation of genes into phylotypes indicated that the system is more complicated. For example, 4 out of 5 N2O reductase denitrifier phylotypes were actually free-living, while the fifth, most abundant phylotype was particle-attached. In the water column, denitrifier and anammox genes were spatially separated with depth with denitrifiers focused on the top section of the OMZ and with anammox becoming abundant slightly deeper and being more dominant at the deep N2 maxima. Interestingly, different phylotypes of denitrifiers have different depth profiles, implying individual adaptations and niches. The presence of measurable ammonia (>200 nM) at the top 20m of the OMZ along with the very low numbers of anammox bacteria is consistent with recent shoaling of the OMZ at the time of sampling. Thus the spatial separation of denitrifiers and anammox at the top of the OMZ may be a transient event due to differences in growth rate and response time. Additionally, assembly of metagenomic reads and clustering of the resulting contigs by tetranucleotide frequency was used to identify denitrifying bacteria and link together gene phylotypes.

da Vinci decoded: does da Vinci stereopsis rely on disparity?

PubMed

Tsirlin, Inna; Wilcox, Laurie M; Allison, Robert S

2012-11-01

In conventional stereopsis, the depth between two objects is computed based on the retinal disparity in the position of matching points in the two eyes. When an object is occluded by another object in the scene, so that it is visible only in one eye, its retinal disparity cannot be computed. Nakayama and Shimojo (1990) found that a precept of quantitative depth between the two objects could still be established for such stimuli and proposed that this precept is based on the constraints imposed by occlusion geometry. They named this and other occlusion-based depth phenomena "da Vinci stereopsis." Subsequent research found quantitative depth based on occlusion geometry in several other classes of stimuli grouped under the term da Vinci stereopsis. However, Nakayama and Shimojo's findings were later brought into question by Gillam, Cook, and Blackburn (2003), who suggested that quantitative depth in their stimuli was perceived based on conventional disparity. In order to understand whether da Vinci stereopsis relies on one type of mechanism or whether its function is stimulus dependent we examine the nature and source of depth in the class of stimuli used by Nakayama and Shimojo (1990). We use three different psychophysical and computational methods to show that the most likely source for depth in these stimuli is occlusion geometry. Based on these experiments and previous data we discuss the potential mechanisms responsible for processing depth from monocular features in da Vinci stereopsis.

Depth profiles of oxygen precipitates in nitride-coated silicon wafers subjected to rapid thermal annealing

NASA Astrophysics Data System (ADS)

Voronkov, V. V.; Falster, R.; Kim, TaeHyeong; Park, SoonSung; Torack, T.

2013-07-01

Silicon wafers, coated with a silicon nitride layer and subjected to high temperature Rapid Thermal Annealing (RTA) in Ar, show—upon a subsequent two-step precipitation anneal cycle (such as 800 °C + 1000 °C)—peculiar depth profiles of oxygen precipitate densities. Some profiles are sharply peaked near the wafer surface, sometimes with a zero bulk density. Other profiles are uniform in depth. The maximum density is always the same. These profiles are well reproduced by simulations assuming that precipitation starts from a uniformly distributed small oxide plates originated from RTA step and composed of oxygen atoms and vacancies ("VO2 plates"). During the first step of the precipitation anneal, an oxide layer propagates around this core plate by a process of oxygen attachment, meaning that an oxygen-only ring-shaped plate emerges around the original plate. These rings, depending on their size, then either dissolve or grow during the second part of the anneal leading to a rich variety of density profiles.

Dynamics of marine bacterial community diversity of the coastal waters of the reefs, inlets, and wastewater outfalls of southeast Florida

PubMed Central

Campbell, Alexandra M; Fleisher, Jay; Sinigalliano, Christopher; White, James R; Lopez, Jose V

2015-01-01

Coastal waters adjacent to populated southeast Florida possess different habitats (reefs, oceanic inlets, sewage outfalls) that may affect the composition of their inherent microbiomes. To determine variation according to site, season, and depth, over the course of 1 year, we characterized the bacterioplankton communities within 38 nearshore seawater samples derived from the Florida Area Coastal Environment (FACE) water quality survey. Six distinct coastal locales were profiled – the Port Everglades and Hillsboro Inlets, Hollywood and Broward wastewater outfalls, and associated reef sites using culture-independent, high-throughput pyrosequencing of the 16S rRNA V4 region. More than 227,000 sequences helped describe longitudinal taxonomic profiles of marine bacteria and archaea. There were 4447 unique operational taxonomic units (OTUs) identified with a mean OTU count of 5986 OTUs across all sites. Bacterial taxa varied significantly by season and by site using weighted and unweighted Unifrac, but depth was only supported by weighted Unifrac, suggesting a change due to presence/absence of certain OTUs. Abundant microbial taxa across all samples included Synechococcus, Pelagibacteraceae, Bacteroidetes, and various Proteobacteria. Unifrac analysis confirmed significant differences at inlet sites relative to reef and outfalls. Inlet-based bacterioplankton significantly differed in greater abundances of Rhodobacteraceae and Cryomorphaceae, and depletion of SAR406 sequences. This study also found higher counts of Firmicutes, Chloroflexi, and wastewater associated SBR1093 bacteria at the outfall and reef sites compared to inlet sites. This study profiles local bacterioplankton populations in a much broader context, beyond culturing and quantitative PCR, and expands upon the work completed by the National Oceanic and Atmospheric Administration FACE program. PMID:25740409

High-sensitivity aeromagnetic survey of the US Atlantic continental margin.

USGS Publications Warehouse

Behrendt, John C.; Klitgord, Kim D.

1980-01-01

The US Geological Survey contracted a high-sensitivity, digital aeromagnetic survey that was flown over the US Atlantic continental margin over a period of 15 months between 1974 and 1976. The 185 000 km of profile data have a relative accuracy approaching a few tenths of a nanotesla, which allowed compilation into maps at a scale of 1:250 000, with a contour interval of 2 nT. Automatic data processing using the Werner method allowed calculations of apparent depth to sources of the magnetic anomalies on all of the profiles, assuming a dike or interface as a source. Comparison of the computed depths to magnetic basement with multichannel seismic profiles across the survey area helped to reduce ambiguities in magnetic depth estimates and enabled interpolation of basement structures between seismic profiles. The resulting map showing depth to basement of the Atlantic continental margin is compatible with available multichannel seismic data, and we consider it a reasonable representation of the base of the sedimentary column. -Authors

Perfect Composition Depth Profiling of Ionic Liquid Surfaces Using High-resolution RBS/ERDA.

PubMed

Nakajima, Kaoru; Zolboo, Enkhbayar; Ohashi, Tomohiro; Lísal, Martin; Kimura, Kenji

2016-01-01

In order to reveal the surface structures of large molecular ionic liquids (ILs), the near-surface elemental depth distributions of 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C n C 1 Im][Tf 2 N], n = 2, 6, 10) were studied using high-resolution Rutherford backscattering spectroscopy (HRBS) in combination with high-resolution elastic recoil detection analysis (HR-ERDA). The elemental depth profiles of all constituent elements, including hydrogen, were derived from HR-ERDA/HRBS measurements, so that the profiles would reproduce both HR-ERDA and HRBS spectra simultaneously. The derived elemental depth profiles agree with state-of-the-art molecular dynamics simulations, indicating the feasibility of this method. A controversy concerning the preferential orientation of [C 2 C 1 Im] at the surface has been resolved by this new combination analysis; namely, the [C 2 C 1 Im] cation has a preferential orientation with the ethyl chain pointing towards the vacuum in the topmost molecular layer.

Depth profiling of high energy nitrogen ions implanted in the <1 0 0>, <1 1 0> and randomly oriented silicon crystals

NASA Astrophysics Data System (ADS)

Erić, M.; Petrović, S.; Kokkoris, M.; Lagoyannis, A.; Paneta, V.; Harissopulos, S.; Telečki, I.

2012-03-01

This work reports on the experimentally obtained depth profiles of 4 MeV 14N2+ ions implanted in the <1 0 0>, <1 1 0> and randomly oriented silicon crystals. The ion fluence was 1017 particles/cm2. The nitrogen depth profiling has been performed using the Nuclear Reaction Analysis (NRA) method, via the study of 14N(d,α0)12C and 14N(d,α1)12C nuclear reactions, and with the implementation of SRIM 2010 and SIMNRA computer simulation codes. For the randomly oriented silicon crystal, change of the density of silicon matrix and the nitrogen "bubble" formation have been proposed as the explanation for the difference between the experimental and simulated nitrogen depth profiles. During the implantation, the RBS/C spectra were measured on the nitrogen implanted and on the virgin crystal spots. These spectra provide information on the amorphization of the silicon crystals induced by the ion implantation.

LINKING Lyα AND LOW-IONIZATION TRANSITIONS AT LOW OPTICAL DEPTH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jaskot, A. E.; Oey, M. S.

2014-08-20

We suggest that low optical depth in the Lyman continuum (LyC) may relate the Lyα emission, C II and Si II absorption, and C II* and Si II* emission seen in high-redshift galaxies. We base this analysis on Hubble Space Telescope Cosmic Origins Spectrograph spectra of four Green Pea (GP) galaxies, which may be analogs of z > 2 Lyα emitters (LAEs). In the two GPs with the strongest Lyα emission, the Lyα line profiles show reduced signs of resonant scattering. Instead, the Lyα profiles resemble the Hα line profiles of evolved star ejecta, suggesting that the Lyα emission originatesmore » from a low column density and similar outflow geometry. The weak C II absorption and presence of non-resonant C II* emission in these GPs support this interpretation and imply a low LyC optical depth along the line of sight. In two additional GPs, weak Lyα emission and strong C II absorption suggest a higher optical depth. These two GPs differ in their Lyα profile shapes and C II* emission strengths, however, indicating different inclinations of the outflows to our line of sight. With these four GPs as examples, we explain the observed trends linking Lyα, C II, and C II* in stacked LAE spectra, in the context of optical depth and geometric effects. Specifically, in some galaxies with strong Lyα emission, a low LyC optical depth may allow Lyα to escape with reduced scattering. Furthermore, C II absorption, C II* emission, and Lyα profile shape can reveal the optical depth, constrain the orientation of neutral outflows in LAEs, and identify candidate LyC emitters.« less

Twoplex 12/13 C6 aniline stable isotope and linkage-specific sialic acid labeling 2D-LC-MS workflow for quantitative N-glycomics.

PubMed

Albrecht, Simone; Mittermayr, Stefan; Smith, Josh; Martín, Silvia Millán; Doherty, Margaret; Bones, Jonathan

2017-01-01

Quantitative glycomics represents an actively expanding research field ranging from the discovery of disease-associated glycan alterations to the quantitative characterization of N-glycans on therapeutic proteins. Commonly used analytical platforms for comparative relative quantitation of complex glycan samples include MALDI-TOF-MS or chromatographic glycan profiling with subsequent data alignment and statistical evaluation. Limitations of such approaches include run-to-run technical variation and the potential introduction of subjectivity during data processing. Here, we introduce an offline 2D LC-MS E workflow for the fractionation and relative quantitation of twoplex isotopically labeled N-linked oligosaccharides using neutral 12 C 6 and 13 C 6 aniline (Δmass = 6 Da). Additional linkage-specific derivatization of sialic acids using 4-(4,6-dimethoxy-1,3,5-trizain-2-yl)-4-methylmorpholinium chloride offered simultaneous and advanced in-depth structural characterization. The potential of the method was demonstrated for the differential analysis of structurally defined N-glycans released from serum proteins of patients diagnosed with various stages of colorectal cancer. The described twoplex 12 C 6 / 13 C 6 aniline 2D LC-MS platform is ideally suited for differential glycomic analysis of structurally complex N-glycan pools due to combination and analysis of samples in a single LC-MS injection and the associated minimization in technical variation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization of near-stoichiometric Ti:LiNbO(3) strip waveguides with varied substrate refractive index in the guiding layer.

PubMed

Zhang, De-Long; Zhang, Pei; Zhou, Hao-Jiang; Pun, Edwin Yue-Bun

2008-10-01

We have demonstrated the possibility that near-stoichiometric Ti:LiNbO(3) strip waveguides are fabricated by carrying out vapor transport equilibration at 1060 degrees C for 12 h on a congruent LiNbO(3) substrate with photolithographically patterned 4-8 microm wide, 115 nm thick Ti strips. Optical characterizations show that these waveguides are single mode at 1.5 microm and show a waveguide loss of 1.3 dB/cm for TM mode and 1.1 dB/cm for TE mode. In the width/depth direction of the waveguide, the mode field follows the Gauss/Hermite-Gauss function. Secondary-ion-mass spectrometry (SIMS) was used to study Ti-concentration profiles in the depth direction and on the surface of the 6 microm wide waveguide. The result shows that the Ti profile follows a sum of two error functions along the width direction and a complementary error function in the depth direction. The surface Ti concentration, 1/e width and depth, and mean diffusivities along the width and depth directions of the guide are similar to 3.0 x 10(21) cm(-3), 3.8 microm, 2.6 microm, 0.30 and 0.14 microm(2)/h, respectively. Micro-Raman analysis was carried out on the waveguide endface to characterize the depth profile of Li composition in the guiding layer. The results show that the depth profile of Li composition also follows a complementary error function with a 1/e depth of 3.64 microm. The mean ([Li(Li)]+[Ti(Li)])/([Nb(Nb)]+[Ti(Nb)]) ratio in the waveguide layer is about 0.98. The inhomogeneous Li-composition profile results in a varied substrate index in the guiding layer. A two-dimensional refractive index profile model in the waveguide is proposed by taking into consideration the varied substrate index and assuming linearity between Ti-induced index change and Ti concentration. The net waveguide surface index increments at 1545 nm are 0.0114 and 0.0212 for ordinary and extraordinary rays, respectively. Based upon the constructed index model, the fundamental mode field profile was calculated using the beam propagation method, and the mode sizes and effective index versus the Ti-strip width were calculated for three lower TM and TE modes using the variational method. An agreement between theory and experiment is obtained.

Decomposition of ultrathin LiF cathode underlayer in organic-based devices evidenced by ToF-SIMS depth profiling

NASA Astrophysics Data System (ADS)

Pakhomov, Georgy L.; Drozdov, Mikhail N.; Travkin, Vlad V.; Bochkarev, Mikhail N.

2017-11-01

In this work we investigate the chemical composition of an archetypal thin-film organic device with the Ag/LiF cathode using the time-of-flight secondary ion mass spectrometry (ToF-SIMS) with depth profiling. The LiF cathode underlayer is partly decomposed because a significant amount of lithium is released into the bulk of the multilayer device. The released lithium diffuses all the way to the substrate, accumulating, as revealed by ToF-SIMS depth profiles, at the interfaces rather than uniformly doping the underlying layers. Particularly, the bottom anode becomes chemically modified.

Analyses of hydrogen in quartz and in sapphire using depth profiling by ERDA at atmospheric pressure: Comparison with resonant NRA and SIMS

NASA Astrophysics Data System (ADS)

Reiche, Ina; Castaing, Jacques; Calligaro, Thomas; Salomon, Joseph; Aucouturier, Marc; Reinholz, Uwe; Weise, Hans-Peter

2006-08-01

Hydrogen is present in anhydrous materials as a result of their synthesis and of their environment during conservation. IBA provides techniques to measure H concentration depth profiles allowing to identify various aspects of the materials including the history of objects such as gemstones used in cultural heritage. A newly established ERDA set-up, using an external microbeam of alpha particles, has been developed to study hydrated near-surface layers in quartz and sapphire by non-destructive H depth profiling in different atmospheres. The samples were also analysed using resonant NRA and SIMS.

Design and implementation of optical imaging and sensor systems for characterization of deep-sea biological camouflage

NASA Astrophysics Data System (ADS)

Haag, Justin Mathew

The visual ecology of deep-sea animals has long been of scientific interest. In the open ocean, where there is no physical structure to hide within or behind, diverse strategies have evolved to solve the problem of camouflage from a potential predator. Simulations of specific predator-prey scenarios have yielded estimates of the range of possible appearances that an animal may exhibit. However, there is a limited amount of quantitative information available related to both animal appearance and the light field at mesopelagic depths (200 m to 1000 m). To mitigate this problem, novel optical instrumentation, taking advantage of recent technological advances, was developed and is described in this dissertation. In the first half of this dissertation, the appearance of mirrored marine animals is quantitatively evaluated. A portable optical imaging scatterometer was developed to measure angular reflectance, described by the bidirectional reflectance distribution function (BRDF), of biological specimens. The instrument allows for BRDF capture from samples of arbitrary size, over a significant fraction of the reflectance hemisphere. Multiple specimens representing two species of marine animals, collected at mesopelagic depths, were characterized using the scatterometer. Low-dimensional parametric models were developed to simplify use of the data sets, and to validate the BRDF method. Results from principal component analysis confirm that BRDF measurements can be used to study intra- and interspecific variability of mirrored marine animal appearance. Collaborative efforts utilizing the BRDF data sets to develop physically-based scattering models are underway. In the second half of this dissertation, another key part of the deep-sea biological camouflage problem is examined. Two underwater radiometers, capable of low-light measurements, were developed to address the lack of available information related to the deep-sea light field. Quantitative comparison of spectral downward irradiance profiles at blue (~470~nm) and green (~560~nm) wavelengths, collected at Pacific and Atlantic field stations, provide insight into the presence of Raman (inelastic) scattering effects at mesopelagic depths. The radiometers were also used to collect in situ flashes of bioluminescence. Collaborations utilizing both the downward irradiance and bioluminescence data sets are planned.

GIS Well Temperature Data from the Roosevelt Hot Springs, Utah FORGE Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gwynn, Mark; Hill, Jay; Allis, Rick

This is a GIS point feature shapefile representing wells, and their temperatures, that are located in the general Utah FORGE area near Milford, Utah. There are also fields that represent interpolated temperature values at depths of 200 m, 1000 m, 2000 m, 3000 m, and 4000 m. in degrees Fahrenheit. The temperature values at specific depths as mentioned above were derived as follows. In cases where the well reached a given depth (200 m and 1, 2, 3, or 4 km), the temperature is the measured temperature. For the shallower wells (and at deeper depths in the wells reaching onemore » or more of the target depths), temperatures were extrapolated from the temperature-depth profiles that appeared to have stable (re-equilibrated after drilling) and linear profiles within the conductive regime (i.e. below the water table or other convective influences such as shallow hydrothermal outflow from the Roosevelt Hydrothermal System). Measured temperatures/gradients from deeper wells (when available and reasonably close to a given well) were used to help constrain the extrapolation to greater depths. Most of the field names in the attribute table are intuitive, however HF = heat flow, intercept = the temperature at the surface (x-axis of the temperature-depth plots) based on the linear segment of the plot that was used to extrapolate the temperature profiles to greater depths, and depth_m is the total well depth. This information is also present in the shapefile metadata.« less

Influence of the tidal front on the three-dimensional distribution of spring phytoplankton community in the eastern Yellow Sea.

PubMed

Choi, Byoung-Ju; Lee, Jung A; Choi, Jae-Sung; Park, Jong-Gyu; Lee, Sang-Ho; Yih, Wonho

2017-04-01

Hydrographic observation and biological samplings were conducted to assess the distribution of phytoplankton community over the sloping shelf of the eastern Yellow Sea in May 2012. The concentration of chlorophyll a was determined and phytoplankton was microscopically examined to conduct quantitative and cluster analyses. A cluster analysis of the phytoplankton species and abundance along four observation lines revealed the three-dimensional structure of the phytoplankton community distribution: the coastal group in the mixed region, the offshore upper layer group preferring stable water column, and the offshore lower layer group. The subsurface maximum of phytoplankton abundance and chlorophyll a concentration appeared as far as 64 km away from the tidal front through the middle layer intrusion. The phytoplankton abundance was high in the shore side of tidal front during the spring tide. The phytoplankton abundance was relatively high at 10-m depth in the mixed region while the concentration of chlorophyll a was high below the depth. The disparity between the profiles of the phytoplankton abundance and the chlorophyll a concentration in the mixed region was related to the depth-dependent species change accompanied by size-fraction of the phytoplankton community. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantitative analysis of imprint shape and its relation to mechanical properties measured by microindentation in bone.

PubMed

Schwiedrzik, J J; Zysset, P K

2015-01-21

Microindentation in bone is a micromechanical testing technique routinely used to extract material properties related to bone quality. As the analysis of microindentation data is based on assumptions about the contact between sample and surface, the aim of this study was to quantify the topological variability of indentations in bone and examine its relationship with mechanical properties. Indentations were performed in dry human and ovine bone in axial and transverse directions and their topology was measured by atomic force microscopy. Statistical shape modeling of the residual imprint allowed to define a mean shape and to describe the variability in terms of 21 principal components related to imprint depth, surface curvature and roughness. The indentation profile of bone was found to be highly consistent and free of any pile up while differing mostly by depth between species and direction. A few of the topological parameters, in particular depth, showed significant but rather weak and inconsistent correlations to variations in mechanical properties. The mechanical response of bone as well as the residual imprint shape was highly consistent within each category. We could thus verify that bone is rather homogeneous in its micromechanical properties and that indentation results are not strongly influenced by small deviations from an ideally flat surface. Copyright © 2014 Elsevier Ltd. All rights reserved.

Strong-field Photoionization of Sputtered Neutral Molecules for Molecular Depth Profiling

PubMed Central

Willingham, D; Brenes, D. A.; Wucher, A

2009-01-01

Molecular depth profiles of an organic thin film of guanine vapor deposited onto a Ag substrate are obtained using a 40 keV C60 cluster ion beam in conjunction with time-of-flight secondary ion mass spectrometric (ToF-SIMS) detection. Strong-field, femtosecond photoionization of intact guanine molecules is used to probe the neutral component of the profile for direct comparison with the secondary ion component. The ability to simultaneously acquire secondary ions and photoionized neutral molecules reveals new fundamental information about the factors that influence the properties of the depth profile. Results show that there is an increased ionization probability for protonated molecular ions within the first 10 nm due to the generation of free protons within the sample. Moreover, there is a 50% increase in fragment ion signal relative to steady state values 25 nm before reaching the guanine/Ag interface as a result of interfacial chemical damage accumulation. An altered layer thickness of 20 nm is observed as a consequence of ion beam induced chemical mixing. In general, we show that the neutral component of a molecular depth profile using the strong-field photoionization technique can be used to elucidate the effects of variations in ionization probability on the yield of molecular ions as well as to aid in obtaining accurate information about depth dependent chemical composition that cannot be extracted from TOF-SIMS data alone. PMID:20495665

The biological pump: Profiles of plankton production and consumption in the upper ocean

NASA Astrophysics Data System (ADS)

Longhurst, Alan R.; Glen Harrison, W.

The ‘biological pump’ mediates flux of carbon to the interior of the ocean by interctions between the components of the vertically-structured pelagic ecosystem of the photic zone. Chlorophyll profiles are not a simple indicator of autotrophic biomass or production, because of non-linearities in the physiology of cells and preferential vertical distribution of taxa. Profiles of numbers or biomass of heterotrophs do not correspond with profiles of consumption, because of depth-selection (taxa, seasons) for reasons unconnected with feeding. Depths of highest plant biomass, chlorophyll and growth rate coincide when these depths are shallow, but become progressively separated in profiles where they are deeper - so that highest growth rate lies progressively shallower than the chloropyll maximum. It is still uncertain how plant biomass is distributed in deep profiles. Depths of greatest heterotroph biomass (mesozooplankton) are usually close to depths of fastest plant growth rate, and thus lie shallower than the chlorophyll maximum in profiles where this itself is deep. This correlation is functional, and relates to the role of heterotrophs in excreting metabolic wastes (especially ammonia), which may fuel a significant component of integrated algal production, especially in the oligotrophic ocean. Some, but not all faecal material from mesozooplankton of the photic zone appears in vertical flux below the pycnocine, depending on the size of the source organisms, and the degree of vertical mixing above the pycnocline. Diel, but probably not seasonal, vertical migration is significant in the vertical flux of dissolved nitrogen. Regional generalisations of the vertical relations of the main components of the ‘biological pump’ now appear within reach, and an approach is suggested.

The Effect of Borehole Flow on Salinity Profiles From Deep Monitor Wells in Hawaii

NASA Astrophysics Data System (ADS)

Rotzoll, K.; Hunt, C. D.; El-Kadi, A. I.

2008-12-01

Ground-water resource management in Hawaii is based partly on salinity profiles from deep wells that are used to monitor the thickness of freshwater lenses and the transition zone between freshwater and saltwater. Vertical borehole flow in these wells may confound understanding of the actual salinity-depth profiles in the basaltic aquifers and lead to misinterpretations that hamper effective water-resource management. Causes and effects of borehole flow on salinity profiles are being evaluated at 40 deep monitor wells in Hawaii. Step- like changes in fluid electrical conductivity with respect to depth are indicative of borehole flow and are evident in almost all available salinity profiles. A regional trend in borehole flow direction, expected from basin-wide ground-water flow dynamics, is evident as major downward flow components in inland recharge areas and major upward flow components in discharge areas near the coast. The midpoint of the transition zone in one deep monitor well showed inconsequential depth displacements in response to barometric pressure and tidal fluctuations and to pumping from nearby wellfields. Commonly, the 1 mS/cm conductivity value is used to indicate the top of the transition zone. Contrary to the more stable midpoint, the depth of the 1 mS/cm conductivity value may be displaced by as much as 200 m in deep monitor wells near pumping wellfields. The displacement is complemented with an increase in conductivity at a particular depth in the upper part of the profile. The observed increase in conductivity is linear with increase in nearby pumpage. The largest deviations from expected aquifer-salinity profiles occur in deep monitor wells located in the area extending from east Pearl Harbor to Kalihi on Oahu, which coincides with the most heavily pumped part of the aquifer.

Migration of fallout radiocaesium in a grassland soil from 1986 to 2001. Part I: activity-depth profiles of (134)Cs and (137)Cs.

PubMed

Schimmack, W; Schultz, W

2006-09-15

The temporal changes of the vertical distribution of (134)Cs (deposited by the Chernobyl fallout in 1986) and (137)Cs (deposited by the Chernobyl and the global fallout) in the soil were investigated at an undisturbed Bavarian grassland site in Germany. At ten sampling dates between 1986 and 2001, the activity density of (134)Cs and (137)Cs was determined in various soil layers down to 80 cm depth. In 2001, the small-scale spatial variability of the radiocaesium activity was determined by sampling five plots within 10 m(2) (coefficient of variation about 20% for the upper soil layers). Between 1987 and 1990, substantial changes of the activity-depth profiles were observed. The percentage depth distributions of (134)Cs and (137)Cs were rather similar. The 50%-depth of the accumulated activity increased from 2.4 cm in 1988 to 5.3 cm in 2001 for (134)Cs and from 2.7 to 5.8 cm for (137)Cs. This indicates that at the study site the migration data of Chernobyl-derived (137)Cs can be estimated by those of total (137)Cs. In the second part of this study, the activity-depth profiles will be evaluated by the convection-dispersion model [Schimmack, W, Feria Márquez, F. Migration of fallout radiocaesium in a grassland soil from 1986 to 2001. Part II: Evaluation of the activity-depth profiles by transport models. Sci Total Environ 2006-this issue].

Fluid Pressure in the Shallow Plate Interface at the Nankai Trough Subduction Zone

NASA Astrophysics Data System (ADS)

Tobin, H. J.; Saffer, D.

2003-12-01

The factors controlling the occurrence, magnitude, and other characteristics of great earthquakes is a fundamental outstanding question in fault physics. Pore fluid pressure is perhaps the most critical yet poorly known parameter governing the strength and seismogenic character of plate boundary faults, but unfortunately cannot be directly inferred through available geophysical sensing methods. Moreover, true in situ fluid pressure has proven difficult to measure even in boreholes. At the Nankai Trough, several hundred meters of sediment are subducted beneath the frontal portion of the accretionary prism. The up-dip portion of the plate interface is therefore hosted in these fine-grained marine sedimentary rocks. ODP Leg 190 and 196 showed that these rapidly-loaded underthrust sediments are significantly overpressured near the deformation front. Here, we attempt to quantitatively infer porosity, pore pressure, and effective normal stress at the plate interface at depths currently inaccessible to drilling. Using seismic reflection interval velocity calibrated at the boreholes to porosity, we quantitatively infer pore pressure to ˜ 20 km down-dip of the deformation front, to a plate interface depth of ˜ 6 km. We have developed a Nankai-specific velocity-porosity transform using ODP cores and logs. We use this function to derive a porosity profile for each of two down-dip seismic sections extracted from a 3-D dataset from the Cape Muroto region. We then calculate pore fluid pressure and effective vertical (fault-normal) stress for the underthrust sediment section using a compaction disequilibrium approach and core-based consolidation test data. Because the pore fluid pressure at the fault interface is likely controlled by that of the top of the underthrust section, this calculation represents a quantitative profile of effective stress and pore pressure at the plate interface. Results show that seismic velocity and porosity increase systematically downdip in the underthrust section, but the increase is suppressed relative to that expected from normally consolidating sediments. The computed pore pressure increases landward from an overpressure ratio (λ * = hydrostatic pressure divided by the lithostatic overburden) of ˜ 0.6 at the deformation front to ˜ 0.77 where sediments have been subducted 15 km. The results of this preliminary analysis suggest that a 3-dimensional mapping of predicted effective normal stress in the seismic data volume is possible.

Quantitative Analysis of Cotton Canopy Size in Field Conditions Using a Consumer-Grade RGB-D Camera.

PubMed

Jiang, Yu; Li, Changying; Paterson, Andrew H; Sun, Shangpeng; Xu, Rui; Robertson, Jon

2017-01-01

Plant canopy structure can strongly affect crop functions such as yield and stress tolerance, and canopy size is an important aspect of canopy structure. Manual assessment of canopy size is laborious and imprecise, and cannot measure multi-dimensional traits such as projected leaf area and canopy volume. Field-based high throughput phenotyping systems with imaging capabilities can rapidly acquire data about plants in field conditions, making it possible to quantify and monitor plant canopy development. The goal of this study was to develop a 3D imaging approach to quantitatively analyze cotton canopy development in field conditions. A cotton field was planted with 128 plots, including four genotypes of 32 plots each. The field was scanned by GPhenoVision (a customized field-based high throughput phenotyping system) to acquire color and depth images with GPS information in 2016 covering two growth stages: canopy development, and flowering and boll development. A data processing pipeline was developed, consisting of three steps: plot point cloud reconstruction, plant canopy segmentation, and trait extraction. Plot point clouds were reconstructed using color and depth images with GPS information. In colorized point clouds, vegetation was segmented from the background using an excess-green (ExG) color filter, and cotton canopies were further separated from weeds based on height, size, and position information. Static morphological traits were extracted on each day, including univariate traits (maximum and mean canopy height and width, projected canopy area, and concave and convex volumes) and a multivariate trait (cumulative height profile). Growth rates were calculated for univariate static traits, quantifying canopy growth and development. Linear regressions were performed between the traits and fiber yield to identify the best traits and measurement time for yield prediction. The results showed that fiber yield was correlated with static traits after the canopy development stage ( R 2 = 0.35-0.71) and growth rates in early canopy development stages ( R 2 = 0.29-0.52). Multi-dimensional traits (e.g., projected canopy area and volume) outperformed one-dimensional traits, and the multivariate trait (cumulative height profile) outperformed univariate traits. The proposed approach would be useful for identification of quantitative trait loci (QTLs) controlling canopy size in genetics/genomics studies or for fiber yield prediction in breeding programs and production environments.

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

PubMed Central

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils. PMID:28611747

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers.

PubMed

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria , Chloroflexi , and Firmicutes increased whereas Cyanobacteria , β -proteobacteria , and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota , Thaumarchaeota , and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

Technical note: GODESS - a profiling mooring in the Gotland Basin

NASA Astrophysics Data System (ADS)

Prien, Ralf D.; Schulz-Bull, Detlef E.

2016-07-01

This note describes a profiling mooring with an interdisciplinary suite of sensors taking profiles between 180 and 30 m depth. It consists of an underwater winch, moored below 180 m depth, and a profiling instrumentation platform. In its described setup it can take about 200 profiles at pre-programmed times or intervals with one set of batteries. This allows for studies over an extended period of time (e.g. two daily profiles over a time of 3 months). The Gotland Deep Environmental Sampling Station (GODESS) in the Eastern Gotland Basin of the Baltic Sea is aimed at investigations of redoxcline dynamics. The described system can be readily adapted to other research foci by changing the profiling instrumentation platform and its payload.

Selectivity of silica species in ocean observed from seasonal and local changes

NASA Astrophysics Data System (ADS)

Tanaka, Miho; Takahashi, Kazuya; Nemoto, Masao; Horimoto, Naho

2013-03-01

Silicic acids, derived from SiO2 (silica), have several chemical forms in solution. Silica is a nutrient for diatoms, which are phytoplankton in oceans. Silica species can be used as a tracer to examine the behavior of silica in nature. The speciation for silica by FAB-MS (fast atom bombardment mass spectrometry) has been carried out for seawater samples from Tokyo Bay and Sagami Bay to investigate the seasonal and locational changes of the depth profiles of silica species. The species, [Si(OH)2O2Na+]-, [Si2(OH)5O2]- ([dimer]-), [Si2(OH)4O3Na+]-, [Si(OH)7O5-] ([cyclic tetramer]-), [Si4(OH)6O6Na+]-, [Si(OH)9O]- ([linear tetramer]-) and [Si4(OH)8O5Na+]- were mainly identified by FAB-MS. The seasonal and locational changes and the reproducibility of depth profiles of silica species were determined from October 2001 to July 2002. The depth profile of the ratio of linear tetramer to cyclic tetramer reflects the activity of diatoms, implying that the linear tetramer is the preferred "food" for diatoms. In particular, the depth profile for the ratio of linear tetramer to cyclic tetramer exhibits a critical changes that depend on the season. Furthermore, the depth profiles for the samples from Sagami Bay (open ocean) indicate that seawater is easily exchanged by ocean currents (the Japan Current). Thus, silica speciation by FAB-MS can give us a new tracer indicating the characteristics of the seawater budget, which change with depth, season and ocean locality.

Application of adenosine triphosphate affinity probe and scheduled multiple-reaction monitoring analysis for profiling global kinome in human cells in response to arsenite treatment.

PubMed

Guo, Lei; Xiao, Yongsheng; Wang, Yinsheng

2014-11-04

Phosphorylation of cellular components catalyzed by kinases plays important roles in cell signaling and proliferation. Quantitative assessment of perturbation in global kinome may provide crucial knowledge for elucidating the mechanisms underlying the cytotoxic effects of environmental toxicants. Here, we utilized an adenosine triphosphate (ATP) affinity probe coupled with stable isotope labeling by amino acids in cell culture (SILAC) to assess quantitatively the arsenite-induced alteration of global kinome in human cells. We constructed a SILAC-compatible kinome library for scheduled multiple-reaction monitoring (MRM) analysis and adopted on-the-fly recalibration of retention time shift, which provided better throughput of the analytical method and enabled the simultaneous quantification of the expression of ∼300 kinases in two LC-MRM runs. With this improved analytical method, we conducted an in-depth quantitative analysis of the perturbation of kinome of GM00637 human skin fibroblast cells induced by arsenite exposure. Several kinases involved in cell cycle progression, including cyclin-dependent kinases (CDK1 and CDK4) and Aurora kinases A, B, and C, were found to be hyperactivated, and the altered expression of CDK1 was further validated by Western analysis. In addition, treatment with a CDK inhibitor, flavopiridol, partially restored the arsenite-induced growth inhibition of human skin fibroblast cells. Thus, sodium arsenite may confer its cytotoxic effect partly through the aberrant activation of CDKs and the resultant perturbation of cell cycle progression. Together, we developed a high-throughput, SILAC-compatible, and MRM-based kinome profiling method and demonstrated that the method is powerful in deciphering the molecular modes of action of a widespread environmental toxicant. The method should be generally applicable for uncovering the cellular pathways triggered by other extracellular stimuli.

Application of Adenosine Triphosphate Affinity Probe and Scheduled Multiple-Reaction Monitoring Analysis for Profiling Global Kinome in Human Cells in Response to Arsenite Treatment

PubMed Central

2015-01-01

Phosphorylation of cellular components catalyzed by kinases plays important roles in cell signaling and proliferation. Quantitative assessment of perturbation in global kinome may provide crucial knowledge for elucidating the mechanisms underlying the cytotoxic effects of environmental toxicants. Here, we utilized an adenosine triphosphate (ATP) affinity probe coupled with stable isotope labeling by amino acids in cell culture (SILAC) to assess quantitatively the arsenite-induced alteration of global kinome in human cells. We constructed a SILAC-compatible kinome library for scheduled multiple-reaction monitoring (MRM) analysis and adopted on-the-fly recalibration of retention time shift, which provided better throughput of the analytical method and enabled the simultaneous quantification of the expression of ∼300 kinases in two LC-MRM runs. With this improved analytical method, we conducted an in-depth quantitative analysis of the perturbation of kinome of GM00637 human skin fibroblast cells induced by arsenite exposure. Several kinases involved in cell cycle progression, including cyclin-dependent kinases (CDK1 and CDK4) and Aurora kinases A, B, and C, were found to be hyperactivated, and the altered expression of CDK1 was further validated by Western analysis. In addition, treatment with a CDK inhibitor, flavopiridol, partially restored the arsenite-induced growth inhibition of human skin fibroblast cells. Thus, sodium arsenite may confer its cytotoxic effect partly through the aberrant activation of CDKs and the resultant perturbation of cell cycle progression. Together, we developed a high-throughput, SILAC-compatible, and MRM-based kinome profiling method and demonstrated that the method is powerful in deciphering the molecular modes of action of a widespread environmental toxicant. The method should be generally applicable for uncovering the cellular pathways triggered by other extracellular stimuli. PMID:25301106

Visual in vivo degradation of injectable hydrogel by real-time and non-invasive tracking using carbon nanodots as fluorescent indicator.

PubMed

Wang, Lei; Li, Baoqiang; Xu, Feng; Li, Ying; Xu, Zheheng; Wei, Daqing; Feng, Yujie; Wang, Yaming; Jia, Dechang; Zhou, Yu

2017-11-01

Visual in vivo degradation of hydrogel by fluorescence-related tracking and monitoring is crucial for quantitatively depicting the degradation profile of hydrogel in a real-time and non-invasive manner. However, the commonly used fluorescent imaging usually encounters limitations, such as intrinsic photobleaching of organic fluorophores and uncertain perturbation of degradation induced by the change in molecular structure of hydrogel. To address these problems, we employed photoluminescent carbon nanodots (CNDs) with low photobleaching, red emission and good biocompatibility as fluorescent indicator for real-time and non-invasive visual in vitro/in vivo degradation of injectable hydrogels that are mixed with CNDs. The in vitro/in vivo toxicity results suggested that CNDs were nontoxic. The embedded CNDs in hydrogels did not diffuse outside in the absence of hydrogel degradation. We had acquired similar degradation kinetics (PBS-Enzyme) between gravimetric and visual determination, and established mathematical equation to quantitatively depict in vitro degradation profile of hydrogels for the predication of in vivo hydrogel degradation. Based on the in vitro data, we developed a visual platform that could quantitatively depict in vivo degradation behavior of new injectable biomaterials by real-time and non-invasive fluorescence tracking. This fluorescence-related visual imaging methodology could be applied to subcutaneous degradation of injectable hydrogel with down to 7 mm depth in small animal trials so far. This fluorescence-related visual imaging methodology holds great potentials for rational design and convenient in vivo screening of biocompatible and biodegradable injectable hydrogels in tissue engineering. Copyright © 2017 Elsevier Ltd. All rights reserved.

IET. Control and equipment building (TAN620) sections. Depth and profile ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

IET. Control and equipment building (TAN-620) sections. Depth and profile of earthen shield tunnels. Ralph M. Parsons 902-4-ANP-620-A-321. Date: February 1954. INEEL index code no. 035-0620-00-693-106906 - Idaho National Engineering Laboratory, Test Area North, Scoville, Butte County, ID

Depth-resolved electronic structure of spintronic nanostructures and complex materials with soft and hard x-ray photoemission

NASA Astrophysics Data System (ADS)

Gray, Alexander

In this dissertation we describe several new directions in the field of x-ray photoelectron spectroscopy, with a particular focus on the enhancement and control of the depth sensitivity and selectivity of the measurement. Enhancement of the depth sensitivity is achieved by going to higher photon energies with hard x-ray excitation and taking advantage of the resulting larger electron inelastic mean-free paths. This novel approach provides a more accurate picture of bulk electronic structure, when compared to the traditional soft x-ray photoelectron spectroscopy (XPS) which, for some systems, may be too strongly influenced by surface effects. We present three case-studies wherein such hard x-ray photoelectron spectroscopy (HAXPES) in the multi-keV regime is used to probe the bulk properties of complex thin-film materials, which would be otherwise impossible to investigate using conventional soft x-ray XPS. Namely, (1) we directly observe the opening of a semiconducting gap in epitaxial Cr0.80Al0.20 alloy thin films and confirm this with theory, (2) we study the electronic and structural properties of near-Heusler FexSi1-x alloy thin films of various composition and degrees of crystallinity, and (3) we observe the Mott metal-to-insulator transition in the ultra-thin epitaxial LaNiO3 films via core-level and valence-band spectroscopies. By performing the experiments at the photon energy of 5.95 keV, the bulk-sensitivity of the measurements, characterized by the inelastic mean-free path of the photoemitted electrons, is enhanced by a factor of 4--7 compared to the conventional soft x-ray photoelectron spectroscopy. The experimental results are compared to calculations performed using various first-principle theoretical approaches, such as the density-functional theory and the one-step theory of photoemission. Furthermore, we present the first results of hard x-ray angle-resolved photoemission measurements (HARPES), at excitation energies of 3.24 and 5.95 keV. In a second aspect of this dissertation, depth selectivity is achieved by setting-up an x-ray standing wave field in the sample by growing it on a synthetic periodic multilayer mirror substrate, which in first-order Bragg reflection acts as the standing-wave generator. The antinodes of the standing wave function as "epicenters" for photoemission, and can be moved in the direction perpendicular to the sample surface by either scanning the incidence angle thetainc, or the photon energy through the Bragg condition. Alternatively, provided that one of the underlying layers in the structure is grown in a shape of a wedge with varying thickness, the standing wave can be scanned vertically though the sample simply by moving the sample laterally under the x-ray measurement spot. We present the first study in which the chemical and electronic-structure profiles of a magnetic tunnel junction La 0.7Sr0.3MnO3/SrTiO3 (LSMO/STO) have been quantitatively determined by a combination of soft and hard x-ray standing-wave excited photoemission. By comparing experiment to x-ray optical calculations, the detailed chemical profile of the constituent layers and their interfaces is quantitatively derived with Angstrom precision. Combined with core-hole multiplet theory incorporating Jahn-Teller distortion, these results indicate a change in the Mn bonding state near the LSMO/STO interface. Our results thus further clarify the reduced performance of LSMO/STO magnetic tunnel junction compared to ideal theoretical expectations. Finally, we demonstrate the addition of depth resolution to the usual two-dimensional images in photoelectron emission microscopy (PEEM) as a further aspect of standing-wave photoemission. We show that standing-wave excited photoelectron microscopy can be used to produce element-specific and depth-selective images of patterned samples. In conjunction with x-ray optical theoretical modeling, quantitative information about the depth-dependent chemical composition of the sample can be extracted from the photoemission data. The good agreement between our experimental results and model calculations suggests that future studies with better spatial and spectral resolution will also yield more detailed information about the interfacial regions. This addition of quantitative depth selectivity to the conventional laterally-resolved soft x-ray photoelectron emission microscopy thus should considerably enhance the capabilities of the PEEM as a research, development and metrology tool for science and industry. (Abstract shortened by UMI.)

Lidar Ratios for Dust Aerosols Derived From Retrievals of CALIPSO Visible Extinction Profiles Constrained by Optical Depths from MODIS-Aqua and CALIPSO/CloudSat Ocean Surface Reflectance Measurements

NASA Technical Reports Server (NTRS)

Young, Stuart A.; Josset, Damien B.; Vaughan, Mark A.

2010-01-01

CALIPSO's (Cloud Aerosol Lidar Infrared Pathfinder Satellite Observations) analysis algorithms generally require the use of tabulated values of the lidar ratio in order to retrieve aerosol extinction and optical depth from measured profiles of attenuated backscatter. However, for any given time or location, the lidar ratio for a given aerosol type can differ from the tabulated value. To gain some insight as to the extent of the variability, we here calculate the lidar ratio for dust aerosols using aerosol optical depth constraints from two sources. Daytime measurements are constrained using Level 2, Collection 5, 550-nm aerosol optical depth measurements made over the ocean by the MODIS (Moderate Resolution Imaging Spectroradiometer) on board the Aqua satellite, which flies in formation with CALIPSO. We also retrieve lidar ratios from night-time profiles constrained by aerosol column optical depths obtained by analysis of CALIPSO and CloudSat backscatter signals from the ocean surface.

Distribution and depth profiles of polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans, and polychlorinated biphenyls in sediment collected from offshore waters of Central Vietnam.

PubMed

Tri, Tran Manh; Anh, Hoang Quoc; Tham, Trinh Thi; Van Quy, Tran; Long, Nguyen Quang; Nhung, Dao Thi; Nakamura, Masafumi; Nishida, Masayo; Maeda, Yasuaki; Van Boi, Luu; Minh, Tu Binh

2016-05-15

Concentrations of PCBs and OCPs were measured in 35 surface sediment samples collected from offshore waters of Central Vietnam. The mean concentrations of PCBs, HCHs, and DDTs in surface sediments were 86.5, 37.0, and 44.5pgg(-1), respectively. Additionally, nine PCDDs, eleven PCDFs, and twelve dl-PCBs were also examined in 19 sediment core samples collected from five locations. Concentration of PCDDs, PCDFs, and dl-PCBs ranged from 200 to 460, 0.39 to 2.9, and 1.6 to 22pgg(-1), respectively. OCDD was detected at the highest concentration, ranged from 100 to 300pgg(-1). Generally, the concentrations of PCDD/Fs at shallower depths were higher, meanwhile the depth profiles of dl-PCBs in sediment cores were different than the depth profiles of PCDD/Fs. The results suggest that the pollution of PCBs might be from many different sources leading to the variation between depths. Copyright © 2016 Elsevier Ltd. All rights reserved.

QUANTITATIVE GENETIC ACTIVITY GRAPHICAL PROFILES FOR USE IN CHEMICAL EVALUATION

EPA Science Inventory

A graphic approach termed a Genetic Activity Profile (GAP) has been developed to display a matrix of data on the genetic and related effects of selected chemical agents. he profiles provide a visual overview of the quantitative (doses) and qualitative (test results) data for each...

Estimation of skin concentrations of topically applied lidocaine at each depth profile.

PubMed

Oshizaka, Takeshi; Kikuchi, Keisuke; Kadhum, Wesam R; Todo, Hiroaki; Hatanaka, Tomomi; Wierzba, Konstanty; Sugibayashi, Kenji

2014-11-20

Skin concentrations of topically administered compounds need to be considered in order to evaluate their efficacies and toxicities. This study investigated the relationship between the skin permeation and concentrations of compounds, and also predicted the skin concentrations of these compounds using their permeation parameters. Full-thickness skin or stripped skin from pig ears was set on a vertical-type diffusion cell, and lidocaine (LID) solution was applied to the stratum corneum (SC) in order to determine in vitro skin permeability. Permeation parameters were obtained based on Fick's second law of diffusion. LID concentrations at each depth of the SC were measured using tape-stripping. Concentration-depth profiles were obtained from viable epidermis and dermis (VED) by analyzing horizontal sections. The corresponding skin concentration at each depth was calculated based on Fick's law using permeation parameters and then compared with the observed value. The steady state LID concentrations decreased linearly as the site became deeper in SC or VED. The calculated concentration-depth profiles of the SC and VED were almost identical to the observed profiles. The compound concentration at each depth could be easily predicted in the skin using diffusion equations and skin permeation data. Thus, this method was considered to be useful for promoting the efficient preparation of topically applied drugs and cosmetics. Copyright © 2014 Elsevier B.V. All rights reserved.

Hyperspectral imaging to investigate the distribution of organic matter and iron down the soil profile

NASA Astrophysics Data System (ADS)

Hobley, Eleanor; Kriegs, Stefanie; Steffens, Markus

2017-04-01

Obtaining reliable and accurate data regarding the spatial distribution of different soil components is difficult due to issues related with sampling scale and resolution on the one hand and laboratory analysis on the other. When investigating the chemical composition of soil, studies frequently limit themselves to two dimensional characterisations, e.g. spatial variability near the surface or depth distribution down the profile, but rarely combine both approaches due to limitations to sampling and analytical capacities. Furthermore, when assessing depth distributions, samples are taken according to horizon or depth increments, resulting in a mixed sample across the sampling depth. Whilst this facilitates mean content estimation per depth increment and therefore reduces analytical costs, the sample information content with regards to heterogeneity within the profile is lost. Hyperspectral imaging can overcome these sampling limitations, yielding high resolution spectral data of down the soil profile, greatly enhancing the information content of the samples. This can then be used to augment horizontal spatial characterisation of a site, yielding three dimensional information into the distribution of spectral characteristics across a site and down the profile. Soil spectral characteristics are associated with specific chemical components of soil, such as soil organic matter or iron contents. By correlating the content of these soil components with their spectral behaviour, high resolution multi-dimensional analysis of soil chemical composition can be obtained. Here we present a hyperspectral approach to the characterisation of soil organic matter and iron down different soil profiles, outlining advantages and issues associated with the methodology.

Complementary Characterization of Cu(In,Ga)Se₂ Thin-Film Photovoltaic Cells Using Secondary Ion Mass Spectrometry, Auger Electron Spectroscopy, and Atom Probe Tomography.

PubMed

Jang, Yun Jung; Lee, Jihye; Jeong, Jeung-Hyun; Lee, Kang-Bong; Kim, Donghwan; Lee, Yeonhee

2018-05-01

To enhance the conversion performance of solar cells, a quantitative and depth-resolved elemental analysis of photovoltaic thin films is required. In this study, we determined the average concentration of the major elements (Cu, In, Ga, and Se) in fabricated Cu(In,Ga)Se2 (CIGS) thin films, using inductively coupled plasma atomic emission spectroscopy, X-ray fluorescence, and wavelengthdispersive electron probe microanalysis. Depth profiling results for CIGS thin films with different cell efficiencies were obtained using secondary ion mass spectrometry and Auger electron spectroscopy to compare the atomic concentrations. Atom probe tomography, a characterization technique with sub-nanometer resolution, was used to obtain three-dimensional elemental mapping and the compositional distribution at the grain boundaries (GBs). GBs are identified by Na increment accompanied by Cu depletion and In enrichment. Segregation of Na atoms along the GB had a beneficial effect on cell performance. Comparative analyses of different CIGS absorber layers using various analytical techniques provide us with understanding of the compositional distributions and structures of high efficiency CIGS thin films in solar cells.

Methodology and Estimates of Scour at Selected Bridge Sites in Alaska

USGS Publications Warehouse

Heinrichs, Thomas A.; Kennedy, Ben W.; Langley, Dustin E.; Burrows, Robert L.

2001-01-01

The U.S. Geological Survey estimated scour depths at 325 bridges in Alaska as part of a cooperative agreement with the Alaska Department of Transportation and Public Facilities. The department selected these sites from approximately 806 State-owned bridges as potentially susceptible to scour during extreme floods. Pier scour and contraction scour were computed for the selected bridges by using methods recommended by the Federal Highway Administration. The U.S. Geological Survey used a four-step procedure to estimate scour: (1) Compute magnitudes of the 100- and 500-year floods. (2) Determine cross-section geometry and hydraulic properties for each bridge site. (3) Compute the water-surface profile for the 100- and 500-year floods. (4) Compute contraction and pier scour. This procedure is unique because the cross sections were developed from existing data on file to make a quantitative estimate of scour. This screening method has the advantage of providing scour depths and bed elevations for comparison with bridge-foundation elevations without the time and expense of a field survey. Four examples of bridge-scour analyses are summarized in the appendix.

Reconstruction of radial thermal conductivity depth profile in case hardened steel rods

NASA Astrophysics Data System (ADS)

Celorrio, Ricardo; Mendioroz, Arantza; Apiñaniz, Estibaliz; Salazar, Agustín; Wang, Chinhua; Mandelis, Andreas

2009-04-01

In this work the surface thermal-wave field (ac temperature) of a solid cylinder illuminated by a modulated light beam is calculated first in two cases: a multilayered cylinder and a cylinder the radial thermal conductivity of which varies continuously. It is demonstrated numerically that, using a few layers of different thicknesses, the surface thermal-wave field of a cylindrical sample with continuously varying radial thermal conductivity can be calculated with high accuracy. Next, an inverse procedure based on the multilayered model is used to reconstruct the radial thermal conductivity profile of hardened C1018 steel rods, the surface temperature of which was measured by photothermal radiometry. The reconstructed thermal conductivity depth profile has a similar shape to those found for flat samples of this material and shows a qualitative anticorrelation with the hardness depth profile.

Ultra-Shallow Depth Profiling of Arsenic Implants in Silicon by Hydride Generation-Inductively Coupled Plasma Atomic Emission Spectrometry

NASA Astrophysics Data System (ADS)

Matsubara, Atsuko; Kojima, Hisao; Itoga, Toshihiko; Kanehori, Keiichi

1995-08-01

High resolution depth profiling of arsenic (As) implanted into silicon wafers by a chemical technique is described. Silicon wafers are precisely etched through repeated oxidation by hydrogen peroxide solution and dissolution of the oxide by hydrofluoric acid solution. The etched silicon thickness is determined by inductively-coupled plasma atomic emission spectrometry (ICP-AES). Arsenic concentration is determined by hydride generation ICP-AES (HG-ICP-AES) with prereduction using potassium iodide. The detection limit of As in a 4-inch silicon wafer is 2.4×1018 atoms/cm3. The etched silicon thickness is controlled to less than 4±2 atomic layers. Depth profiling of an ultra-shallow As diffusion layer with the proposed method shows good agreement with profiling using the four-probe method or secondary ion mass spectrometry.

A porewater - based stable isotope approach for the investigation of subsurface hydrological processes

NASA Astrophysics Data System (ADS)

Garvelmann, J.; Külls, C.; Weiler, M.

2011-10-01

Predicting and understanding subsurface flowpaths is still a crucial issue in hydrological research. We present an experimental approach to reveal present and past subsurface flowpaths of water in the unsaturated and saturated zone. Two hillslopes in a humid moutainous catchment have been investigated. The H2O(liquid) - H2O(vapor) equilibration laser spectroscopy method was used to obtain high resolution δ2H vertical depth profiles of porewater at various points along a fall line of a pasture hillslope in the southern Black Forest, Germany. The Porewater Stable Isotope Profile (PSIP) approach was developed to use the integrated information of several vertical depth profiles of deuterium along two transects at the hillslopes. Different shapes of depth profiles were observed in relation to hillslope position. The statistical variability (inter-quartile range and standard deviation) of each profile was used to characterize different types of depth profiles. The profiles upslope or with a weak affinity for saturation as indicated by a low topographic wetness index preserve the isotopic input signal by precipitation with a distinct seasonal variability. These observations indicate mainly vertical movement of soil water in the upper part of the hillslope before sampling. The profiles downslope or at locations with a strong affinity for saturation do not show a similar seasonal isotopic signal. The input signal is erased in the foothills and a large proportion of pore water samples are close to the isotopic values of δ2H in stream water during base flow. Near the stream indications for efficient mixing of water from lateral subsurface flow paths with vertical percolation are found.

Geophysical and Chemical Weathering Signatures Across the Deep Weathered-Unweathered Granite Boundary of the Calhoun Critical Zone Observatory

NASA Astrophysics Data System (ADS)

Richter, D., Jr.; Bacon, A. R.; Brantley, S. L.; Holbrook, W. S.

2015-12-01

To understand the relationship between geophysical measurements and chemical weathering at Earth's surface, we combine comprehensive chemical and physical analyses of a 70-m granite weathering profile in the Southern Piedmont in the southeastern United States. The research site is in the uplands of the Calhoun Critical Zone Observatory and is similar to many geomorphically stable, ancient, and highly-weathered Ultisol soils of the region. Surface and downhole geophysical analyses suggest significant physical changes to depths of about 40 m, where geophysical properties are consistent with competent and unweathered granite. At this depth, surface refraction velocities increase to >4.5 km/s; variations in downhole sonic velocities decrease by more than two-fold; and deviations in the downhole caliper log sharply decrease as well. Forty meters depth is also the depth of initiation of plagioclase feldspar weathering, as inferred from bulk geochemical measurement of the full 70-m deep core. Specifically, element-depth profiles, cast as mass transfer coefficient profiles using Ti and Zr as immobile elements, document inferred loss of plagioclase in the depth interval between 15 and 40-m depth. Plagioclase feldspar is the most abundant of the highly reactive minerals in the granite. Such a wide reaction front is characteristic of weathering granites. Some loss of K is observed at these depths but most K loss, as well as Mg loss, occurs at shallower depths. Nearby geophysical profiles and 3D stress models have been interpreted as showing that seismic velocities decrease at 40 m depth due to opening of fractures as rock is exhumed toward the surface. Given our interpretations of both the geochemical and geophysical data, we infer that the onset of chemical weathering of feldspar coincides with the opening of these fractures. The data highlight the ability of geochemistry and geophysics to complement each other and enrich our understanding of Earth's Critical Zone.

Elemental depth profiling in transparent conducting oxide thin film by X-ray reflectivity and grazing incidence X-ray fluorescence combined analysis

NASA Astrophysics Data System (ADS)

Rotella, H.; Caby, B.; Ménesguen, Y.; Mazel, Y.; Valla, A.; Ingerle, D.; Detlefs, B.; Lépy, M.-C.; Novikova, A.; Rodriguez, G.; Streli, C.; Nolot, E.

2017-09-01

The optical and electrical properties of transparent conducting oxide (TCO) thin films are strongly linked with the structural and chemical properties such as elemental depth profile. In R&D environments, the development of non-destructive characterization techniques to probe the composition over the depth of deposited films is thus necessary. The combination of Grazing-Incidence X-ray Fluorescence (GIXRF) and X-ray reflectometry (XRR) is emerging as a fab-compatible solution for the measurement of thickness, density and elemental profile in complex stacks. Based on the same formalism, both techniques can be implemented on the same experimental set-up and the analysis can be combined in a single software in order to refine the sample model. While XRR is sensitive to the electronic density profile, GIXRF is sensitive to the atomic density (i. e. the elemental depth profile). The combination of both techniques allows to get simultaneous information about structural properties (thickness and roughness) as well as the chemical properties. In this study, we performed a XRR-GIXRF combined analysis on indium-free TCO thin films (Ga doped ZnO compound) in order to correlate the optical properties of the films with the elemental distribution of Ga dopant over the thickness. The variation of optical properties due to annealing process were probed by spectroscopic ellipsometry measurements. We studied the evolution of atomic profiles before and after annealing process. We show that the blue shift of the band gap in the optical absorption edge is linked to a homogenization of the atomic profiles of Ga and Zn over the layer after the annealing. This work demonstrates that the combination of the techniques gives insight into the material composition and makes the XRR-GIXRF combined analysis a promising technique for elemental depth profiling.

Estimating surface visibility at Hong Kong from ground-based LIDAR, sun photometer and operational MODIS products.

PubMed

Shahzad, Muhammad I; Nichol, Janet E; Wang, Jun; Campbell, James R; Chan, Pak W

2013-09-01

Hong Kong's surface visibility has decreased in recent years due to air pollution from rapid social and economic development in the region. In addition to deteriorating health standards, reduced visibility disrupts routine civil and public operations, most notably transportation and aviation. Regional estimates of visibility solved operationally using available ground and satellite-based estimates of aerosol optical properties and vertical distribution may prove more effective than standard reliance on a few existing surface visibility monitoring stations. Previous studies have demonstrated that such satellite measurements correlate well with near-surface optical properties, despite these sensors do not consider range-resolved information and indirect parameterizations necessary to solve relevant parameters. By expanding such analysis to include vertically resolved aerosol profile information from an autonomous ground-based lidar instrument, this work develops six models for automated assessment of surface visibility. Regional visibility is estimated using co-incident ground-based lidar, sun photometer visibility meter and MODerate-resolution maging Spectroradiometer (MODIS) aerosol optical depth data sets. Using a 355 nm extinction coefficient profile solved from the lidar MODIS AOD (aerosol optical depth) is scaled down to the surface to generate a regional composite depiction of surface visibility. These results demonstrate the potential for applying passive satellite depictions of broad-scale aerosol optical properties together with a ground-based surface lidar and zenith-viewing sun photometer for improving quantitative assessments of visibility in a city such as Hong Kong.

Object Recognition in Flight: How Do Bees Distinguish between 3D Shapes?

PubMed Central

Werner, Annette; Stürzl, Wolfgang; Zanker, Johannes

2016-01-01

Honeybees (Apis mellifera) discriminate multiple object features such as colour, pattern and 2D shape, but it remains unknown whether and how bees recover three-dimensional shape. Here we show that bees can recognize objects by their three-dimensional form, whereby they employ an active strategy to uncover the depth profiles. We trained individual, free flying honeybees to collect sugar water from small three-dimensional objects made of styrofoam (sphere, cylinder, cuboids) or folded paper (convex, concave, planar) and found that bees can easily discriminate between these stimuli. We also tested possible strategies employed by the bees to uncover the depth profiles. For the card stimuli, we excluded overall shape and pictorial features (shading, texture gradients) as cues for discrimination. Lacking sufficient stereo vision, bees are known to use speed gradients in optic flow to detect edges; could the bees apply this strategy also to recover the fine details of a surface depth profile? Analysing the bees’ flight tracks in front of the stimuli revealed specific combinations of flight maneuvers (lateral translations in combination with yaw rotations), which are particularly suitable to extract depth cues from motion parallax. We modelled the generated optic flow and found characteristic patterns of angular displacement corresponding to the depth profiles of our stimuli: optic flow patterns from pure translations successfully recovered depth relations from the magnitude of angular displacements, additional rotation provided robust depth information based on the direction of the displacements; thus, the bees flight maneuvers may reflect an optimized visuo-motor strategy to extract depth structure from motion signals. The robustness and simplicity of this strategy offers an efficient solution for 3D-object-recognition without stereo vision, and could be employed by other flying insects, or mobile robots. PMID:26886006

Object Recognition in Flight: How Do Bees Distinguish between 3D Shapes?

PubMed

Werner, Annette; Stürzl, Wolfgang; Zanker, Johannes

2016-01-01

Honeybees (Apis mellifera) discriminate multiple object features such as colour, pattern and 2D shape, but it remains unknown whether and how bees recover three-dimensional shape. Here we show that bees can recognize objects by their three-dimensional form, whereby they employ an active strategy to uncover the depth profiles. We trained individual, free flying honeybees to collect sugar water from small three-dimensional objects made of styrofoam (sphere, cylinder, cuboids) or folded paper (convex, concave, planar) and found that bees can easily discriminate between these stimuli. We also tested possible strategies employed by the bees to uncover the depth profiles. For the card stimuli, we excluded overall shape and pictorial features (shading, texture gradients) as cues for discrimination. Lacking sufficient stereo vision, bees are known to use speed gradients in optic flow to detect edges; could the bees apply this strategy also to recover the fine details of a surface depth profile? Analysing the bees' flight tracks in front of the stimuli revealed specific combinations of flight maneuvers (lateral translations in combination with yaw rotations), which are particularly suitable to extract depth cues from motion parallax. We modelled the generated optic flow and found characteristic patterns of angular displacement corresponding to the depth profiles of our stimuli: optic flow patterns from pure translations successfully recovered depth relations from the magnitude of angular displacements, additional rotation provided robust depth information based on the direction of the displacements; thus, the bees flight maneuvers may reflect an optimized visuo-motor strategy to extract depth structure from motion signals. The robustness and simplicity of this strategy offers an efficient solution for 3D-object-recognition without stereo vision, and could be employed by other flying insects, or mobile robots.

Episodic thermal perturbations associated with groundwater flow: An example from Kilauea Volcano, Hawaii

USGS Publications Warehouse

Hurwitz, S.; Ingebritsen, S.E.; Sorey, M.L.

2002-01-01

Temperature measurements in deep drill holes on volcano summits or upper flanks allow a quantitative analysis of groundwater induced heat transport within the edifice. We present a new temperature-depth profile from a deep well on the summit of Kilauea Volcano, Hawaii, and analyze it in conjunction with a temperature profile measured 26 years earlier. We propose two groundwater flow models to interpret the complex temperature profiles. The first is a modified confined lateral flow model (CLFM) with a continuous flux of hydrothermal fluid. In the second, transient flow model (TFM), slow conductive cooling follows a brief, advective heating event. We carry out numerical simulations to examine the timescales associated with each of the models. Results for both models are sensitive to the initial conditions, and with realistic initial conditions it takes between 750 and 1000 simulation years for either model to match the measured temperature profiles. With somewhat hotter initial conditions, results are consistent with onset of a hydrothermal plume ???550 years ago, coincident with initiation of caldera subsidence. We show that the TFM is consistent with other data from hydrothermal systems and laboratory experiments and perhaps is more appropriate for this highly dynamic environment. The TFM implies that volcano-hydrothermal systems may be dominated by episodic events and that thermal perturbations may persist for several thousand years after hydrothermal flow has ceased.

Fire debris analysis for forensic fire investigation using laser induced breakdown spectroscopy (LIBS)

NASA Astrophysics Data System (ADS)

Choi, Soojin; Yoh, Jack J.

2017-08-01

The possibility verification of the first attempt to apply LIBS to arson investigation was performed. LIBS has capabilities for real time in-situ analysis and depth profiling. It can provide valuable information about the fire debris that are complementary to the classification of original sample components and combustion residues. In this study, fire debris was analyzed to determine the ignition source and existence of a fire accelerant using LIBS spectra and depth profiling analysis. Fire debris chemical composition and carbon layer thickness determines the possible ignition source while the carbon layer thickness of combusted samples represents the degree of sample carbonization. When a sample is combusted with fire accelerants, a thicker carbon layer is formed because the burning rate is increased. Therefore, depth profiling can confirm the existence of combustion accelerants, which is evidence of arson. Also investigation of fire debris by depth profiling is still possible when a fire is extinguished with water from fire hose. Such data analysis and in-situ detection of forensic signals via the LIBS may assist fire investigation at crime scenes.

Defining the ecologically relevant mixed-layer depth for Antarctica's coastal seas

NASA Astrophysics Data System (ADS)

Carvalho, Filipa; Kohut, Josh; Oliver, Matthew J.; Schofield, Oscar

2017-01-01

Mixed-layer depth (MLD) has been widely linked to phytoplankton dynamics in Antarctica's coastal regions; however, inconsistent definitions have made intercomparisons among region-specific studies difficult. Using a data set with over 20,000 water column profiles corresponding to 32 Slocum glider deployments in three coastal Antarctic regions (Ross Sea, Amundsen Sea, and West Antarctic Peninsula), we evaluated the relationship between MLD and phytoplankton vertical distribution. Comparisons of these MLD estimates to an applied definition of phytoplankton bloom depth, as defined by the deepest inflection point in the chlorophyll profile, show that the maximum of buoyancy frequency is a good proxy for an ecologically relevant MLD. A quality index is used to filter profiles where MLD is not determined. Despite the different regional physical settings, we found that the MLD definition based on the maximum of buoyancy frequency best describes the depth to which phytoplankton can be mixed in Antarctica's coastal seas.

Crack depth profiling using guided wave angle dependent reflectivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Volker, Arno, E-mail: arno.volker@tno.nl; Pahlavan, Lotfollah, E-mail: arno.volker@tno.nl; Blacquiere, Gerrit, E-mail: arno.volker@tno.nl

2015-03-31

Tomographic corrosion monitoring techniques have been developed, using two rings of sensors around the circumference of a pipe. This technique is capable of providing a detailed wall thickness map, however this might not be the only type of structural damage. Therefore this concept is expanded to detect and size cracks and small corrosion defects like root corrosion. The expanded concept uses two arrays of guided-wave transducers, collecting both reflection and transmission data. The data is processed such that the angle-dependent reflectivity is obtained without using a baseline signal of a defect-free situation. The angle-dependent reflectivity is the input of anmore » inversion scheme that calculates a crack depth profile. From this profile, the depth and length of the crack can be determined. Preliminary experiments show encouraging results. The depth sizing accuracy is in the order of 0.5 mm.« less

OCT structure, COB location and magmatic type of the S Angolan & SE Brazilian margins from integrated quantitative analysis of deep seismic reflection and gravity anomaly data

NASA Astrophysics Data System (ADS)

Cowie, Leanne; Kusznir, Nick; Horn, Brian

2014-05-01

Integrated quantitative analysis using deep seismic reflection data and gravity inversion have been applied to the S Angolan and SE Brazilian margins to determine OCT structure, COB location and magmatic type. Knowledge of these margin parameters are of critical importance for understanding rifted continental margin formation processes and in evaluating petroleum systems in deep-water frontier oil and gas exploration. The OCT structure, COB location and magmatic type of the S Angolan and SE Brazilian rifted continental margins are much debated; exhumed and serpentinised mantle have been reported at these margins. Gravity anomaly inversion, incorporating a lithosphere thermal gravity anomaly correction, has been used to determine Moho depth, crustal basement thickness and continental lithosphere thinning. Residual Depth Anomaly (RDA) analysis has been used to investigate OCT bathymetric anomalies with respect to expected oceanic bathymetries and subsidence analysis has been used to determine the distribution of continental lithosphere thinning. These techniques have been validated for profiles Lusigal 12 and ISE-01 on the Iberian margin. In addition a joint inversion technique using deep seismic reflection and gravity anomaly data has been applied to the ION-GXT BS1-575 SE Brazil and ION-GXT CS1-2400 S Angola deep seismic reflection lines. The joint inversion method solves for coincident seismic and gravity Moho in the time domain and calculates the lateral variations in crustal basement densities and velocities along the seismic profiles. Gravity inversion, RDA and subsidence analysis along the ION-GXT BS1-575 profile, which crosses the Sao Paulo Plateau and Florianopolis Ridge of the SE Brazilian margin, predict the COB to be located SE of the Florianopolis Ridge. Integrated quantitative analysis shows no evidence for exhumed mantle on this margin profile. The joint inversion technique predicts oceanic crustal thicknesses of between 7 and 8 km thickness with normal oceanic basement seismic velocities and densities. Beneath the Sao Paulo Plateau and Florianopolis Ridge, joint inversion predicts crustal basement thicknesses between 10-15km with high values of basement density and seismic velocities under the Sao Paulo Plateau which are interpreted as indicating a significant magmatic component within the crustal basement. The Sao Paulo Plateau and Florianopolis Ridge are separated by a thin region of crustal basement beneath the salt interpreted as a regional transtensional structure. Sediment corrected RDAs and gravity derived "synthetic" RDAs are of a similar magnitude on oceanic crust, implying negligible mantle dynamic topography. Gravity inversion, RDA and subsidence analysis along the S Angolan ION-GXT CS1-2400 profile suggests that exhumed mantle, corresponding to a magma poor margin, is absent..The thickness of earliest oceanic crust, derived from gravity and deep seismic reflection data, is approximately 7km consistent with the global average oceanic crustal thicknesses. The joint inversion predicts a small difference between oceanic and continental crustal basement density and seismic velocity, with the change in basement density and velocity corresponding to the COB independently determined from RDA and subsidence analysis. The difference between the sediment corrected RDA and that predicted from gravity inversion crustal thickness variation implies that this margin is experiencing approximately 500m of anomalous uplift attributed to mantle dynamic uplift.

SU-E-T-614: Derivation of Equations to Define Inflection Points and Its Analysis in Flattening Filter Free Photon Beams Based On the Principle of Polynomial function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muralidhar, K Raja; Komanduri, K

2014-06-01

Purpose: The objective of this work is to present a mechanism for calculating inflection points on profiles at various depths and field sizes and also a significant study on the percentage of doses at the inflection points for various field sizes and depths for 6XFFF and 10XFFF energy profiles. Methods: Graphical representation was done on Percentage of dose versus Inflection points. Also using the polynomial function, the authors formulated equations for calculating spot-on inflection point on the profiles for 6X FFF and 10X FFF energies for all field sizes and at various depths. Results: In a flattening filter free radiationmore » beam which is not like in Flattened beams, the dose at inflection point of the profile decreases as field size increases for 10XFFF. Whereas in 6XFFF, the dose at the inflection point initially increases up to 10x10cm2 and then decreases. The polynomial function was fitted for both FFF beams for all field sizes and depths. For small fields less than 5x5 cm2 the inflection point and FWHM are almost same and hence analysis can be done just like in FF beams. A change in 10% of dose can change the field width by 1mm. Conclusion: The present study, Derivative of equations based on the polynomial equation to define inflection point concept is precise and accurate way to derive the inflection point dose on any FFF beam profile at any depth with less than 1% accuracy. Corrections can be done in future studies based on the multiple number of machine data. Also a brief study was done to evaluate the inflection point positions with respect to dose in FFF energies for various field sizes and depths for 6XFFF and 10XFFF energy profiles.« less

Use of glancing angle X-ray powder diffractometry to depth-profile phase transformations during dissolution of indomethacin and theophylline tablets.

PubMed

Debnath, Smita; Predecki, Paul; Suryanarayanan, Raj

2004-01-01

The purpose of this study was (i) to develop glancing angle x-ray powder diffractometry (XRD) as a method for profiling phase transformations as a function of tablet depth; and (ii) to apply this technique to (a) study indomethacin crystallization during dissolution of partially amorphous indomethacin tablets and to (b) profile anhydrate --> hydrate transformations during dissolution of theophylline tablets. The intrinsic dissolution rates of indomethacin and theophylline were determined after different pharmaceutical processing steps. Phase transformations during dissolution were evaluated by various techniques. Transformation in the bulk and on the tablet surface was characterized by conventional XRD and scanning electron microscopy, respectively. Glancing angle XRD enabled us to profile these transformations as a function of depth from the tablet surface. Pharmaceutical processing resulted in a decrease in crystallinity of both indomethacin and theophylline. When placed in contact with the dissolution medium, while indomethacin recrystallized, theophylline anhydrate rapidly converted to theophylline monohydrate. Due to intimate contact with the dissolution medium, drug transformation occurred to a greater extent at or near the tablet surface. Glancing angle XRD enabled us to depth profile the extent of phase transformations as a function of the distance from the tablet surface. The processed sample (both indomethacin and theophylline) transformed more rapidly than did the corresponding unprocessed drug. Several challenges associated with the glancing angle technique, that is, the effects of sorbed water, phase transformations during the experimental timescale, and the influence of phase transformation on penetration depth, were addressed. Increased solubility, and consequently dissolution rate, is one of the potential advantages of metastable phases. This advantage is negated if, during dissolution, the metastable to stable transformation rate > dissolution rate. Glancing angle XRD enabled us to quantify and thereby profile phase transformations as a function of compact depth. The technique has potential utility in monitoring surface reactions, both chemical decomposition and physical transformations, in pharmaceutical systems.

CBCL Pediatric Bipolar Disorder Profile and ADHD: Comorbidity and Quantitative Trait Loci Analysis

ERIC Educational Resources Information Center

McGough, James J.; Loo, Sandra K.; McCracken, James T.; Dang, Jeffery; Clark, Shaunna; Nelson, Stanley F.; Smalley, Susan L.

2008-01-01

The pediatric bipolar disorder profile of the Child Behavior checklist is used to differentiate patterns of comorbidity and to search for quantitative trait loci in multiple affected ADHD sibling pairs. The CBCL-PBD profiling identified 8 percent of individuals with severe psychopathology and increased rates of oppositional defiant, conduct and…

LOGISTIC FUNCTION PROFILE FIT: A least-squares program for fitting interface profiles to an extended logistic function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirchhoff, William H.

2012-09-15

The extended logistic function provides a physically reasonable description of interfaces such as depth profiles or line scans of surface topological or compositional features. It describes these interfaces with the minimum number of parameters, namely, position, width, and asymmetry. Logistic Function Profile Fit (LFPF) is a robust, least-squares fitting program in which the nonlinear extended logistic function is linearized by a Taylor series expansion (equivalent to a Newton-Raphson approach) with no apparent introduction of bias in the analysis. The program provides reliable confidence limits for the parameters when systematic errors are minimal and provides a display of the residuals frommore » the fit for the detection of systematic errors. The program will aid researchers in applying ASTM E1636-10, 'Standard practice for analytically describing sputter-depth-profile and linescan-profile data by an extended logistic function,' and may also prove useful in applying ISO 18516: 2006, 'Surface chemical analysis-Auger electron spectroscopy and x-ray photoelectron spectroscopy-determination of lateral resolution.' Examples are given of LFPF fits to a secondary ion mass spectrometry depth profile, an Auger surface line scan, and synthetic data generated to exhibit known systematic errors for examining the significance of such errors to the extrapolation of partial profiles.« less

Quantitative determination of sulfur content in concrete with laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Weritz, F.; Ryahi, S.; Schaurich, D.; Taffe, A.; Wilsch, G.

2005-08-01

Laser-induced breakdown spectroscopy has been employed for the investigation of the sulfur content of concrete. Sulfur compounds are a natural but minor component in building materials. The ingress of sulfates or sulfuric acid constitutes a major risk of chemical aggression for concrete. There is a need for a fast method, which can be used on-site and is able to investigate a wide range of different measuring points, so that damages can be characterized. For quantitative determination the sulfur spectral line at 921.3 nm is used. The optimum ambient atmosphere has been determined by comparison of measurements accomplished under air, argon and helium atmosphere. Reference samples have been produced and calibration curves have been determined, the results of LIBS measurements are compared with results from chemical analysis. Defining a limit for the intensity ratio of a calcium and a oxygen spectral line can reduce the influence of the heterogeneity of the material, so that only spectra with a high amount of cementitious material are evaluated. Depth profiles and spatial resolved sulfur distributions are presented measured on concrete cores originating from a highly sulfate contaminated clarifier.

Laser depth profiling of diffusion and alpha ejection profiles in Durango apatite: testing the fundamental parameters of apatite (U-Th)/He dating

NASA Astrophysics Data System (ADS)

van Soest, M. C.; Monteleone, B. D.; Boyce, J. W.; Hodges, K.

2009-12-01

Since its development (e.g. Zeitler et al., 1987, Lippolt et al., 1994, Farley et al., 1996, Wolf et al., 1996) as a viable low temperature thermochronological method (U-Th)/He dating of apatite has become a popular and widely applied low temperature thermochronometer. The method has been applied with success to a great variety of geological problems, and the fundamental parameters of the method: the bulk diffusion parameters of helium in apatite, and the calculated theoretical helium stopping distance in apatite used to correct the ages for the effects of alpha ejection appear sound. However, the development of the UV laser microprobe technique for the (U-Th)/He method (Boyce et al., 2006) allows for in-situ testing of the helium bulk diffusion parameters (Farley, 2000) and can provide a direct measurement of the alpha ejection distance in apatite. So, with the ultimate goal of further developing the in-situ (U-Th)/He dating method and micro-analytical depth profiling techniques to constrain cooling histories in natural grains, we conducted a helium depth profiling study of induced diffusion and natural alpha ejection profiles in Durango apatite. For the diffusion depth profiling, a Durango crystal was cut in slabs oriented parallel and perpendicular to the crystal c-axis. The slabs were polished and heated using different temperature and time schedules to induce predictable diffusion profiles based on the bulk helium diffusion parameters in apatite. Depth profiling of the 4He diffusion profiles was done using an ArF excimer laser. The measured diffusion depth profiles at 350°, 400°, and 450° C coincide well with the predicted bulk diffusion curves, independent of slab orientation, but the 300° C profiles consistently deviate significantly. The possible cause for this deviation is currently being investigated. Alpha ejection profiling was carried out on crystal margins from two different Durango apatite crystals, several faces from each crystal were analyzed to evaluate the potential effects of crystallographic orientation on alpha ejection. The results from both crystals were very reproducible irrespective of crystal surface used and confirm the findings of Monteleone et al. (2008) that the measured alpha ejection profiles deviate significantly from and are shorter than the calculated theoretical average value. Efforts are currently underway to better constrain the measured alpha ejection distance and measure alpha ejection profiles in apatite crystals other than Durango apatite. References: Boyce, J. et al. (2006) GCA 70, pp. 3031-3039. Farley, K. et al. (1996) GCA 60, pp. 4223-4229. Farley, K. (2006) JGR SE 105, p. 2903-2914. Lippolt, H. et al. (1994) Chem Geol 112, pp. 179-191. Monteleone, B. et al. (2008) Eos Trans AGU, 89 Fall Meeting V53B-2162. Wolf, R. et al. (1996) GCA 60, pp. 4231-4240. Zeitler, P. et al. (1987) GCA 51, pp. 2865-2868.

Vertical Profiles of Light-Absorbing Aerosol: A Combination of In-situ and AERONET Observations during NASA DISCOVER-AQ

NASA Astrophysics Data System (ADS)

Ziemba, L. D.; Beyersdorf, A. J.; Chen, G.; Corr, C.; Crumeyrolle, S.; Giles, D. M.; Holben, B. N.; Hudgins, C.; Martin, R.; Moore, R.; Shook, M.; Thornhill, K. L., II; Winstead, E.; Anderson, B. E.

2014-12-01

Understanding the vertical profile of atmospheric aerosols plays a vital role in utilizing spaceborne, column-integrated satellite observations. The properties and distribution of light-absorbing aerosol are particularly uncertain despite significant air quality and climate ramifications. Advanced retrieval algorithms are able to derive complex aerosol properties (e.g., wavelength-dependent absorption coefficient and single scattering albedo) from remote-sensing measurements, but quantitative relationships to surface conditions remain a challenge. Highly systematic atmospheric profiling during four unique deployments for the NASA DISCOVER-AQ project (Baltimore, MD, 2011; San Joaquin Valley, CA, 2013; Houston, TX, 2013; Denver, CO, 2014) allow statistical assessment of spatial, temporal, and source-related variability for light-absorbing aerosol properties in these distinct regions. In-situ sampling in conjunction with a dense network of AERONET sensors also allows evaluation of the sensitivity, limitations, and advantages of remote-sensing data products over a wide range of conditions. In-situ aerosol and gas-phase observations were made during DISCOVER-AQ aboard the NASA P-3B aircraft. Aerosol absorption coefficients were measured by a Particle Soot Absorption Photometer (PSAP). Approximately 200 profiles for each of the four deployments were obtained, from the surface (25-300m altitude) to 5 km, and are used to calculate absorption aerosol optical depths (AAODs). These are quantitatively compared to AAOD derived from AERONET Level 1.5 retrievals to 1) explore discrepancies between measurements, 2) quantify the fraction of AAOD that exists directly at the surface and is often missed by airborne sampling, and 3) evaluate the potential for deriving ground-level black carbon (BC) concentrations for air quality prediction. Aerosol size distributions are used to assess absorption contributions from mineral dust, both at the surface and aloft. SP2 (Single Particle Soot Photometer) mixing state and coating thickness analyses will be explored to explain in-situ/AERONET discrepancies, and ground-based absorption coefficient and BC-mass observations will be utilized whenever possible to fully obtain the true absorption vertical profile.

Calculation of effective penetration depth in X-ray diffraction for pharmaceutical solids.

PubMed

Liu, Jodi; Saw, Robert E; Kiang, Y-H

2010-09-01

The use of the glancing incidence X-ray diffraction configuration to depth profile surface phase transformations is of interest to pharmaceutical scientists. The Parratt equation has been used to depth profile phase changes in pharmaceutical compacts. However, it was derived to calculate 1/e penetration at glancing incident angles slightly below the critical angle of condensed matter and is, therefore, applicable to surface studies of materials such as single crystalline nanorods and metal thin films. When the depth of interest is 50-200 microm into the surface, which is typical for pharmaceutical solids, the 1/e penetration depth, or skin depth, can be directly calculated from an exponential absorption law without utilizing the Parratt equation. In this work, we developed a more relevant method to define X-ray penetration depth based on the signal detection limits of the X-ray diffractometer. Our definition of effective penetration depth was empirically verified using bilayer compacts of varying known thicknesses of mannitol and lactose.

NanoSIMS Imaging Alternation Layers of a Leached SON68 Glass Via A FIB-made Wedged Crater

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yi-Chung; Schreiber, Daniel K.; Neeway, James J.

2014-11-01

Currently, nuclear wastes are commonly immobilized into glasses because of their long-term durability. Exposure to water for long periods of time, however, will eventually corrode the waste form and is the leading potential avenue for radionuclide release into the environment. Because such slow processes cannot be experimentally tested, the prediction of release requires a thorough understanding the mechanisms governing glass corrosion. In addition, due to the exceptional durability of glass, much of the testing must be performed on high-surface-area powders. A technique that can provide accurate compositional profiles with very precise depth resolution for non-flat samples would be a majormore » benefit to the field. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling is an excellent tool that has long been used to examine corrosion layers of glass. The roughness of the buried corrosion layers, however, causes the corresponding SIMS depth profiles to exhibit erroneously wide interfaces. In this study, NanoSIMS was used to image the cross-section of the corrosion layers of a leached SON68 glass sample. A wedged crater was prepared by a focused ion beam (FIB) instrument to obtain a 5× improvement in depth resolution for NanoSIMS measurements. This increase in resolution allowed us to confirm that the breakdown of the silica glass network is further from the pristine glass than a second dissolution front for boron, another glass former. The existence of these two distinct interfaces, separated by only ~20 nm distance in depth, was not apparent by traditional ToF-SIMS depth profiling but has been confirmed also by atom probe tomography. This novel sample geometry will be a major benefit to efficient NanoSIMS sampling of irregular interfaces at the nanometer scale that would otherwise be obscured within ToF-SIMS depth profiles.« less

Measurements of Raman crystallinity profiles in thin-film microcrystalline silicon solar cells

NASA Astrophysics Data System (ADS)

Choong, G.; Vallat-Sauvain, E.; Multone, X.; Fesquet, L.; Kroll, U.; Meier, J.

2013-06-01

Wedge-polished thin film microcrystalline silicon solar cells are prepared and used for micro-Raman measurements. Thereby, the variations of the Raman crystallinity with depth are accessed easily. Depth resolution limits of the measurement set-up are established and calculations evidencing the role of optical limits are presented. Due to this new technique, Raman crystallinity profiles of two microcrystalline silicon cells give first hints for the optimization of the profile leading to improved electrical performance of such devices.

Sharing the slope: depth partitioning of agariciid corals and associated Symbiodinium across shallow and mesophotic habitats (2-60 m) on a Caribbean reef

PubMed Central

2013-01-01

Background Scleractinian corals and their algal endosymbionts (genus Symbiodinium) exhibit distinct bathymetric distributions on coral reefs. Yet, few studies have assessed the evolutionary context of these ecological distributions by exploring the genetic diversity of closely related coral species and their associated Symbiodinium over large depth ranges. Here we assess the distribution and genetic diversity of five agariciid coral species (Agaricia humilis, A. agaricites, A. lamarcki, A. grahamae, and Helioseris cucullata) and their algal endosymbionts (Symbiodinium) across a large depth gradient (2-60 m) covering shallow to mesophotic depths on a Caribbean reef. Results The five agariciid species exhibited distinct depth distributions, and dominant Symbiodinium associations were found to be species-specific, with each of the agariciid species harbouring a distinct ITS2-DGGE profile (except for a shared profile between A. lamarcki and A. grahamae). Only A. lamarcki harboured different Symbiodinium types across its depth distribution (i.e. exhibited symbiont zonation). Phylogenetic analysis (atp6) of the coral hosts demonstrated a division of the Agaricia genus into two major lineages that correspond to their bathymetric distribution (“shallow”: A. humilis / A. agaricites and “deep”: A. lamarcki / A. grahamae), highlighting the role of depth-related factors in the diversification of these congeneric agariciid species. The divergence between “shallow” and “deep” host species was reflected in the relatedness of the associated Symbiodinium (with A. lamarcki and A. grahamae sharing an identical Symbiodinium profile, and A. humilis and A. agaricites harbouring a related ITS2 sequence in their Symbiodinium profiles), corroborating the notion that brooding corals and their Symbiodinium are engaged in coevolutionary processes. Conclusions Our findings support the hypothesis that the depth-related environmental gradient on reefs has played an important role in the diversification of the genus Agaricia and their associated Symbiodinium, resulting in a genetic segregation between coral host-symbiont communities at shallow and mesophotic depths. PMID:24059868

Shipboard Acoustic Current Profiling during the Coastal Ocean Dynamics Experiment,

DTIC Science & Technology

1985-05-01

average profile based on the bottori depth estimated from the ship’s posit ion. in the CODEU region. an efficient computer routine was developed for... forex ~and and( port ward comnport ent s of V. at conistant z ., the depth Iill ships coordi- nlatv (’S(Chap 2). The data cort- from I -mintIe

Investigating the Fundamentals of Molecular Depth Profiling Using Strong-field Photoionization of Sputtered Neutrals

PubMed Central

Willingham, D.; Brenes, D. A.; Winograd, N.; Wucher, A.

2010-01-01

Molecular depth profiles of model organic thin films were performed using a 40 keV C60+ cluster ion source in concert with TOF-SIMS. Strong-field photoionization of intact neutral molecules sputtered by 40 keV C60+ primary ions was used to analyze changes in the chemical environment of the guanine thin films as a function of ion fluence. Direct comparison of the secondary ion and neutral components of the molecular depth profiles yields valuable information about chemical damage accumulation as well as changes in the molecular ionization probability. An analytical protocol based on the erosion dynamics model is developed and evaluated using guanine and trehalose molecular secondary ion signals with and without comparable laser photoionization data. PMID:26269660

An iterative algorithm for determining depth profiles of collection probability by electron-beam-induced current

NASA Astrophysics Data System (ADS)

Konovalov, Igor; Breitenstein, Otwin

2001-01-01

An iterative algorithm for the derivation of depth profiles of the minority carrier collection probability in a semiconductor with or without a coating on the top is presented using energy-resolved electron-beam-induced current measurements in planar geometry. The calculation is based on the depth-dose function of Everhart and Hoff (Everhart T E and Hoff P H 1971 J. Appl. Phys. 42 5837) and on the penetration-range function of Kanaya and Okayama (Kanaya K and Okayama S 1972 J. Phys. D: Appl. Phys. 5 43) or on that of Fitting (Fitting H-J 1974 Phys. Status Solidi/ a 26 525). It can also be performed with any other depth-dose functions. Using this algorithm does not require us to make any assumptions on the shape of the collection profile within the depth of interest. The influence of an absorbing top contact and/or a limited thickness of the semiconductor layer appear in the result, but can also be taken explicitly into account. Examples using silicon and CIS solar cells as well as a GaAs LED are presented.

An angle-resolved, wavelength-dispersive x-ray fluorescence spectrometer for depth profile analysis of ion-implanted semiconductors using synchrotron radiation

NASA Astrophysics Data System (ADS)

Schmitt, W.; Hormes, J.; Kuetgens, U.; Gries, W. H.

1992-01-01

An apparatus for angle-resolved, wavelength-dispersive x-ray fluorescence spectroscopy with synchrotron radiation has been built and tested at the beam line BN2 of the Bonn electron stretcher and accelerator (ELSA). The apparatus is to be used for nondestructive depth profile analysis of ion-implanted semiconductors as part of the multinational Versailles Project of Advanced Materials and Standards (VAMAS) project on ion-implanted reference materials. In particular, the centroid depths of depth profiles of various implants is to be determined by use of the angle-resolved signal ratio technique. First results of measurements on implants of phosphorus (100 keV, 1016 cm-2) and sulfur (200 keV, 1014 cm-2) in silicon wafers using ``white'' synchrotron radiation are presented and suggest that it should be generally possible to measure the centroid depth of an implant at dose densities as low as 1014 cm-2. Some of the apparative and technical requirements are discussed which are peculiar to the use of synchrotron radiation in general and to the use of nonmonochromatized radiation in particular.

A porewater-based stable isotope approach for the investigation of subsurface hydrological processes

NASA Astrophysics Data System (ADS)

Garvelmann, J.; Külls, C.; Weiler, M.

2012-02-01

Predicting and understanding subsurface flowpaths is still a crucial issue in hydrological research. We present an experimental approach to reveal present and past subsurface flowpaths of water in the unsaturated and saturated zone. Two hillslopes in a humid mountainous catchment have been investigated. The H2O(liquid) - H2O(vapor) equilibration laser spectroscopy method was used to obtain high resolution δ2H vertical depth profiles of pore water at various points along two fall lines of a pasture hillslope in the southern Black Forest, Germany. The Porewater-based Stable Isotope Profile (PSIP) approach was developed to use the integrated information of several vertical depth profiles of deuterium along transects at the hillslope. Different shapes of depth profiles were observed in relation to hillslope position. The statistical variability (inter-quartile range and standard deviation) of each profile was used to characterize different types of depth profiles. The profiles upslope or with a weak affinity for saturation as indicated by a low topographic wetness index preserve the isotopic input signal by precipitation with a distinct seasonal variability. These observations indicate mainly vertical movement of soil water in the upper part of the hillslope before sampling. The profiles downslope or at locations with a strong affinity for saturation do not show a similar seasonal isotopic signal. The input signal is erased in the foothills and a large proportion of pore water samples are close to the isotopic values of δ2H in streamwater during base flow conditions indicating the importance of the groundwater component in the catchment. Near the stream indications for efficient mixing of water from lateral subsurface flow paths with vertical percolation are found.

Chemical analysis of solids with sub-nm depth resolution by using a miniature LIMS system designed for in situ space research

NASA Astrophysics Data System (ADS)

Riedo, Andreas; Grimaudo, Valentine; Moreno-García, Pavel; Brigitte Neuland, Maike; Tulej, Marek; Broekmann, Peter; Wurz, Peter

2015-04-01

Sensitive elemental and isotope analysis of solid samples are of considerable interest in nowadays in situ space research. For context in situ analysis, high spatial resolution is also of substantial importance. While the measurements conducted with high lateral resolution can provide compositional details of the surface of highly heterogeneous materials, depth profiling measurements yield information on compositional details of surface and subsurface. The mass spectrometric analysis with the vertical resolution at sub-µm levels is of special consideration and can deliver important information on processes, which may have modified the surface. Information on space weathering effects can be readily determined when the sample composition of the surface and sub-surface is studied with high vertical resolution. In this contribution we will present vertical depth resolution measurements conducted by our sensitive miniature laser ablation ionization time-of-flight mass spectrometer (160mm x Ø 60mm) designed for in situ space research [1-3]. The mass spectrometer is equipped with a fs-laser system (~190fs pulse width, λ = 775nm), which is used for ablation and ionization of the sample material [2]. Laser radiation is focussed on the target material to a spot size of about 10-20 µm in diameter. Mass spectrometric measurements are conducted with a mass resolution (m/Δm) of about 400-500 (at 56Fe mass peak) and with a superior dynamic range of more than eight orders of magnitude. The depth profiling performance studies were conducted on 10µm thick Cu films that were deposited by an additive-assisted electrochemical procedure on Si-wafers. The presented measurement study will show that the current instrument prototype is able to conduct quantitative chemical (elemental and isotope) analysis of solids with a vertical resolution at sub-nm level. Contaminants, incorporated by using additives (polymers containing e.g. C, N, O, S) and with layer thickness of a few nanometres, can be fully resolved [1]. The current measurement performance, including the sensitivity and the high vertical depth resolution, opens new perspectives for future applications in the laboratory, e.g. measurements of Genesis samples, and new measurement capabilities for in situ space research. References 1)V. Grimaudo, P. Moreno-García, M.B. Neuland, M. Tulej, P. Broekmann, P. Wurz and A. Riedo, "High-resolution chemical depth profiling of solid material using a miniature laser ablation/ionization mass spectrometer", Anal. Chem., 2015, submitted. 2)A. Riedo, M. Neuland, S. Meyer, M. Tulej, and P. Wurz, "Coupling of LMS with a fs-laser ablation ion source: elemental and isotope composition measurements", J. Anal. At. Spectrom., 2013, 28, 1256. 3)Tulej et al. CAMAM: A Miniature Laser Ablation Ionisation Mass Spectrometer and Microscope-Camera System for In Situ Investigation of the Composition and Morphology of Extraterrestrial Materials, Geostand. Geoanal. Res., 2014, doi: 10.1111/j.1751-908X.2014.00302.x

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium

PubMed Central

2014-01-01

We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the United States Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for junction discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed, for these and qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings. PMID:25150838

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

PubMed Central

2012-01-01

Background RNA sequencing (RNA-Seq) has emerged as a powerful approach for the detection of differential gene expression with both high-throughput and high resolution capabilities possible depending upon the experimental design chosen. Multiplex experimental designs are now readily available, these can be utilised to increase the numbers of samples or replicates profiled at the cost of decreased sequencing depth generated per sample. These strategies impact on the power of the approach to accurately identify differential expression. This study presents a detailed analysis of the power to detect differential expression in a range of scenarios including simulated null and differential expression distributions with varying numbers of biological or technical replicates, sequencing depths and analysis methods. Results Differential and non-differential expression datasets were simulated using a combination of negative binomial and exponential distributions derived from real RNA-Seq data. These datasets were used to evaluate the performance of three commonly used differential expression analysis algorithms and to quantify the changes in power with respect to true and false positive rates when simulating variations in sequencing depth, biological replication and multiplex experimental design choices. Conclusions This work quantitatively explores comparisons between contemporary analysis tools and experimental design choices for the detection of differential expression using RNA-Seq. We found that the DESeq algorithm performs more conservatively than edgeR and NBPSeq. With regard to testing of various experimental designs, this work strongly suggests that greater power is gained through the use of biological replicates relative to library (technical) replicates and sequencing depth. Strikingly, sequencing depth could be reduced as low as 15% without substantial impacts on false positive or true positive rates. PMID:22985019

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing.

PubMed

Robles, José A; Qureshi, Sumaira E; Stephen, Stuart J; Wilson, Susan R; Burden, Conrad J; Taylor, Jennifer M

2012-09-17

RNA sequencing (RNA-Seq) has emerged as a powerful approach for the detection of differential gene expression with both high-throughput and high resolution capabilities possible depending upon the experimental design chosen. Multiplex experimental designs are now readily available, these can be utilised to increase the numbers of samples or replicates profiled at the cost of decreased sequencing depth generated per sample. These strategies impact on the power of the approach to accurately identify differential expression. This study presents a detailed analysis of the power to detect differential expression in a range of scenarios including simulated null and differential expression distributions with varying numbers of biological or technical replicates, sequencing depths and analysis methods. Differential and non-differential expression datasets were simulated using a combination of negative binomial and exponential distributions derived from real RNA-Seq data. These datasets were used to evaluate the performance of three commonly used differential expression analysis algorithms and to quantify the changes in power with respect to true and false positive rates when simulating variations in sequencing depth, biological replication and multiplex experimental design choices. This work quantitatively explores comparisons between contemporary analysis tools and experimental design choices for the detection of differential expression using RNA-Seq. We found that the DESeq algorithm performs more conservatively than edgeR and NBPSeq. With regard to testing of various experimental designs, this work strongly suggests that greater power is gained through the use of biological replicates relative to library (technical) replicates and sequencing depth. Strikingly, sequencing depth could be reduced as low as 15% without substantial impacts on false positive or true positive rates.

Community structure and function of planktonic Crenarchaeota: changes with depth in the South China Sea.

PubMed

Hu, Anyi; Jiao, Nianzhi; Zhang, Chuanlun L

2011-10-01

Marine Crenarchaeota represent a widespread and abundant microbial group in marine ecosystems. Here, we investigated the abundance, diversity, and distribution of planktonic Crenarchaeota in the epi-, meso-, and bathypelagic zones at three stations in the South China Sea (SCS) by analysis of crenarchaeal 16S rRNA gene, ammonia monooxygenase gene amoA involved in ammonia oxidation, and biotin carboxylase gene accA putatively involved in archaeal CO(2) fixation. Quantitative PCR analyses indicated that crenarchaeal amoA and accA gene abundances varied similarly with archaeal and crenarchaeal 16S rRNA gene abundances at all stations, except that crenarchaeal accA genes were almost absent in the epipelagic zone. Ratios of the crenarchaeal amoA gene to 16S rRNA gene abundances decreased ~2.6 times from the epi- to bathypelagic zones, whereas the ratios of crenarchaeal accA gene to marine group I crenarchaeal 16S rRNA gene or to crenarchaeal amoA gene abundances increased with depth, suggesting that the metabolism of Crenarchaeota may change from the epi- to meso- or bathypelagic zones. Denaturing gradient gel electrophoresis profiling of the 16S rRNA genes revealed depth partitioning in archaeal community structures. Clone libraries of crenarchaeal amoA and accA genes showed two clusters: the "shallow" cluster was exclusively derived from epipelagic water and the "deep" cluster was from meso- and/or bathypelagic waters, suggesting that niche partitioning may take place between the shallow and deep marine Crenarchaeota. Overall, our results show strong depth partitioning of crenarchaeal populations in the SCS and suggest a shift in their community structure and ecological function with increasing depth.

Wettability of AFM tip influences the profile of interfacial nanobubbles

NASA Astrophysics Data System (ADS)

Teshima, Hideaki; Takahashi, Koji; Takata, Yasuyuki; Nishiyama, Takashi

2018-02-01

To accurately characterize the shape of interfacial nanobubbles using atomic force microscopy (AFM), we investigated the effect of wettability of the AFM tip while operating in the peak force tapping (PFT) mode. The AFM tips were made hydrophobic and hydrophilic by Teflon AF coating and oxygen plasma treatment, respectively. It was found that the measured base radius of nanobubbles differed between AFM height images and adhesion images, and that this difference depended on the tip wettability. The force curves obtained during the measurements were also different depending on the wettability, especially in the range of the tip/nanobubble interaction and in the magnitude of the maximum attractive force in the retraction period. The difference suggests that hydrophobic tips penetrate the gas/liquid interface of the nanobubbles, with the three phase contact line being pinned on the tip surface; hydrophilic tips on the other hand do not penetrate the interface. We then quantitatively estimated the pinning position and recalculated the true profiles of the nanobubbles by comparing the height images and adhesion images. As the AFM tip was made more hydrophilic, the penetration depth decreased and eventually approached zero. This result suggests that the PFT measurement using a hydrophilic tip is vital for the acquisition of reliable nanobubble profiles.

Utilizing the Vertical Variability of Precipitation to Improve Radar QPE

NASA Technical Reports Server (NTRS)

Gatlin, Patrick N.; Petersen, Walter A.

2016-01-01

Characteristics of the melting layer and raindrop size distribution can be exploited to further improve radar quantitative precipitation estimation (QPE). Using dual-polarimetric radar and disdrometers, we found that the characteristic size of raindrops reaching the ground in stratiform precipitation often varies linearly with the depth of the melting layer. As a result, a radar rainfall estimator was formulated using D(sub m) that can be employed by polarimetric as well as dual-frequency radars (e.g., space-based radars such as the GPM DPR), to lower the bias and uncertainty of conventional single radar parameter rainfall estimates by as much as 20%. Polarimetric radar also suffers from issues associated with sampling the vertical distribution of precipitation. Hence, we characterized the vertical profile of polarimetric parameters (VP3)-a radar manifestation of the evolving size and shape of hydrometeors as they fall to the ground-on dual-polarimetric rainfall estimation. The VP3 revealed that the profile of ZDR in stratiform rainfall can bias dual-polarimetric rainfall estimators by as much as 50%, even after correction for the vertical profile of reflectivity (VPR). The VP3 correction technique that we developed can improve operational dual-polarimetric rainfall estimates by 13% beyond that offered by a VPR correction alone.

Using Sediment Profile Imagery (SPI) to Quantify ...

EPA Pesticide Factsheets

We present the results of monthly sediment and water quality surveys to evaluate the impact of intermittent, seasonal hypoxia on benthic habitat condition. This study was conducted in the Pensacola Bay (Florida) estuary across nine sites extending from the mouth of the Escambia River down-estuary to the outlet into the Gulf of Mexico. The sites span the full salinity gradient and cover a range of sediment types and dissolved oxygen statuses. Monthly sediment profile imagery (SPI) was captured from each site in conjunction with water column conductivity-temperature-depth (CTD) profiles and sediment grabs to evaluate sediment characteristics and macrobenthic community composition. The results of this study will be used to evaluate the use of SPI to determine effects of water quality on the health of benthic communities in Gulf Coast estuaries. Whereas recent water quality management efforts in Florida (e.g., numeric nutrient criteria, marine dissolved oxygen standard) assumed linkages between dissolved oxygen and aquatic life use attainment based on laboratory tests, SPI methods can potentially provide an assessment of these relationships in realistic field settings. The work presented here is in support of better indicators and endpoints and will help improve quantitative relationships between nutrient pollution and ecosystem condition. The audience that would be interested in this presentation includes scientists and managers from across the southeastern U

PSP toxin levels and plankton community composition and abundance in size-fractionated vertical profiles during spring/summer blooms of the toxic dinoflagellate Alexandrium fundyense in the Gulf of Maine and on Georges Bank, 2007, 2008, and 2010: 1. Toxin levels.

PubMed

Deeds, Jonathan R; Petitpas, Christian M; Shue, Vangie; White, Kevin D; Keafer, Bruce A; McGillicuddy, Dennis J; Milligan, Peter J; Anderson, Donald M; Turner, Jefferson T

2014-05-01

As part of the NOAA ECOHAB funded Gulf of Maine Toxicity (GOMTOX) project, we determined Alexandrium fundyense abundance, paralytic shellfish poisoning (PSP) toxin composition, and concentration in quantitatively-sampled size-fractionated (20-64, 64-100, 100-200, 200-500, and > 500 μm) particulate water samples, and the community composition of potential grazers of A. fundyense in these size fractions, at multiple depths (typically 1, 10, 20 m, and near-bottom) during 10 large-scale sampling cruises during the A. fundyense bloom season (May-August) in the coastal Gulf of Maine and on Georges Bank in 2007, 2008, and 2010. Our findings were as follows: (1) when all sampling stations and all depths were summed by year, the majority (94% ± 4%) of total PSP toxicity was contained in the 20-64 μm size fraction; (2) when further analyzed by depth, the 20-64 μm size fraction was the primary source of toxin for 97% of the stations and depths samples over three years; (3) overall PSP toxin profiles were fairly consistent during the three seasons of sampling with gonyautoxins (1, 2, 3, and 4) dominating (90.7% ± 5.5%), followed by the carbamate toxins saxitoxin (STX) and neosaxitoxin (NEO) (7.7% ± 4.5%), followed by n-sulfocarbamoyl toxins (C1 and 2, GTX5) (1.3% ± 0.6%), followed by all decarbamoyl toxins (dcSTX, dcNEO, dcGTX2&3) (< 1%), although differences were noted between PSP toxin compositions for nearshore coastal Gulf of Maine sampling stations compared to offshore Georges Bank sampling stations for 2 out of 3 years; (4) surface cell counts of A. fundyense were a fairly reliable predictor of the presence of toxins throughout the water column; and (5) nearshore surface cell counts of A. fundyense in the coastal Gulf of Maine were not a reliable predictor of A. fundyense populations offshore on Georges Bank for 2 out of the 3 years sampled.

PSP toxin levels and plankton community composition and abundance in size-fractionated vertical profiles during spring/summer blooms of the toxic dinoflagellate Alexandrium fundyense in the Gulf of Maine and on Georges Bank, 2007, 2008, and 2010: 1. Toxin levels

PubMed Central

Deeds, Jonathan R.; Petitpas, Christian M.; Shue, Vangie; White, Kevin D.; Keafer, Bruce A.; McGillicuddy, Dennis J.; Milligan, Peter J.; Anderson, Donald M.; Turner, Jefferson T.

2014-01-01

As part of the NOAA ECOHAB funded Gulf of Maine Toxicity (GOMTOX)1 project, we determined Alexandrium fundyense abundance, paralytic shellfish poisoning (PSP) toxin composition, and concentration in quantitatively-sampled size-fractionated (20–64, 64–100, 100–200, 200–500, and > 500 μm) particulate water samples, and the community composition of potential grazers of A. fundyense in these size fractions, at multiple depths (typically 1, 10, 20 m, and near-bottom) during 10 large-scale sampling cruises during the A. fundyense bloom season (May–August) in the coastal Gulf of Maine and on Georges Bank in 2007, 2008, and 2010. Our findings were as follows: (1) when all sampling stations and all depths were summed by year, the majority (94% ± 4%) of total PSP toxicity was contained in the 20–64 μm size fraction; (2) when further analyzed by depth, the 20–64 μm size fraction was the primary source of toxin for 97% of the stations and depths samples over three years; (3) overall PSP toxin profiles were fairly consistent during the three seasons of sampling with gonyautoxins (1, 2, 3, and 4) dominating (90.7% ± 5.5%), followed by the carbamate toxins saxitoxin (STX) and neosaxitoxin (NEO) (7.7% ± 4.5%), followed by n-sulfocarbamoyl toxins (C1 and 2, GTX5) (1.3% ± 0.6%), followed by all decarbamoyl toxins (dcSTX, dcNEO, dcGTX2&3) (< 1%), although differences were noted between PSP toxin compositions for nearshore coastal Gulf of Maine sampling stations compared to offshore Georges Bank sampling stations for 2 out of 3 years; (4) surface cell counts of A. fundyense were a fairly reliable predictor of the presence of toxins throughout the water column; and (5) nearshore surface cell counts of A. fundyense in the coastal Gulf of Maine were not a reliable predictor of A. fundyense populations offshore on Georges Bank for 2 out of the 3 years sampled. PMID:25076816

TU-AB-BRA-12: Quality Assurance of An Integrated Magnetic Resonance Image Guided Adaptive Radiotherapy Machine Using Cherenkov Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andreozzi, J; Bruza, P; Saunders, S

Purpose: To investigate the viability of using Cherenkov imaging as a fast and robust method for quality assurance tests in the presence of a magnetic field, where other instruments can be limited. Methods: Water tank measurements were acquired from a clinically utilized adaptive magnetic resonance image guided radiation therapy (MR-IGRT) machine with three multileaf-collimator equipped 60Co sources. Cherenkov imaging used an intensified charge coupled device (ICCD) camera placed 3.5m from the treatment isocenter, looking down the bore of the 0.35T MRI into a water tank. Images were post-processed to make quantitative comparison between Cherenkov light intensity with both film andmore » treatment planning system predictions, in terms of percent depth dose curves as well as lateral beam profile measurements. A TG-119 commissioning test plan (C4: C-Shape) was imaged in real-time at 6.33 frames per second to investigate the temporal and spatial resolution of the Cherenkov imaging technique. Results: A .33mm/pixel Cherenkov image resolution was achieved across 1024×1024 pixels in this setup. Analysis of the Cherenkov image of a 10.5×10.5cm treatment beam in the water tank successfully measured the beam width at the depth of maximum dose within 1.2% of the film measurement at the same point. The percent depth dose curve for the same beam was on average within 2% of ionization chamber measurements for corresponding depths between 3–100mm. Cherenkov video of the TG-119 test plan provided qualitative agreement with the treatment planning system dose predictions, and a novel temporal verification of the treatment. Conclusions: Cherenkov imaging was successfully used to make QA measurements of percent depth dose curves and cross beam profiles of MRI-IGRT radiotherapy machines after only several seconds of beam-on time and data capture; both curves were extracted from the same data set. Video-rate imaging of a dynamic treatment plan provided new information regarding temporal dose deposition. This study has been funded by NIH grants R21EB17559 and R01CA109558, as well as Norris Cotton Cancer Center Pilot funding.« less

A new method for depth profiling reconstruction in confocal microscopy

NASA Astrophysics Data System (ADS)

Esposito, Rosario; Scherillo, Giuseppe; Mensitieri, Giuseppe

2018-05-01

Confocal microscopy is commonly used to reconstruct depth profiles of chemical species in multicomponent systems and to image nuclear and cellular details in human tissues via image intensity measurements of optical sections. However, the performance of this technique is reduced by inherent effects related to wave diffraction phenomena, refractive index mismatch and finite beam spot size. All these effects distort the optical wave and cause an image to be captured of a small volume around the desired illuminated focal point within the specimen rather than an image of the focal point itself. The size of this small volume increases with depth, thus causing a further loss of resolution and distortion of the profile. Recently, we proposed a theoretical model that accounts for the above wave distortion and allows for a correct reconstruction of the depth profiles for homogeneous samples. In this paper, this theoretical approach has been adapted for describing the profiles measured from non-homogeneous distributions of emitters inside the investigated samples. The intensity image is built by summing the intensities collected from each of the emitters planes belonging to the illuminated volume, weighed by the emitters concentration. The true distribution of the emitters concentration is recovered by a new approach that implements this theoretical model in a numerical algorithm based on the Maximum Entropy Method. Comparisons with experimental data and numerical simulations show that this new approach is able to recover the real unknown concentration distribution from experimental profiles with an accuracy better than 3%.

Global distribution of plant-extractable water capacity of soil

USGS Publications Warehouse

Dunne, K.A.; Willmott, C.J.

1996-01-01

Plant-extractable water capacity of soil is the amount of water that can be extracted from the soil to fulfill evapotranspiration demands. It is often assumed to be spatially invariant in large-scale computations of the soil-water balance. Empirical evidence, however, suggests that this assumption is incorrect. In this paper, we estimate the global distribution of the plant-extractable water capacity of soil. A representative soil profile, characterized by horizon (layer) particle size data and thickness, was created for each soil unit mapped by FAO (Food and Agriculture Organization of the United Nations)/Unesco. Soil organic matter was estimated empirically from climate data. Plant rooting depths and ground coverages were obtained from a vegetation characteristic data set. At each 0.5?? ?? 0.5?? grid cell where vegetation is present, unit available water capacity (cm water per cm soil) was estimated from the sand, clay, and organic content of each profile horizon, and integrated over horizon thickness. Summation of the integrated values over the lesser of profile depth and root depth produced an estimate of the plant-extractable water capacity of soil. The global average of the estimated plant-extractable water capacities of soil is 8??6 cm (Greenland, Antarctica and bare soil areas excluded). Estimates are less than 5, 10 and 15 cm - over approximately 30, 60, and 89 per cent of the area, respectively. Estimates reflect the combined effects of soil texture, soil organic content, and plant root depth or profile depth. The most influential and uncertain parameter is the depth over which the plant-extractable water capacity of soil is computed, which is usually limited by root depth. Soil texture exerts a lesser, but still substantial, influence. Organic content, except where concentrations are very high, has relatively little effect.

Improving depth resolutions in positron beam spectroscopy by concurrent ion-beam sputtering

NASA Astrophysics Data System (ADS)

John, Marco; Dalla, Ayham; Ibrahim, Alaa M.; Anwand, Wolfgang; Wagner, Andreas; Böttger, Roman; Krause-Rehberg, Reinhard

2018-05-01

The depth resolution of mono-energetic positron annihilation spectroscopy using a positron beam is shown to improve by concurrently removing the sample surface layer during positron beam spectroscopy. During ion-beam sputtering with argon ions, Doppler-broadening spectroscopy is performed with energies ranging from 3 keV to 5 keV allowing for high-resolution defect studies just below the sputtered surface. With this technique, significantly improved depth resolutions could be obtained even at larger depths when compared to standard positron beam experiments which suffer from extended positron implantation profiles at higher positron energies. Our results show that it is possible to investigate layered structures with a thickness of about 4 microns with significantly improved depth resolution. We demonstrated that a purposely generated ion-beam induced defect profile in a silicon sample could be resolved employing the new technique. A depth resolution of less than 100 nm could be reached.

Dating a tropical ice core by time-frequency analysis of ion concentration depth profiles

NASA Astrophysics Data System (ADS)

Gay, M.; De Angelis, M.; Lacoume, J.-L.

2014-09-01

Ice core dating is a key parameter for the interpretation of the ice archives. However, the relationship between ice depth and ice age generally cannot be easily established and requires the combination of numerous investigations and/or modelling efforts. This paper presents a new approach to ice core dating based on time-frequency analysis of chemical profiles at a site where seasonal patterns may be significantly distorted by sporadic events of regional importance, specifically at the summit area of Nevado Illimani (6350 m a.s.l.), located in the eastern Bolivian Andes (16°37' S, 67°46' W). We used ion concentration depth profiles collected along a 100 m deep ice core. The results of Fourier time-frequency and wavelet transforms were first compared. Both methods were applied to a nitrate concentration depth profile. The resulting chronologies were checked by comparison with the multi-proxy year-by-year dating published by de Angelis et al. (2003) and with volcanic tie points. With this first experiment, we demonstrated the efficiency of Fourier time-frequency analysis when tracking the nitrate natural variability. In addition, we were able to show spectrum aliasing due to under-sampling below 70 m. In this article, we propose a method of de-aliasing which significantly improves the core dating in comparison with annual layer manual counting. Fourier time-frequency analysis was applied to concentration depth profiles of seven other ions, providing information on the suitability of each of them for the dating of tropical Andean ice cores.

Experimental validation of a Monte Carlo proton therapy nozzle model incorporating magnetically steered protons.

PubMed

Peterson, S W; Polf, J; Bues, M; Ciangaru, G; Archambault, L; Beddar, S; Smith, A

2009-05-21

The purpose of this study is to validate the accuracy of a Monte Carlo calculation model of a proton magnetic beam scanning delivery nozzle developed using the Geant4 toolkit. The Monte Carlo model was used to produce depth dose and lateral profiles, which were compared to data measured in the clinical scanning treatment nozzle at several energies. Comparisons were also made between measured and simulated off-axis profiles to test the accuracy of the model's magnetic steering. Comparison of the 80% distal dose fall-off values for the measured and simulated depth dose profiles agreed to within 1 mm for the beam energies evaluated. Agreement of the full width at half maximum values for the measured and simulated lateral fluence profiles was within 1.3 mm for all energies. The position of measured and simulated spot positions for the magnetically steered beams agreed to within 0.7 mm of each other. Based on these results, we found that the Geant4 Monte Carlo model of the beam scanning nozzle has the ability to accurately predict depth dose profiles, lateral profiles perpendicular to the beam axis and magnetic steering of a proton beam during beam scanning proton therapy.

Quantitative Microbial Community Analysis of Three Different Sulfidic Mine Tailing Dumps Generating Acid Mine Drainage▿

PubMed Central

Kock, Dagmar; Schippers, Axel

2008-01-01

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 109 cells g−1 dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general. PMID:18586975

Quantitative microbial community analysis of three different sulfidic mine tailing dumps generating acid mine drainage.

PubMed

Kock, Dagmar; Schippers, Axel

2008-08-01

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 10(9) cells g(-1) dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general.

Magnetic nonuniformity and thermal hysteresis of magnetism in a manganite thin film.

PubMed

Singh, Surendra; Fitzsimmons, M R; Lookman, T; Thompson, J D; Jeen, H; Biswas, A; Roldan, M A; Varela, M

2012-02-17

We measured the chemical and magnetic depth profiles of a single crystalline (La(1-x)Pr(x))(1-y)Ca(y)MnO(3-δ) (x=0.52±0.05, y=0.23±0.04, δ=0.14±0.10) film grown on a NdGaO(3) substrate using x-ray reflectometry, electron microscopy, electron energy-loss spectroscopy, and polarized neutron reflectometry. Our data indicate that the film exhibits coexistence of different magnetic phases as a function of depth. The magnetic depth profile is correlated with a variation of chemical composition with depth. The thermal hysteresis of ferromagnetic order in the film suggests a first-order ferromagnetic transition at low temperatures.

Development of nanotopography during SIMS characterization of thin films of Ge1-xSnx alloy

NASA Astrophysics Data System (ADS)

Secchi, M.; Demenev, E.; Colaux, J. L.; Giubertoni, D.; Dell'Anna, R.; Iacob, E.; Gwilliam, R. M.; Jeynes, C.; Bersani, M.

2015-11-01

This work presents a study of application of secondary ion mass spectrometry (SIMS) to measure tin concentration in Ge1-xSnx alloy with x higher than solid solubility ∼1%, i.e. well above the diluted regime where SIMS measurements usually provide the most reliable quantitative results. SIMS analysis was performed on Sn+ ion implanted Ge films, epitaxially deposited on Si, and on chemical vapor deposition deposited Ge0.93Sn0.07 alloy. Three SIMS conditions were investigated, varying primary beam ion species and secondary ion polarity keeping 1 keV impact energy. Best depth profile accuracy, best agreement with the fluences measured by Rutherford backscattering spectrometry, good detection limit (∼1 × 1017 at/cm3) and depth resolution (∼2 nm/decade) are achieved in Cs+/SnCs+ configuration. However, applied sputtering conditions (Cs+ 1 keV, 64° incidence vs. normal) induced an early formation of surface topography on the crater bottom resulting in significant variation of sputtering yield. Atomic force microscopy shows a peculiar topography developed on Ge: for oblique incidence, a topography consisting in a sequence of dots and ripples was observed on the crater bottom. This behavior is unusual for grazing incidence and has been observed to increase with the Cs+ fluence. Rotating sample during sputtering prevents this ripple formation and consequently improves the depth accuracy.

Quantitative study of the correlation between cerebellar retraction factors and hearing loss following microvascular decompression for hemifacial spasm.

PubMed

Li, Ning; Zhao, Wei-Guo; Pu, Chun-Hua; Yang, Wen-Lei

2018-01-01

This prospective study quantitatively measured the cerebellar retraction factors, including retraction distance, depth and duration, and evaluated their potential relationship to the development of hearing loss after microvascular decompression (MVD) for hemifacial spasm (HFS). One hundred ten patients with primary HFS who underwent MVD in our department were included into this study. The cerebellar retraction factors were quantitatively measured on preoperative MR and timed during MVD. Associations of cerebellar retraction and other factors to postoperative hearing loss were analyzed. Eleven (10%) patients developed hearing loss after MVD. Compared with the group without hearing loss, the cerebellar retraction distance, depth and duration of the group with hearing loss were significantly greater (p < 0.05). Multivariate regression analysis showed that greater cerebellar retraction depth and longer retraction duration were significantly associated with a higher incidence of postoperative hearing impairment (p < 0.05). This study strongly suggested a correlation between the cerebellar retraction factors, especially retraction depth and duration, and possibility of hearing loss following MVD for HFS.

Compositional analysis and depth profiling of thin film CrO{sub 2} by heavy ion ERDA and standard RBS: a comparison

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khamlich, S., E-mail: skhamlich@gmail.com; Department of Chemistry, Tshwane University of Technology, Private Bag X 680, Pretoria, 0001; The African Laser Centre, CSIR campus, P.O. Box 395, Pretoria

2012-08-15

Chromium dioxide (CrO{sub 2}) thin film has generated considerable interest in applied research due to the wide variety of its technological applications. It has been extensively investigated in recent years, attracting the attention of researchers working on spintronic heterostructures and in the magnetic recording industry. However, its synthesis is usually a difficult task due to its metastable nature and various synthesis techniques are being investigated. In this work a polycrystalline thin film of CrO{sub 2} was prepared by electron beam vaporization of Cr{sub 2}O{sub 3} onto a Si substrate. The polycrystalline structure was confirmed through XRD analysis. The stoichiometry andmore » elemental depth distribution of the deposited film were measured by ion beam nuclear analytical techniques heavy ion elastic recoil detection analysis (ERDA) and Rutherford backscattering spectrometry (RBS), which both have relative advantage over non-nuclear spectrometries in that they can readily provide quantitative information about the concentration and distribution of different atomic species in a layer. Moreover, the analysis carried out highlights the importance of complementary usage of the two techniques to obtain a more complete description of elemental content and depth distribution in thin films. - Graphical abstract: Heavy ion elastic recoil detection analysis (ERDA) and Rutherford backscattering spectrometry (RBS) both have relative advantage over non-nuclear spectrometries in that they can readily provide quantitative information about the concentration and distribution of different atomic species in a layer. Highlights: Black-Right-Pointing-Pointer Thin films of CrO{sub 2} have been grown by e-beam evaporation of Cr{sub 2}O{sub 3} target in vacuum. Black-Right-Pointing-Pointer The composition was determined by heavy ion-ERDA and RBS. Black-Right-Pointing-Pointer HI-ERDA and RBS provided information on the light and heavy elements, respectively.« less

Geochemistry of organic carbon and trace elements in boreal stratified lakes during different seasons

NASA Astrophysics Data System (ADS)

Moreva, O. Y.; Pokrovsky, O. S.; Shirokova, L. S.; Viers, J.

2008-12-01

Our knowledge of chemical fluxes in the system rock-soils-rivers-ocean of boreal and glacial landscapes is limited by the least studied part, i.e., the river water transformation between the lake and the river systems. Dissolved organic carbon (DOC), nutrients, major and trace elements are being leached from soil profile to the river but subjected to chemical transformation in the lakes due to phytoplankton and bacterial activity. As a result, many lakes in boreal regions are quite different in chemical composition compared to surrounding rivers and demonstrate important chemical stratification. The main processes responsible for chemical stratification in lakes are considered to be i) diffusion fluxes from the sediment to the bottom water accompanied by sulfate reduction and methanogenesis in the sediments and ii) dissolution/mineralization of precipitating organic matter (mineral fraction, detritus, plankton pellets) in the bottom layer horizons under anoxic conditions. Up to present time, distinguishing between two processes remains difficult. This paper is aimed at filling this gap via detailed geochemical analysis of DOC and trace elements in the water column profiles of three typical stratified lakes of Arkhangelsk region in Kenozersky National Parc (64° N) in winter (glacial) and in summer period. Concentration of most trace elements (Li, B, Al, Ti, V, Cr, Ni, Co, Zn, As, Rb, Sr, Y, Zr, Mo, Sb, Ba, REEs, Th, U) are not subjected to strong variations along the water column, despite the presence of strong or partial redox stratification. Apparently, these elements are not significantly controlled by production/mineralization processes and redox phenomena in the water column, or the influence of these processes is not pronounced under the control by the allochtonous river water input. In particularly, the stability of titanium and aluminum concentration along the depth profile and their independence of iron behavior suggest the important control by dissolved organic matter. Therefore, organo-ferric colloids controlling petrogenic elements speciation in soil and river waters are being replaced by autochthonous organic colloids in the lake system. The same observation is true for some heavy metals such as nickel, copper and zinc, whereas cobalt, as limiting component, is being strongly removed from the photic zone or it is coprecipitating with manganese hydroxide. Results of the present work allow quantitative evaluation of the role of redox processes in the bottom horizons and organic detritus degradation in the creation of chemical stratification of small lakes with high DOC concentration. Further insights on geochemical migration of trace elements in lakes require : i) study of colloidal speciation using in-situ dialysis; ii) monitoring the annual and seasonal dynamics of redox processes and TE concentration variation along the profile; iii) quantitative assessment of bacterial degradation of suspended OM and Mn and Fe redox reactions along the depth profile; iv) setting the sedimentary traps for evaluation of suspended material fluxes, and, v) thorough study of chemical composition of interstitial pore waters.

Possibilities of LA-ICP-MS technique for the spatial elemental analysis of the recent fish scales: Line scan vs. depth profiling

NASA Astrophysics Data System (ADS)

Holá, Markéta; Kalvoda, Jiří; Nováková, Hana; Škoda, Radek; Kanický, Viktor

2011-01-01

LA-ICP-MS and solution based ICP-MS in combination with electron microprobe are presented as a method for the determination of the elemental spatial distribution in fish scales which represent an example of a heterogeneous layered bone structure. Two different LA-ICP-MS techniques were tested on recent common carp ( Cyprinus carpio) scales: A line scan through the whole fish scale perpendicular to the growth rings. The ablation crater of 55 μm width and 50 μm depth allowed analysis of the elemental distribution in the external layer. Suitable ablation conditions providing a deeper ablation crater gave average values from the external HAP layer and the collagen basal plate. Depth profiling using spot analysis was tested in fish scales for the first time. Spot analysis allows information to be obtained about the depth profile of the elements at the selected position on the sample. The combination of all mentioned laser ablation techniques provides complete information about the elemental distribution in the fish scale samples. The results were compared with the solution based ICP-MS and EMP analyses. The fact that the results of depth profiling are in a good agreement both with EMP and PIXE results and, with the assumed ways of incorporation of the studied elements in the HAP structure, suggests a very good potential for this method.

Two-dimensional interferometric characterization of laser-induced refractive index profiles in bulk Topas polymer

NASA Astrophysics Data System (ADS)

Hessler, Steffen; Rosenberger, Manuel; Schmauss, Bernhard; Hellmann, Ralf

2018-01-01

In this paper we precisely determine laser-induced refractive index profiles created in cyclic olefin copolymer Topas 6017 employing a sophisticated phase shifting Mach-Zehnder interferometry approach. Beyond the usual one-dimensional modification depth measurement we highlight that for straight waveguide structures also a two-dimensional refractive index distribution can be directly obtained providing full information of a waveguide's exact cross section and its gradient refractive index contrast. Deployed as direct data input in optical waveguide simulation, the evaluated 2D refractive index profiles permit a detailed calculation of the waveguides' actual mode profiles. Furthermore, conventional one-dimensional interferometric measurements for refractive index depth profiles with varying total imposed laser fluence of a 248 nm KrF excimer laser are included to investigate the effect on refractive index modification depth. Maximum surface refractive index increase turns out to attain up to 1.86 ·10-3 enabling laser-written optical waveguide channels. Additionally, a comprehensive optical material characterization in terms of dispersion, thermo-optic coefficient and absorption measurement of unmodified and UV-modified Topas 6017 is carried out.

Principal component analysis of TOF-SIMS spectra, images and depth profiles: an industrial perspective

NASA Astrophysics Data System (ADS)

Pacholski, Michaeleen L.

2004-06-01

Principal component analysis (PCA) has been successfully applied to time-of-flight secondary ion mass spectrometry (TOF-SIMS) spectra, images and depth profiles. Although SIMS spectral data sets can be small (in comparison to datasets typically discussed in literature from other analytical techniques such as gas or liquid chromatography), each spectrum has thousands of ions resulting in what can be a difficult comparison of samples. Analysis of industrially-derived samples means the identity of most surface species are unknown a priori and samples must be analyzed rapidly to satisfy customer demands. PCA enables rapid assessment of spectral differences (or lack there of) between samples and identification of chemically different areas on sample surfaces for images. Depth profile analysis helps define interfaces and identify low-level components in the system.

Depth-profile investigations of triterpenoid varnishes by KrF excimer laser ablation and laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Theodorakopoulos, C.; Zafiropulos, V.

2009-07-01

The ablation properties of aged triterpenoid dammar and mastic films were investigated using a Krypton Fluoride excimer laser (248 nm, 25 ns). Ablation rate variations between surface and bulk layers indicated changes of the ablation mechanisms across the depth profiles of the films. In particular, after removal of the uppermost surface varnish layers there was a reduction of the ablation step in the bulk that was in line with a significant reduction of carbon dimer emission beneath the surface layers as detected by laser-induced breakdown spectroscopy. The results are explicable by the generation of condensation, cross-linking and oxidative gradients across the depth profile of triterpenoid varnish films during the aging degradation process, which were recently quantified and established on the molecular level.

Silver/oxygen depth profile in coins by using laser ablation, mass quadrupole spectrometer and X-rays fluorescence

NASA Astrophysics Data System (ADS)

Cutroneo, M.; Torrisi, L.; Caridi, F.; Sayed, R.; Gentile, C.; Mondio, G.; Serafino, T.; Castrizio, E. D.

2013-05-01

Silver coins belonging to different historical periods were investigated to determine the Ag/O atomic ratio depth profiles. Laser ablation has been employed to remove, in high vacuum, the first superficial layers of the coins. Mass quadrupole spectrometry has been used to detect the Ag and the O atomic elements vaporized from the coin surface. The depth profile allowed to determine the thickness of the oxidation layer indicating that, in general, it is high in old coins. A complementary technique, using scanning electron microscope and the associated XRF microprobe, have been devoted to confirm the measurements of Ag/O atomic ratio measured with the laser-coupled mass spectrometry. The oxidation layer thicknesses range between about 25 and 250 microns.

Electrophysiological mapping of the accessory olfactory bulb of the rabbit (Oryctolagus cuniculus).

PubMed

van Groen, T; Ruardy, L; da Silva, F H

1986-07-01

Field potentials elicited by electrical stimulation of the vomeronasal nerve were measured in the accessory olfactory bulb of the rabbit. Maps were made of the distribution of surface field potentials and of the corresponding depth profiles. The surface maps followed closely the contours of the accessory olfactory bulb: at the frontal border the field potential tended to zero and at the center of the structure the field potential attained a maximum. Depth profiles of the field potentials through the accessory olfactory bulb presented a surface-negative wave and, in depth, a positive wave. The polarity reversal occurred at the deep part of the granule cell layer. The zero equipotential line followed closely the curvature of the granule cell layer. Current source density analysis of the depth profiles revealed a main sink at the external plexiform and granule cell layers. This indicates that the main activity in the accessory olfactory bulb is generated by the synapses between the mitral cells and the granule cells as is found in the main olfactory bulb.

Characterization of drug-eluting stent (DES) materials with cluster secondary ion mass spectrometry (SIMS)

NASA Astrophysics Data System (ADS)

Mahoney, Christine M.; Patwardhan, Dinesh V.; Ken McDermott, M.

2006-07-01

Secondary ion mass spectrometry (SIMS) employing an SF 5+ polyatomic primary ion source was utilized to analyze several materials commonly used in drug-eluting stents (DES). Poly(ethylene- co-vinyl acetate) (PEVA), poly(lactic- co-glycolic acid) (PLGA) and various poly(urethanes) were successfully depth profiled using SF 5+ bombardment. The resultant molecular depth profiles obtained from these polymeric films showed very little degradation in molecular signal as a function of increasing SF 5+ primary ion dose when experiments were performed at low temperatures (signal was maintained for doses up to ˜5 × 10 15 ions/cm 2). Temperature was determined to be an important parameter in both the success of the depth profiles and the mass spectral analysis of the polymers. In addition to the pristine polymer films, paclitaxel (drug released in Taxus™ stent) containing PLGA films were also characterized, where it was confirmed that both drug and polymer signals could be monitored as a function of depth at lower paclitaxel concentrations (10 wt%).

Tracking the Subsurface Signal of Decadal Climate Warming to Quantify Vertical Groundwater Flow Rates

NASA Astrophysics Data System (ADS)

Bense, V. F.; Kurylyk, B. L.

2017-12-01

Sustained ground surface warming on a decadal time scale leads to an inversion of thermal gradients in the upper tens of meters. The magnitude and direction of vertical groundwater flow should influence the propagation of this warming signal, but direct field observations of this phenomenon are rare. Comparison of temperature-depth profiles in boreholes in the Veluwe area, Netherlands, collected in 1978-1982 and 2016 provided such direct measurement. We used these repeated profiles to track the downward propagation rate of the depth at which the thermal gradient is zero. Numerical modeling of the migration of this thermal gradient "inflection point" yielded estimates of downward groundwater flow rates (0-0.24 m a-1) that generally concurred with known hydrogeological conditions in the area. We conclude that analysis of inflection point depths in temperature-depth profiles impacted by surface warming provides a largely untapped opportunity to inform sustainable groundwater management plans that rely on accurate estimates of long-term vertical groundwater fluxes.

Retrieving cloud, dust and ozone abundances in the Martian atmosphere using SPICAM/UV nadir spectra

NASA Astrophysics Data System (ADS)

Willame, Y.; Vandaele, A. C.; Depiesse, C.; Lefèvre, F.; Letocart, V.; Gillotay, D.; Montmessin, F.

2017-08-01

We present the retrieval algorithm developed to analyse nadir spectra from SPICAM/UV aboard Mars-Express. The purpose is to retrieve simultaneously several parameters of the Martian atmosphere and surface: the dust optical depth, the ozone total column, the cloud opacity and the surface albedo. The retrieval code couples the use of an existing complete radiative transfer code, an inversion method and a cloud detection algorithm. We describe the working principle of our algorithm and the parametrisation used to model the required absorption, scattering and reflection processes of the solar UV radiation that occur in the Martian atmosphere and at its surface. The retrieval method has been applied on 4 Martian years of SPICAM/UV data to obtain climatologies of the different quantities under investigation. An overview of the climatology is given for each species showing their seasonal and spatial distributions. The results show a good qualitative agreement with previous observations. Quantitative comparisons of the retrieved dust optical depths indicate generally larger values than previous studies. Possible shortcomings in the dust modelling (altitude profile) have been identified and may be part of the reason for this difference. The ozone results are found to be influenced by the presence of clouds. Preliminary quantitative comparisons show that our retrieved ozone columns are consistent with other results when no ice clouds are present, and are larger for the cases with clouds at high latitude. Sensitivity tests have also been performed showing that the use of other a priori assumptions such as the altitude distribution or some scattering properties can have an important impact on the retrieval.

Dissolved Ti in the US GEOTRACES Atlantic Transect

NASA Astrophysics Data System (ADS)

Murray, R. W.; Moran, S.; Kelly, R. P.; Kelley, K. A.; Graham, D.

2012-12-01

The concentration of Ti in sediment and settling particles is often used as a lithogenic tracer, based on the assumption that its inventory is dominated by the mineralogically-bound component. Given Ti's overall refractory geochemical nature and that it is the 9th most abundant element in the crust, Ti offers several advantages for such use. However, there are suggestions in various literatures (deep-sea carbonates, coastal/estuarine waters and porewaters, and the few extant open ocean data) that Ti may have a quantitatively significant labile behavior that challenges the assumption of its lithogenic exclusivity. We report on a new technique developed to measure dissolved Ti in open ocean seawater. We will present data from SAFe and GEOTRACES intercalibration standards, as well as from complete depth profiles along the US Atlantic GEOTRACES sections sampled in 2010 and 2011. Following work of Biller et al. (2012, Mar. Chem., 130, 12-), preconcentration in our method is achieved via the NOBIAS-chelate PA1 resin of Sohrin et al. (2008, Anal. Chem., 80, 6267-). We achieve a 12-fold concentration from 60 ml of seawater, and samples are analyzed in triplicate. Samples are UV-oxidized prior to column treatment. We have quantified dissolved Ti both by Isotope Dilution quadrupole ICP-MS (ID-ICP-MS) and also by linear calibrations to Ti-free seawaters spiked with variable Ultra High Purity Ti to mimic natural range of abundances. We achieve a total procedural blank of 10 pM, with a detection limit of 6 pM. Ongoing improvements are oriented towards a smaller initial volume of seawater sample. Our results of intercalibration standards S1, D2, GS, and GD agree well with those generated by Croot (2011, Anal. Chem., 83, 6395-) using cathodic stripping voltammetry. We also have analyzed GSP, D1, and NASS-6. Of particular interest is intercalibration standard GD, taken from 2000 m at the BATS location for which Orians et al. (1990, Nature, 348, 322-) have published the only extant data for dissolved Ti in the open Atlantic. Croot's values and our values both agree well with Orians' original analyses, which not only confirms our respective analytical approaches but also suggests that the GEOTRACES rosette system, small parts of which contain Ti, does not contaminate seawater samples for Ti. We also present data from the 2011 GEOTRACES station taken at BATS in the western Atlantic and at Station 11 from the 2010 GEOTRACES transect in the eastern Atlantic. Our profile to 2000 m (= 213 pM) is similar to that of Orians et al. (1990) to the same depth, but extends deeper to 3597 m. Unlike the deep Pacific profile of Orians et al. (1990) from Station PAPA, which extends to 3860 m and reaches a maximum of 263 pM at that depth, our BATS profile is essentially invariant with depth below 2000 m. We observe a similar deepwater distribution at Station 11, which shows an increase from 60 pM near the surface to a maximum of 180 pM at 700 m, followed perhaps by a slight decrease to 130 pM at 3300 m depth.

Inorganic material profiling using Arn+ cluster: Can we achieve high quality profiles?

NASA Astrophysics Data System (ADS)

Conard, T.; Fleischmann, C.; Havelund, R.; Franquet, A.; Poleunis, C.; Delcorte, A.; Vandervorst, W.

2018-06-01

Retrieving molecular information by sputtering of organic systems has been concretized in the last years due to the introduction of sputtering by large gas clusters which drastically eliminated the compound degradation during the analysis and has led to strong improvements in depth resolution. Rapidly however, a limitation was observed for heterogeneous systems where inorganic layers or structures needed to be profiled concurrently. As opposed to organic material, erosion of the inorganic layer appears very difficult and prone to many artefacts. To shed some light on these problems we investigated a simple system consisting of aluminum delta layer(s) buried in a silicon matrix in order to define the most favorable beam conditions for practical analysis. We show that counterintuitive to the small energy/atom used and unlike monoatomic ion sputtering, the information depth obtained with large cluster ions is typically very large (∼10 nm) and that this can be caused both by a large roughness development at early stages of the sputtering process and by a large mixing zone. As a consequence, a large deformation of the Al intensity profile is observed. Using sample rotation during profiling significantly improves the depth resolution while sample temperature has no significant effect. The determining parameter for high depth resolution still remains the total energy of the cluster instead of the energy per atom in the cluster.

How well Can We Classify SWOT-derived Water Surface Profiles?

NASA Astrophysics Data System (ADS)

Frasson, R. P. M.; Wei, R.; Picamilh, C.; Durand, M. T.

2015-12-01

The upcoming Surface Water Ocean Topography (SWOT) mission will detect water bodies and measure water surface elevation throughout the globe. Within its continental high resolution mask, SWOT is expected to deliver measurements of river width, water elevation and slope of rivers wider than ~50 m. The definition of river reaches is an integral step of the computation of discharge based on SWOT's observables. As poorly defined reaches can negatively affect the accuracy of discharge estimations, we seek strategies to break up rivers into physically meaningful sections. In the present work, we investigate how accurately we can classify water surface profiles based on simulated SWOT observations. We assume that most river sections can be classified as either M1 (mild slope, with depth larger than the normal depth), or A1 (adverse slope with depth larger than the critical depth). This assumption allows the classification to be based solely on the second derivative of water surface profiles, with convex profiles being classified as A1 and concave profiles as M1. We consider a HEC-RAS model of the Sacramento River as a representation of the true state of the river. We employ the SWOT instrument simulator to generate a synthetic pass of the river, which includes our best estimates of height measurement noise and geolocation errors. We process the resulting point cloud of water surface heights with the RiverObs package, which delineates the river center line and draws the water surface profile. Next, we identify inflection points in the water surface profile and classify the sections between the inflection points. Finally, we compare our limited classification of simulated SWOT-derived water surface profile to the "exact" classification of the modeled Sacramento River. With this exercise, we expect to determine if SWOT observations can be used to find inflection points in water surface profiles, which would bring knowledge of flow regimes into the definition of river reaches.

In-Depth Interviewing as Qualitative Investigation.

ERIC Educational Resources Information Center

Books, Marilyn

A discussion of in-depth interviewing as a method for research on language teaching and learning situates the technique within the continuum of research methodology and differentiates it from quantitative research methods. The strengths and weaknesses of in-depth interviewing are examined, methods of sampling are discussed, and advice on the…

Integrating depth functions and hyper-scale terrain analysis for 3D soil organic carbon modeling in agricultural fields at regional scale

NASA Astrophysics Data System (ADS)

Ramirez-Lopez, L.; van Wesemael, B.; Stevens, A.; Doetterl, S.; Van Oost, K.; Behrens, T.; Schmidt, K.

2012-04-01

Soil Organic Carbon (SOC) represents a key component in the global C cycle and has an important influence on the global CO2 fluxes between terrestrial biosphere and atmosphere. In the context of agricultural landscapes, SOC inventories are important since soil management practices have a strong influence on CO2 fluxes and SOC stocks. However, there is lack of accurate and cost-effective methods for producing high spatial resolution of SOC information. In this respect, our work is focused on the development of a three dimensional modeling approach for SOC monitoring in agricultural fields. The study area comprises ~420 km2 and includes 4 of the 5 agro-geological regions of the Grand-Duchy of Luxembourg. The soil dataset consist of 172 profiles (1033 samples) which were not sampled specifically for this study. This dataset is a combination of profile samples collected in previous soil surveys and soil profiles sampled for other research purposes. The proposed strategy comprises two main steps. In the first step the SOC distribution within each profile (vertical distribution) is modeled. Depth functions for are fitted in order to summarize the information content in the profile. By using these functions the SOC can be interpolated at any depth within the profiles. The second step involves the use of contextual terrain (ConMap) features (Behrens et al., 2010). These features are based on the differences in elevation between a given point location in the landscape and its circular neighbourhoods at a given set of different radius. One of the main advantages of this approach is that it allows the integration of several spatial scales (eg. local and regional) for soil spatial analysis. In this work the ConMap features are derived from a digital elevation model of the area and are used as predictors for spatial modeling of the parameters of the depth functions fitted in the previous step. In this poster we present some preliminary results in which we analyze: i. The use of different depth functions, ii. The use of different machine learning approaches for modeling the parameters of the fitted depth functions using the ConMap features and iii. The influence of different spatial scales on the SOC profile distribution variability. Keywords: 3D modeling, Digital soil mapping, Depth functions, Terrain analysis. Reference Behrens, T., K. Schmidt, K., Zhu, A.X. Scholten, T. 2010. The ConMap approach for terrain-based digital soil mapping. European Journal of Soil Science, v. 61, p.133-143.

Using Vertical electrical sounding survey and refraction seismic survey for determining the geological layers depths, the structural features and assessment groundwater in Aqaba area in South Jordan.

NASA Astrophysics Data System (ADS)

Akawwi, Emad; Alzoubi, Abdallah; Ben Abraham, Zvi; Rahamn Abo Alades, Abdel; Alrzouq, Rami; Tiber, Gidon; Neimi, Tina

2010-05-01

The study area is the Aqaba region (Southern wadi Araba basin). Aqaba region area located at 87900 and 89000 North and 147000 and 158000 East (Palestine grid). Tectonically Aqaba area lies within the tectonic plate boundary along the Arabian and African plate slide. This plate boundary comprises numerous and shot fault segments. The main aims of this study are to assessing the groundwater potential and its quality, to explain the subsurface geological conditions and support the ongoing geological, environmental and hydrogeological studies. Therefore, it was anticipated that the results of the geophysical surveying will give many different important parameters as The subsurface geological features, thicknesses of the different lithological units, depth to the bed rocks and depth to the water table. The groundwater can apply an important role in ensuring sustainable water supply in the area. This study was carried out in order to assess groundwater condition, geological layers thicknesses and structural features in Aqaba area by using vertical electrical sounding (VES) surveys and refraction seismic techniques. There are three geoelectrical cross section were carried out at different sites by using the Schlumberger array. The first cross section indicated three layers of different resistivity. The second cross section indicated four layers of different resistivity. The third geoelectrical cross sections indicated three layers. The refraction seismic method also has been conducted in the same area as VES. About 12 refraction seismic profiles have been carried out in the study area. The length of the first profile was 745 m at the direction N-S. This profile indicated two different layers with a different velocities. The length of the second profile was 1320 m with E-W direction. This profile indicated two different layers. The length of the third profile was about 515 m with a direction SE-NW. It recognized two different layers with a different velocities. The fourth profile was N-S direction and the length of this profile was 950 m. Two different layers were recognized along this profile. The fifth profile was located N-S with length about 340 m. Two layers were recognized from this profile. The sixth profile was located N-S direction and the length about 575 m. Three layers were recognized from this profile. The direction of the seventh profile was N-S with a length of about 235 m. two different layers were recognized the top layer was unconsolidated alluvium. The profile number 8 was located N-S with length about 232 m. two layers were conducted from this profile. The direction of ninth profile was NW-SE with length about 565 m. two layers were conducted along this profile. The length of the tenth profile was 235 m and the direction was N-S. Two layers with a different velocities were detected along this profile. Profile number eleven was located SW-NE with length about 475 m. two layers were recognized from this profile. The length of the last profile was 375 m with direction SE-NW. Two layers were conducted from this profile. It was found that the shallow aquifers exist at a depths ranging from 4 to 19 m and the relatively deep aquifers from 24 to 60 m below the ground surface. Keywords: Vertical electrical sounding, Aqaba, Resistivity, Groundwater, Layer depth, Geoelectrical.

Online, efficient and precision laser profiling of bronze-bonded diamond grinding wheels based on a single-layer deep-cutting intermittent feeding method

NASA Astrophysics Data System (ADS)

Deng, Hui; Chen, Genyu; He, Jie; Zhou, Cong; Du, Han; Wang, Yanyi

2016-06-01

In this study, an online, efficient and precision laser profiling approach that is based on a single-layer deep-cutting intermittent feeding method is described. The effects of the laser cutting depth and the track-overlap ratio of the laser cutting on the efficiency, precision and quality of laser profiling were investigated. Experiments on the online profiling of bronze-bonded diamond grinding wheels were performed using a pulsed fiber laser. The results demonstrate that an increase in the laser cutting depth caused an increase in the material removal efficiency during the laser profiling process. However, the maximum laser profiling efficiency was only achieved when the laser cutting depth was equivalent to the initial surface contour error of the grinding wheel. In addition, the selection of relatively high track-overlap ratios of laser cutting for the profiling of grinding wheels was beneficial with respect to the increase in the precision of laser profiling, whereas the efficiency and quality of the laser profiling were not affected by the change in the track-overlap ratio. After optimized process parameters were employed for online laser profiling, the circular run-out error and the parallelism error of the grinding wheel surface decreased from 83.1 μm and 324.6 μm to 11.3 μm and 3.5 μm, respectively. The surface contour precision of the grinding wheel significantly improved. The highest surface contour precision for grinding wheels of the same type that can be theoretically achieved after laser profiling is completely dependent on the peak power density of the laser. The higher the laser peak power density is, the higher the surface contour precision of the grinding wheel after profiling.

Laser characterization of the depth profile of complex refractive index of PMMA implanted with 50 keV silicon ions

NASA Astrophysics Data System (ADS)

Stefanov, Ivan L.; Stoyanov, Hristiyan Y.; Petrova, Elitza; Russev, Stoyan C.; Tsutsumanova, Gichka G.; Hadjichristov, Georgi B.

2013-03-01

The depth profile of the complex refractive index of silicon ion (Si+) implanted polymethylmethacrylate (PMMA) is studied, in particular PMMA implanted with Si+ ions accelerated to a relatively low energy of 50 keV and at a fluence of 3.2 × 1015 cm-2. The ion-modified material with nano-clustered structure formed in the near(sub)surface layer of a thickness of about 100 nm is optically characterized by simulation based on reflection ellipsometry measurements at a wavelength of 632.8 nm (He-Ne laser). Being of importance for applications of ion-implanted PMMA in integrated optics, optoelectronics and optical communications, the effect of the index depth profile of Si+-implanted PMMA on the profile of the reflected laser beam due to laser-induced thermo-lensing in reflection is also analyzed upon illumination with a low power cw laser (wavelength 532 nm, optical power 10 - 50 mW).

Prevalence and Reliability of Phonological, Surface, and Mixed Profiles in Dyslexia: A Review of Studies Conducted in Languages Varying in Orthographic Depth

ERIC Educational Resources Information Center

Sprenger-Charolles, Liliane; Siegel, Linda S.; Jimenez, Juan E.; Ziegler, Johannes C.

2011-01-01

The influence of orthographic transparency on the prevalence of dyslexia subtypes was examined in a review of multiple-case studies conducted in languages differing in orthographic depth (English, French, and Spanish). Cross-language differences are found in the proportion of dissociated profiles as a function of the dependent variables (speed or…

Neogene Uplift and Magmatism of Anatolia: Insights From Drainage Analysis and Basaltic Geochemistry

NASA Astrophysics Data System (ADS)

McNab, F.; Ball, P. W.; Hoggard, M. J.; White, N. J.

2018-01-01

It is agreed that mantle dynamics have played a role in generating and maintaining the elevated topography of Anatolia during Neogene times. However, there is debate about the relative importance of subduction zone and asthenospheric processes. Key issues concern onset and cause of regional uplift, thickness of the lithospheric plate, and the presence/absence of temperature and/or compositional anomalies within the convecting mantle. Here, we tackle these interlinked issues by analyzing and modeling two disparate suites of observations. First, a drainage inventory of 1,844 longitudinal river profiles is assembled. This database is inverted to calculate the variation of Neogene regional uplift through time and space by minimizing the misfit between observed and calculated river profiles subject to independent calibration. Our results suggest that regional uplift commenced at 20 Ma in the east and propagated westward. Second, we have assembled a database of geochemical analyses of basaltic rocks. Two different approaches have been used to quantitatively model this database with a view to determining the depth and degree of asthenospheric melting across Anatolia. Our results suggest that melting occurs at depths as shallow as 60 km in the presence of mantle potential temperatures as high as 1400°C. There is evidence that temperatures are higher in the east, consistent with the pattern of subplate shear wave velocity anomalies. Our combined results are consistent with isostatic and admittance analyses and suggest that elevated asthenospheric temperatures beneath thinned Anatolian lithosphere have played a first-order role in generating and maintaining regional dynamic topography and basaltic magmatism.

Profiling and characterization of sialylated N-glycans by 2D-HPLC (HIAX/PGC) with online orbitrap MS/MS and offline MSn.

PubMed

Hanneman, Andrew J S; Strand, James; Huang, Chi-Ting

2014-02-01

Glycosylation is a critical parameter used to evaluate protein quality and consistency. N-linked glycan profiling is fundamental to the support of biotherapeutic protein manufacturing from early stage process development through drug product commercialization. Sialylated glycans impact the serum half-life of receptor-Fc fusion proteins (RFPs), making their quality and consistency a concern during the production of fusion proteins. Here, we describe an analytical approach providing both quantitative profiling and in-depth mass spectrometry (MS)-based structural characterization of sialylated RFP N-glycans. Aiming to efficiently link routine comparability studies with detailed structural characterization, an integrated workflow was implemented employing fluorescence detection, online positive and negative ion tandem mass spectrometry (MS/MS), and offline static nanospray ionization-sequential mass spectrometry (NSI-MS(n)). For routine use, high-performance liquid chromatography profiling employs established fluorescence detection of 2-aminobenzoic acid derivatives (2AA) and hydrophilic interaction anion-exchange chromatography (HIAX) charge class separation. Further characterization of HIAX peak fractions is achieved by online (-) ion orbitrap MS/MS, offering the advantages of high mass accuracy and data-dependent MS/MS. As required, additional characterization uses porous graphitized carbon in the second chromatographic dimension to provide orthogonal (+) ion MS/MS spectra and buffer-free liquid chromatography peak eluants that are optimum for offline (+)/(-) NSI-MS(n) investigations to characterize low-abundance species and specific moieties including O-acetylation and sulfation. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association.

Automated X-ray quality control of catalytic converters

NASA Astrophysics Data System (ADS)

Shashishekhar, N.; Veselitza, D.

2017-02-01

Catalytic converters are devices attached to the exhaust system of automobile or other engines to eliminate or substantially reduce polluting emissions. They consist of coated substrates enclosed in a stainless steel housing. The substrate is typically made of ceramic honeycombs; however stainless steel foil honeycombs are also used. The coating is usually a slurry of alumina, silica, rare earth oxides and platinum group metals. The slurry also known as the wash coat is applied to the substrate in two doses, one on each end of the substrate; in some cases multiple layers of coating are applied. X-ray imaging is used to inspect the applied coating depth on a substrate to confirm compliance with quality requirements. Automated image analysis techniques are employed to measure the coating depth from the X-ray image. Coating depth is assessed by analysis of attenuation line profiles in the image. Edge detection algorithms with noise reduction and outlier rejection are used to calculate the coating depth at a specified point along an attenuation line profile. Quality control of the product is accomplished using several attenuation line profile regions for coating depth measurements, with individual pass or fail criteria specified for each region.

Alkyl nitrate (C1-C3) depth profiles in the tropical Pacific Ocean

NASA Astrophysics Data System (ADS)

Dahl, E. E.; Yvon-Lewis, S. A.; Saltzman, E. S.

2007-01-01

This paper reports the first depth profile measurements of methyl, ethyl, isopropyl and n-propyl nitrates in the tropical Pacific Ocean. Depth profile measurements were made at 22 stations during the Project Halocarbon Air Sea Exchange cruise, in warm pool, equatorial, subequatorial, and gyre waters. The highest concentrations, up to several hundred pM of methyl nitrate, were observed in the central Pacific within 8 degrees of the equator. In general, alkyl nitrate levels were highest in the surface mixed layer, and decreased with depth below the mixed layer. The spatial distribution of the alkyl nitrates suggests that there is a strong source associated with biologically productive ocean regions, that is characterized by high ratios of methyl:ethyl nitrate. However, the data do not allow discrimination between direct biological emissions and photochemistry as production mechanisms. Alkyl nitrates were consistently detectable at several hundred meters depth. On the basis of the estimated chemical loss rate of these compounds, we conclude that deep water alkyl nitrates must be produced in situ. Possible sources include free radical processes initiated by radioactive decay or cosmic rays, enzymatically mediated reactions involving bacteria, or unidentified chemical mechanisms involving dissolved organic matter.

Changes in prescribed doses for the Seattle neutron therapy system

NASA Astrophysics Data System (ADS)

Popescu, A.

2008-06-01

From the beginning of the neutron therapy program at the University of Washington Medical Center, the neutron dose distribution in tissue has been calculated using an in-house treatment planning system called PRISM. In order to increase the accuracy of the absorbed dose calculations, two main improvements were made to the PRISM treatment planning system: (a) the algorithm was changed by the addition of an analytical expression of the central axis wedge factor dependence with field size and depth developed at UWMC. Older versions of the treatment-planning algorithm used a constant central axis wedge factor; (b) a complete newly commissioned set of measured data was introduced in the latest version of PRISM. The new version of the PRISM algorithm allowed for the use of the wedge profiles measured at different depths instead of one wedge profile measured at one depth. The comparison of the absorbed dose calculations using the old and the improved algorithm showed discrepancies mainly due to the missing central axis wedge factor dependence with field size and depth and due to the absence of the wedge profiles at depths different from 10 cm. This study concludes that the previously reported prescribed doses for neutron therapy should be changed.

Depth Profiles in Maize ( Zea mays L.) Seeds Studied by Photoacoustic Spectroscopy

NASA Astrophysics Data System (ADS)

Hernández-Aguilar, C.; Domínguez-Pacheco, A.; Cruz-Orea, A.; Zepeda-Bautista, R.

2015-06-01

Photoacoustic spectroscopy (PAS) has been used to analyze agricultural seeds and can be applied to the study of seed depth profiles of these complex samples composed of different structures. The sample depth profile can be obtained through the photoacoustic (PA) signal, amplitude, and phase at different light modulation frequencies. The PA signal phase is more sensitive to changes of thermal properties in layered samples than the PA signal amplitude. Hence, the PA signal phase can also be used to characterize layers at different depths. Thus, the objective of the present study was to obtain the optical absorption spectra of maize seeds ( Zea mays L.) by means of PAS at different light modulation frequencies (17 Hz, 30 Hz, and 50 Hz) and comparing these spectra with the ones obtained from the phase-resolved method in order to separate the optical absorption spectra of seed pericarp and endosperm. The results suggest the possibility of using the phase-resolved method to obtain optical absorption spectra of different seed structures, at different depths, without damaging the seed. Thus, PAS could be a nondestructive method for characterization of agricultural seeds and thus improve quality control in the food industry.

Regional correlations of VS30 averaged over depths less than and greater than 30 meters

USGS Publications Warehouse

Boore, David M.; Thompson, Eric M.; Cadet, Héloïse

2011-01-01

Using velocity profiles from sites in Japan, California, Turkey, and Europe, we find that the time-averaged shear-wave velocity to 30 m (VS30), used as a proxy for site amplification in recent ground-motion prediction equations (GMPEs) and building codes, is strongly correlated with average velocities to depths less than 30 m (VSz, with z being the averaging depth). The correlations for sites in Japan (corresponding to the KiK-net network) show that VSz is systematically larger for a given VSz than for profiles from the other regions. The difference largely results from the placement of the KiK-net station locations on rock and rocklike sites, whereas stations in the other regions are generally placed in urban areas underlain by sediments. Using the KiK-net velocity profiles, we provide equations relating VS30 to VSz for z ranging from 5 to 29 m in 1-m increments. These equations (and those for California velocity profiles given in Boore, 2004b) can be used to estimate VS30 from VSz for sites in which velocity profiles do not extend to 30 m. The scatter of the residuals decreases with depth, but, even for an averaging depth of 5 m, a variation in logVS30 of ±1 standard deviation maps into less than a 20% uncertainty in ground motions given by recent GMPEs at short periods. The sensitivity of the ground motions to VS30 uncertainty is considerably larger at long periods (but is less than a factor of 1.2 for averaging depths greater than about 20 m). We also find that VS30 is correlated with VSz for z as great as 400 m for sites of the KiK-net network, providing some justification for using VS30 as a site-response variable for predicting ground motions at periods for which the wavelengths far exceed 30 m.

Improved depth profiling with slow positrons of ion implantation-induced damage in silicon

NASA Astrophysics Data System (ADS)

Fujinami, M.; Miyagoe, T.; Sawada, T.; Akahane, T.

2003-10-01

Variable-energy positron annihilation spectroscopy (VEPAS) has been extensively applied to study defects in near-surface regions and buried interfaces, but there is an inherent limit for depth resolution due to broadening of the positron implantation profile. In order to overcome this limit and obtain optimum depth resolution, iterative chemical etching of the sample surface and VEPAS measurement are employed. This etch-and-measure technique is described in detail and the capabilities are illustrated by investigating the depth profile of defects in Si after B and P implantations with 2×1014/cm2 at 100 keV followed by annealing. Defect tails can be accurately examined and the extracted defect profile is proven to extend beyond the implanted ion range predicted by the Monte Carlo code TRIM. This behavior is more remarkable for P ion implantation than B, and the mass difference of the implanted ions is strongly related to it. No significant difference is recognized in the annealing behavior between B and P implantations. After annealing at 300 °C, the defect profile is hardly changed, but the ratio of the characteristic Doppler broadening, S, a parameter for defects, to that for the bulk Si rises by 0.01, indicating that divacancies, V2, are transformed into V4. Annealing at more than 500 °C causes diffusion of the defects toward the surface and positron traps are annealed out at 800 °C. It is proved that this resolution-enhanced VEPAS can eliminate some discrepancies in defect profiles extracted by conventional means.

Three-dimensional dosimetry of small megavoltage radiation fields using radiochromic gels and optical CT scanning

NASA Astrophysics Data System (ADS)

Babic, Steven; McNiven, Andrea; Battista, Jerry; Jordan, Kevin

2009-04-01

The dosimetry of small fields as used in stereotactic radiotherapy, radiosurgery and intensity-modulated radiation therapy can be challenging and inaccurate due to partial volume averaging effects and possible disruption of charged particle equilibrium. Consequently, there exists a need for an integrating, tissue equivalent dosimeter with high spatial resolution to avoid perturbing the radiation beam and artificially broadening the measured beam penumbra. In this work, radiochromic ferrous xylenol-orange (FX) and leuco crystal violet (LCV) micelle gels were used to measure relative dose factors (RDFs), percent depth dose profiles and relative lateral beam profiles of 6 MV x-ray pencil beams of diameter 28.1, 9.8 and 4.9 mm. The pencil beams were produced via stereotactic collimators mounted on a Varian 2100 EX linear accelerator. The gels were read using optical computed tomography (CT). Data sets were compared quantitatively with dosimetric measurements made with radiographic (Kodak EDR2) and radiochromic (GAFChromic® EBT) film, respectively. Using a fast cone-beam optical CT scanner (Vista™), corrections for diffusion in the FX gel data yielded RDFs that were comparable to those obtained by minimally diffusing LCV gels. Considering EBT film-measured RDF data as reference, cone-beam CT-scanned LCV gel data, corrected for scattered stray light, were found to be in agreement within 0.5% and -0.6% for the 9.8 and 4.9 mm diameter fields, respectively. The validity of the scattered stray light correction was confirmed by general agreement with RDF data obtained from the same LCV gel read out with a laser CT scanner that is less prone to the acceptance of scattered stray light. Percent depth dose profiles and lateral beam profiles were found to agree within experimental error for the FX gel (corrected for diffusion), LCV gel (corrected for scattered stray light), and EBT and EDR2 films. The results from this study reveal that a three-dimensional dosimetry method utilizing optical CT-scanned radiochromic gels allows for the acquisition of a self-consistent volumetric data set in a single exposure, with sufficient spatial resolution to accurately characterize small fields.

Simple measures of channel habitat complexity predict transient hydraulic storage in streams

EPA Science Inventory

Stream thalweg depth profiles (along path of greatest channel depth) and woody debris tallies have recently become components of routine field procedures for quantifying physical habitat in national stream monitoring efforts. Mean residual depth, standard deviation of thalweg dep...

Optical nanoscopy of high T c cuprate nanoconstriction devices patterned by helium ion beams

DOE PAGES

Gozar, Adrian; Litombe, N. E.; Hoffman, Jennifer E.; ...

2017-02-06

Helium ion beams (HIB) focused to subnanometer scales have emerged as powerful tools for high-resolution imaging as well as nanoscale lithography, ion milling, or deposition. Quantifying irradiation effects is an essential step toward reliable device fabrication, but most of the depth profiling information is provided by computer simulations rather than the experiment. Here, we demonstrate the use of atomic force microscopy (AFM) combined with scanning near-field optical microscopy (SNOM) to provide three-dimensional (3D) dielectric characterization of high-temperature superconductor devices fabricated by HIB. By imaging the infrared dielectric response obtained from light demodulation at multiple harmonics of the AFM tapping frequency,more » we find that amorphization caused by the nominally 0.5 nm HIB extends throughout the entire 26.5 nm thickness of the cuprate film and by ~500 nm laterally. This unexpectedly widespread damage in morphology and electronic structure can be attributed to a helium depth distribution substantially modified by the internal device interfaces. Lastly, our study introduces AFM-SNOM as a quantitative tomographic technique for noninvasive 3D characterization of irradiation damage in a wide variety of nanoscale devices.« less

Profiles of eight working mothers who practiced exclusive breastfeeding in Depok, Indonesia.

PubMed

Februhartanty, Judhiastuty; Wibowo, Yulianti; Fahmida, Umi; Roshita, Airin

2012-02-01

Exclusive breastfeeding practice is generally low because of multifaceted factors internally within mothers themselves and also the surroundings. In addition, studies have consistently found that maternal employment outside the home is related to shorter duration of exclusive breastfeeding. With all these challenges, it is interesting that there are some mothers who manage to exclusively breastfeed their infants. Therefore, this report aims at exploring the characteristics of working mothers who are able to practice exclusive breastfeeding. The original study population was non-working and working mothers who have infants around 1 to 6 months old. The study design is an observational study with a mixed methods approach using a quantitative study (survey) and qualitative methods (in-depth interview) in sequential order. In addition, in-depth interviews with family members, midwives, supervisors at work, and community health workers were also included to accomplish a holistic picture of the situation. The study concludes that self-efficacy and confidence of the breastfeeding mothers characterize the practice of exclusive breastfeeding. Good knowledge that was acquired way before the mothers got pregnant suggests a predisposing factor to the current state of confidence. Home support from the father enhances the decision to sustain breastfeeding.

Structural diagnostics of the tropopause inversion layer and its evolution

NASA Astrophysics Data System (ADS)

Gettelman, A.; Wang, T.

2015-01-01

The Tropopause Inversion Layer (TIL) is marked by a peak in static stability directly above the tropopause. The TIL is quantitatively defined with new diagnostics using Global Positioning System Radio Occultation temperature soundings and reanalysis data. A climatology of the TIL is developed from reanalysis data (1980-2011) using diagnostics for the position, depth, and strength of the TIL based on the TIL peak in static stability. TIL diagnostics have defined relationships to the synoptic situation in the Upper Troposphere and Lower Stratosphere. The TIL is present nearly all the time. The TIL becomes hard to define in the subtropics where tropical air overlies midlatitude air, in a region of complex static stability profiles. The mean position of the subtropical TIL gradient is sharp and is co-located with the subtropical tropopause break. Over the period 1980-2011 the TIL depth below the tropopause has decreased by 5% per decade and increased above the tropical tropopause by a similar percentage. Furthermore, the latitude of the abrupt change in the TIL from tropical to extratropical in the lower stratosphere appears to have shifted poleward in each hemisphere by ˜1° latitude per decade, depending on the diagnostic examined. Reanalysis trends should be treated with caution.

Observation of changes in the metallurgical characteristics of Ni-Cr alloys using Nd:YAG laser welding

PubMed Central

Choi, SM

2014-01-01

This study aimed to determine the effect of hardness change according to penetration depth in the laser fusing zone and observed the correlation of the microstructure as an Nd:YAG laser was irradiated to Ni-Cr alloy for dental use by setting the spot diameter size to various conditions. In all groups, the hardness depth profiles in the laser fusing zone and heat-affected zone (HAZ) had larger values than those of the base metal. In addition, the hardness values in places beyond the fusing zone and the HAZ were measured as being quantitatively lower. The observation result of the diffusion of the constituent elements and microstructure using field emission scanning electron microscopy, energy-dispersive spectroscopy, and electron probe microanalyzer showed that the fusing zone revealed a much finer dendritic form than the base metal due to the self-quenching effect after welding, while no change in constituent elements was found although some evaporation of the main elements was observed. In addition, Mo- and Si-combined intermetallic compounds were formed on the interdendritic area. Through this study, the laser fusing zone had better hardenability due to the intermetallic compound and grain refinement effect. PMID:25342985

Detection and imaging of corrosion around wing skin fasteners using the dripless bubbler ultrasonic scanner

NASA Astrophysics Data System (ADS)

Hsu, David K.; Barnard, Daniel J.

1998-03-01

The galvanic action between steel fasteners and aluminum wing skins of aircraft often leads to hidden exfoliation corrosion around the countersink surface of the fastener heads. To detect and evaluate the severity of such corrosion defects, the Dripless Bubbler ultrasonic scanner was applied. This technique uses a focused beam of high frequency ultrasound in a closed-cycle, water-coupled scan of wing skin test panels containing corroded and uncorroded fasteners. With full waveform acquisition, not only the lateral extent but also the depth profile of the corrosions around the fastener heads were mapped out, subject to shadowing of defects at different depth. The technique is capable of providing quantitative assessment of the severity of the corrosion. In tests conducted to evaluate different techniques, the Dripless Bubbler has shown high probability of detection and low false call rate. The presence of paint on the surface did not degrade the performance of the technique. In addition, the Dripless Bubbler was also used on wing skin panels containing repair 'blend-out' regions that had 0.020' to 0.100' of metal removed from the surface by grinding. Corrosions around fasteners in the blend-out regions were also detected.

Benthopelagic megafauna assemblages of the Rio Grande Rise (SW Atlantic)

NASA Astrophysics Data System (ADS)

Perez, Jose Angel Alvarez; Kitazato, Hiroshi; Sumida, Paulo Yukio Gomes; Sant'Ana, Rodrigo; Mastella, Angélica Maffini

2018-04-01

The Rio Grande Rise (RGR) is a large and geomorphologically complex structure of the deep SW Atlantic Ocean. In 2013, the 600-1200 m deep plateau of the most prominent topographic component of the RGR (named Alpha) was explored during two dives of the manned submersible Shinkai 6500 (30°22‧15‧‧S - 36°02‧02‧‧W and 31°05‧58‧‧S - 34°02‧40‧‧W). Video profiles recorded during these dives were analyzed for description of benthopelagic megafauna (fish and crustaceans) assemblages, and quantitative assessment of structuring factors (depth, topography and habitat types). Fishes represented over 92% (462) of all benthopelagic megafauna, divided into 11 orders and 17 families. Over half of fish records were Macrouridae, Synaphobranchidae and Chaunacidae. Megafauna abundance varied at different spatial scales, being higher in shallower habitats ( 600 m) dominated by branched suspension feeders (mostly sponges and cnidarians). Beta-diversity and community structure were related to habitat diversity. Because the RGR is vast and may comprise numerous distinctive habitats associated with depth, topography and water mass dynamics, fauna diversity may be high and patchy.

A (137)Cs erosion model with moving boundary.

PubMed

Yin, Chuan; Ji, Hongbing

2015-12-01

A novel quantitative model of the relationship between diffused concentration changes and erosion rates using assessment of soil losses was developed. It derived from the analysis of surface soil (137)Cs flux variation under persistent erosion effect and based on the principle of geochemistry kinetics moving boundary. The new moving boundary model improves the basic simplified transport model (Zhang et al., 2008), and mainly applies to uniform rainfall areas which show a long-time soil erosion. The simulation results for this kind of erosion show under a long-time soil erosion, the influence of (137)Cs concentration will decrease exponentially with increasing depth. Using the new model fit to the measured (137)Cs depth distribution data in Zunyi site, Guizhou Province, China which has typical uniform rainfall provided a good fit with R(2) = 0.92. To compare the soil erosion rates calculated by the simple transport model and the new model, we take the Kaixian reference profile as example. The soil losses estimated by the previous simplified transport model are greater than those estimated by the new moving boundary model, which is consistent with our expectations. Copyright © 2015 Elsevier Ltd. All rights reserved.

GPR studies over the tsunami affected Karaikal beach, Tamil Nadu, south India

NASA Astrophysics Data System (ADS)

Loveson, V. J.; Gujar, A. R.; Barnwal, R.; Khare, Richa; Rajamanickam, G. V.

2014-08-01

In this study, results of GPR profiling related to mapping of subsurface sedimentary layers at tsunami affected Karaikal beach are presented . A 400 MHz antenna was used for profiling along 262 m stretch of transect from beach to backshore areas with penetration of about 2.0 m depth (50 ns two-way travel time). The velocity analysis was carried out to estimate the depth information along the GPR profile. Based on the significant changes in the reflection amplitude, three different zones are marked and the upper zone is noticed with less moisture compared to other two (saturated) zones. The water table is noticed to vary from 0.5 to 0.75 m depth (12-15 ns) as moving away from the coastline. Buried erosional surface is observed at 1.5 m depth (40-42 ns), which represents the limit up to which the extreme event acted upon. In other words, it is the depth to which the tsunami sediments have been piled up to about 1.5 m thickness. Three field test pits were made along the transect and sedimentary sequences were recorded. The sand layers, especially, heavy mineral layers, recorded in the test pits indicate a positive correlation with the amplitude and velocity changes in the GPR profile. Such interpretation seems to be difficult in the middle zone due to its water saturation condition. But it is fairly clear in the lower zone located just below the erosional surface where the strata is comparatively more compact. The inferences from the GPR profile thus provide a lucid insight to the subsurface sediment sequences of the tsunami sediments in the Karaikal beach.

Variations in bacterial and fungal community composition along the soil depth profiles determined by pyrosequencing

NASA Astrophysics Data System (ADS)

Ko, D.; Yoo, G.; Jun, S. C.; Yun, S. T.; Chung, H.

2015-12-01

Soil microorganisms play key roles in nutrient cycling, and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depth, we analyzed soil microbial activities and bacterial and fungal community composition in a soil profile of a fallow field located in central Korea. Soil samples were taken using 120-cm soil cores. To analyze the composition of bacterial and fungal communities, barcoded pyrosequnecing analysis of 16S rRNA genes (bacteria) and ITS region (fungi) was conducted. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1 and 17.5%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3 and 0.4%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively), a dominant fungal group at this site, showed no significant difference along the soil profile. To examine the vertical difference of microbial activities, activity of five extracellular enzymes that take part in cycling of C, N, and P in soil ecosystems, beta-1,4-glucosidase, cellobiohydrolase, beta-1,4-xylosidase, beta-1,4-N-acetylglucosaminidase, and acid phosphatase were analyzed. The soil enzyme activity declined with soil depth. For example, acid phosphatase activity was 88.5 (± 14.6 (± 1 SE)), 30.0 (± 5.9), 18.0 (± 3.5), 14.1 (± 3.7), and 10.7 (± 3.8) nmol g-1 hr-1, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of soil microbial communities and their relationship with biogeochemical factors.

Microbial Nitrogen Cycling Associated with the Early Diagenesis of Organic Matter in Subseafloor Sediments

NASA Astrophysics Data System (ADS)

Zhao, R.

2015-12-01

The early diagenesis of organic matter is the major energy source of marine sedimentary biosphere and thus controls its population size; however, the vertical distribution of any functional groups along with the diagenesis of organic matter is remained unclear, especially for those microbes involved in nitrogen transformation which serve as a major control on the nitrogen flux between reservoirs. Here we investigated the vertical distributions of various functional groups in five sediment cores retrieved from Arctic Mid-Ocean Ridge (AMOR), with emphasis on the nitrifiers, denitrifiers and anaerobic ammonium oxidizing bacteria (anammox). We observed the clear geochemical zonation associated with organic matter diagenesis in the sediments based on the pore water profiles of oxygen, nitrate, ammonium, manganese and sulfate, with distinct geochemical transition zones at the boundaries of geochemical zones, including oxic-anoxic transition zone (OATZ) and nitrate-manganese reduction zone (NMTZ). Nitrate was produced in surface oxygenated sediments and nitrate consumption mainly took place at the NMTZ, splitted between re-oxidation of ammonium and manganese (II). Abundances of ammonia oxidizers, nitrite oxidizers, and denitrifiers, estimated through quantitative PCR targeting their respective functional genes, generally decrease with depth, but constantly elevated around the OATZ, NMTZ, and manganese-reduction zone as well. Anammox bacteria were only detected around the NMTZ where both nitrate/nitrite and ammonium are available. These depth profiles of functional groups were also confirmed by the community structure profiling by prokaryotic 16S rRNA gene tag pyrosequencing. Cell-specific rates of nitrification and denitrification, calculated from the bulk net reaction rates divided by functional group abundances, were similar to those values from oligotrophic sediments like North Pond and thus suggested that nitrifiers and denitirifiers populations were in maintenance state. This study illustrated the microbial nitrogen transformation accompanying the early diagenesis of organic matter in marine sediments, which scenario might be occurring in a wide range of stratified environments on Earth.

Laser beam shaping for biomedical microscopy techniques

NASA Astrophysics Data System (ADS)

Laskin, Alexander; Kaiser, Peter; Laskin, Vadim; Ostrun, Aleksei

2016-04-01

Uniform illumination of a working field is very important in optical systems of confocal microscopy and various implementations of fluorescence microscopy like TIR, SSIM, STORM, PALM to enhance performance of these laser-based research techniques. Widely used TEM00 laser sources are characterized by essentially non-uniform Gaussian intensity profile which leads usually to non-uniform intensity distribution in a microscope working field or in a field of microlenses array of a confocal microscope optical system, this non-uniform illumination results in instability of measuring procedure and reducing precision of quantitative measurements. Therefore transformation of typical Gaussian distribution of a TEM00 laser to flat-top (top hat) profile is an actual technical task, it is solved by applying beam shaping optics. Due to high demands to optical image quality the mentioned techniques have specific requirements to a uniform laser beam: flatness of phase front and extended depth of field, - from this point of view the microscopy techniques are similar to holography and interferometry. There are different refractive and diffractive beam shaping approaches used in laser industrial and scientific applications, but only few of them are capable to fulfil the optimum conditions for beam quality required in discussed microscopy techniques. We suggest applying refractive field mapping beam shapers πShaper, which operational principle presumes almost lossless transformation of Gaussian to flat-top beam with flatness of output wavefront, conserving of beam consistency, providing collimated low divergent output beam, high transmittance, extended depth of field, negligible wave aberration, and achromatic design provides capability to work with several lasers with different wavelengths simultaneously. The main function of a beam shaper is transformation of laser intensity profile, further beam transformation to provide optimum for a particular technique spot size and shape has to be realized by an imaging optical system which can include microscope objectives and tube lenses. This paper will describe design basics of refractive beam shapers and optical layouts of their applying in microscopy systems. Examples of real implementations and experimental results will be presented as well.

Depth profiling and imaging capabilities of an ultrashort pulse laser ablation time of flight mass spectrometer

PubMed Central

Cui, Yang; Moore, Jerry F.; Milasinovic, Slobodan; Liu, Yaoming; Gordon, Robert J.; Hanley, Luke

2012-01-01

An ultrafast laser ablation time-of-flight mass spectrometer (AToF-MS) and associated data acquisition software that permits imaging at micron-scale resolution and sub-micron-scale depth profiling are described. The ion funnel-based source of this instrument can be operated at pressures ranging from 10−8 to ∼0.3 mbar. Mass spectra may be collected and stored at a rate of 1 kHz by the data acquisition system, allowing the instrument to be coupled with standard commercial Ti:sapphire lasers. The capabilities of the AToF-MS instrument are demonstrated on metal foils and semiconductor wafers using a Ti:sapphire laser emitting 800 nm, ∼75 fs pulses at 1 kHz. Results show that elemental quantification and depth profiling are feasible with this instrument. PMID:23020378

Chemical depth profiles of the GaAs/native oxide interface

NASA Technical Reports Server (NTRS)

Grunthaner, P. J.; Vasquez, R. P.; Grunthaner, F. J.

1980-01-01

The final-state oxidation products and their distribution in thin native oxides (30-40 A) on GaAs have been studied using X-ray photoelectron spectroscopy in conjunction with chemical depth profiling. Extended room-temperature-oxidation conditions have been chosen to allow the native oxide to attain its equilibrium composition and structure. The work emphasizes the use of chemical depth-profiling methods which make it possible to examine the variation in chemical reactivity of the oxide structure. A minimum of two distinct regions of Ga2O3 with differing chemical reactivity is observed. Chemical shift data indicate the presence of As2O3 in the oxide together with an elemental As overlayer at the interface. A change in relative charge transfer between oxygen and both arsenic and gallium-oxide species is observed in the region of the interface.

Modeling and parameterization of photoelectrons emitted in condensed matter by linearly polarized synchrotron radiation

NASA Astrophysics Data System (ADS)

Jablonski, A.

2018-01-01

Growing availability of synchrotron facilities stimulates an interest in quantitative applications of hard X-ray photoemission spectroscopy (HAXPES) using linearly polarized radiation. An advantage of this approach is the possibility of continuous variation of radiation energy that makes it possible to control the sampling depth for a measurement. Quantitative applications are based on accurate and reliable theory relating the measured spectral features to needed characteristics of the surface region of solids. A major complication in the case of polarized radiation is an involved structure of the photoemission cross-section for hard X-rays. In the present work, details of the relevant formalism are described and algorithms implementing this formalism for different experimental configurations are proposed. The photoelectron signal intensity may be considerably affected by variation in the positioning of the polarization vector with respect to the surface plane. This information is critical for any quantitative application of HAXPES by polarized X-rays. Different quantitative applications based on photoelectrons with energies up to 10 keV are considered here: (i) determination of surface composition, (ii) estimation of sampling depth, and (iii) measurements of an overlayer thickness. Parameters facilitating these applications (mean escape depths, information depths, effective attenuation lengths) were calculated for a number of photoelectron lines in four elemental solids (Si, Cu, Ag and Au) in different experimental configurations and locations of the polarization vector. One of the considered configurations, with polarization vector located in a plane perpendicular to the surface, was recommended for quantitative applications of HAXPES. In this configurations, it was found that the considered parameters vary weakly in the range of photoelectron emission angles from normal emission to about 50° with respect to the surface normal. The averaged values of the mean escape depth and effective attenuation length were approximated with accurate predictive formulas. The predicted effective attenuation lengths were compared with published values; major discrepancies observed can be ascribed to a possibility of discontinuous structure of the deposited overlayer.

The perception of three-dimensionality across continuous surfaces

NASA Technical Reports Server (NTRS)

Stevens, Kent A.

1989-01-01

The apparent three-dimensionality of a viewed surface presumably corresponds to several internal preceptual quantities, such as surface curvature, local surface orientation, and depth. These quantities are mathematically related for points within the silhouette bounds of a smooth, continuous surface. For instance, surface curvature is related to the rate of change of local surface orientation, and surface orientation is related to the local gradient of distance. It is not clear to what extent these 3D quantities are determined directly from image information rather than indirectly from mathematically related forms, by differentiation or by integration within boundary constraints. An open empirical question, for example, is to what extent surface curvature is perceived directly, and to what extent it is quantitative rather than qualitative. In addition to surface orientation and curvature, one derives an impression of depth, i.e., variations in apparent egocentric distance. A static orthographic image is essentially devoid of depth information, and any quantitative depth impression must be inferred from surface orientation and other sources. Such conversion of orientation to depth does appear to occur, and even to prevail over stereoscopic depth information under some circumstances.

Depth profiling of galvanoaluminium-nickel coatings on steel by UV- and VIS-LIBS

NASA Astrophysics Data System (ADS)

Nagy, T. O.; Pacher, U.; Giesriegl, A.; Weimerskirch, M. J. J.; Kautek, W.

2017-10-01

Laser-induced depth profiling was applied to the investigation of galvanised steel sheets as a typical modern multi-layer coating system for environmental corrosion protection. The samples were ablated stepwise by the use of two different wavelengths of a frequency-converted Nd:YAG-laser, 266 nm and 532 nm, with a pulse duration of τ = 4 ns at fluences ranging from F = 50 to 250 J cm-2. The emission light of the resulting plasma was analysed as a function of both penetration depth and elemental spectrum in terms of linear correlation analysis. Elemental depth profiles were calculated and compared to EDX-cross sections of the cut sample. A proven mathematical algorithm designed for the reconstruction of layer structures from distorted emission traces caused by the Gaussian ablation profile can even resolve thin intermediate layers in terms of depth and thickness. The obtained results were compared to a purely thermally controlled ablation model. Thereby light-plasma coupling is suggested to be a possible cause of deviations in the ablation behaviour of Al. The average ablation rate h as a function of fluence F for Ni ranges from 1 to 3.5 μm/pulse for λ = 266 nm as well as for λ = 532 nm. In contrast, the range of h for Al differs from 2 to 4 μm/pulse for λ = 532 nm and 4 to 8 μm/pulse for λ = 266 nm in the exact same fluence range on the exact same sample.

Identification of novel biomarker candidates for hypertrophic cardiomyopathy and other cardiovascular diseases leading to heart failure.

PubMed

Rehulkova, H; Rehulka, P; Myslivcova Fucikova, A; Stulik, J; Pudil, R

2016-11-23

In-depth proteome discovery analysis represents new strategy in an effort to identify novel reliable specific protein markers for hypertrophic cardiomyopathy and other life threatening cardiovascular diseases. To systematically identify novel protein biomarkers of cardiovascular diseases with high mortality we employed an isobaric tag for relative and absolute quantitation (iTRAQ) proteome technology to make comparative analysis of plasma samples obtained from patients suffering from non-obstructive hypertrophic cardiomyopathy, stable dilated cardiomyopathy, aortic valve stenosis, chronic stable coronary artery disease and stable arterial hypertension. We found 128 plasma proteins whose abundances were uniquely regulated among the analyzed cardiovascular pathologies. 49 of them have not been described yet. Additionally, application of statistical exploratory analyses of the measured protein profiles indicated the relationship in pathophysiology of the examined cardiovascular pathologies.

Parametric Modeling in Action: High Accuracy Seismology of Kepler DAV Stars

NASA Astrophysics Data System (ADS)

Giammichele, N.; Fontaine, G.; Charpinet, S.; Brassard, P.; Greiss, S.

2015-06-01

We summarize here the efforts made on the quantitative seismic analyses performed on two ZZ Ceti stars observed with the Kepler satellite. One of them, KIC 11911480, is located close to the blue edge of the instability strip, while the other, GD 1212, is found at the red edge. We emphasize the need for parameterized modeling and the forward approach to uniquely establish the fundamental parameters of the stars. We show how the internal structures as well as rotation profiles are unravelled to surprisingly large depths for degenerates such as ZZ Ceti stars, which further confirms the loss of stellar angular momentum before the white dwarf stage detected previously in GW Vir pulsating white dwarfs. This opens up interesting prospects for the new mission to come, Kepler-2, in the field of white dwarf asteroseismology.

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.

PubMed

Guertin, Michael J; Cullen, Amy E; Markowetz, Florian; Holding, Andrew N

2018-04-17

A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide changes in occupancy. Analysis-based normalization methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor (TF) binding, these assumptions do not hold true. The challenges in normalization are confounded by experimental variability during sample preparation, processing and recovery. We present a novel normalization strategy utilizing an internal standard of unchanged peaks for reference. Our method can be readily applied to monitor genome-wide changes by ChIP-seq that are otherwise lost or misrepresented through analytical normalization. We compare our approach to normalization by total read depth and two alternative methods that utilize external experimental controls to study TF binding. We successfully resolve the key challenges in quantitative ChIP-seq analysis and demonstrate its application by monitoring the loss of Estrogen Receptor-alpha (ER) binding upon fulvestrant treatment, ER binding in response to estrodiol, ER mediated change in H4K12 acetylation and profiling ER binding in patient-derived xenographs. This is supported by an adaptable pipeline to normalize and quantify differential TF binding genome-wide and generate metrics for differential binding at individual sites.

Quantitative proteomics and terminomics to elucidate the role of ubiquitination and proteolysis in adaptive immunity.

PubMed

Klein, Theo; Viner, Rosa I; Overall, Christopher M

2016-10-28

Adaptive immunity is the specialized defence mechanism in vertebrates that evolved to eliminate pathogens. Specialized lymphocytes recognize specific protein epitopes through antigen receptors to mount potent immune responses, many of which are initiated by nuclear factor-kappa B activation and gene transcription. Most, if not all, pathways in adaptive immunity are further regulated by post-translational modification (PTM) of signalling proteins, e.g. phosphorylation, citrullination, ubiquitination and proteolytic processing. The importance of PTMs is reflected by genetic or acquired defects in these pathways that lead to a dysfunctional immune response. Here we discuss the state of the art in targeted proteomics and systems biology approaches to dissect the PTM landscape specifically regarding ubiquitination and proteolysis in B- and T-cell activation. Recent advances have occurred in methods for specific enrichment and targeted quantitation. Together with improved instrument sensitivity, these advances enable the accurate analysis of often rare PTM events that are opaque to conventional proteomics approaches, now rendering in-depth analysis and pathway dissection possible. We discuss published approaches, including as a case study the profiling of the N-terminome of lymphocytes of a rare patient with a genetic defect in the paracaspase protease MALT1, a key regulator protease in antigen-driven signalling, which was manifested by elevated linear ubiquitination.This article is part of the themed issue 'Quantitative mass spectrometry'. © 2016 The Authors.

Depth to Curie temperature across the central Red Sea from magnetic data using the de-fractal method

NASA Astrophysics Data System (ADS)

Salem, Ahmed; Green, Chris; Ravat, Dhananjay; Singh, Kumar Hemant; East, Paul; Fairhead, J. Derek; Mogren, Saad; Biegert, Ed

2014-06-01

The central Red Sea rift is considered to be an embryonic ocean. It is characterised by high heat flow, with more than 90% of the heat flow measurements exceeding the world mean and high values extending to the coasts - providing good prospects for geothermal energy resources. In this study, we aim to map the depth to the Curie isotherm (580 °C) in the central Red Sea based on magnetic data. A modified spectral analysis technique, the “de-fractal spectral depth method” is developed and used to estimate the top and bottom boundaries of the magnetised layer. We use a mathematical relationship between the observed power spectrum due to fractal magnetisation and an equivalent random magnetisation power spectrum. The de-fractal approach removes the effect of fractal magnetisation from the observed power spectrum and estimates the parameters of depth to top and depth to bottom of the magnetised layer using iterative forward modelling of the power spectrum. We applied the de-fractal approach to 12 windows of magnetic data along a profile across the central Red Sea from onshore Sudan to onshore Saudi Arabia. The results indicate variable magnetic bottom depths ranging from 8.4 km in the rift axis to about 18.9 km in the marginal areas. Comparison of these depths with published Moho depths, based on seismic refraction constrained 3D inversion of gravity data, showed that the magnetic bottom in the rift area corresponds closely to the Moho, whereas in the margins it is considerably shallower than the Moho. Forward modelling of heat flow data suggests that depth to the Curie isotherm in the centre of the rift is also close to the Moho depth. Thus Curie isotherm depths estimated from magnetic data may well be imaging the depth to the Curie temperature along the whole profile. Geotherms constrained by the interpreted Curie isotherm depths have subsequently been calculated at three points across the rift - indicating the variation in the likely temperature profile with depth.

Reconstructing Space- and Energy-Dependent Exciton Generation in Solution-Processed Inverted Organic Solar Cells.

PubMed

Wang, Yuheng; Zhang, Yajie; Lu, Guanghao; Feng, Xiaoshan; Xiao, Tong; Xie, Jing; Liu, Xiaoyan; Ji, Jiahui; Wei, Zhixiang; Bu, Laju

2018-04-25

Photon absorption-induced exciton generation plays an important role in determining the photovoltaic properties of donor/acceptor organic solar cells with an inverted architecture. However, the reconstruction of light harvesting and thus exciton generation at different locations within organic inverted device are still not well resolved. Here, we investigate the film depth-dependent light absorption spectra in a small molecule donor/acceptor film. Including depth-dependent spectra into an optical transfer matrix method allows us to reconstruct both film depth- and energy-dependent exciton generation profiles, using which short-circuit current and external quantum efficiency of the inverted device are simulated and compared with the experimental measurements. The film depth-dependent spectroscopy, from which we are able to simultaneously reconstruct light harvesting profile, depth-dependent composition distribution, and vertical energy level variations, provides insights into photovoltaic process. In combination with appropriate material processing methods and device architecture, the method proposed in this work will help optimizing film depth-dependent optical/electronic properties for high-performance solar cells.

Quantitative proteomic study of Aspergillus Fumigatus secretome revealed deamidation of secretory enzymes.

PubMed

Adav, Sunil S; Ravindran, Anita; Sze, Siu Kwan

2015-04-24

Aspergillus sp. plays an essential role in lignocellulosic biomass recycling and is also exploited as cell factories for the production of industrial enzymes. This study profiled the secretome of Aspergillus fumigatus when grown with cellulose, xylan and starch by high throughput quantitative proteomics using isobaric tags for relative and absolute quantification (iTRAQ). Post translational modifications (PTMs) of proteins play a critical role in protein functions. However, our understanding of the PTMs in secretory proteins is limited. Here, we present the identification of PTMs such as deamidation of secreted proteins of A. fumigatus. This study quantified diverse groups of extracellular secreted enzymes and their functional classification revealed cellulases and glycoside hydrolases (32.9%), amylases (0.9%), hemicellulases (16.2%), lignin degrading enzymes (8.1%), peptidases and proteases (11.7%), chitinases, lipases and phosphatases (7.6%), and proteins with unknown function (22.5%). The comparison of quantitative iTRAQ results revealed that cellulose and xylan stimulates expression of specific cellulases and hemicellulases, and their abundance level as a function of substrate. In-depth data analysis revealed deamidation as a major PTM of key cellulose hydrolyzing enzymes like endoglucanases, cellobiohydrolases and glucosidases. Hemicellulose degrading endo-1,4-beta-xylanase, monosidases, xylosidases, lignin degrading laccase, isoamyl alcohol oxidase and oxidoreductases were also found to be deamidated. The filamentous fungi play an essential role in lignocellulosic biomass recycling and fungal strains belonging to Aspergillus were also exploited as cell factories for the production of organic acids, pharmaceuticals, and industrially important enzymes. In this study, extracellular proteins secreted by thermophilic A. fumigatus when grown with cellulose, xylan and starch were profiled using isobaric tags for relative and absolute quantification (iTRAQ) by adopting liquid chromatography tandem mass spectrometry. The comparison of quantitative iTRAQ results revealed that cellulose and xylan stimulate expression of specific cellulases and hemicellulases, and expression level as a function of substrate. Post translational modifications revealed deamidation of key cellulases including endoglucanases, cellobiohydrolases and glucosidases; and hemicellulases and lignin degrading enzymes. The knowledge on deamidated enzymes along with specific sites of modifications could be crucial information for further functional studies of these enzymes of A. fumigatus. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantitative analysis of fracture surface by roughness and fractal method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, X.W.; Tian, J.F.; Kang, Y.

1995-09-01

In recent years there has been extensive research and great development in Quantitative Fractography, which acts as an integral part of fractographic analysis. A prominent technique for studying the fracture surface is based on fracture profile generation and the major means for characterizing the profile quantitatively are roughness and fractal methods. By this way, some quantitative indexes such as the roughness parameters R{sub L} for profile and R{sub S} for surface, fractal dimensions D{sub L} for profile and D{sub S} for surface can be measured. Given the relationships between the indexes and the mechanical properties of materials, it is possiblemore » to achieve the goal of protecting materials from fracture. But, as the case stands, the theory and experimental technology of quantitative fractography are still imperfect and remain to be studied further. Recently, Gokhale and Underwood et al have proposed an assumption-free method for estimating the surface roughness by vertically sectioning the fracture surface with sections at an angle of 120 deg with each other, which could be expressed as follows: R{sub S} = {ovr R{sub L}{center_dot}{Psi}} where {Psi} is the profile structure factor. This method is based on the classical sterological principles and verified with the aid of computer simulations for some ruled surfaces. The results are considered to be applicable to fracture surfaces with any arbitrary complexity and anisotropy. In order to extend the detail applications to this method in quantitative fractography, the authors made a study on roughness and fractal methods dependent on this method by performing quantitative measurements on some typical low-temperature impact fractures.« less

Magnetic and chemical nonuniformity in Ga{sub 1-x}Mn{sub x}As films as probed by polarized neutron and x-ray reflectometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirby, B. J.; Borchers, J. A.; Rhyne, J. J.

We have used complementary neutron and x-ray reflectivity techniques to examine the depth profiles of a series of as-grown and annealed Ga{sub 1-x}Mn{sub x}As thin films. A magnetization gradient is observed for two as-grown films and originates from a nonuniformity of Mn at interstitial sites, and not from local variations in Mn at Ga sites. Furthermore, we see that the depth-dependent magnetization can vary drastically among as-grown Ga{sub 1-x}Mn{sub x}As films despite being deposited under seemingly similar conditions. These results imply that the depth profile of interstitial Mn is dependent not only on annealing, but is also extremely sensitive tomore » initial growth conditions. We observe that annealing improves the magnetization by producing a surface layer that is rich in Mn and O, indicating that the interstitial Mn migrates to the surface. Finally, we expand upon our previous neutron reflectivity study of Ga{sub 1-x}Mn{sub x}As, by showing how the depth profile of the chemical composition at the surface and through the film thickness is directly responsible for the complex magnetization profiles observed in both as-grown and annealed films.« less

Magnetic and chemical nonuniformity in Ga{sub 1-x}Mn{sub x}As as probed with neutron & x-ray reflectivfity.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirby, B. J.; Borchers, J. A.; Rhyne, J. J.

We have used complementary neutron and x-ray reflectivity techniques to examine the depth profiles of a series of as-grown and annealed Ga{sub 1-x}Mn{sub x}As thin films. A magnetization gradient is observed for two as-grown films and originates from a nonuniformity of Mn at interstitial sites, and not from local variations in Mn at Ga sites. Furthermore, we see that the depth-dependent magnetization can vary drastically among as-grown Ga{sub 1-x}Mn{sub x}As films despite being deposited under seemingly similar conditions. These results imply that the depth profile of interstitial Mn is dependent not only on annealing, but is also extremely sensitive tomore » initial growth conditions. We observe that annealing improves the magnetization by producing a surface layer that is rich in Mn and O, indicating that the interstitial Mn migrates to the surface. Finally, we expand upon our previous neutron reflectivity study of Ga{sub 1-x}Mn{sub x}As, by showing how the depth profile of the chemical composition at the surface and through the film thickness is directly responsible for the complex magnetization profiles observed in both as-grown and annealed films.« less

On the temperature dependence of Na migration in thin SiO 2 films during ToF-SIMS O 2+ depth profiling

NASA Astrophysics Data System (ADS)

Krivec, Stefan; Detzel, Thomas; Buchmayr, Michael; Hutter, Herbert

2010-10-01

The detection of Na in insulating samples by means of time of flight-secondary ion mass spectrometry (ToF-SIMS) depth profiling has always been a challenge. In particular the use of O 2+ as sputter species causes a severe artifact in the Na depth distribution due to Na migration under the influence of an internal electrical filed. In this paper we address the influence of the sample temperature on this artifact. It is shown that the transport of Na is a dynamic process in concordance with the proceeding sputter front. Low temperatures mitigated the migration process by reducing the Na mobility in the target. In the course of this work two sample types have been investigated: (i) A Na doped PMMA layer, deposited on a thin SiO 2 film. Here, the incorporation behavior of Na into SiO 2 during depth profiling is demonstrated. (ii) Na implanted into a thin SiO 2 film. By this sample type the migration behavior could be examined when defects, originating from the implantation process, are present in the SiO 2 target. In addition, we propose an approach for the evaluation of an implanted Na profile, which is unaffected by the migration process.

How Confocal Is Confocal Raman Microspectroscopy on the Skin? Impact of Microscope Configuration and Sample Preparation on Penetration Depth Profiles.

PubMed

Lunter, Dominique Jasmin

2016-01-01

The aim of the study was to elucidate the effect of sample preparation and microscope configuration on the results of confocal Raman microspectroscopic evaluation of the penetration of a pharmaceutical active into the skin (depth profiling). Pig ear skin and a hydrophilic formulation containing procaine HCl were used as a model system. The formulation was either left on the skin during the measurement, or was wiped off or washed off prior to the analysis. The microscope configuration was varied with respect to objectives and pinholes used. Sample preparation and microscope configuration had a tremendous effect on the results of depth profiling. Regarding sample preparation, the best results could be observed when the formulation was washed off the skin prior to the analysis. Concerning microscope configuration, the use of a 40 × 0.6 numerical aperture (NA) objective in combination with a 25-µm pinhole or a 100 × 1.25 NA objective in combination with a 50-µm pinhole was found to be advantageous. Complete removal of the sample from the skin before the analysis was found to be crucial. A thorough analysis of the suitability of the chosen microscope configuration should be performed before acquiring concentration depth profiles. © 2016 S. Karger AG, Basel.

Observations of pockmark flow structure in Belfast Bay, Maine, Part 1: current-induced mixing

USGS Publications Warehouse

Fandel, Christina L.; Lippmann, Thomas C.; Irish, James D.; Brothers, Laura L.

2017-01-01

Field observations of current profiles and temperature, salinity, and density structure were used to examine vertical mixing within two pockmarks in Belfast Bay, Maine. The first is located in 21 m water depth (sea level to rim), nearly circular in shape with a 45 m rim diameter and 12 m rim-to-bottom relief. The second is located in 25 m water depth, more elongated in shape with an approximately 80 m (36 m) major (minor) axis length at the rim, and 17 m relief. Hourly averaged current profiles were acquired from bottom-mounted acoustic Doppler current profilers deployed on the rim and center of each pockmark over successive 42 h periods in July 2011. Conductivity–temperature–depth casts at the rim and center of each pockmark show warmer, fresher water in the upper water column, evidence of both active and fossil thermocline structure 5–8 m above the rim, and well-mixed water below the rim to the bottom. Vertical velocities show up- and down-welling events that extend into the depths of each pockmark. An observed temperature change at both the rim and center occurs coincident with an overturning event below the rim, and suggests active mixing of the water column into the depths of each pockmark. Vertical profiles of horizontal velocities show depth variation at both the center and rim consistent with turbulent logarithmic current boundary layers, and suggest that form drag may possibly be influencing the local flow regime. While resource limitations prevented observation of the current structure and water properties at a control site, the acquired data suggest that active mixing and overturning within the sampled pockmarks occur under typical benign conditions, and that current flows are influenced by upstream bathymetric irregularities induced by distant pockmarks.

Determining the vertical evolution of hydrodynamic parameters in weathered and fractured south Indian crystalline-rock aquifers: insights from a study on an instrumented site

NASA Astrophysics Data System (ADS)

Boisson, A.; Guihéneuf, N.; Perrin, J.; Bour, O.; Dewandel, B.; Dausse, A.; Viossanges, M.; Ahmed, S.; Maréchal, J. C.

2015-02-01

Due to extensive irrigation, most crystalline aquifers of south India are overexploited. Aquifer structure consists of an upper weathered saprolite followed by a fractured zone whose fracture density decreases with depth. To achieve sustainable management, the evolution of hydrodynamic parameters (transmissivity and storage coefficient) by depth in the south Indian context should be quantified. Falling-head borehole permeameter tests, injection tests, flowmeter profiles, single-packer tests and pumping tests were carried out in the unsaturated saprolite and saturated fractured granite. Results show that the saprolite is poorly transmissive (T fs = 3 × 10-7 to 8.5 × 10-8 m2 s-1) and that the most conductive part of the aquifer corresponds to the bottom of the saprolite and the upper part of the fractured rock (T = 1.0 × 10-3 to 7.0 × 10-4 m2 s-1). The transmissivity along the profile is mostly controlled by two distinct conductive zones without apparent vertical hydraulic connection. The transmissivity and storage coefficient both decrease with depth depending on the saturation of the main fracture zones, and boreholes are not exploitable after a certain depth (27.5 m on the investigated section). The numerous investigations performed allow a complete quantification with depth of the hydrodynamic parameters along the weathering profile, and a conceptual model is presented. Hydrograph observations (4 years) are shown to be relevant as a first-order characterization of the media and diffusivity evolution with depth. The evolution of these hydrodynamic parameters along the profile has a great impact on groundwater prospecting, exploitation and transport properties in such crystalline rock aquifers.

Mars Sample Return: The Value of Depth Profiles

NASA Technical Reports Server (NTRS)

Hausrath, E. M.; Navarre-Sitchler, A. K.; Moore, J.; Sak, P. B.; Brantley, S. L.; Golden, D. C.; Sutter, B.; Schroeder, C.; Socki, R.; Morris, R. V.;

Quantitative light-induced fluorescence technology for quantitative evaluation of tooth wear

NASA Astrophysics Data System (ADS)

Kim, Sang-Kyeom; Lee, Hyung-Suk; Park, Seok-Woo; Lee, Eun-Song; de Josselin de Jong, Elbert; Jung, Hoi-In; Kim, Baek-Il

2017-12-01

Various technologies used to objectively determine enamel thickness or dentin exposure have been suggested. However, most methods have clinical limitations. This study was conducted to confirm the potential of quantitative light-induced fluorescence (QLF) using autofluorescence intensity of occlusal surfaces of worn teeth according to enamel grinding depth in vitro. Sixteen permanent premolars were used. Each tooth was gradationally ground down at the occlusal surface in the apical direction. QLF-digital and swept-source optical coherence tomography images were acquired at each grinding depth (in steps of 100 μm). All QLF images were converted to 8-bit grayscale images to calculate the fluorescence intensity. The maximum brightness (MB) values of the same sound regions in grayscale images before (MB) and phased values after (MB) the grinding process were calculated. Finally, 13 samples were evaluated. MB increased over the grinding depth range with a strong correlation (r=0.994, P<0.001). In conclusion, the fluorescence intensity of the teeth and grinding depth was strongly correlated in the QLF images. Therefore, QLF technology may be a useful noninvasive tool used to monitor the progression of tooth wear and to conveniently estimate enamel thickness.

The potential of high-frequency profiling to assess vertical and seasonal patterns of phytoplankton dynamics in lakes: An extension of the Plankton Ecology Group (PEG) model

USGS Publications Warehouse

Brentrup, Jennifer A.; Williamson, Craig E.; Colom-Montero, William; Eckert, Werner; de Eyto, Elvira; Grossart, Hans-Peter; Huot, Yannick; Isles, Peter D. F.; Knoll, Lesley B.; Leach, Taylor H.; McBride, Christopher G.; Pierson, Don; Pomati, Francesco; Read, Jordan S.; Rose, Kevin C.; Samal, Nihar R.; Staehr, Peter A.; Winslow, Luke A.

2016-01-01

The use of high-frequency sensors on profiling buoys to investigate physical, chemical, and biological processes in lakes is increasing rapidly. Profiling buoys with automated winches and sensors that collect high-frequency chlorophyll fluorescence (ChlF) profiles in 11 lakes in the Global Lake Ecological Observatory Network (GLEON) allowed the study of the vertical and temporal distribution of ChlF, including the formation of subsurface chlorophyll maxima (SSCM). The effectiveness of 3 methods for sampling phytoplankton distributions in lakes, including (1) manual profiles, (2) single-depth buoys, and (3) profiling buoys were assessed. High-frequency ChlF surface data and profiles were compared to predictions from the Plankton Ecology Group (PEG) model. The depth-integrated ChlF dynamics measured by the profiling buoy data revealed a greater complexity that neither conventional sampling nor the generalized PEG model captured. Conventional sampling techniques would have missed SSCM in 7 of 11 study lakes. Although surface-only ChlF data underestimated average water column ChlF, at times by nearly 2-fold in 4 of the lakes, overall there was a remarkable similarity between surface and mean water column data. Contrary to the PEG model’s proposed negligible role for physical control of phytoplankton during the growing season, thermal structure and light availability were closely associated with ChlF seasonal depth distribution. Thus, an extension of the PEG model is proposed, with a new conceptual framework that explicitly includes physical metrics to better predict SSCM formation in lakes and highlight when profiling buoys are especially informative.

Full skin quantitative optical coherence elastography achieved by combining vibration and surface acoustic wave methods

NASA Astrophysics Data System (ADS)

Li, Chunhui; Guan, Guangying; Huang, Zhihong; Wang, Ruikang K.; Nabi, Ghulam

2015-03-01

By combining with the phase sensitive optical coherence tomography (PhS-OCT), vibration and surface acoustic wave (SAW) methods have been reported to provide elastography of skin tissue respectively. However, neither of these two methods can provide the elastography in full skin depth in current systems. This paper presents a feasibility study on an optical coherence elastography method which combines both vibration and SAW in order to give the quantitative mechanical properties of skin tissue with full depth range, including epidermis, dermis and subcutaneous fat. Experiments are carried out on layered tissue mimicking phantoms and in vivo human forearm and palm skin. A ring actuator generates vibration while a line actuator were used to excited SAWs. A PhS-OCT system is employed to provide the ultrahigh sensitive measurement of the generated waves. The experimental results demonstrate that by the combination of vibration and SAW method the full skin bulk mechanical properties can be quantitatively measured and further the elastography can be obtained with a sensing depth from ~0mm to ~4mm. This method is promising to apply in clinics where the quantitative elasticity of localized skin diseases is needed to aid the diagnosis and treatment.

Estimation and correction of produced light from prompt gamma photons on luminescence imaging of water for proton therapy dosimetry

NASA Astrophysics Data System (ADS)

Yabe, Takuya; Komori, Masataka; Toshito, Toshiyuki; Yamaguchi, Mitsutaka; Kawachi, Naoki; Yamamoto, Seiichi

2018-02-01

Although the luminescence images of water during proton-beam irradiation using a cooled charge-coupled device camera showed almost the same ranges of proton beams as those measured by an ionization chamber, the depth profiles showed lower Bragg peak intensities than those measured by an ionization chamber. In addition, a broad optical baseline signal was observed in depths that exceed the depth of the Bragg peak. We hypothesize that this broad baseline signal originates from the interaction of proton-induced prompt gamma photons with water. These prompt gamma photons interact with water to form high-energy Compton electrons, which may cause luminescence or Cherenkov emission from depths exceeding the location of the Bragg peak. To clarify this idea, we measured the luminescence images of water during the irradiations of protons in water with minimized parallax errors, and also simulated the produced light by the interactions of prompt gamma photons with water. We corrected the measured depth profiles of the luminescence images by subtracting the simulated distributions of the produced light by the interactions of prompt gamma photons in water. Corrections were also conducted using the estimated depth profiles of the light of the prompt gamma photons, as obtained from the off-beam areas of the luminescence images of water. With these corrections, we successfully obtained depth profiles that have almost identical distributions as the simulated dose distributions for protons. The percentage relative height of the Bragg peak with corrections to that of the simulation data increased to 94% from 80% without correction. Also, the percentage relative offset heights of the deeper part of the Bragg peak with corrections decreased to 0.2%-0.4% from 4% without correction. These results indicate that the luminescence imaging of water has potential for the dose distribution measurements for proton therapy dosimetry.

A comparison of upper mantle subcontinental electrical conductivity for North America, Europe, and Asia.

USGS Publications Warehouse

Campbell, W.H.; Schiffmacher, E.R.

1986-01-01

Spherical harmonic analysis coefficients of the external and internal parts of the quiet-day geomagnetic field variations (Sq), separated for the N American, European, Central Asian and E Asian regions, were used to determine conductivity profiles to depths of about 600km by the Schmucker equivalent-substitute conductor method. All 3 regions showed a roughly exponential increase of conductivity with depth. Distinct discontinuities seemed to be evident near 255-300km and near 450-600km. Regional differences in the conductivity profiles were shown by the functional fittings to the data. For depths less than about 275km, the N American conductivities seemed to be significantly higher than the other regions. For depths greater than about 300km, the E Asian conductivities were largest. -Authors

Chemical characteristics of hadal waters in the Izu-Ogasawara Trench of the western Pacific Ocean.

PubMed

Gamo, Toshitaka; Shitashima, Kiminori

2018-01-01

Vertical profiles of potential temperature, salinity, and some chemical components were obtained at a trench station (29°05'N, 142°51'E; depth = 9768 m) in the Izu-Ogasawara (Bonin) Trench in 1984 and 1994 to characterize the hadal waters below ∼6000 m depth. We compared portions of both the 1984 and 1994 profiles with nearby data obtained between 1976 and 2013. Results demonstrated that the hadal waters had slightly higher potential temperature and nitrate and lower dissolved oxygen than waters at sill depths (∼6000 m) outside the trench, probably due to the effective accumulation of geothermal heat and active biological processes inside the trench. The silicate, iron, and manganese profiles in 1984 showed slight but significant increases below ∼6000 m depth, suggesting that these components may have been intermittently supplied from the trench bottom. Significant amounts of 222 Rn in excess over 226 Ra were detected in the hadal waters up to 2675 m from the bottom, reflecting laterally supplied 222 Rn from the trench walls.

Modern Material Analysis Instruments Add a New Dimension to Materials Characterization and Failure Analysis

NASA Technical Reports Server (NTRS)

Panda, Binayak

2009-01-01

Modern analytical tools can yield invaluable results during materials characterization and failure analysis. Scanning electron microscopes (SEMs) provide significant analytical capabilities, including angstrom-level resolution. These systems can be equipped with a silicon drift detector (SDD) for very fast yet precise analytical mapping of phases, as well as electron back-scattered diffraction (EBSD) units to map grain orientations, chambers that admit large samples, variable pressure for wet samples, and quantitative analysis software to examine phases. Advanced solid-state electronics have also improved surface and bulk analysis instruments: Secondary ion mass spectroscopy (SIMS) can quantitatively determine and map light elements such as hydrogen, lithium, and boron - with their isotopes. Its high sensitivity detects impurities at parts per billion (ppb) levels. X-ray photo-electron spectroscopy (XPS) can determine oxidation states of elements, as well as identifying polymers and measuring film thicknesses on coated composites. This technique is also known as electron spectroscopy for chemical analysis (ESCA). Scanning Auger electron spectroscopy (SAM) combines surface sensitivity, spatial lateral resolution (10 nm), and depth profiling capabilities to describe elemental compositions of near and below surface regions down to the chemical state of an atom.

Communication Profiles of Psychiatric Residents and Attending Physicians in Medication-Management Appointments: A Quantitative Pilot Study

ERIC Educational Resources Information Center

Castillo, Enrico G.; Pincus, Harold A.; Wieland, Melissa; Roter, Debra; Larson, Susan; Houck, Patricia; Reynolds, Charles F.; Cruz, Mario

2012-01-01

Objective: The authors quantitatively examined differences in psychiatric residents' and attending physicians' communication profiles and voice tones. Methods: Audiotaped recordings of 49 resident-patient and 35 attending-patient medication-management appointments at four ambulatory sites were analyzed with the Roter Interaction Analysis System…

Towards quantitative usage of EMI-data for Digital Soil Mapping

NASA Astrophysics Data System (ADS)

Nüsch, A.-K.; Wunderlich, T.; Kathage, S.; Werban, U.; Dietrich, P.

2009-04-01

As formulated in the Thematic Strategy for Soil Protection prepared by the European Commission soil degradation is a serious problem in Europe. The degradation is driven or exacerbated by human activity and has a direct impact on water and air quality, biodiversity, climate and human life-quality. High-resolution soil property maps are one major prerequisite for the specific protection of soil function and restoration of degraded soils as well as sustainable land use, water and environmental management. However, the currently available techniques for (digital) soil mapping still have deficiencies in terms of reliability and precision, the feasibility of investigation of large areas (e.g. catchments and landscapes) and the assessment of soil degradation threats at this scale. The focus of the iSOIL (Interactions between soil related science - Linking geophysics, soil science and digital soil mapping) project is on improving fast and reliable mapping of soil properties, soil functions and soil degradation threats. This requires the improvement as well as integration of geophysical and spectroscopic measurement techniques in combination with advanced soil sampling approaches, pedometrical and pedophysical approaches. Many commercially available geophysical sensors and equipment (EMI, DC, gamma-spectroscopy, magnetics) are ready to use for measurements of different parameters. Data collection with individual sensors is well developed and numerously described. However comparability of data of different sensor types as well as reproducibility of data is not self-evident. In particular handling of sensors has to be carried out accurately, e.g. consistent calibration. Soil parameters will be derived from geophysical properties to create comprehensive soil maps. Therefore one prerequisite is the comparison of different geophysical properties not only qualitative but also quantitative. At least reproducibility is one of the most important conditions for monitoring tasks. The first parameter we focussed on is apparent electrical conductivity (ECa). It is an important geophysical properity in soil science since soil parameters (water content, etc.) can be deduced. Nowadays mobile geophysical platforms allow to survey large areas comprehensively in a short time period. These platforms have been equipped with EM38DD (Geonics) and Profiler EMP-400 (GSSI) - two different types of electromagnetic induction (EMI) instruments - within first iSOIL field campaign. While EM38DD measures in horizontal and vertical mode at the same time, Profiler measures three frequencies simultaneously and magnetic susceptibility additionally. Coil separation of the instruments is nearly the same, so penetration depth is similar. On the other hand, frequencies are arbitrary at Profiler but fixed at EM38DD. These differences in penetration depth have to taken into account. By our measurement we tested the comparability of the data to show differences between instruments of the same type (EM38DD-EM38DD) using different settings, and different types (EM38DD-Profiler). Moreover both sensors work in continuous as well in discontinuous mode. The results show that quality of data is comparable, but the quantities are varying. This has to be considered for further interpretations and monitoring. In the next steps we have to determine how to convert relative data into absolute data since ECa data from different locations are not comparable to each other in a quantitative way. In the talk we will give an introduction in the application of EMI for soil monitoring, followed by an overview about comparability and reproducibility of data.

The stable isotope composition of halite and sulfate of hyperarid soils and its relation to aqueous transport

NASA Astrophysics Data System (ADS)

Amundson, Ronald; Barnes, Jaime D.; Ewing, Stephanie; Heimsath, Arjun; Chong, Guillermo

2012-12-01

Halite (NaCl) and gypsum or anhydrite (CaSO4) are water-soluble minerals found in soils of the driest regions of Earth, and only modest attention has been given to the hydrological processes that distribute these salts vertically in soil profiles. The two most notable chloride and sulfate-rich deserts on earth are the Dry Valleys of Antarctica and the Atacama Desert of Chile. While each is hyperarid, they possess very different hydrological regimes. We first show, using previously published S and O isotope data for sulfate minerals, that downward migration of water and sulfate is the primary mechanism responsible for depth profiles of sulfate concentration, and S and O isotopes, in both deserts. In contrast, we found quite different soluble Cl concentration and Cl isotope profiles between the two deserts. For Antarctic soils with an ice layer near the soil surface, the Cl concentrations increase with decreasing soil depth, whereas the ratio of 37Cl/35Cl increases. Based on previous field observations by others, we found that thermally driven upward movement of brine during the winter, described by an advection/diffusion model, qualitatively mimics the observed profiles. In contrast, in the Atacama Desert where rare but relatively large rains drive Cl downward through the profiles, Cl concentrations and 37Cl/35Cl ratios increased with depth. The depth trends in Cl isotopes are more closely explained by a Rayleigh-like model of downward fluid flow. The isotope profiles, and our modeling, reveal the similarities and differences between these two very arid regions on Earth, and are relevant for constraining models of fluid flow in arid zone soil and vadose zone hydrology.

High-resolution phylogenetic microbial community profiling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structuresmore » at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.« less

Genome-wide profiling of DNA-binding proteins using barcode-based multiplex Solexa sequencing.

PubMed

Raghav, Sunil Kumar; Deplancke, Bart

2012-01-01

Chromatin immunoprecipitation (ChIP) is a commonly used technique to detect the in vivo binding of proteins to DNA. ChIP is now routinely paired to microarray analysis (ChIP-chip) or next-generation sequencing (ChIP-Seq) to profile the DNA occupancy of proteins of interest on a genome-wide level. Because ChIP-chip introduces several biases, most notably due to the use of a fixed number of probes, ChIP-Seq has quickly become the method of choice as, depending on the sequencing depth, it is more sensitive, quantitative, and provides a greater binding site location resolution. With the ever increasing number of reads that can be generated per sequencing run, it has now become possible to analyze several samples simultaneously while maintaining sufficient sequence coverage, thus significantly reducing the cost per ChIP-Seq experiment. In this chapter, we provide a step-by-step guide on how to perform multiplexed ChIP-Seq analyses. As a proof-of-concept, we focus on the genome-wide profiling of RNA Polymerase II as measuring its DNA occupancy at different stages of any biological process can provide insights into the gene regulatory mechanisms involved. However, the protocol can also be used to perform multiplexed ChIP-Seq analyses of other DNA-binding proteins such as chromatin modifiers and transcription factors.

Near-real-time processing of a ceilometer network assisted with sun-photometer data: monitoring a dust outbreak over the Iberian Peninsula

NASA Astrophysics Data System (ADS)

Cazorla, Alberto; Andrés Casquero-Vera, Juan; Román, Roberto; Guerrero-Rascado, Juan Luis; Toledano, Carlos; Cachorro, Victoria E.; Orza, José Antonio G.; Cancillo, María Luisa; Serrano, Antonio; Titos, Gloria; Pandolfi, Marco; Alastuey, Andres; Hanrieder, Natalie; Alados-Arboledas, Lucas

2017-10-01

The interest in the use of ceilometers for optical aerosol characterization has increased in the last few years. They operate continuously almost unattended and are also much less expensive than lidars; hence, they can be distributed in dense networks over large areas. However, due to the low signal-to-noise ratio it is not always possible to obtain particle backscatter coefficient profiles, and the vast number of data generated require an automated and unsupervised method that ensures the quality of the profiles inversions. In this work we describe a method that uses aerosol optical depth (AOD) measurements from the AERONET network that it is applied for the calibration and automated quality assurance of inversion of ceilometer profiles. The method is compared with independent inversions obtained by co-located multiwavelength lidar measurements. A difference smaller than 15 % in backscatter is found between both instruments. This method is continuously and automatically applied to the Iberian Ceilometer Network (ICENET) and a case example during an unusually intense dust outbreak affecting the Iberian Peninsula between 20 and 24 February 2016 is shown. Results reveal that it is possible to obtain quantitative optical aerosol properties (particle backscatter coefficient) and discriminate the quality of these retrievals with ceilometers over large areas. This information has a great potential for alert systems and model assimilation and evaluation.

High-resolution phylogenetic microbial community profiling

DOE PAGES

Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin; ...

2016-02-09

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structuresmore » at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.« less

In situ probing of temperature in radio frequency thermal plasma using Yttrium ion emission lines during synthesis of yttria nanoparticles

NASA Astrophysics Data System (ADS)

Dhamale, G. D.; Tiwari, N.; Mathe, V. L.; Bhoraskar, S. V.; Ghorui, S.

2017-07-01

Particle feeding is used in the most important applications of radio frequency (r.f.) thermal plasmas like synthesis of nanoparticles and particle spheroidization. The study reports an in-situ investigation of radial distribution of temperature in such devices using yttrium ion emission lines under different rates of particle loading during synthesis of yttria nanoparticles. A number of interesting facts about the response of r.f. plasma to the rate of particle loading, hitherto unknown, are revealed. Observed phenomena are supported with experimental data from fast photographic experiments and actual synthesis results. The use of the Abel inversion technique together with simultaneous multi-track acquisition of emission spectra from different spatial locations using a CCD based spectrometer allowed us to extract accurate distribution of temperature inside the plasma in the presence of inherent instabilities. The temperature profiles of this type of plasma have been measured possibly for the first time while particles are being fed into the plasma. Observed changes in the temperature profiles as the particle feed rate increases are very significant. Reaction forces resulting from particle evaporation, and increased skin depth owing to the decrease in electrical conductivity in the edge region are proposed as the two different mechanisms to account for the observed changes in the temperature profile as the powder feed rate is increased. Quantitative analyses supporting the proposed mechanisms are presented.

Study of the photovoltaic effect in thin film barium titanate

NASA Technical Reports Server (NTRS)

Grannemann, W. W.; Dharmadhikari, V. S.

1982-01-01

The basic mechanism associated with the photovoltaic phenomena observed in the R.F. sputtered BaTiO3/silicon system is presented. Series of measurements of short circuit photocurrents and open circuit photovoltage were made. The composition depth profiles and the interface characteristics of the BaTiO3/silicon system were investigated for a better understanding of the electronic properties. A Scanning Auger Microprobe combined with ion in depth profiling were used.

Auger compositional depth profiling of the metal contact-TlBr interface

NASA Astrophysics Data System (ADS)

Nelson, A. J.; Swanberg, E. L.; Voss, L. F.; Graff, R. T.; Conway, A. M.; Nikolic, R. J.; Payne, S. A.; Kim, H.; Cirignano, L.; Shah, K.

2015-08-01

Degradation of room temperature operation of TlBr radiation detectors with time is thought to be due to electromigration of Tl and Br vacancies within the crystal as well as the metal contacts migrating into the TlBr crystal itself due to electrochemical reactions at the metal/TlBr interface. Scanning Auger electron spectroscopy (AES) in combination with sputter depth profiling was used to investigate the metal contact surface/interfacial structure on TlBr devices. Device-grade TlBr was polished and subjected to a 32% HCl etch to remove surface damage and create a TlBr1-xClx surface layer prior to metal contact deposition. Auger compositional depth profiling results reveal non-equilibrium interfacial diffusion after device operation in both air and N2 at ambient temperature. These results improve our understanding of contact/device degradation versus operating environment for further enhancing radiation detector performance.

Depth profiling the solid electrolyte interphase on lithium titanate (Li4Ti5O12) using synchrotron-based photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Nordh, Tim; Younesi, Reza; Brandell, Daniel; Edström, Kristina

2015-10-01

The presence of a surface layer on lithium titanate (Li4Ti5O12, LTO) anodes, which has been a topic of debate in scientific literature, is here investigated with tunable high surface sensitive synchrotron-based photoelectron spectroscopy (PES) to obtain a reliable depth profile of the interphase. Li||LTO cells with electrolytes consisting of 1 M lithium hexafluorophosphate dissolved in ethylene carbonate:diethyl carbonate (LiPF6 in EC:DEC) were cycled in two different voltage windows of 1.0-2.0 V and 1.4-2.0 V. LTO electrodes were characterized after 5 and 100 cycles. Also the pristine electrode as such, and an electrode soaked in the electrolyte were analyzed by varying the photon energies enabling depth profiling of the outermost surface layer. The main components of the surface layer were found to be ethers, P-O containing compounds, and lithium fluoride.

The electrical conductivity of the Earth's upper mantle as estimated from satellite measured magnetic field variations. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Didwall, E. M.

1981-01-01

Low latitude magnetic field variations (magnetic storms) caused by large fluctuations in the equatorial ring current were derived from magnetic field magnitude data obtained by OGO 2, 4, and 6 satellites over an almost 5 year period. Analysis procedures consisted of (1) separating the disturbance field into internal and external parts relative to the surface of the Earth; (2) estimating the response function which related to the internally generated magnetic field variations to the external variations due to the ring current; and (3) interpreting the estimated response function using theoretical response functions for known conductivity profiles. Special consideration is given to possible ocean effects. A temperature profile is proposed using conductivity temperature data for single crystal olivine. The resulting temperature profile is reasonable for depths below 150-200 km, but is too high for shallower depths. Apparently, conductivity is not controlled solely by olivine at shallow depths.

Identification of Chinese medicinal fungus Cordyceps sinensis by depth-profiling mid-infrared photoacoustic spectroscopy

NASA Astrophysics Data System (ADS)

Du, Changwen; Zhou, Jianmin; Liu, Jianfeng

2017-02-01

With increased demand for Cordyceps sinensis it needs rapid methods to meet the challenge of identification raised in quality control. In this study Cordyceps sinensis from four typical natural habitats in China was characterized by depth-profiling Fourier transform infrared photoacoustic spectroscopy. Results demonstrated that Cordyceps sinensis samples resulted in typical photoacoustic spectral appearance, but heterogeneity was sensed in the whole sample; due to the heterogeneity Cordyceps sinensis was represented by spectra of four groups including head, body, tail and leaf under a moving mirror velocity of 0.30 cm s- 1. The spectra of the four groups were used as input of a probabilistic neural network (PNN) to identify the source of Cordyceps sinensis, and all the samples were correctly identified by the PNN model. Therefore, depth-profiling Fourier transform infrared photoacoustic spectroscopy provides novel and unique technique to identify Cordyceps sinensis, which shows great potential in quality control of Cordyceps sinensis.

Surface influence upon vertical profiles in the nocturnal boundary layer

NASA Astrophysics Data System (ADS)

Garratt, J. R.

1983-05-01

Near-surface wind profiles in the nocturnal boundary layer, depth h, above relatively flat, tree-covered terrain are described in the context of the analysis of Garratt (1980) for the unstable atmospheric boundary layer. The observations at two sites imply a surface-based transition layer, of depth z *, within which the observed non-dimensional profiles Φ M 0 are a modified form of the inertial sub-layer relation Φ _M ( {{z L}} = ( {{{1 + 5_Z } L}} ) according to Φ _M^{{0}} ˜eq ( {{{1 + 5z} L}} )exp [ { - 0.7( {{{1 - z} z}_ * } )] , where z is height above the zero-plane displacement and L is the Monin-Obukhov length. At both sites the depth z * is significantly smaller than the appropriate neutral value ( z * N ) found from the previous analysis, as might be expected in the presence of a buoyant sink for turbulent kinetic energy.

Nondestructive depth profile of the chemical state of ultrathin Al2O3/Si interface

NASA Astrophysics Data System (ADS)

Lee, Jong Cheol; Oh, S.-J.

2004-05-01

We investigated a depth profile of the chemical states of an Al2O3/Si interface using nondestructive photon energy-dependent high-resolution x-ray photoelectron spectroscopy (HRXPS). The Si 2p binding energy, attributed to the oxide interfacial layer (OIL), was found to shift from 102.1 eV to 102.9 eV as the OIL region closer to Al2O3 layer was sampled, while the Al 2p binding energy remains the same. This fact strongly suggests that the chemical state of the interfacial layer is not Al silicate as previously believed. We instead propose from the HRXPS of Al 2p and Si 2p depth-profile studies that the chemical states of the Al2O3/Si interface mainly consist of SiO2 and Si2O3.

Long-Term Observations of Ocean Biogeochemistry with Nitrate and Oxygen Sensors in Apex Profiling Floats

NASA Astrophysics Data System (ADS)

Johnson, K. S.; Coletti, L.; Jannasch, H.; Martz, T.; Swift, D.; Riser, S.

2008-12-01

Long-term, autonomous observations of ocean biogeochemical cycles are now feasible with chemical sensors in profiling floats. These sensors will enable decadal-scale observations of trends in global ocean biogeochemical cycles. Here, we focus on measurements on nitrate and dissolved oxygen. The ISUS (In Situ Ultraviolet Spectrophotometer) optical nitrate sensor has been adapted to operate in a Webb Research, Apex profiling float. The Apex float is of the type used in the Argo array and is designed for multi-year, expendable deployments in the ocean. Floats park at 1000 m depth and make 60 nitrate and oxygen measurements at depth intervals ranging from 50 m below 400 m to 5 m in the upper 100 m as they profile to the surface. All data are transmitted to shore using the Iridium telemetry system and they are available on the Internet in near-real time. Floats equipped with ISUS and an Aanderaa oxygen sensor are capable of making 280 vertical profiles from 1000 m. At a 5 day cycle time, the floats should have nearly a four year endurance. Three floats have now been deployed at the Hawaii Ocean Time series station (HOT), Ocean Station Papa (OSP) in the Gulf of Alaska and at 50 South, 30 East in the Southern Ocean. Two additional floats are designated for deployment at the Bermuda Atlantic Time Series station (BATS) and in the Drake Passage. The HOT float has made 56 profiles over 260 days and should continue operating for 3 more years. Nitrate concentrations are in excellent agreement with the long-term mean observed at HOT. No significant long-term drift in sensor response has occurred. A variety of features have been observed in the HOT nitrate data that are linked to contemporaneous changes in oxygen production and mesoscale dynamics. The impacts of these features will be briefly described. The Southern Ocean float has operated for 200 days and is now observing reinjection of nitrate into surface waters as winter mixing occurs(surface nitrate > 24 micromolar). We expect that the OSP and Southern Ocean floats will provide a quantitative measurement of the timing and magnitude of the spring bloom via the drawdown of surface nitrate. We are funded through NSF and NOPP to continue float deployments at HOT, BATS, OSP and the Southern Ocean for the next 3 years and to refine the sensor so it can be offered as a commercial option for all float users. New sensors in development for float deployments include a stable ISFET pH sensor.

Studying Degradation in Lithium-Ion Batteries by Depth Profiling with Lithium-Nuclear Reaction Analysis

NASA Astrophysics Data System (ADS)

Schulz, Adam

Lithium ion batteries (LIBs) are secondary (rechargeable) energy storage devices that lose the ability to store charge, or degrade, with time. This charge capacity loss stems from unwanted reactions such as the continual growth of the solid electrolyte interphase (SEI) layer on the negative carbonaceous electrode. Parasitic reactions consume mobile lithium, the byproducts of which deposit as SEI layer. Introducing various electrolyte additives and coatings on the positive electrode reduce the rate of SEI growth and lead to improved calendar lifetimes of LIBs respectively. There has been substantial work both electrochemically monitoring and computationally modeling the development of the SEI layer. Additionally, a plethora of spectroscopic techniques have been employed in an attempt to characterize the components of the SEI layer. Despite lithium being the charge carrier in LIBs, depth profiles of lithium in the SEI are few. Moreover, accurate depth profiles relating capacity loss to lithium in the SEI are virtually non-existent. Better quantification of immobilized lithium would lead to improved understanding of the mechanisms of capacity loss and allow for computational and electrochemical models dependent on true materials states. A method by which to prepare low variability, high energy density electrochemical cells for depth profiling with the non-destructive technique, lithium nuclear reaction analysis (Li-NRA), is presented here. Due to the unique and largely non-destructive nature of Li-NRA we are able to perform repeated measurement on the same sample and evaluate the variability of the technique. By using low variability electrochemical cells along with this precise spectroscopic technique, we are able to confidently report trends of lithium concentration while controlling variables such as charge state, age and electrolyte composition. Conversion of gamma intensity versus beam energy, rendered by NRA, to Li concentration as a function of depth requires calibration and modeling of the nuclear stopping power of the substrate (electrode material). A methodology to accurately convert characteristic gamma intensity versus beam energy raw data to Li % as a function of depth is presented. Depth profiles are performed on the electrodes of commercial LIBs charged to different states of charge and aged to different states of health. In-lab created Li-ion cells are prepared with different electrolytes and then depth profiled by Li-NRA. It was found lithium accumulates within the solid electrolyte interphase (SEI) layer with the square root of time, consistent with previous reports. When vinylene carbonate (VC) is introduced to electrolyte lithium accumulates at a rapidly reduced rate as compared to cells containing ethylene carbonte (EC). Additionally, lithium concentration within the positive electrode surface was observed to decrease linearly with time independent of electrolyte tested. Future experiments to be conducted to finish the work and the underpinnings of a materials based capacity loss model are proposed.

Scanning photoelectron microscope for nanoscale three-dimensional spatial-resolved electron spectroscopy for chemical analysis.

PubMed

Horiba, K; Nakamura, Y; Nagamura, N; Toyoda, S; Kumigashira, H; Oshima, M; Amemiya, K; Senba, Y; Ohashi, H

2011-11-01

In order to achieve nondestructive observation of the three-dimensional spatially resolved electronic structure of solids, we have developed a scanning photoelectron microscope system with the capability of depth profiling in electron spectroscopy for chemical analysis (ESCA). We call this system 3D nano-ESCA. For focusing the x-ray, a Fresnel zone plate with a diameter of 200 μm and an outermost zone width of 35 nm is used. In order to obtain the angular dependence of the photoelectron spectra for the depth-profile analysis without rotating the sample, we adopted a modified VG Scienta R3000 analyzer with an acceptance angle of 60° as a high-resolution angle-resolved electron spectrometer. The system has been installed at the University-of-Tokyo Materials Science Outstation beamline, BL07LSU, at SPring-8. From the results of the line-scan profiles of the poly-Si/high-k gate patterns, we achieved a total spatial resolution better than 70 nm. The capability of our system for pinpoint depth-profile analysis and high-resolution chemical state analysis is demonstrated. © 2011 American Institute of Physics

Depth Profile of Induced Magnetic Polarization in Cu Layers of Co/Cu(111) Metallic Superlattices by Resonant X-ray Magnetic Scattering at the Cu K Absorption Edge

NASA Astrophysics Data System (ADS)

Uegaki, Shin; Yoshida, Akihiro; Hosoito, Nobuyoshi

2015-03-01

We investigated induced spin polarization of 4p conduction electrons in Cu layers of antiferromagnetically (AFM) and ferromagnetically (FM) coupled Co/Cu(111) metallic superlattices by resonant X-ray magnetic scattering at the Cu K absorption edge. Magnetic reflectivity profiles of the two superlattices were measured in the magnetic saturation state with circularly polarized synchrotron radiation X-rays at 8985 eV. Depth profiles of the resonant magnetic scattering length of Cu, which corresponds to the induced spin polarization of Cu, were evaluated in the two Co/Cu superlattices by analyzing the observed magnetic reflectivity profiles. We demonstrated that the spin polarization induced in the Cu layer was distributed around the Co/Cu interfaces with an attenuation length of several Å in both AFM and FM coupled superlattices. The uniform component, which exists in Au layers of Fe/Au(001) superlattices, was not found in the depth distribution of induced magnetic polarization in the Cu layers of Co/Cu(111) superlattices.

Numerical analysis of dysplasia-associated changes in depth-dependent light scattering profile of cervical epithelium

NASA Astrophysics Data System (ADS)

Arifler, Dizem; MacAulay, Calum; Follen, Michele; Guillaud, Martial

2013-06-01

Dysplastic progression is known to be associated with changes in morphology and internal structure of cells. A detailed assessment of the influence of these changes on cellular scattering response is needed to develop and optimize optical diagnostic techniques. In this study, we first analyzed a set of quantitative histopathologic images from cervical biopsies and we obtained detailed information on morphometric and photometric features of segmented epithelial cell nuclei. Morphometric parameters included average size and eccentricity of the best-fit ellipse. Photometric parameters included optical density measures that can be related to dielectric properties and texture characteristics of the nuclei. These features enabled us to construct realistic three-dimensional computational models of basal, parabasal, intermediate, and superficial cell nuclei that were representative of four diagnostic categories, namely normal (or negative for dysplasia), mild dysplasia, moderate dysplasia, and severe dysplasia or carcinoma in situ. We then employed the finite-difference time-domain method, a popular numerical tool in electromagnetics, to compute the angle-resolved light scattering properties of these representative models. Results indicated that a high degree of variability can characterize a given diagnostic category, but scattering from moderately and severely dysplastic or cancerous nuclei was generally observed to be stronger compared to scattering from normal and mildly dysplastic nuclei. Simulation results also pointed to significant intensity level variations among different epithelial depths. This suggests that intensity changes associated with dysplastic progression need to be analyzed in a depth-dependent manner.

Sea surface cooling in the Northern South China Sea observed using Chinese Sea-wing Underwater Glider measurements

NASA Astrophysics Data System (ADS)

Qiu, C.; Mao, H.; Wu, J.

2016-02-01

Based on 26 days of Chinese Seawing underwater Glider measurements and satellite microwave data, we documented cooling of the upper mixed layer of the ocean in response to changes in the wind in the Northern South China Sea (NSCS) from September 19, 2014, to October 15, 2014. The Seawing underwater glider measured 177 profiles of temperature, salinity, and pressure within a 55 km נ55 km area, and reached a depth of 1000 m at a temporal resolution of 4 h. The study area experienced two cooling events, Cooling I and Cooling II, according to their timing. During Cooling I, water temperature at 1m depth (T1) decreased by 1.0°C, and the corresponding satellitederived surface winds increased locally by 4.2 m/s. During Cooling II, T1 decreased sharply by 1.7°C within a period of 4 days; sea surface winds increased by 7 m/s and covered the entire NSCS. The corresponding mixed layer depth (MLD) deepened sharply from 30 m to 60 m during Cooling II, and remained steady during Cooling I. We estimated temperature tendencies using a ML model. High resolution Seawing underwater glider measurements provided an estimation of MLD migration, allowing us to obtain the temporal entrainment rate of cool sub thermocline water. Quantitative analysis confirmed that the entrainment rate and latent heat flux were the two major components that regulated cooling of the ML, and that the Ekman advection and sensible heat flux were small.

Galaxy Zoo: quantitative visual morphological classifications for 48 000 galaxies from CANDELS

NASA Astrophysics Data System (ADS)

Simmons, B. D.; Lintott, Chris; Willett, Kyle W.; Masters, Karen L.; Kartaltepe, Jeyhan S.; Häußler, Boris; Kaviraj, Sugata; Krawczyk, Coleman; Kruk, S. J.; McIntosh, Daniel H.; Smethurst, R. J.; Nichol, Robert C.; Scarlata, Claudia; Schawinski, Kevin; Conselice, Christopher J.; Almaini, Omar; Ferguson, Henry C.; Fortson, Lucy; Hartley, William; Kocevski, Dale; Koekemoer, Anton M.; Mortlock, Alice; Newman, Jeffrey A.; Bamford, Steven P.; Grogin, N. A.; Lucas, Ray A.; Hathi, Nimish P.; McGrath, Elizabeth; Peth, Michael; Pforr, Janine; Rizer, Zachary; Wuyts, Stijn; Barro, Guillermo; Bell, Eric F.; Castellano, Marco; Dahlen, Tomas; Dekel, Avishai; Ownsworth, Jamie; Faber, Sandra M.; Finkelstein, Steven L.; Fontana, Adriano; Galametz, Audrey; Grützbauch, Ruth; Koo, David; Lotz, Jennifer; Mobasher, Bahram; Mozena, Mark; Salvato, Mara; Wiklind, Tommy

2017-02-01

We present quantified visual morphologies of approximately 48 000 galaxies observed in three Hubble Space Telescope legacy fields by the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS) and classified by participants in the Galaxy Zoo project. 90 per cent of galaxies have z ≤ 3 and are observed in rest-frame optical wavelengths by CANDELS. Each galaxy received an average of 40 independent classifications, which we combine into detailed morphological information on galaxy features such as clumpiness, bar instabilities, spiral structure, and merger and tidal signatures. We apply a consensus-based classifier weighting method that preserves classifier independence while effectively down-weighting significantly outlying classifications. After analysing the effect of varying image depth on reported classifications, we also provide depth-corrected classifications which both preserve the information in the deepest observations and also enable the use of classifications at comparable depths across the full survey. Comparing the Galaxy Zoo classifications to previous classifications of the same galaxies shows very good agreement; for some applications, the high number of independent classifications provided by Galaxy Zoo provides an advantage in selecting galaxies with a particular morphological profile, while in others the combination of Galaxy Zoo with other classifications is a more promising approach than using any one method alone. We combine the Galaxy Zoo classifications of `smooth' galaxies with parametric morphologies to select a sample of featureless discs at 1 ≤ z ≤ 3, which may represent a dynamically warmer progenitor population to the settled disc galaxies seen at later epochs.

Design of a modulated orthovoltage stereotactic radiosurgery system.

PubMed

Fagerstrom, Jessica M; Bender, Edward T; Lawless, Michael J; Culberson, Wesley S

2017-07-01

To achieve stereotactic radiosurgery (SRS) dose distributions with sharp gradients using orthovoltage energy fluence modulation with inverse planning optimization techniques. A pencil beam model was used to calculate dose distributions from an orthovoltage unit at 250 kVp. Kernels for the model were derived using Monte Carlo methods. A Genetic Algorithm search heuristic was used to optimize the spatial distribution of added tungsten filtration to achieve dose distributions with sharp dose gradients. Optimizations were performed for depths of 2.5, 5.0, and 7.5 cm, with cone sizes of 5, 6, 8, and 10 mm. In addition to the beam profiles, 4π isocentric irradiation geometries were modeled to examine dose at 0.07 mm depth, a representative skin depth, for the low energy beams. Profiles from 4π irradiations of a constant target volume, assuming maximally conformal coverage, were compared. Finally, dose deposition in bone compared to tissue in this energy range was examined. Based on the results of the optimization, circularly symmetric tungsten filters were designed to modulate the orthovoltage beam across the apertures of SRS cone collimators. For each depth and cone size combination examined, the beam flatness and 80-20% and 90-10% penumbrae were calculated for both standard, open cone-collimated beams as well as for optimized, filtered beams. For all configurations tested, the modulated beam profiles had decreased penumbra widths and flatness statistics at depth. Profiles for the optimized, filtered orthovoltage beams also offered decreases in these metrics compared to measured linear accelerator cone-based SRS profiles. The dose at 0.07 mm depth in the 4π isocentric irradiation geometries was higher for the modulated beams compared to unmodulated beams; however, the modulated dose at 0.07 mm depth remained <0.025% of the central, maximum dose. The 4π profiles irradiating a constant target volume showed improved statistics for the modulated, filtered distribution compared to the standard, open cone-collimated distribution. Simulations of tissue and bone confirmed previously published results that a higher energy beam (≥ 200 keV) would be preferable, but the 250 kVp beam was chosen for this work because it is available for future measurements. A methodology has been described that may be used to optimize the spatial distribution of added filtration material in an orthovoltage SRS beam to result in dose distributions with decreased flatness and penumbra statistics compared to standard open cones. This work provides the mathematical foundation for a novel, orthovoltage energy fluence-modulated SRS system. © 2017 American Association of Physicists in Medicine.

Microbial community changes as a possible factor controlling carbon sequestration in subsoil

NASA Astrophysics Data System (ADS)

Strücker, Juliane; Jörgensen, Rainer Georg

2015-04-01

In order to gain more knowledge regarding the microbial community and their influence on carbon sequestration in subsoil two depth profiles with different soil organic carbon (SOC) concentrations were sampled. The SOC concentrations developed naturally due to deposition and erosion. This experiment offers the opportunity to investigate to which extend natural SOC availability or other subsoil specific conditions influence the composition and the functional diversity of the microbial community and in return if there is any evidence how the microbial community composition affects carbon sequestration under these conditions. Soil samples were taken at four different depths on two neighbouring arable sites; one Kolluvisol with high SOC concentrations (8-12 g/kg) throughout the profile and one Luvisol with low SOC concentrations (3-4 g/kg) below 30 cm depth. The multi substrate induced respiration (MSIR) method was used to identify shifts in the functional diversity of the microbial community along the depth profiles. Amino sugars Muramic Acid and Glucosamine were measured as indicators for bacterial and fungal residues and ergosterol was determined as marker for saprotrophic fungi. The results of the discriminant analysis of the respiration values obtained from the 17 substrates used in the MSIR show that the substrate use in subsoil is different from the substrate use in topsoil. The amino sugar analysis and the ratio of ergosterol to microbial biomass C indicate that the fungal dominance of the microbial community decreases with depth. The results from this study support previous findings, which also observed decreasing fungal dominance with depth. Furthermore the MSIR approach shows clearly that not only the composition of the microbial community but also their substrate use changes with depth. Thus, a different microbial community with altered substrate requirements could be an important reason for enhanced carbon sequestration in subsoil. The fact that the MSIR was also able to differentiate between the two sites proves the assumption that resources are an important factor controlling the functional diversity of the microbial community, as abiotic factors are very similar for the two profiles, but the sites show a different depth gradient for SOC.

Application of acoustic-Doppler current profiler and expendable bathythermograph measurements to the study of the velocity structure and transport of the Gulf Stream

NASA Technical Reports Server (NTRS)

Joyce, T. M.; Dunworth, J. A.; Schubert, D. M.; Stalcup, M. C.; Barbour, R. L.

1988-01-01

The degree to which Acoustic-Doppler Current Profiler (ADCP) and expendable bathythermograph (XBT) data can provide quantitative measurements of the velocity structure and transport of the Gulf Stream is addressed. An algorithm is used to generate salinity from temperature and depth using an historical Temperature/Salinity relation for the NW Atlantic. Results have been simulated using CTD data and comparing real and pseudo salinity files. Errors are typically less than 2 dynamic cm for the upper 800 m out of a total signal of 80 cm (across the Gulf Stream). When combined with ADCP data for a near-surface reference velocity, transport errors in isopycnal layers are less than about 1 Sv (10 to the 6th power cu m/s), as is the difference in total transport for the upper 800 m between real and pseudo data. The method is capable of measuring the real variability of the Gulf Stream, and when combined with altimeter data, can provide estimates of the geoid slope with oceanic errors of a few parts in 10 to the 8th power over horizontal scales of 500 km.

Multivariate inference of pathway activity in host immunity and response to therapeutics

PubMed Central

Goel, Gautam; Conway, Kara L.; Jaeger, Martin; Netea, Mihai G.; Xavier, Ramnik J.

2014-01-01

Developing a quantitative view of how biological pathways are regulated in response to environmental factors is central for understanding of disease phenotypes. We present a computational framework, named Multivariate Inference of Pathway Activity (MIPA), which quantifies degree of activity induced in a biological pathway by computing five distinct measures from transcriptomic profiles of its member genes. Statistical significance of inferred activity is examined using multiple independent self-contained tests followed by a competitive analysis. The method incorporates a new algorithm to identify a subset of genes that may regulate the extent of activity induced in a pathway. We present an in-depth evaluation of specificity, robustness, and reproducibility of our method. We benchmarked MIPA's false positive rate at less than 1%. Using transcriptomic profiles representing distinct physiological and disease states, we illustrate applicability of our method in (i) identifying gene–gene interactions in autophagy-dependent response to Salmonella infection, (ii) uncovering gene–environment interactions in host response to bacterial and viral pathogens and (iii) identifying driver genes and processes that contribute to wound healing and response to anti-TNFα therapy. We provide relevant experimental validation that corroborates the accuracy and advantage of our method. PMID:25147207

Investigating mechanically induced phase response of the tissue by using high-speed phase-resolved optical coherence tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ling, Yuye; Hendon, Christine P.

2017-02-01

Phase-resolved optical coherence tomography (OCT), a functional extension of OCT, provides depth-resolved phase information with extra contrast. In cardiology, changes in the mechanical properties have been associated with tissue remodeling and disease progression. Here we present the capability of profiling structural deformation of the sample in vivo by using a highly stable swept source OCT system The system, operating at 1300 nm, has an A-line acquisition rate of 200 kHz. We measured the phase noise floor to be 6.5 pm±3.2 pm by placing a cover slip in the sample arm, while blocking the reference arm. We then conducted a vibrational frequency test by measuring the phase response from a polymer membrane stimulated by a pure tone acoustic wave from 10 kHz to 80 kHz. The measured frequency response agreed with the known stimulation frequency with an error < 0.005%. We further measured the phase response of 7 fresh swine hearts obtained from Green Village Packing Company through a mechanical stretching test, within 24 hours of sacrifice. The heart tissue was cut into a 1 mm slices and fixed on two motorized stages. We acquired 100,000 consecutive M-scans, while the sample is stretched at a constant velocity of 10 um/s. The depth-resolved phase image presents linear phase response over time at each depth, but the slope varies among tissue types. Our future work includes refining our experiment protocol to quantitatively measured the elastic modulus of the tissue in vivo and building a tissue classifier based on depth-resolved phase information.

Probing neural tissue with airy light-sheet microscopy: investigation of imaging performance at depth within turbid media

NASA Astrophysics Data System (ADS)

Nylk, Jonathan; McCluskey, Kaley; Aggarwal, Sanya; Tello, Javier A.; Dholakia, Kishan

2017-02-01

Light-sheet microscopy (LSM) has received great interest for fluorescent imaging applications in biomedicine as it facilitates three-dimensional visualisation of large sample volumes with high spatiotemporal resolution whilst minimising irradiation of, and photo-damage to the specimen. Despite these advantages, LSM can only visualize superficial layers of turbid tissues, such as mammalian neural tissue. Propagation-invariant light modes have played a key role in the development of high-resolution LSM techniques as they overcome the natural divergence of a Gaussian beam, enabling uniform and thin light-sheets over large distances. Most notably, Bessel and Airy beam-based light-sheet imaging modalities have been demonstrated. In the single-photon excitation regime and in lightly scattering specimens, Airy-LSM has given competitive performance with advanced Bessel-LSM techniques. Airy and Bessel beams share the property of self-healing, the ability of the beam to regenerate its transverse beam profile after propagation around an obstacle. Bessel-LSM techniques have been shown to increase the penetration-depth of the illumination into turbid specimens but this effect has been understudied in biologically relevant tissues, particularly for Airy beams. It is expected that Airy-LSM will give a similar enhancement over Gaussian-LSM. In this paper, we report on the comparison of Airy-LSM and Gaussian-LSM imaging modalities within cleared and non-cleared mouse brain tissue. In particular, we examine image quality versus tissue depth by quantitative spatial Fourier analysis of neural structures in virally transduced fluorescent tissue sections, showing a three-fold enhancement at 50 μm depth into non-cleared tissue with Airy-LSM. Complimentary analysis is performed by resolution measurements in bead-injected tissue sections.

Quantitative evaluation of the voice range profile in patients with voice disorder.

PubMed

Ikeda, Y; Masuda, T; Manako, H; Yamashita, H; Yamamoto, T; Komiyama, S

1999-01-01

In 1953, Calvet first displayed the fundamental frequency (pitch) and sound pressure level (intensity) of a voice on a two-dimensional plane and created a voice range profile. This profile has been used to evaluate clinically various vocal disorders, although such evaluations to date have been subjective without quantitative assessment. In the present study, a quantitative system was developed to evaluate the voice range profile utilizing a personal computer. The area of the voice range profile was defined as the voice volume. This volume was analyzed in 137 males and 175 females who were treated for various dysphonias at Kyushu University between 1984 and 1990. Ten normal subjects served as controls. The voice volume in cases with voice disorders significantly decreased irrespective of the disease and sex. Furthermore, cases having better improvement after treatment showed a tendency for the voice volume to increase. These findings illustrated the voice volume as a useful clinical test for evaluating voice control in cases with vocal disorders.

{sup 14}C depth profiles in Apollo 15 and 17 cores and lunar rock 68815

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jull, A.J.T.; Cloudt, S.; Donahue, D.J.

1998-09-01

Accelerator mass spectrometry (AMS) was used to measure the activity vs. depth profiles of {sup 14}C produced by both solar cosmic rays (SCR) and galactic cosmic rays (GCR) in Apollo 15 lunar cores 15001-6 and 15008, Apollo 17 core 76001, and lunar rock 68815. Calculated GCR production rates are in good agreement with {sup 14}C measurements at depths below {approximately}10 cm. Carbon-14 produced by solar protons was observed in the top few cm of the Apollo 15 cores and lunar rock 68815, with near-surface values as high as 66 dpm/kg in 68815. Only low levels of SCR-produced {sup 14}C weremore » observed in the Apollo 17 core 76001. New cross sections for production of {sup 14}C by proton spallation on O, Si, Al, Mg, Fe, and Ni were measured using AMS. These cross sections are essential for the analysis of the measured {sup 14}C depth profiles. The best fit to the activity-depth profiles for solar-proton-produced {sup 14}C measured in the tops of both the Apollo 15 cores and 68815 was obtained for an exponential rigidity spectral shape R{sub 0} of 110--115 MV and a 4 {pi} flux (J{sub 10}, Ep > 10 MeV) of 103--108 protons/cm{sup 2}/s. These values of R{sub 0} are higher, indicating a harder rigidity, and the solar-proton fluxes are higher than those determined from {sup 10}Be, {sup 26}Al, and {sup 53}Mn measurements.« less

Using Uranium-series isotopes to understand processes of rapid soil formation in tropical volcanic settings: an example from Basse-Terre, French Guadeloupe

NASA Astrophysics Data System (ADS)

Ma, Lin

2015-04-01

Lin Ma1, Yvette Pereyra1, Peter B Sak2, Jerome Gaillardet3, Heather L Buss4 and Susan L Brantley5, (1) University of Texas at El Paso, El Paso, TX, United States, (2) Dickinson College, Carlisle, PA, United States, (3) Institute de Physique d Globe Paris, Paris, France, (4) University of Bristol, Bristol, United Kingdom, (5) Pennsylvania State University Main Campus, University Park, PA, United States Uranium-series isotopes fractionate during chemical weathering and their activity ratios can be used to determine timescales and rates of soil formation. Such soil formation rates provide important information to understand processes related to rapid soil formation in tropical volcanic settings, especially with respect to their fertility and erosion. Recent studies also highlighted the use of U-series isotopes to trace and quantify atmospheric inputs to surface soils. Such a process is particularly important in providing mineral nutrients to ecosystems in highly depleted soil systems such as the tropical soils. Here, we report U-series isotope compositions in thick soil profiles (>10 m) developed on andesitic pyroclastic flows in Basse-Terre Island of French Guadeloupe. Field observations have shown heterogeneity in color and texture in these thick profiles. However, major element chemistry and mineralogy show some general depth trends. The main minerals present throughout the soil profile are halloysite and gibbsite. Chemically immobile elements such as Al, Fe, and Ti show a depletion profile relative to Th while elements such as K, Mn, and Si show a partial depletion profile at depth. Mobile elements such as Ca, Mg, and Sr have undergone intensive weathering at depths, and an addition profile near the surface, most likely related to atmospheric inputs. (238U/232Th) activity ratios in one soil profile from the Brad David watershed in this study ranged from 0.374 to 1.696, while the (230Th/232Th) ratios ranged from 0.367 to 1.701. A decrease of (238U/232Th) in the deep soil profile depth is observed, and then an increase to the surface. The (230Th /232Th) ratios showed a similar trend as (238U/232Th). Marine aerosols and atmospheric dust from the Sahara region are most likely responsible for the addition of U in shallow soils. Intensive chemical weathering is responsible for the loss of U at depth, consistent with these observations of major element chemistry and mineralogy. Furthermore, U-series chemical weathering model suggests that the weathering duration from 12m to 4m depth in this profile is about 250kyr, with a weathering advancing rate of ~30 m/Ma. The rate is also about one order of magnitude lower than the weathering rate (~300 m/Ma) determined by river chemistry for this watershed. In this profile, the augered core didn't reach the unweathered bedrock. Hence, the derived slow weathering rate most likely represents the intensive weathering of clay minerals, while the transformation of fresh bedrock to regolith occurs at much great depth beneath the thick regolith. The marine aerosols and atmospheric dust are important sources of mineral nutrients for highly depleted surface soils.

Psychosocial framework for understanding psychological distress among survivors of the November 26, 2008 Mumbai terror attack: beyond traumatic experiences and emergency medical care.

PubMed

Joseph, Jacquleen; Jaswal, Surinder

2014-06-01

The field of "Public Health in Disasters and Complex Emergencies" is replete with either epidemiological studies or studies in the area of hospital preparedness and emergency care. The field is dominated by hospital-based or emergency phase-related literature, with very little attention on long-term health and mental health consequences. The social science, or the public mental health perspective, too, is largely missing. It is in this context that the case report of the November 26, 2008 Mumbai terror attack survivors is presented to bring forth the multi-dimensional and dynamic long-term impacts, and their consequences for psychological well-being, two years after the incident. Based on literature, the report formulates a theoretical framework through which the lived experiences of the survivors is analyzed and understood from a social science perspective. This report is an outcome of the ongoing work with the survivors over a period of two years. A mixed methodology was used. It quantitatively captures the experience of 231 families following the attack, and also uses a self-reporting questionnaire (SRQ), SRQ20, to understand the psychological distress. In-depth qualitative case studies constructed from the process records and in-depth interviews focus on lived experiences of the survivors and explain the patterns emerging from the quantitative analysis. This report outlines the basic profile of the survivors, the immediate consequences of the attack, the support received, psychological consequences, and the key factors contributing to psychological distress. Through analysis of the key factors and the processes emerging from the lived experiences that explain the progression of vulnerability to psychological distress, this report puts forth a psychosocial framework for understanding psychological distress among survivors of the November 26, 2008 Mumbai terror attack.

Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clair, Geremy; Piehowski, Paul D.; Nicola, Teodora

Global proteomics approaches allow characterization of whole tissue lysates to an impressive depth. However, it is now increasingly recognized that to better understand the complexity of multicellular organisms, global protein profiling of specific spatially defined regions/substructures of tissues (i.e. spatially-resolved proteomics) is essential. Laser capture microdissection (LCM) enables microscopic isolation of defined regions of tissues preserving crucial spatial information. However, current proteomics workflows entail several manual sample preparation steps and are challenged by the microscopic mass-limited samples generated by LCM, and that impact measurement robustness, quantification, and throughput. Here, we coupled LCM with a fully automated sample preparation workflow thatmore » with a single manual step allows: protein extraction, tryptic digestion, peptide cleanup and LC-MS/MS analysis of proteomes from microdissected tissues. Benchmarking against the current state of the art in ultrasensitive global proteomic analysis, our approach demonstrated significant improvements in quantification and throughput. Using our LCM-SNaPP proteomics approach, we characterized to a depth of more than 3,400 proteins, the ontogeny of protein changes during normal lung development in laser capture microdissected alveolar tissue containing ~4,000 cells per sample. Importantly, the data revealed quantitative changes for 350 low abundance transcription factors and signaling molecules, confirming earlier transcript-level observations and defining seven modules of coordinated transcription factor/signaling molecule expression patterns, suggesting that a complex network of temporal regulatory control directs normal lung development with epigenetic regulation fine-tuning pre-natal developmental processes. Our LCM-proteomics approach facilitates efficient, spatially-resolved, ultrasensitive global proteomics analyses in high-throughput that will be enabling for several clinical and biological applications.« less

Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions

NASA Astrophysics Data System (ADS)

Olivieri, Giorgia; Parry, Krista M.; Powell, Cedric J.; Tobias, Douglas J.; Brown, Matthew A.

2016-04-01

Over the past decade, energy-dependent ambient pressure X-ray photoelectron spectroscopy (XPS) has emerged as a powerful analytical probe of the ion spatial distributions at the vapor (vacuum)-aqueous electrolyte interface. These experiments are often paired with complementary molecular dynamics (MD) simulations in an attempt to provide a complete description of the liquid interface. There is, however, no systematic protocol that permits a straightforward comparison of the two sets of results. XPS is an integrated technique that averages signals from multiple layers in a solution even at the lowest photoelectron kinetic energies routinely employed, whereas MD simulations provide a microscopic layer-by-layer description of the solution composition near the interface. Here, we use the National Institute of Standards and Technology database for the Simulation of Electron Spectra for Surface Analysis (SESSA) to quantitatively interpret atom-density profiles from MD simulations for XPS signal intensities using sodium and potassium iodide solutions as examples. We show that electron inelastic mean free paths calculated from a semi-empirical formula depend strongly on solution composition, varying by up to 30% between pure water and concentrated NaI. The XPS signal thus arises from different information depths in different solutions for a fixed photoelectron kinetic energy. XPS signal intensities are calculated using SESSA as a function of photoelectron kinetic energy (probe depth) and compared with a widely employed ad hoc method. SESSA simulations illustrate the importance of accounting for elastic-scattering events at low photoelectron kinetic energies (<300 eV) where the ad hoc method systematically underestimates the preferential enhancement of anions over cations. Finally, some technical aspects of applying SESSA to liquid interfaces are discussed.

Isomer-specific profiling of N-glycans derived from human serum for potential biomarker discovery in pancreatic cancer.

PubMed

Liu, Yufei; Wang, Chang; Wang, Ran; Wu, Yike; Zhang, Liang; Liu, Bi-Feng; Cheng, Liming; Liu, Xin

2018-06-15

Glycosylation is one of the most important post-translational modifications of protein. Recently, global profiling of human serum glycomics has become a noninvasive method for cancer-related biomarker discovery and many studies have focused on compositional glycan profiling. In contrast, structure-specific glycan profiling may provide more potential biomarkers with higher specificity than compositional profiling. In this work, N-glycans released from human serum were neutralized with methylamine and reduced by ammonia-borane complex prior to profiling using nanoLC-ESI-MS with porous graphitized carbon (PGC) and relative abundances of over 280 isomers were compared between pancreatic cancer (PC) cases (n = 32) and healthy controls (n = 32). Statistical analysis identified 25 specific-isomeric biomarkers with significant differences (p-value < 0.05). ROC and PCA analysis were performed to assess the potential biomarkers which were identified as being significantly altered in cancer. The AUCs of the significantly changed specific-isomers were ranging from 0.712 to 0.949. In addition, with the combination of all potential biomarkers, a higher AUC of 0.976 with sensitivity (93.5%) and specificity (90.6%) was obtained. Overall, the proposed strategy coupled to relative quantitative analysis of isomeric glycans make it possible to discover new biomarkers for the diagnosis of PC. Pancreatic cancer (PC) has a poor prognosis with a five-year survival rate <5%. Therefore, a strategy for accurate diagnosis of PC is indeed required. In this paper, a dual-derivatized strategy for structure-specific glycan profiling has been used and according to our best knowledge, this is the first application of this strategy for PC biomarker discovery, in which the separation, identification and relative quantification of isomeric glycans can be simultaneously obtained. In addition, by in-depth analysis of isomeric glycans, the full description of the stereo- and region- diversity of glycans can also be achieved, which might provide more potential information for PC biomarker discovery. Copyright © 2018 Elsevier B.V. All rights reserved.

DNA profiling, telomere analysis and antioxidant properties as tools for monitoring ex situ seed longevity

PubMed Central

Donà, M.; Balestrazzi, A.; Mondoni, A.; Rossi, G.; Ventura, L.; Buttafava, A.; Macovei, A.; Sabatini, M. E.; Valassi, A.; Carbonera, D.

2013-01-01

Background and Aims The germination test currently represents the most used method to assess seed viability in germplasm banks, despite the difficulties caused by the occurrence of seed dormancy. Furthermore, seed longevity can vary considerably across species and populations from different environments, and studies related to the eco-physiological processes underlying such variations are still limited in their depth. The aim of the present work was the identification of reliable molecular markers that might help in monitoring seed deterioration. Methods Dry seeds were subjected to artificial ageing and collected at different time points for molecular/biochemical analyses. DNA damage was measured using the RAPD (random amplified polymorphic DNA) approach while the seed antioxidant profile was obtained using both the DPPH (1,1-diphenyl, 2-picrylhydrazyl) assay and the Folin–Ciocalteu reagent method. Electron paramagnetic resonance (EPR) provided profiles of free radicals. Quantitative real-time polymerase chain reaction (QRT-PCR) was used to assess the expression profiles of the antioxidant genes MT2 (type 2 metallothionein) and SOD (superoxide dismutase). A modified QRT-PCR protocol was used to determine telomere length. Key Results The RAPD profiles highlighted different capacities of the two Silene species to overcome DNA damage induced by artificial ageing. The antioxidant profiles of dry and rehydrated seeds revealed that the high-altitude taxon Silene acaulis was characterized by a lower antioxidant specific activity. Significant upregulation of the MT2 and SOD genes was observed only in the rehydrated seeds of the low-altitude species. Rehydration resulted in telomere lengthening in both Silene species. Conclusions Different seed viability markers have been selected for plant species showing inherent variation of seed longevity. RAPD analysis, quantification of redox activity of non-enzymatic antioxidant compounds and gene expression profiling provide deeper insights to study seed viability during storage. Telomere lengthening is a promising tool to discriminate between short- and long-lived species. PMID:23532044

CRUSTAL REFRACTION PROFILE OF THE LONG VALLEY CALDERA, CALIFORNIA, FROM THE JANUARY 1983 MAMMOTH LAKES EARTHQUAKE SWARM.

USGS Publications Warehouse

Luetgert, James H.; Mooney, Walter D.

1985-01-01

Seismic-refraction profiles recorded north of Mammoth Lakes, California, using earthquake sources from the January 1983 swarm complement earlier explosion refraction profiles and provide velocity information from deeper in the crust in the area of the Long Valley caldera. Eight earthquakes from a depth range of 4. 9 to 8. 0 km confirm the observation of basement rocks with seismic velocities ranging from 5. 8 to 6. 4 km/sec extending at least to depths of 20 km. The data provide further evidence for the existence of a partial melt zone beneath Long Valley caldera and constrain its geometry. Refs.

OCT structure, COB location and magmatic type of the SE Brazilian & S Angolan margins from integrated quantitative analysis of deep seismic reflection and gravity anomaly data

NASA Astrophysics Data System (ADS)

Cowie, L.; Kusznir, N. J.; Horn, B.

2013-12-01

Knowledge of ocean-continent transition (OCT) structure, continent-ocean boundary (COB) location and magmatic type are of critical importance for understanding rifted continental margin formation processes and in evaluating petroleum systems in deep-water frontier oil and gas exploration. The OCT structure, COB location and magmatic type of the SE Brazilian and S Angolan rifted continental margins are much debated; exhumed and serpentinised mantle have been reported at these margins. Integrated quantitative analysis using deep seismic reflection data and gravity inversion have been used to determine OCT structure, COB location and magmatic type for the SE Brazilian and S Angolan margins. Gravity inversion has been used to determine Moho depth, crustal basement thickness and continental lithosphere thinning. Residual Depth Anomaly (RDA) analysis has been used to investigate OCT bathymetric anomalies with respect to expected oceanic bathymetries and subsidence analysis has been used to determine the distribution of continental lithosphere thinning. These techniques have been validated on the Iberian margin for profiles IAM9 and ISE-01. In addition a joint inversion technique using deep seismic reflection and gravity anomaly data has been applied to the ION-GXT BS1-575 SE Brazil and ION-GXT CS1-2400 S Angola. The joint inversion method solves for coincident seismic and gravity Moho in the time domain and calculates the lateral variations in crustal basement densities and velocities along profile. Gravity inversion, RDA and subsidence analysis along the S Angolan ION-GXT CS1-2400 profile has been used to determine OCT structure and COB location. Analysis suggests that exhumed mantle, corresponding to a magma poor margin, is absent beneath the allochthonous salt. The thickness of earliest oceanic crust, derived from gravity and deep seismic reflection data is approximately 7km. The joint inversion predicts crustal basement densities and seismic velocities which are slightly less than expected for 'normal' oceanic crust. The difference between the sediment corrected RDA and that predicted from gravity inversion crustal thickness variation implies that this margin is experiencing ~300m of anomalous uplift attributed to mantle dynamic uplift. Gravity inversion, RDA and subsidence analysis have also been used to determine OCT structure and COB location along the ION-GXT BS1-575 profile, crossing the Sao Paulo Plateau and Florianopolis Ridge of the SE Brazilian margin. Gravity inversion, RDA and subsidence analysis predict the COB to be located SE of the Florianopolis Ridge. Analysis shows no evidence for exhumed mantle on this margin profile. The joint inversion technique predicts normal oceanic basement seismic velocities and densities and beneath the Sao Paulo Plateau and Florianopolis Ridge predicts crustal basement thicknesses between 10-15km. The Sao Paulo Plateau and Florianopolis Ridge are separated by a thin region of crustal basement beneath the salt interpreted as a regional transtensional structure. Sediment corrected RDAs and gravity derived 'synthetic' RDAs are of a similar magnitude on oceanic crust, implying negligible mantle dynamic topography.

Extreme precipitation depths for Texas, excluding the Trans-Pecos region

USGS Publications Warehouse

Lanning-Rush, Jennifer; Asquith, William H.; Slade, Raymond M.

1998-01-01

Storm durations of 1, 2, 3, 4, 5, and 6 days were investigated for this report. The extreme precipitation depth for a particular area is estimated from an “extreme precipitation curve” (an upper limit or envelope curve developed from graphs of extreme precipitation depths for each climatic region). The extreme precipitation curves were determined using precipitation depth-duration information from a subset (24 “extreme” storms) of 213 “notable” storms documented throughout Texas. The extreme precipitation curves can be used to estimate extreme precipitation depth for a particular area. The extreme precipitation depth represents a limiting depth, which can provide useful comparative information for more quantitative analyses.

LA-ICP-MS depth profile analysis of apatite: Protocol and implications for (U-Th)/He thermochronometry

NASA Astrophysics Data System (ADS)

Johnstone, Samuel; Hourigan, Jeremy; Gallagher, Christopher

2013-05-01

Heterogeneous concentrations of α-producing nuclides in apatite have been recognized through a variety of methods. The presence of zonation in apatite complicates both traditional α-ejection corrections and diffusive models, both of which operate under the assumption of homogeneous concentrations. In this work we develop a method for measuring radial concentration profiles of 238U and 232Th in apatite by laser ablation ICP-MS depth profiling. We then focus on one application of this method, removing bias introduced by applying inappropriate α-ejection corrections. Formal treatment of laser ablation ICP-MS depth profile calibration for apatite includes construction and calibration of matrix-matched standards and quantification of rates of elemental fractionation. From this we conclude that matrix-matched standards provide more robust monitors of fractionation rate and concentrations than doped silicate glass standards. We apply laser ablation ICP-MS depth profiling to apatites from three unknown populations and small, intact crystals of Durango fluorapatite. Accurate and reproducible Durango apatite dates suggest that prolonged exposure to laser drilling does not impact cooling ages. Intracrystalline concentrations vary by at least a factor of 2 in the majority of the samples analyzed, but concentration variation only exceeds 5x in 5 grains and 10x in 1 out of the 63 grains analyzed. Modeling of synthetic concentration profiles suggests that for concentration variations of 2x and 10x individual homogeneous versus zonation dependent α-ejection corrections could lead to age bias of >5% and >20%, respectively. However, models based on measured concentration profiles only generated biases exceeding 5% in 13 of the 63 cases modeled. Application of zonation dependent α-ejection corrections did not significantly reduce the age dispersion present in any of the populations studied. This suggests that factors beyond homogeneous α-ejection corrections are the dominant source of overdispersion in apatite (U-Th)/He cooling ages.

SU-F-T-487: On-Site Beam Matching of An Elekta Infinity with Agility MLC with An Elekta Versa HD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, C; Garcia, M; Mason, B

2016-06-15

Purpose: Historically, beam matching of similar Linear Accelerators has been accomplished by sending beam data to the manufacturer to match at their factory. The purpose of this work is to demonstrate that fine beam matching can be carried out on-site as part of the acceptance test, with similar or better results. Methods: Initial scans of a 10 × 10 Percent depth dose (PDD) and a 40 × 40 beam profile at the depth of Dmax, for 6MV and 10 MV were taken to compare with the standard beam data from the Versa. The energy was then adjusted and the beammore » steered to achieve agreement between the depth dose and the horns of the beam profile. This process was repeated until the best agreement between PDD and profiles was achieved. Upon completion, all other clinical data were measured to verify match. This included PDD, beam profiles, output factors and Wedge factors. For electron beams PDD’s were matched and the beam profiles verified for the final beam energy. Confirmatory PDD and beam profiles for clinical field sizes, as well as Output Factors were measured. Results: The average difference in PDD’s for 6MV and 10MV were within 0.4% for both wedged and open fields. Beam profile comparisons over the central 80% of the field, at multiple depths, show agreement of 0.8% or less for both wedged and open fields. Average output factor agreement over all field sizes was 0.4% for 6MV and 0.2 % for 10MV. Wedge factors agreement was less than 0.6% for both photon energies over all field sizes. Electron PDD agreed to 0.5mm. Cone ratios agreed to 1% or less. Conclusion: This work indicates that beam matching can be carried out on-site simply and quickly. The results of this beam matching can achieve similar or better results than factory matching.« less

The GEORIFT 2013 wide-angle seismic profile, along Pripyat-Dnieper-Donets Basin

NASA Astrophysics Data System (ADS)

Starostenko, Vitaliy; Janik, Tomasz; Yegorova, Tamara; Czuba, Wojciech; Sroda, Piotr; Lysynchuk, Dmytro; Aizberg, Roman; Garetsky, Radim; Karataev, German; Gribik, Yaroslav; Farfuliak, Lliudmyla; Kolomiyets, Katerina; Omelchenko, Victor; Gryn, Dmytro; Guterch, Aleksander; Komminaho, Kari; Legostaeva, Olga; Thybo, Hans; Tiira, Timo; Tolkunov, Anatoly

2017-04-01

The GEORIFT 2013 deep seismic sounding (DSS) experiment was carried in August 2013 on territory of Belarus and Ukraine in wide international co-operation. The aim of the work is to study basin architecture and the deep structure of the Pripyat-Dnieper-Donets Basin (PDDB), which is the deepest and best studied Palaeozoic rift basin in Europe. The PDDB locates in the southern part of the East European Craton (EEC) and crosses in NW direction the Sarmatia, the southernmost of three major segments forming the EEC. The long PDDB was formed by Late Devonian rifting in the arch of the ancient Sarmatian shield. During the Late Devonian, rifting, associated with domal basement uplift and magmatism, was widespread in the EEC from the PDDB rift basin in the south to Eastern Barents Sea in the north. The GEORIFT 2013 runs in NW-SE direction along the PDDB and crosses the Pripyat Trough and Dnieper Graben separated by Bragin uplift of the basement. The total profile length was 675 km: 315 km on the Belarusian territory and 360 km in Ukraine. The field acquisition included 14 shot points (charge 600-1000 kg of TNT), and 309 recording stations every 2.2 km. The data quality of the data was good, with visible first arrivals even up to 670 km. We present final model of the structure to the depth of 80 km. Ray-tracing forward modelling (SEIS83 package) was used for the modelling of the seismic data. The thickness of the sedimentary layer (Vp < 6.0 km/s) changes along the profile from 1-4 km in the NW, through 5 km in the central part, to 10-13 km in the SE part of the profile. In 330-530 km distance range, an updoming of the lower crust (with Vp of 7.1 km/s) to 25 km depth is observed. Large variations in the internal structure of the crust and the Moho topography were detected. The depth of the Moho varies from 47 km in the northwestern part of the model, to 40 km in central part, and to 38 km in the southeastern part of the profile. The sub-Moho velocities are 8.25 km/s. Second, near-horizontal mantle discontinuity was found in the northwestern part of the profile at the depth of 50-47 km. It dips to the depth of 60 km at distances of 360-405 km, similarly as on crossing EUROBRIDGE'97 profile (Thybo et al., 2003). In the central part of the profile (distances 180-330 km and 300-480 km) two reflectors were found in the lower lithosphere at depths of about 62 km and 75 km, respectively.

Assessing XCTD Fall Rate Errors using Concurrent XCTD and CTD Profiles in the Southern Ocean

NASA Astrophysics Data System (ADS)

Millar, J.; Gille, S. T.; Sprintall, J.; Frants, M.

2010-12-01

Refinements in the fall rate equation for XCTDs are not as well understood as those for XBTs, due in part to the paucity of concurrent and collocated XCTD and CTD profiles. During February and March 2010, the Diapycnal and Isopycnal Mixing Experiment in the Southern Ocean (DIMES) conducted 31 collocated 1000-meter XCTD and CTD casts in the Drake Passage. These XCTD/CTD profile pairs are closely matched in space and time, with a mean distance between casts of 1.19 km and a mean lag time of 39 minutes. The profile pairs are well suited to address the XCTD fall rate problem specifically in higher latitude waters, where existing fall rate corrections have rarely been assessed. Many of these XCTD/CTD profile pairs reveal an observable depth offset in measurements of both temperature and conductivity. Here, the nature and extent of this depth offset is evaluated.

Impact energy and retained dose uniformity in enhanced glow discharge plasma immersion ion implantation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Q. Y.; Fu, Ricky K. Y.; Chu, Paul K.

2009-08-10

The implantation energy and retained dose uniformity in enhanced glow discharge plasma immersion ion implantation (EGD-PIII) is investigated numerically and experimentally. Depth profiles obtained from different samples processed by EGD-PIII and traditional PIII are compared. The retained doses under different pulse widths are calculated by integrating the area under the depth profiles. Our results indicate that the improvement in the impact energy and retained dose uniformity by this technique is remarkable.

pH variation and influence in an autotrophic nitrogen removing biofilm system using an efficient numerical solution strategy.

PubMed

Vangsgaard, Anna Katrine; Mauricio-Iglesias, Miguel; Valverde-Pérez, Borja; Gernaey, Krist V; Sin, Gürkan

2013-01-01

A pH simulator consisting of an efficient numerical solver of a system of nine nonlinear equations was constructed and implemented in the modeling software MATLAB. The pH simulator was integrated in a granular biofilm model and used to simulate the pH profiles within granules performing the nitritation-anammox process for a range of operating points. The simulation results showed that pH profiles were consistently increasing with increasing depth into the granule, since the proton-producing aerobic ammonium-oxidizing bacteria (AOB) were located close to the granule surface. Despite this pH profile, more NH3 was available for AOB than for anaerobic ammonium oxidizers, located in the center of the granules. However, operating at a higher oxygen loading resulted in steeper changes in pH over the depth of the granule and caused the NH3 concentration profile to increase from the granule surface towards the center. The initial value of the background charge and influent bicarbonate concentration were found to greatly influence the simulation result and should be accurately measured. Since the change in pH over the depth of the biofilm was relatively small, the activity potential of the microbial groups affected by the pH did not change more than 5% over the depth of the granules.

Quantitative depth resolved microcirculation imaging with optical coherence tomography angiography (Part ΙΙ): Microvascular network imaging.

PubMed

Gao, Wanrong

2017-04-17

In this work, we review the main phenomena that have been explored in OCT angiography to image the vessels of the microcirculation within living tissues with the emphasis on how the different processing algorithms were derived to circumvent specific limitations. Parameters are then discussed that can quantitatively describe the depth-resolved microvascular network for possible clinic diagnosis applications. Finally,future directions in continuing OCT development are discussed. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Towards Understanding Soil Forming in Santa Clotilde Critical Zone Observatory: Modelling Soil Mixing Processes in a Hillslope using Luminescence Techniques

NASA Astrophysics Data System (ADS)

Sanchez, A. R.; Laguna, A.; Reimann, T.; Giráldez, J. V.; Peña, A.; Wallinga, J.; Vanwalleghem, T.

2017-12-01

Different geomorphological processes such as bioturbation and erosion-deposition intervene in soil formation and landscape evolution. The latter processes produce the alteration and degradation of the materials that compose the rocks. The degree to which the bedrock is weathered is estimated through the fraction of the bedrock which is mixing in the soil either vertically or laterally. This study presents an analytical solution for the diffusion-advection equation to quantify bioturbation and erosion-depositions rates in profiles along a catena. The model is calibrated with age-depth data obtained from profiles using the luminescence dating based on single grain Infrared Stimulated Luminescence (IRSL). Luminescence techniques contribute to a direct measurement of the bioturbation and erosion-deposition processes. Single-grain IRSL techniques is applied to feldspar minerals of fifteen samples which were collected from four soil profiles at different depths along a catena in Santa Clotilde Critical Zone Observatory, Cordoba province, SE Spain. A sensitivity analysis is studied to know the importance of the parameters in the analytical model. An uncertainty analysis is carried out to stablish the better fit of the parameters to the measured age-depth data. The results indicate a diffusion constant at 20 cm in depth of 47 (mm2/year) in the hill-base profile and 4.8 (mm2/year) in the hilltop profile. The model has high uncertainty in the estimation of erosion and deposition rates. This study reveals the potential of luminescence single-grain techniques to quantify pedoturbation processes.

Condition and biochemical profile of blue mussels (Mytilus edulis L.) cultured at different depths in a cold water coastal environment

NASA Astrophysics Data System (ADS)

Gallardi, Daria; Mills, Terry; Donnet, Sebastien; Parrish, Christopher C.; Murray, Harry M.

2017-08-01

The growth and health of cultured blue mussels (Mytilus edulis) are affected by environmental conditions. Typically, culture sites are situated in sheltered areas near shore (i.e., < 1 km distance from land, < 20 m depth); however, land runoff, user conflicts and environmental impact in coastal areas are concerns and interest in developing deep water (> 20 m depth) mussel culture has been growing. This study evaluated the effect of culture depth on blue mussels in a cold water coastal environment (Newfoundland, Canada). Culture depth was examined over two years from September 2012 to September 2014; mussels from three shallow water (5 m) and three deep water (15 m) sites were compared for growth and biochemical composition; culture depths were compared for temperature and chlorophyll a. Differences between the two years examined were noted, possibly due to harsh winter conditions in the second year of the experiment. In both years shallow and deep water mussels presented similar condition; in year 2 deep water mussels had a significantly better biochemical profile. Lipid and glycogen analyses showed seasonal variations, but no significant differences between shallow and deep water were noted. Fatty acid profiles showed a significantly higher content of omega-3 s (20:5ω3; EPA) and lower content of bacterial fatty acids in deep water sites in year 2. Everything considered, deep water appeared to provide a more favorable environment for mussel growth than shallow water under harsher weather conditions.

Variable-Depth Liner Evaluation Using Two NASA Flow Ducts

NASA Technical Reports Server (NTRS)

Jones, M. G.; Nark, D. M.; Watson, W. R.; Howerton, B. M.

2017-01-01

Four liners are investigated experimentally via tests in the NASA Langley Grazing Flow Impedance Tube. These include an axially-segmented liner and three liners that use reordering of the chambers. Chamber reordering is shown to have a strong effect on the axial sound pressure level profiles, but a limited effect on the overall attenuation. It is also shown that bent chambers can be used to reduce the liner depth with minimal effects on the attenuation. A numerical study is also conducted to explore the effects of a planar and three higher-order mode sources based on the NASA Langley Curved Duct Test Rig geometry. A four-segment liner is designed using the NASA Langley CDL code with a Python-based optimizer. Five additional liner designs, four with rearrangements of the first liner segments and one with a redistribution of the individual chambers, are evaluated for each of the four sources. The liner configuration affects the sound pressure level profile much more than the attenuation spectra for the planar and first two higher-order mode sources, but has a much larger effect on the SPL profiles and attenuation spectra for the last higher-order mode source. Overall, axially variable-depth liners offer the potential to provide improved fan noise reduction, regardless of whether the axially variable depths are achieved via a distributed array of chambers (depths vary from chamber to chamber) or a group of zones (groups of chambers for which the depth is constant).

The effects of the depth of web on the bending behaviour of triangular web profile steel beam section

NASA Astrophysics Data System (ADS)

De'nan, Fatimah; Keong, Choong Kok; Hashim, Nor Salwani

2017-10-01

Due to extensive usage of corrugated web in construction, this paper performs finite element analysis to investigate the web thickness effects on the bending behaviour of Triangular Web Profile (TRIWP) steel section. A TRIWP steel section which are consists two flanges attached to a triangular profile web plate. This paper analyzes two categories of TRIWP steel sections which are D×100×6×3 mm and D×75×5×2 mm. It was observed that for steel section D×100×6×3 mm (TRIWP1), the deflection about minor and major axis increased as the span length increased. Meanwhile, the deflection about major axis decreased when depth of the web increased. About minor axis, the deflection increased for 3m and 4m span, while the deflection at 4.8m decreased with increment the depth of web. However, when the depth of the web exceeds 250mm, deflection at 3m and 4m were increased. For steel section D×75×5×2 mm (TRIWP2), the result was different with TRIWP1 steel section, where the deflection in both major and minor directions increased with the increment of span length and decreased with increment the depth of web. It shows that the deflection increased proportionally with the depth of web. Therefore, deeper web should be more considered because it resulted in smaller deflection.

Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning.

PubMed

Liu, Xian; Chen, Chengrong; Wang, Weijin; Hughes, Jane M; Lewis, Tom; Hou, Enqing; Shen, Jupei

2015-11-01

Soil biogeochemical cycles are largely mediated by microorganisms, while fire significantly modifies biogeochemical cycles mainly via altering microbial community and substrate availability. Majority of studies on fire effects have focused on the surface soil; therefore, our understanding of the vertical distribution of microbial communities and the impacts of fire on nitrogen (N) dynamics in the soil profile is limited. Here, we examined the changes of soil denitrification capacity (DNC) and denitrifying communities with depth under different burning regimes, and their interaction with environmental gradients along the soil profile. Results showed that soil depth had a more pronounced impact than the burning treatment on the bacterial community size. The abundance of 16S rRNA and denitrification genes (narG, nirK, and nirS) declined exponentially with soil depth. Surprisingly, the nosZ-harboring denitrifiers were enriched in the deeper soil layers, which was likely to indicate that the nosZ-harboring denitrifiers could better adapt to the stress conditions (i.e., oxygen deficiency, nutrient limitation, etc.) than other denitrifiers. Soil nutrients, including dissolved organic carbon (DOC), total soluble N (TSN), ammonium (NH(4)(+)), and nitrate (NO(3)(-)), declined significantly with soil depth, which probably contributed to the vertical distribution of denitrifying communities. Soil DNC decreased significantly with soil depth, which was negligible in the depths below 20 cm. These findings have provided new insights into niche separation of the N-cycling functional guilds along the soil profile, under a varied fire disturbance regime.

Hydrogen analysis depth calibration by CORTEO Monte-Carlo simulation

NASA Astrophysics Data System (ADS)

Moser, M.; Reichart, P.; Bergmaier, A.; Greubel, C.; Schiettekatte, F.; Dollinger, G.

2016-03-01

Hydrogen imaging with sub-μm lateral resolution and sub-ppm sensitivity has become possible with coincident proton-proton (pp) scattering analysis (Reichart et al., 2004). Depth information is evaluated from the energy sum signal with respect to energy loss of both protons on their path through the sample. In first order, there is no angular dependence due to elastic scattering. In second order, a path length effect due to different energy loss on the paths of the protons causes an angular dependence of the energy sum. Therefore, the energy sum signal has to be de-convoluted depending on the matrix composition, i.e. mainly the atomic number Z, in order to get a depth calibrated hydrogen profile. Although the path effect can be calculated analytically in first order, multiple scattering effects lead to significant deviations in the depth profile. Hence, in our new approach, we use the CORTEO Monte-Carlo code (Schiettekatte, 2008) in order to calculate the depth of a coincidence event depending on the scattering angle. The code takes individual detector geometry into account. In this paper we show, that the code correctly reproduces measured pp-scattering energy spectra with roughness effects considered. With more than 100 μm thick Mylar-sandwich targets (Si, Fe, Ge) we demonstrate the deconvolution of the energy spectra on our current multistrip detector at the microprobe SNAKE at the Munich tandem accelerator lab. As a result, hydrogen profiles can be evaluated with an accuracy in depth of about 1% of the sample thickness.

Regional correlations of V s30 and velocities averaged over depths less than and greater than 30 meters

USGS Publications Warehouse

Boore, D.M.; Thompson, E.M.; Cadet, H.

2011-01-01

Using velocity profiles from sites in Japan, California, Turkey, and Europe, we find that the time-averaged shear-wave velocity to 30 m (V S30), used as a proxy for site amplification in recent ground-motion prediction equations (GMPEs) and building codes, is strongly correlated with average velocities to depths less than 30 m (V Sz, with z being the averaging depth). The correlations for sites in Japan (corresponding to the KiK-net network) show that V S30 is systematically larger for a given V Sz than for profiles from the other regions. The difference largely results from the placement of the KiK-net station locations on rock and rocklike sites, whereas stations in the other regions are generally placed in urban areas underlain by sediments. Using the KiK-net velocity profiles, we provide equations relating V S30 to V Sz for z ranging from 5 to 29 m in 1-m increments. These equations (and those for California velocity profiles given in Boore, 2004b) can be used to estimate V S30 from V Sz for sites in which velocity profiles do not extend to 30 m. The scatter of the residuals decreases with depth, but, even for an averaging depth of 5 m, a variation in log V S30 of 1 standard deviation maps into less than a 20% uncertainty in ground motions given by recent GMPEs at short periods. The sensitivity of the ground motions to V S30 uncertainty is considerably larger at long periods (but is less than a factor of 1.2 for averaging depths greater than about 20 m). We also find that V S30 is correlated with V Sz for z as great as 400 m for sites of the KiK-net network, providing some justification for using V S30 as a site-response variable for predicting ground motions at periods for which the wavelengths far exceed 30 m.

Accessory Mineral Depth-Profiling Applied to the Corsican Lower Crust: A Continuous Thermal History of Mesozoic Continental Rifting

NASA Astrophysics Data System (ADS)

Seymour, N. M.; Stockli, D. F.; Beltrando, M.; Smye, A.

2015-12-01

Despite advances in understanding the structural development of hyperextended magma-poor rift margins, the temporal and thermal evolution of lithospheric hyperextension during rifting remains only poorly understood. In contrast to classic pure-shear models, multi-stage rift models that include depth-dependent thinning predict significant lower-crustal reheating during the necking phase due to buoyant rise of the asthenosphere. The Santa Lucia nappe of NE Corsica is an ideal laboratory to test for lower-crustal reheating as it preserves Permian lower crust exhumed from granulitic conditions during Mesozoic Tethyan rifting. This study presents the first use of apatite U-Pb depth-profile thermochronology in conjunction with novel rutile U-Pb and zircon U-Pb thermo- and geochronology to reconstruct a continuous t-T path to constrain the syn-rift thermal evolution of this exposed lower-crustal section. LASS-ICP-MS depth-profile analyses of zircon reveal thin (<10 μm) ~210-180 Ma overgrowths on 300-270 Ma cores in lower-crustal lithologies, indicative of renewed thermal activity during Mesozoic rifting. Cooling due to rapid rift margin exhumation is recorded by the topology of rutile and apatite depth profiles caused by thermally-activated volume diffusion at T >400°C. Lower-crustal rutile reveal a rounded progression from core plateaus at ~170 Ma to 150-145 Ma at the outer 8-10 μm of grains while middle-crustal apatite records 170 Ma cores grading to 140-135 Ma rims. Inverse modeling of rutile profiles suggests the lower crust cooled from 700°C at 200 Ma to 425°C at 140 Ma. Middle-crustal apatite yield a two-stage history, with rapid cooling from 500°C at 200 Ma to 420°C at ~180 Ma followed by slow cooling to 400°C by 160 Ma. Combined with zircon overgrowth ages, these data indicate the Santa Lucia nappe underwent a thermal pulse in the late Triassic-early Jurassic associated with depth-dependent thinning and hyperextension of the Corsican margin.

Vegetation change alters soil profile δ15N values at the landscape scale in a subtropical savanna

NASA Astrophysics Data System (ADS)

Zhou, Y.; Mushinski, R. M.; Hyodo, A.; Wu, X. B.; Boutton, T. W.

2017-12-01

The assessment of spatial variation in soil δ15N could provide integrative insights on soil N cycling processes across multiple spatial scales. However, little is known about spatial patterns of δ15N within soil profiles in arid and semiarid ecosystems, especially those undergoing vegetation change with a distinct shift in dominance and/or functional type. We quantified how changes from grass to woody plant dominance altered spatial patterns of δ15N throughout a 1.2 m soil profile by collecting 320 spatially-specific soil cores in a 160 m × 100 m subtropical savanna landscape that has undergone encroachment by Prosopis glandulosa (an N2-fixer) during the past century. Leaf δ15N was comparable among different plant life-forms, while fine roots from woody species had significantly lower δ15N than herbaceous species across this landscape. Woody encroachment significantly decreased soil δ15N throughout the entire soil profile, and created horizontal spatial patterns of soil δ15N that strongly resembled the spatial distribution of woody patches and were evident within each depth increment. The lower soil δ15N values that characterized areas beneath woody canopies were mostly due to the encroaching woody species, especially the N2-fixer P. glandulosa, which delivered 15N-depleted organic matter via root turnover to soils along the profile. Soil δ15N increased with depth, reached maximum values at an intermediate depth, and decreased at greater depths. Higher δ15N values at intermediate soil depths were correlated with the presence of a subsurface clay-rich argillic horizon across this landscape which may favor more rapid rates of N-cycling processes that can cause N losses and 15N enrichment of the residual soil N. These results indicate that succession from grassland to woodland has altered spatial variation in soil δ15N across the landscape and to considerable depth, suggesting significant changes in the relative rates of N-inputs vs. N-losses in this subtropical system after vegetation change.

Positron depth profiling of the structural and electronic structure transformations of hydrogenated Mg-based thin films

NASA Astrophysics Data System (ADS)

Eijt, S. W. H.; Kind, R.; Singh, S.; Schut, H.; Legerstee, W. J.; Hendrikx, R. W. A.; Svetchnikov, V. L.; Westerwaal, R. J.; Dam, B.

2009-02-01

We report positron depth-profiling studies on the hydrogen sorption behavior and phase evolution of Mg-based thin films. We show that the main changes in the depth profiles resulting from the hydrogenation to the respective metal hydrides are related to a clear broadening in the observed electron momentum densities in both Mg and Mg2Ni films. This shows that positron annihilation methods are capable of monitoring these metal-to-insulator transitions, which form the basis for important applications of these types of films in switchable mirror devices and hydrogen sensors in a depth-sensitive manner. Besides, some of the positrons trap at the boundaries of columnar grains in the otherwise nearly vacancy-free Mg films. The combination of positron annihilation and x-ray diffraction further shows that hydrogen loading at elevated temperatures, in the range of 480-600 K, leads to a clear Pd-Mg alloy formation of the Pd catalyst cap layer. At the highest temperatures, the hydrogenation induces a partial delamination of the ˜5 nm thin capping layer, as sensitively monitored by positron depth profiling of the fraction of ortho-positronium formed at interface with the cap layer. The delamination effectively blocks the hydrogen cycling. In Mg-Si bilayers, we investigated the reactivity upon hydrogen loading and heat treatments near 480 K, which shows that Mg2Si formation is fast relative to MgH2. The combination of positron depth profiling and transmission electron microscopy shows that hydrogenation promotes a complete conversion to Mg2Si for this destabilized metal hydride system, while a partially unreacted, Mg-rich amorphous prelayer remains on top of Mg2Si after a single heat treatment in an inert gas environment. Thin film studies indicate that the difficulty of rehydrogenation of Mg2Si is not primarily the result from slow hydrogen dissociation at surfaces, but is likely hindered by the presence of a barrier for removal of Mg from the readily formed Mg2Si.

Hemispheric aerosol vertical profiles: anthropogenic impacts on optical depth and cloud nuclei.

PubMed

Clarke, Antony; Kapustin, Vladimir

2010-09-17

Understanding the effect of anthropogenic combustion upon aerosol optical depth (AOD), clouds, and their radiative forcing requires regionally representative aerosol profiles. In this work, we examine more than 1000 vertical profiles from 11 major airborne campaigns in the Pacific hemisphere and confirm that regional enhancements in aerosol light scattering, mass, and number are associated with carbon monoxide from combustion and can exceed values in unperturbed regions by more than one order of magnitude. Related regional increases in a proxy for cloud condensation nuclei (CCN) and AOD imply that direct and indirect aerosol radiative effects are coupled issues linked globally to aged combustion. These profiles constrain the influence of combustion on regional AOD and CCN suitable for challenging climate model performance and informing satellite retrievals.

Influence of Annealing on the Depth Microstructure of the Shot Peened Duplex Stainless Steel at Elevated Temperature

NASA Astrophysics Data System (ADS)

Feng, Qiang; She, Jia; Xiang, Yong; Wu, Xianyun; Wang, Chengxi; Jiang, Chuanhai

The depth profiles of residual stresses and lattice parameters in the surface layers of shot peened duplex stainless steel at elevated temperature were investigated utilizing X-ray diffraction analysis. At each deformation depth, residual stress distributions in both ferrite and austenite were studied by X-ray diffraction stress analysis which is performed on the basis of the sin2ψ method and the lattice parameters were explored by Rietveld method. The results reveal that difference changes of depth residual compressive stress profiles between ferrite and austenite under the same annealing condition are resulted from the diverse coefficient of thermal expansion, dislocation density, etc. for different phases in duplex stainless steel. The relaxations of depth residual stresses in austenite are more obvious than those in ferrite. The lattice parameters decrease in the surface layer with the extending of annealing time, however, they increase along the depth after annealing for 16min. The change of the depth lattice parameters can be ascribed to both thermal expansion and the relaxation of residual stress. The different changes of microstructure at elevated temperature between ferrite and austenite are discussed.

Measurement of sound speed vs. depth in South Pole ice for neutrino astronomy

NASA Astrophysics Data System (ADS)

Abbasi, R.; Abdou, Y.; Ackermann, M.; Adams, J.; Aguilar, J. A.; Ahlers, M.; Andeen, K.; Auffenberg, J.; Bai, X.; Baker, M.; Barwick, S. W.; Bay, R.; Bazo Alba, J. L.; Beattie, K.; Beatty, J. J.; Bechet, S.; Becker, J. K.; Becker, K.-H.; Benabderrahmane, M. L.; Berdermann, J.; Berghaus, P.; Berley, D.; Bernardini, E.; Bertrand, D.; Besson, D. Z.; Bissok, M.; Blaufuss, E.; Boersma, D. J.; Bohm, C.; Bolmont, J.; Böser, S.; Botner, O.; Bradley, L.; Braun, J.; Breder, D.; Castermans, T.; Chirkin, D.; Christy, B.; Clem, J.; Cohen, S.; Cowen, D. F.; D'Agostino, M. V.; Danninger, M.; Day, C. T.; De Clercq, C.; Demirörs, L.; Depaepe, O.; Descamps, F.; Desiati, P.; de Vries-Uiterweerd, G.; DeYoung, T.; Diaz-Velez, J. C.; Dreyer, J.; Dumm, J. P.; Duvoort, M. R.; Edwards, W. R.; Ehrlich, R.; Eisch, J.; Ellsworth, R. W.; Engdegård, O.; Euler, S.; Evenson, P. A.; Fadiran, O.; Fazely, A. R.; Feusels, T.; Filimonov, K.; Finley, C.; Foerster, M. M.; Fox, B. D.; Franckowiak, A.; Franke, R.; Gaisser, T. K.; Gallagher, J.; Ganugapati, R.; Gerhardt, L.; Gladstone, L.; Goldschmidt, A.; Goodman, J. A.; Gozzini, R.; Grant, D.; Griesel, T.; Groß, A.; Grullon, S.; Gunasingha, R. M.; Gurtner, M.; Ha, C.; Hallgren, A.; Halzen, F.; Han, K.; Hanson, K.; Hasegawa, Y.; Heise, J.; Helbing, K.; Herquet, P.; Hickford, S.; Hill, G. C.; Hoffman, K. D.; Hoshina, K.; Hubert, D.; Huelsnitz, W.; Hülß, J.-P.; Hulth, P. O.; Hultqvist, K.; Hussain, S.; Imlay, R. L.; Inaba, M.; Ishihara, A.; Jacobsen, J.; Japaridze, G. S.; Johansson, H.; Joseph, J. M.; Kampert, K.-H.; Kappes, A.; Karg, T.; Karle, A.; Kelley, J. L.; Kenny, P.; Kiryluk, J.; Kislat, F.; Klein, S. R.; Klepser, S.; Knops, S.; Kohnen, G.; Kolanoski, H.; Köpke, L.; Kowalski, M.; Kowarik, T.; Krasberg, M.; Kuehn, K.; Kuwabara, T.; Labare, M.; Lafebre, S.; Laihem, K.; Landsman, H.; Lauer, R.; Leich, H.; Lennarz, D.; Lucke, A.; Lundberg, J.; Lünemann, J.; Madsen, J.; Majumdar, P.; Maruyama, R.; Mase, K.; Matis, H. S.; McParland, C. P.; Meagher, K.; Merck, M.; Mészáros, P.; Middell, E.; Milke, N.; Miyamoto, H.; Mohr, A.; Montaruli, T.; Morse, R.; Movit, S. M.; Münich, K.; Nahnhauer, R.; Nam, J. W.; Nießen, P.; Nygren, D. R.; Odrowski, S.; Olivas, A.; Olivo, M.; Ono, M.; Panknin, S.; Patton, S.; Pérez de los Heros, C.; Petrovic, J.; Piegsa, A.; Pieloth, D.; Pohl, A. C.; Porrata, R.; Potthoff, N.; Price, P. B.; Prikockis, M.; Przybylski, G. T.; Rawlins, K.; Redl, P.; Resconi, E.; Rhode, W.; Ribordy, M.; Rizzo, A.; Rodrigues, J. P.; Roth, P.; Rothmaier, F.; Rott, C.; Roucelle, C.; Rutledge, D.; Ryckbosch, D.; Sander, H.-G.; Sarkar, S.; Satalecka, K.; Schlenstedt, S.; Schmidt, T.; Schneider, D.; Schukraft, A.; Schulz, O.; Schunck, M.; Seckel, D.; Semburg, B.; Seo, S. H.; Sestayo, Y.; Seunarine, S.; Silvestri, A.; Slipak, A.; Spiczak, G. M.; Spiering, C.; Stamatikos, M.; Stanev, T.; Stephens, G.; Stezelberger, T.; Stokstad, R. G.; Stoufer, M. C.; Stoyanov, S.; Strahler, E. A.; Straszheim, T.; Sulanke, K.-H.; Sullivan, G. W.; Swillens, Q.; Taboada, I.; Tarasova, O.; Tepe, A.; Ter-Antonyan, S.; Terranova, C.; Tilav, S.; Tluczykont, M.; Toale, P. A.; Tosi, D.; Turčan, D.; van Eijndhoven, N.; Vandenbroucke, J.; Van Overloop, A.; Vogt, C.; Voigt, B.; Walck, C.; Waldenmaier, T.; Walter, M.; Wendt, C.; Westerhoff, S.; Whitehorn, N.; Wiebusch, C. H.; Wiedemann, A.; Wikström, G.; Williams, D. R.; Wischnewski, R.; Wissing, H.; Woschnagg, K.; Xu, X. W.; Yodh, G.; Yoshida, S.; IceCube Collaboration

2010-06-01

We have measured the speed of both pressure waves and shear waves as a function of depth between 80 and 500 m depth in South Pole ice with better than 1% precision. The measurements were made using the South Pole Acoustic Test Setup (SPATS), an array of transmitters and sensors deployed in the ice at the South Pole in order to measure the acoustic properties relevant to acoustic detection of astrophysical neutrinos. The transmitters and sensors use piezoceramics operating at ˜5-25 kHz. Between 200 m and 500 m depth, the measured profile is consistent with zero variation of the sound speed with depth, resulting in zero refraction, for both pressure and shear waves. We also performed a complementary study featuring an explosive signal propagating vertically from 50 to 2250 m depth, from which we determined a value for the pressure wave speed consistent with that determined for shallower depths, higher frequencies, and horizontal propagation with the SPATS sensors. The sound speed profile presented here can be used to achieve good acoustic source position and emission time reconstruction in general, and neutrino direction and energy reconstruction in particular. The reconstructed quantities could also help separate neutrino signals from background.

CO2 dynamics in the Amargosa Desert: Fluxes and isotopic speciation in a deep unsaturated zone

USGS Publications Warehouse

Walvoord, Michelle Ann; Striegl, Robert G.; Prudic, David E.; Stonestrom, David A.

2005-01-01

Natural unsaturated-zone gas profiles at the U.S. Geological Survey's Amargosa Desert Research Site, near Beatty, Nevada, reveal the presence of two physically and isotopically distinct CO2 sources, one shallow and one deep. The shallow source derives from seasonally variable autotrophic and heterotrophic respiration in the root zone. Scanning electron micrograph results indicate that at least part of the deep CO2 source is associated with calcite precipitation at the 110-m-deep water table. We use a geochemical gas-diffusion model to explore processes of CO2 production and behavior in the unsaturated zone. The individual isotopic species 12CO2, 13CO2, and 14CO2 are treated as separate chemical components that diffuse and react independently. Steady state model solutions, constrained by the measured δ13C (in CO2), and δ14C (in CO2) profiles, indicate that the shallow CO2 source from root and microbial respiration composes ∼97% of the annual average total CO2 production at this arid site. Despite the small contribution from deep CO2 production amounting to ∼0.1 mol m−2 yr−1, upward diffusion from depth strongly influences the distribution of CO2 and carbon isotopes in the deep unsaturated zone. In addition to diffusion from deep CO2 production, 14C exchange with a sorbed CO2 phase is indicated by the modeled δ14C profiles, confirming previous work. The new model of carbon-isotopic profiles provides a quantitative approach for evaluating fluxes of carbon under natural conditions in deep unsaturated zones.

Mapping patterns of soil properties and soil moisture using electromagnetic induction to investigate the impact of land use changes on soil processes

NASA Astrophysics Data System (ADS)

Robinet, Jérémy; von Hebel, Christian; van der Kruk, Jan; Govers, Gerard; Vanderborght, Jan

2016-04-01

As highlighted by many authors, classical or geophysical techniques for measuring soil moisture such as destructive soil sampling, neutron probes or Time Domain Reflectometry (TDR) have some major drawbacks. Among other things, they provide point scale information, are often intrusive and time-consuming. ElectroMagnetic Induction (EMI) instruments are often cited as a promising alternative hydrogeophysical methods providing more efficiently soil moisture measurements ranging from hillslope to catchment scale. The overall objective of our research project is to investigate whether a combination of geophysical techniques at various scales can be used to study the impact of land use change on temporal and spatial variations of soil moisture and soil properties. In our work, apparent electrical conductivity (ECa) patterns are obtained with an EM multiconfiguration system. Depth profiles of ECa were subsequently inferred through a calibration-inversion procedure based on TDR data. The obtained spatial patterns of these profiles were linked to soil profile and soil water content distributions. Two catchments with contrasting land use (agriculture vs. natural forest) were selected in a subtropical region in the south of Brazil. On selected slopes within the catchments, combined EMI and TDR measurements were carried out simultaneously, under different atmospheric and soil moisture conditions. Ground-truth data for soil properties were obtained through soil sampling and auger profiles. The comparison of these data provided information about the potential of the EMI technique to deliver qualitative and quantitative information about the variability of soil moisture and soil properties.

El Nino-southern oscillation: A coupled response to the greenhouse effect?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, De-Zheng

The purpose of this article to elucidate the link between the El Nino-Southern Oscillation (ENSO) and radiative forcing (of which the greenhouse effect is a major part). A unified theory for the tropical Pacific climate is developed by considering the response of the coupled ocean-atmosphere to a changing radiative forcing. The hypothesis is that both the zonal surface sea temperature (SST) gradients and ENSO are a coupled response to the strong radiative heating or the tropical warmth. Owing to ocean-atmosphere interaction, the stronger the radiative heating, the larger the zonal SST gradients. When the SST gradients exceed a critical value,more » however, the ocean-atmosphere interaction in the cold-tongue region is too strong for the coupled system to hold steady. Consequently, the coupled system enters an oscillatory state. These coupled dynamics are examined in a simple mathematical model whose behavior is consistent with the hypothesis. With a linear temperature profile throughout the depth of subsurface ocean, the model predicts that both the magnitude and period of the oscillation increase with increases in radiative forcing or the greenhouse effect. The increase in the magnitude of the oscillation largely comes from an enhancement of the magnitude of the cold anomalies, while the increase in the period mostly comes from a prolonged duration of the warm events. With a profile in which the lapse rate decreases with depth, the sensitivity is more moderate. The simplicity of the model prevents a quantitative simulation of the sensitivity of ENSO to increases in the greenhouse effect, but qualitatively the model results support the empirical interpretation of the prolonged duration of the 1990-1995 ENSO event. 5 refs., 7 figs.« less

Simulation and experimental verification of prompt gamma-ray emissions during proton irradiation.

PubMed

Schumann, A; Petzoldt, J; Dendooven, P; Enghardt, W; Golnik, C; Hueso-González, F; Kormoll, T; Pausch, G; Roemer, K; Fiedler, F

2015-05-21

Irradiation with protons and light ions offers new possibilities for tumor therapy but has a strong need for novel imaging modalities for treatment verification. The development of new detector systems, which can provide an in vivo range assessment or dosimetry, requires an accurate knowledge of the secondary radiation field and reliable Monte Carlo simulations. This paper presents multiple measurements to characterize the prompt γ-ray emissions during proton irradiation and benchmarks the latest Geant4 code against the experimental findings. Within the scope of this work, the total photon yield for different target materials, the energy spectra as well as the γ-ray depth profile were assessed. Experiments were performed at the superconducting AGOR cyclotron at KVI-CART, University of Groningen. Properties of the γ-ray emissions were experimentally determined. The prompt γ-ray emissions were measured utilizing a conventional HPGe detector system (Clover) and quantitatively compared to simulations. With the selected physics list QGSP_BIC_HP, Geant4 strongly overestimates the photon yield in most cases, sometimes up to 50%. The shape of the spectrum and qualitative occurrence of discrete γ lines is reproduced accurately. A sliced phantom was designed to determine the depth profile of the photons. The position of the distal fall-off in the simulations agrees with the measurements, albeit the peak height is also overestimated. Hence, Geant4 simulations of prompt γ-ray emissions from irradiation with protons are currently far less reliable as compared to simulations of the electromagnetic processes. Deviations from experimental findings were observed and quantified. Although there has been a constant improvement of Geant4 in the hadronic sector, there is still a gap to close.

Lithological influences on contemporary and long-term regolith weathering at the Luquillo Critical Zone Observatory

USGS Publications Warehouse

Buss, Heather L.; Lara, Maria Chapela; Moore, Oliver; Kurtz, Andrew C.; Schulz, Marjorie S.; White, Arthur F.

2017-01-01

Lithologic differences give rise to the differential weatherability of the Earth’s surface and globally variable silicate weathering fluxes, which provide an important negative feedback on climate over geologic timescales. To isolate the influence of lithology on weathering rates and mechanisms, we compare two nearby catchments in the Luquillo Critical Zone Observatory in Puerto Rico, which have similar climate history, relief and vegetation, but differ in bedrock lithology. Regolith and pore water samples with depth were collected from two ridgetops and at three sites along a slope transect in the volcaniclastic Bisley catchment and compared to existing data from the granitic Río Icacos catchment. The depth variations of solid-state and pore water chemistry and quantitative mineralogy were used to calculate mass transfer (tau) and weathering solute profiles, which in turn were used to determine weathering mechanisms and to estimate weathering rates.Regolith formed on both lithologies is highly leached of most labile elements, although Mg and K are less depleted in the granitic than in the volcaniclastic profiles, reflecting residual biotite in the granitic regolith not present in the volcaniclastics. Profiles of both lithologies that terminate at bedrock corestones are less weathered at depth, near the rock-regolith interfaces. Mg fluxes in the volcaniclastics derive primarily from dissolution of chlorite near the rock-regolith interface and from dissolution of illite and secondary phases in the upper regolith, whereas in the granitic profile, Mg and K fluxes derive from biotite dissolution. Long-term mineral dissolution rates and weathering fluxes were determined by integrating mass losses over the thickness of solid-state weathering fronts, and are therefore averages over the timescale of regolith development. Resulting long-term dissolution rates for minerals in the volcaniclastic regolith include chlorite: 8.9 × 10−14 mol m−2 s−1, illite: 2.1 × 10−14 mol m−2 s−1 and kaolinite: 4.0 × 10−14 mol m−2 s−1. Long-term weathering fluxes are several orders of magnitude lower in the granitic regolith than in the volcaniclastic, despite higher abundances of several elements in the granitic regolith. Contemporary weathering fluxes were determined from net (rain-corrected) solute profiles and thus represent rates over the residence time of water in the regolith. Contemporary weathering fluxes within the granitic regolith are similar to the long-term fluxes. In contrast, the long-term fluxes are faster than the contemporary fluxes in the volcaniclastic regolith. Contemporary fluxes in the granitic regolith are generally also slightly faster than in the volcaniclastic. The differences in weathering fluxes over space and time between these two watersheds indicate significant lithologic control of chemical weathering mechanisms and rates.

Three dimensional characterization of laser ablation craters using high resolution X-ray computed tomography

NASA Astrophysics Data System (ADS)

Galmed, A. H.; du Plessis, A.; le Roux, S. G.; Hartnick, E.; Von Bergmann, H.; Maaza, M.

2018-01-01

Laboratory X-ray computed tomography is an emerging technology for the 3D characterization and dimensional analysis of many types of materials. In this work we demonstrate the usefulness of this characterization method for the full three dimensional analysis of laser ablation craters, in the context of a laser induced breakdown spectroscopy setup. Laser induced breakdown spectroscopy relies on laser ablation for sampling the material of interest. We demonstrate here qualitatively (in images) and quantitatively (in terms of crater cone angles, depths, diameters and volume) laser ablation crater analysis in 3D for metal (aluminum) and rock (false gold ore). We show the effect of a Gaussian beam profile on the resulting crater geometry, as well as the first visual evidence of undercutting in the rock sample, most likely due to ejection of relatively large grains. The method holds promise for optimization of laser ablation setups especially for laser induced breakdown spectroscopy.

Informing urban carbon emissions with atmospheric observations: motivation, methods, and reducing uncertainties.

NASA Astrophysics Data System (ADS)

Kort, E. A.; Ware, J.; Duren, R. M.; Schimel, D.; Miller, C. E.; Decola, P.

2014-12-01

Urban regions play a dominant role in the anthropogenic perturbation to atmospheric carbon dioxide and methane. With increasing urbanization (notably in developing nations) and increasing emissions, quantitative observational information on emissions of CO2 and CH4 becomes critical for improved understanding of the global carbon cycle and for carbon management/policy decisions. In this presentation, we will discuss the impact uncertainty in anthropogenic emissions has on global carbon-climate understanding, providing broad geophysical motivation for urban studies. We will further discuss observations of urban regions at different scales (satellite vs. in-situ), and investigate the information content of these complementary methods for answering targeted questions on both global carbon fluxes and regional management decisions. Finally, we will present new attempts at reducing uncertainty in high-resolution inversions leveraging remotely sensed aerosol profiles to constrain both mixing depths and vertical distributions of trace gases.

Droplet barcoding for single cell transcriptomics applied to embryonic stem cells

PubMed Central

Klein, Allon M; Mazutis, Linas; Akartuna, Ilke; Tallapragada, Naren; Veres, Adrian; Li, Victor; Peshkin, Leonid; Weitz, David A; Kirschner, Marc W

2015-01-01

Summary It has long been the dream of biologists to map gene expression at the single cell level. With such data one might track heterogeneous cell sub-populations, and infer regulatory relationships between genes and pathways. Recently, RNA sequencing has achieved single cell resolution. What is limiting is an effective way to routinely isolate and process large numbers of individual cells for quantitative in-depth sequencing. We have developed a high-throughput droplet-microfluidic approach for barcoding the RNA from thousands of individual cells for subsequent analysis by next-generation sequencing. The method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. We analyzed mouse embryonic stem cells, revealing in detail the population structure and the heterogeneous onset of differentiation after LIF withdrawal. The reproducibility of these high-throughput single cell data allowed us to deconstruct cell populations and infer gene expression relationships. PMID:26000487

Correlation between Ti source/drain contact and performance of InGaZnO-based thin film transistors

NASA Astrophysics Data System (ADS)

Choi, Kwang-Hyuk; Kim, Han-Ki

2013-02-01

Ti contact properties and their electrical contribution to an amorphous InGaZnO (a-IGZO) semiconductor-based thin film transistor (TFT) were investigated in terms of chemical, structural, and electrical considerations. TFT device parameters were quantitatively studied by a transmission line method. By comparing various a-IGZO TFT parameters with those of different Ag and Ti source/drain electrodes, Ti S/D contact with an a-IGZO channel was found to lead to a negative shift in VT (-Δ 0.52 V). This resulted in higher saturation mobility (8.48 cm2/Vs) of a-IGZO TFTs due to effective interfacial reaction between Ti and an a-IGZO semiconducting layer. Based on transmission electron microcopy, x-ray photoelectron depth profile analyses, and numerical calculation of TFT parameters, we suggest a possible Ti contact mechanism on semiconducting a-IGZO channel layers for TFTs.

Experimental and Numerical Analysis of Microstructures and Stress States of Shot-Peened GH4169 Superalloys

NASA Astrophysics Data System (ADS)

Hu, Dianyin; Gao, Ye; Meng, Fanchao; Song, Jun; Wang, Rongqiao

2018-04-01

Combining experiments and finite element analysis (FEA), a systematic study was performed to analyze the microstructural evolution and stress states of shot-peened GH4169 superalloy over a variety of peening intensities and coverages. A dislocation density evolution model was integrated into the representative volume FEA model to quantitatively predict microstructural evolution in the surface layers and compared with experimental results. It was found that surface roughness and through-depth residual stress profile are more sensitive to shot-peening intensity compared to coverage due to the high kinetic energy involved. Moreover, a surface nanocrystallization layer was discovered in the top surface region of GH4169 for all shot-peening conditions. However, the grain refinement was more intensified under high shot-peening coverage, under which enough time was permitted for grain refinement. The grain size gradient predicted by the numerical framework showed good agreement with experimental observations.

Observed Characteristics and Origins of Meltwaters Exported from Jakobshavn and Ilulissat Icefjord, Greenland

NASA Astrophysics Data System (ADS)

Beaird, N.; Straneo, F.; Jenkins, W. J.

2017-12-01

Jakobshavn Isbrae has undergone rapid retreat in recent decades and is now among the largest sources of anomalous ice discharge from Greenland's shrinking ice sheet. The characteristics, distribution, and pathways of meltwater sourced from Jakobshavn can have important impacts on ecosystems and regional, perhaps global, ocean circulation. Here we report on novel geochemical (noble gas) observations that enable a quantitative description of the meltwaters exiting Ilulissat Icefjord into Disko Bay, including the partition into Submarine Meltwater sources and Subglacial Discharge sources. We identify a coastally-trapped plume outside of the fjord mouth consistent with a coastal current flowing north. The plume extends to 100 m depth, and 10 km offshore. Temperature and salinity profiles inside the fjord suggest a deep-reaching buoyancy-forced overturning feeding this outflow. Relatively high Submarine Meltwater concentration (2.5%) imply a substantial contribution of iceberg meltwater to the fjord. Subglacial Discharge concentrations in the plume reach 6%.

Single-Shot Laser Ablation Split-Stream (SS-LASS) Analysis Depth Profiling

NASA Astrophysics Data System (ADS)

Kylander-Clark, A. R.; Stearns, M. A.; Viete, D. R.; Cottle, J. M.; Hacker, B. R.

2014-12-01

Laser ablation depth profiling of geochronometers—such as zircon, monazite, titanite and rutile—has become popular in recent years as a tool to both determine date vs. depth or trace-element (TE) composition vs. depth; the former allows the dating of thin rims and, potentially, inversion of Pb-loss profiles for thermal histories, whereas the latter can yield insight into changes in PTX or mineral parageneses and inversion of trace-element profiles for thermal histories. In this study, we combine both techniques, enabling simultaneous acquisition of U-Th/Pb isotopic ratios and trace-element compositions, by joining a 193 nm excimer laser to a multi-collector ICP-MS and single-collector ICP-MS. The simultaneous acquisition allows direct shot-by-shot linkage between time and petrology, expanding our ability to understand the evolution of complex geologic systems. We construct each depth profile by capturing the analyte with a succession of individual laser pulses (each ~100 nm deep) . This has two main advantages over a typical time-dependent analysis of a multi-shot routine composed of tens to hundreds of shots and a several μm deep hole. 1) The reference material is analyzed between each shot for a more-accurate standardization of each aliquot of ablated material. 2) There is no mixing of material ablated from successive laser pulses during transmission to the ICP. The method is limited by count rate, which depends on spot size, excavation rate, instrument sensitivity, etc., and, for single-collector ICP, the switching time, which limits the number of elements that can be analyzed and their total counts. We explore the latter theoretically and experimentally to provide insight on both the ideal number of elements to measure and the dwell time in any given sample. Examples of the utility of SS-LASS include the comparison of apparent Pb loss to diffusion profiles of trace elements in rims of metamorphic rutile and titanite, as well as the determination of the timing and petrologic conditions of thin zircon rims in metamorphic rocks.

The Wire Flyer Towed Profiling System

NASA Astrophysics Data System (ADS)

Roman, C.; Ullman, D. S.; Hebert, D.

2016-02-01

The Wire Flyer is an autonomous profiling vehicle that slides up and down a standard towed cable in a controlled manner using the lift created by wing foils. The vehicle is able to create high resolution water-column sections within a specified depth band in an automated manner. The Wire Flyer is different than standard undulating tow bodies in that it decouples the vehicle's motion from the tow cable dynamics. Due to this separation the vehicle is able to profile with nearly 1:1 horizontal to vertical motion. A heavy depressor weight is fixed to the end of the cable and the cable shape remains relatively static during operation. The vehicle uses a closed loop wing angle controller to achieve desired vertical velocities between 0 and 2.5 m/s for ship speeds between 1.5 and 2.5 m/s. During typical operations, updated commands and condensed data samples can be sent to and from the vehicle via an acoustic modem to adjust the profiling pattern to ensure the desired coverage. The current 1000 meter rated vehicle is equipped with a SBE 49 FastCAT CTD, and can carry additional sensors for oxygen, Chlorophyll fluorescence and acoustic echosounding. Results showing the vehicle performance as well as the quality of the processed CTD data will be presented from three test cruises to the New England Shelf Break Front. Many shallow and deep sections were obtained with horizontal resolution that is not otherwise achievable with undulating tow bodies, underway CTDs, standard CTD tow-yos, gliders or free swimming AUVs. A typical survey at ship speeds of 3-4 knots can profile over a depth band between 200 and 600 meters depth with a repeat cycle length of less than 1 km. The vehicle concept is depth independent and could work with a full ocean depth design. Application areas for the system include sub-meso scale observations of fronts, vent and seep plumes, oxygen minimum layers, mixing and mid-water bioacoustics.

Soil profiles' development and differentiation as revealed by their magnetic signal

NASA Astrophysics Data System (ADS)

Jordanova, Neli; Jordanova, Diana

2017-04-01

Soil profiles' development is a major theme in soil science research, as far as it gives basic information on soil genesis and classification. The use of soil magnetic properties as indicators for physical and geochemical conditions during pedogenesis received great attention during the last decade mainly in relation to paleoclimate reconstructions. However, tracking the observed general relationships with respect to degree of soil differentiation would lead to capitalization of this knowledge and its further utilization as pedogenic indicator. Here we present an overview of the observed relationships and depth variations of magnetic characteristics along ten soil profiles of Chernozems, Luvisols and Planosols from Bulgaria. Depending on the general soil group considered, different relationships between depth distribution of the relative amount of superparamagnetic (SP), single domain (SD) and larger pseudo single domain (PSD) to multi domain (MD) ferrimagnetic fractions are revealed. The profiles of the soil group with pronounced accumulation of organic matter in the mineral topsoil (Chernozems and Phaeozems) a systematic shift in the relative maxima of SP- and SD- like concentration proxies is observed with the increase of profile differentiation. In contrast, the group of soils with clay-enriched subsoil horizon (e.g. Luvisols) shows different evolution of the depth distribution of the grain-size proxy parameters. The increase of profile's degradation leads to a decrease in the amount of the SP fraction and a split in its maxima into two depth intervals related to the eluvial and illuvial horizons respectively. Along with this tendency, the maximum of the SD fraction moves to progressively deeper levels of the illuvial horizon. The third soil group of the Planosols is characterized by specific re-distribution of the iron oxides, caused by the oscillating oxidation - reduction fluctuations within the profile. The diagnostic eluvial and illuvial soil horizons are enriched with stable SD magnetite-like fraction, likely originating from ferrihydrite transformations under repeating oxidative - reductive conditions. The major magnetic phase in illuvial horizons is hematite, while in eluvial and C-horizons magnetite dominates. These different trends in the evolution of mineralogy and magnetic grain size fractions along the depth of the various soil groups are useful indicators of the soil chemistry, as well as the dynamics of the main soil forming processes.

Field tests of a down-hole TDR profiling water content measurement system

USDA-ARS?s Scientific Manuscript database

Accurate soil profile water content monitoring at multiple depths has previously been possible only using the neutron probe (NP), but with great effort and at unsatisfactory intervals. Despite the existence of several capacitance systems for profile water content measurements, accuracy and spatial r...

Surface analysis and depth profiling of corrosion products formed in lead pipes used to supply low alkalinity drinking water.

PubMed

Davidson, C M; Peters, N J; Britton, A; Brady, L; Gardiner, P H E; Lewis, B D

2004-01-01

Modern analytical techniques have been applied to investigate the nature of lead pipe corrosion products formed in pH adjusted, orthophosphate-treated, low alkalinity water, under supply conditions. Depth profiling and surface analysis have been carried out on pipe samples obtained from the water distribution system in Glasgow, Scotland, UK. X-ray diffraction spectrometry identified basic lead carbonate, lead oxide and lead phosphate as the principal components. Scanning electron microscopy/energy-dispersive x-ray spectrometry revealed the crystalline structure within the corrosion product and also showed spatial correlations existed between calcium, iron, lead, oxygen and phosphorus. Elemental profiling, conducted by means of secondary ion mass spectrometry (SIMS) and secondary neutrals mass spectrometry (SNMS) indicated that the corrosion product was not uniform with depth. However, no clear stratification was apparent. Indeed, counts obtained for carbonate, phosphate and oxide were well correlated within the depth range probed by SIMS. SNMS showed relationships existed between carbon, calcium, iron, and phosphorus within the bulk of the scale, as well as at the surface. SIMS imaging confirmed the relationship between calcium and lead and suggested there might also be an association between chloride and phosphorus.

A study of using femtosecond LIBS in analyzing metallic thin film-semiconductor interface

NASA Astrophysics Data System (ADS)

Galmed, A. H.; Kassem, A. K.; von Bergmann, H.; Harith, M. A.

2011-01-01

Metals and metal alloys are usually employed as interconnections to guide electrical signals between components into the very large scale integrated (VLSI) devices. These devices demand higher complexity, better performance and lower cost. Thin film is a common geometry for these metallic applications, requiring a substrate for rigidity. Accurate depth profile analysis of coatings is becoming increasingly important with expanding industrial use in technological fields. A number of articles devoted to LIBS applications for depth-resolved analysis have been published in recent years. In the present work, we are studying the ability of femtosecond LIBS to make depth profiling for a Ti thin film of thickness 213 nm deposited onto a silicon (100) substrate before and after thermal annealing. The measurements revealed that an average ablation rates of 15 nm per pulse have been achieved. The thin film was examined using X-Ray Diffraction (XRD) and Atomic Force Microscope (AFM), while the formation of the interface was examined using Rutherford Back Scattering (RBS) before and after annealing. To verify the depth profiling results, a theoretical simulation model is presented that gave a very good agreement with the experimental results.

Effects of Radiation on Oxide Materials.

DTIC Science & Technology

1981-11-01

argon sputtering. The results show that this technique is quite successful and makes it possible to profile implanted Na that fits the theoretical ...the finite escape depth of the photoionized electrons. Thicker (100 R) oxides were used for depth-profiling XPS measurements. 6.3.2 Results--30-R Films... Scofield , J. Electron Spectrosc. 8, 129 (1976). 63 SOFT SILICON DIOXIOE ON SILICON (WET GROWN) 12 . 0 1 10 o - AUGER z 0 ,- C- IS" SI - 2S Z N-I i sI-P 2 0

Clustering single cells: a review of approaches on high-and low-depth single-cell RNA-seq data.

PubMed

Menon, Vilas

2017-12-11

Advances in single-cell RNA-sequencing technology have resulted in a wealth of studies aiming to identify transcriptomic cell types in various biological systems. There are multiple experimental approaches to isolate and profile single cells, which provide different levels of cellular and tissue coverage. In addition, multiple computational strategies have been proposed to identify putative cell types from single-cell data. From a data generation perspective, recent single-cell studies can be classified into two groups: those that distribute reads shallowly over large numbers of cells and those that distribute reads more deeply over a smaller cell population. Although there are advantages to both approaches in terms of cellular and tissue coverage, it is unclear whether different computational cell type identification methods are better suited to one or the other experimental paradigm. This study reviews three cell type clustering algorithms, each representing one of three broad approaches, and finds that PCA-based algorithms appear most suited to low read depth data sets, whereas gene clustering-based and biclustering algorithms perform better on high read depth data sets. In addition, highly related cell classes are better distinguished by higher-depth data, given the same total number of reads; however, simultaneous discovery of distinct and similar types is better served by lower-depth, higher cell number data. Overall, this study suggests that the depth of profiling should be determined by initial assumptions about the diversity of cells in the population, and that the selection of clustering algorithm(s) is subsequently based on the depth of profiling will allow for better identification of putative transcriptomic cell types. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Dissolved oxygen stratification and response to thermal structure and long-term climate change in a large and deep subtropical reservoir (Lake Qiandaohu, China).

PubMed

Zhang, Yunlin; Wu, Zhixu; Liu, Mingliang; He, Jianbo; Shi, Kun; Zhou, Yongqiang; Wang, Mingzhu; Liu, Xiaohan

2015-05-15

From January 2010 to March 2014, detailed depth profiles of water temperature, dissolved oxygen (DO), and chromophoric dissolved organic matter (CDOM) were collected at three sites in Lake Qiandaohu, a large, deep subtropical reservoir in China. Additionally, we assessed the changes in DO stratification over the past 61 years (1953-2013) based on our empirical models and long-term air temperature and transparency data. The DO concentration never fell below 2 mg/L, the critical value for anoxia, and the DO depth profiles were closely linked to the water temperature depth profiles. In the stable stratification period in summer and autumn, the significant increase in CDOM in the metalimnion explained the decrease in DO due to the oxygen consumed by CDOM. Well-developed oxygen stratification was detected at the three sites in spring, summer and autumn and was associated with thermal stratification. Oxycline depth was significantly negatively correlated with daily air temperature and thermocline thickness but significantly positively correlated with thermocline depth during the stratification weakness period (July-February). However, there were no significant correlations among these parameters during the stratification formation period (March-June). The increase of 1.67 °C in yearly average daily air temperature between 1980 and 2013 and the decrease of 0.78 m in Secchi disk depth caused a decrease of 1.65 m and 2.78 m in oxycline depth, respectively, facilitating oxygen stratification and decreasing water quality. Therefore, climate warming has had a substantial effect on water quality through changing the DO regime in Lake Qiandaohu. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantification of microbial activity in subsurface environments using a hydrogenase enzyme assay

NASA Astrophysics Data System (ADS)

Adhikari, R. R.; Nickel, J.; Kallmeyer, J.

2012-04-01

The subsurface biosphere is the largest microbial ecosystem on Earth. Despite its large size and extensive industrial exploitation, very little is known about the role of microbial activity in the subsurface. Subsurface microbial activity plays a fundamental role in geochemical cycles of carbon and other biologically important elements. How the indigenous microbial communities are supplied with energy is one of the most fundamental questions in subsurface research. It is still an enigma how these communities can survive with such recalcitrant carbon over geological time scales. Despite its usually very low concentration, hydrogen is an important element in subsurface environments. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways; they either obtain protons from the radiolysis of water and/or cleavage of hydrogen generated by the alteration of basaltic crust, or they dispose of protons by formation of water. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy-generating metabolic processes to electron acceptors such as carbon dioxide or sulfate. H2ase activity can therefore be used as a measure for total microbial activity as it targets a key metabolic compound rather than a specific turnover process. Using a highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey and in marine subsurface sediments of the Barents Sea. Additionally, sulfate reduction rates (SRRs) were measured to compare the results of the H2ase enzyme assay with the quantitatively most important electron acceptor process. H2ase activity was found at all sites, measured values and distribution of activity varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3 d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3 d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3 d-1 down to a depth of 1.60 m. At all sites the SRR profile followed the H2ase activity profile until SRR declined to values close to the minimum detection limit (~10 pmol cm-3 d-1). H2ase activity increased again after SRR declined, indicating that other microbial processes are becoming quantitatively more important. The H2ase and SRR data show that our assay has a potential to become a valuable tool to measure total subsurface microbial activity.

Fluid overpressures and strength of the sedimentary upper crust

NASA Astrophysics Data System (ADS)

Suppe, John

2014-12-01

The classic crustal strength-depth profile based on rock mechanics predicts a brittle strength σ1 -σ3 = κ(ρbar gz -Pf) that increases linearly with depth as a consequence of [1] the intrinsic brittle pressure dependence κ plus [2] an assumption of hydrostatic pore-fluid pressure, Pf = ρwgz. Many deep borehole stress data agree with a critical state of failure of this form. In contrast, fluid pressures greater than hydrostatic ρbar gz >Pf >ρw gz are normally observed in clastic continental margins and shale-rich mountain belts. Therefore we explore the predicted shapes of strength-depth profiles using data from overpressured regions, especially those dominated by the widespread disequilibrium-compaction mechanism, in which fluid pressures are hydrostatic above the fluid-retention depth zFRD and overpressured below, increasing parallel to the lithostatic gradient ρbar gz . Both brittle crustal strength and frictional fault strength below the zFRD must be constant with depth because effective stress (ρbar gz -Pf) is constant, in contrast with the classic linearly increasing profile. Borehole stress and fluid-pressure measurements in several overpressured deforming continental margins agree with this constant-strength prediction, with the same pressure-dependence κ as the overlying hydrostatic strata. The role of zFRD in critical-taper wedge mechanics and jointing is illustrated. The constant-strength approximation is more appropriate for overpressured crust than classic linearly increasing models.

Contaminant transport in soil with depth-dependent reaction coefficients and time-dependent boundary conditions.

PubMed

Gao, Guangyao; Fu, Bojie; Zhan, Hongbin; Ma, Ying

2013-05-01

Predicting the fate and movement of contaminant in soils and groundwater is essential to assess and reduce the risk of soil contamination and groundwater pollution. Reaction processes of contaminant often decreased monotonously with depth. Time-dependent input sources usually occurred at the inlet of natural or human-made system such as radioactive waste disposal site. This study presented a one-dimensional convection-dispersion equation (CDE) for contaminant transport in soils with depth-dependent reaction coefficients and time-dependent inlet boundary conditions, and derived its analytical solution. The adsorption coefficient and degradation rate were represented as sigmoidal functions of soil depth. Solute breakthrough curves (BTCs) and concentration profiles obtained from CDE with depth-dependent and constant reaction coefficients were compared, and a constant effective reaction coefficient, which was calculated by arithmetically averaging the depth-dependent reaction coefficient, was proposed to reflect the lumped depth-dependent reaction effect. With the effective adsorption coefficient and degradation rate, CDE could produce similar BTCs and concentration profiles as those from CDE with depth-dependent reactions in soils with moderate chemical heterogeneity. In contrast, the predicted concentrations of CDE with fitted reaction coefficients at a certain depth departed significantly from those of CDE with depth-dependent reactions. Parametric analysis was performed to illustrate the effects of sinusoidally and exponentially decaying input functions on solute BTCs. The BTCs and concentration profiles obtained from the solutions for finite and semi-infinite domain were compared to investigate the effects of effluent boundary condition. The finite solution produced higher concentrations at the increasing limb of the BTCs and possessed a higher peak concentration than the semi-infinite solution which had a slightly long tail. Furthermore, the finite solution gave a higher concentration in the immediate vicinity of the exit boundary than the semi-infinite solution. The applicability of the proposed model was tested with a field herbicide and tracer leaching experiment in an agricultural area of northeastern Greece. The simulation results indicated that the proposed CDE with depth-dependent reaction coefficients was able to capture the evolution of metolachlor concentration at the upper soil depths. However, the simulation results at deep depths were not satisfactory as the proposed model did not account for preferential flow observed in the field. Copyright © 2013 Elsevier Ltd. All rights reserved.

Addressing the contribution of climate and vegetation cover on hillslope denudation, Chilean Coastal Cordillera (26°-38°S)

NASA Astrophysics Data System (ADS)

Schaller, M.; Ehlers, T. A.; Lang, K. A. H.; Schmid, M.; Fuentes-Espoz, J. P.

2018-05-01

The Earth surface is modulated by interactions among tectonics, climate, and biota. The influence of each of these factors on hillslope denudation rates is difficult to disentangle. The Chilean Coastal Cordillera offers a strong climate and vegetation gradient from arid and unvegetated in the North to humid and vegetated in the South. A similar (convergent) plate tectonic boundary lies to the West of the Coastal Cordillera. We present eight depth profiles analyzed for in situ-produced cosmogenic 10Be in four study areas. These profiles reveal denudation rates of soil-mantled hillslopes and the depth of mobile layers. Depth profiles were investigated from both S- and N-facing mid-slope positions. Results indicate the depth of the mobile layers in the four study areas increase from N to S in latitude. When mixing is present in the mobile layers they are completely mixed. In the S- and N-facing hillslopes of each study area, mid-slope positions do not show a systematic change in depth of the mobile layers nor in denudation rates based on cosmogenic depth profiles. From N to S in latitude, modelled denudation rates of hillslopes increase from ∼0.46 to ∼5.65 cm/kyr and then decrease to ∼3.22 cm/kyr in the southernmost, highest vegetation cover, study area. Calculated turnover times of soils decrease from ∼30 to ∼11 kyr and then increase to ∼22 kyr. In this work, the increasing denudation rates are attributed to increasing mean annual precipitation from N to S. However, despite the ongoing increase in precipitation from N to S, the denudation rate in the southernmost location does not continue to increase due to the protective nature of increasing vegetation cover. This indicates a vegetation induced non-linear relationship with denudation rates.

Quantitative Serum Nuclear Magnetic Resonance Metabolomics in Large-Scale Epidemiology: A Primer on -Omic Technologies

PubMed Central

Kangas, Antti J; Soininen, Pasi; Lawlor, Debbie A; Davey Smith, George; Ala-Korpela, Mika

2017-01-01

Abstract Detailed metabolic profiling in large-scale epidemiologic studies has uncovered novel biomarkers for cardiometabolic diseases and clarified the molecular associations of established risk factors. A quantitative metabolomics platform based on nuclear magnetic resonance spectroscopy has found widespread use, already profiling over 400,000 blood samples. Over 200 metabolic measures are quantified per sample; in addition to many biomarkers routinely used in epidemiology, the method simultaneously provides fine-grained lipoprotein subclass profiling and quantification of circulating fatty acids, amino acids, gluconeogenesis-related metabolites, and many other molecules from multiple metabolic pathways. Here we focus on applications of magnetic resonance metabolomics for quantifying circulating biomarkers in large-scale epidemiology. We highlight the molecular characterization of risk factors, use of Mendelian randomization, and the key issues of study design and analyses of metabolic profiling for epidemiology. We also detail how integration of metabolic profiling data with genetics can enhance drug development. We discuss why quantitative metabolic profiling is becoming widespread in epidemiology and biobanking. Although large-scale applications of metabolic profiling are still novel, it seems likely that comprehensive biomarker data will contribute to etiologic understanding of various diseases and abilities to predict disease risks, with the potential to translate into multiple clinical settings. PMID:29106475

Heat dissipation sensors of variable length for the measurement of sap flow in trees with deep sapwood.

PubMed

James, Shelley A; Clearwater, Michael J; Meinzer, Frederick C; Goldstein, Guillermo

2002-03-01

Robust thermal dissipation sensors of variable length (3 to 30 cm) were developed to overcome limitations to the measurement of radial profiles of sap flow in large-diameter tropical trees with deep sapwood. The effective measuring length of the custom-made sensors was reduced to 1 cm at the tip of a thermally nonconducting shaft, thereby minimizing the influence of nonuniform sap flux density profiles across the sapwood. Sap flow was measured at different depths and circumferential positions in the trunks of four trees at the Parque Natural Metropolitano canopy crane site, Panama City, Republic of Panama. Sap flow was detected to a depth of 24 cm in the trunks of a 1-m-diameter Anacardium excelsum (Bertero & Balb. ex Kunth) Skeels tree and a 0.65-m-diameter Ficus insipida Willd. tree, and to depths of 7 cm in a 0.34-m-diameter Cordia alliodora (Ruiz & Pav.) Cham. trunk, and 17 cm in a 0.47-m-diameter Schefflera morototoni (Aubl.) Maguire, Steyerm. & Frodin trunk. Sap flux density was maximal in the outermost 4 cm of sapwood and declined with increasing sapwood depth. Considerable variation in sap flux density profiles was observed both within and among the trees. In S. morototoni, radial variation in sap flux density was associated with radial variation in wood properties, particularly vessel lumen area and distribution. High variability in radial and circumferential sap flux density resulted in large errors when measurements of sap flow at a single depth, or a single radial profile, were used to estimate whole-plant water use. Diurnal water use ranged from 750 kg H2O day-1 for A. excelsum to 37 kg H2O day-1 for C. alliodora.

Observing continental boundary-layer structure and evolution over the South African savannah using a ceilometer

NASA Astrophysics Data System (ADS)

Gierens, Rosa T.; Henriksson, Svante; Josipovic, Micky; Vakkari, Ville; van Zyl, Pieter G.; Beukes, Johan P.; Wood, Curtis R.; O'Connor, Ewan J.

2018-05-01

The atmospheric boundary layer (BL) is the atmospheric layer coupled to the Earth's surface at relatively short timescales. A key quantity is the BL depth, which is important in many applied areas of weather and climate such as air-quality forecasting. Studying BLs in climates and biomes across the globe is important, particularly in the under-sampled southern hemisphere. The present study is based on a grazed grassland-savannah area in northwestern South Africa during October 2012-August 2014. Ceilometers are probably the cheapest method for measuring continuous aerosol profiles up to several kilometers above ground and are thus an ideal tool for long-term studies of BLs. A ceilometer-estimated BL depth is based on profiles of attenuated backscattering coefficients from atmospheric aerosols; the sharpest drop often occurs at BL top. Based on this, we developed a new method for layer detection that we call the signal-limited layer method. The new algorithm was applied to ceilometer profiles which thus classified BL into classic regime types: daytime convective mixing, and a double layer at night of surface-based stable with a residual layer above it. We employed wavelet fitting to increase successful BL estimation for noisy profiles. The layer-detection algorithm was supported by an eddy-flux station, rain gauges, and manual inspection. Diurnal cycles were often clear, with BL depth detected for 50% of the daytime typically being 1-3 km, and for 80% of the night-time typically being a few hundred meters. Variability was also analyzed with respect to seasons and years. Finally, BL depths were compared with ERA-Interim estimates of BL depth to show reassuring agreement.

Crustal structure of the southern Dead Sea basin derived from project DESIRE wide-angle seismic data

NASA Astrophysics Data System (ADS)

Mechie, J.; Abu-Ayyash, K.; Ben-Avraham, Z.; El-Kelani, R.; Qabbani, I.; Weber, M.

2009-07-01

As part of the DEad Sea Integrated REsearch project (DESIRE) a 235 km long seismic wide-angle reflection/refraction (WRR) profile was completed in spring 2006 across the Dead Sea Transform (DST) in the region of the southern Dead Sea basin (DSB). The DST with a total of about 107 km multi-stage left-lateral shear since about 18 Ma ago, accommodates the movement between the Arabian and African plates. It connects the spreading centre in the Red Sea with the Taurus collision zone in Turkey over a length of about 1100 km. With a sedimentary infill of about 10 km in places, the southern DSB is the largest pull-apart basin along the DST and one of the largest pull-apart basins on Earth. The WRR measurements comprised 11 shots recorded by 200 three-component and 400 one-component instruments spaced 300 m to 1.2 km apart along the whole length of the E-W trending profile. Models of the P-wave velocity structure derived from the WRR data show that the sedimentary infill associated with the formation of the southern DSB is about 8.5 km thick beneath the profile. With around an additional 2 km of older sediments, the depth to the seismic basement beneath the southern DSB is about 11 km below sea level beneath the profile. Seismic refraction data from an earlier experiment suggest that the seismic basement continues to deepen to a maximum depth of about 14 km, about 10 km south of the DESIRE profile. In contrast, the interfaces below about 20 km depth, including the top of the lower crust and the Moho, probably show less than 3 km variation in depth beneath the profile as it crosses the southern DSB. Thus the Dead Sea pull-apart basin may be essentially an upper crustal feature with upper crustal extension associated with the left-lateral motion along the DST. The boundary between the upper and lower crust at about 20 km depth might act as a decoupling zone. Below this boundary the two plates move past each other in what is essentially a shearing motion. Thermo-mechanical modelling of the DSB supports such a scenario. As the DESIRE seismic profile crosses the DST about 100 km north of where the DESERT seismic profile crosses the DST, it has been possible to construct a crustal cross-section of the region before the 107 km left-lateral shear on the DST occurred.

Stability of Zircon and its Isotopic Ratios in High-Temperature Fluids: Long-Term (4 months) Isotope Exchange Experiment at 850 °C and 50 MPa

NASA Astrophysics Data System (ADS)

Bindeman, Ilya N.; Schmitt, Axel K.; Lundstrom, Craig C.; Hervig, Richard L.

2018-05-01

Stability of zircon in hydrothermal fluids and vanishingly slow rates of diffusion identify zircon as a reliable recorder of its formation conditions in recent and ancient rocks. Debate, however, persists on how rapidly oxygen and key trace elements (e.g., Li, B, Pb) diffuse when zircon is exposed to hot aqueous fluids. Here, we report results of a nano- to micrometer-scale investigation of isotopic exchange using natural zircon from Mesa Falls Tuff (Yellowstone) treated with quartz-saturated, isotopically (18O, D, 7Li, and 11B) labeled water with a nominal δ18O value of +450‰ over 4 months at 850°C and 50 MPa. Frontside (crystal rim inwards) δ18O depth profiling of zircon by magnetic sector SIMS shows initially high but decreasing 18O/16O over a 130 nm non-Fickian profile, with a decay length comparable to the signal from surficial Au coating deposited onto zircon. In contrast, backside (crystal interior outwards) depth profiling on a 2-3 µm thick wafer cut and thinned from treated zircon by focused ion beam (FIB) milling lacks any significant increase in 18O/16O during penetration of the original surface layer. Near-surface time-of-flight (TOF-SIMS) frontside profiles of uncoated zircon from 4-month and 1-day-long experiments as well as untreated zircons display similar enrichments of 18O over a distance of 20 nm. All frontside 18O profiles are here interpreted as transient surface signals from nm-thick surface enrichment or contamination unrelated to diffusion. Likewise, frontside depth profiling of H, Li, and B isotopes are similar for long- and short-duration experiments. Additionally, surface U-Pb dating of zircon from the 4-month experiment returned U-Pb ages by depth profiling with 1 µm penetration that were identical to untreated samples. Frontside and backside depth-profiling thus demonstrate that diffusive 18O enrichment in the presence of H2O is much slower than predicted from experiments in Watson and Cherniak (1997). Instead, intracrystalline exchange of oxygen between fluid and zircon in wet experimental conditions with excess silica occurred over length-scales equivalent to those predicted for dry diffusion. Oxygen diffusion coefficients even under wet conditions and elevated temperatures (850 °C) are <1-3×10-23 m2/sec, underscoring a virtual lack of oxygen diffusion and an outstanding survivability of zircons

Analysis of Solar Wind Samples Returned by Genesis Using Laser Post Ionization Secondary Neutral Mass Spectrometry

NASA Astrophysics Data System (ADS)

Veryovkin, I. V.; Calaway, W. F.; Tripa, C. E.; Pellin, M. J.; Burnett, D. S.

2005-12-01

A new secondary neutral mass spectrometry (SNMS) instrument implementing laser post ionization (LPI) of ion sputtered and laser desorbed neutral species has been developed and constructed for the specific purpose of quantitative analysis of metallic elements at ultra trace levels in solar wind collector samples returned to Earth by the Genesis Discovery mission. The first LPI SNMS measurements are focusing on determining Al, Ca, Cr, and Mg in these samples. These measurements provide the first concentration and isotopic abundances determinations for several key metallic elements and also elucidate possible fractionation effects between the photosphere and the solar wind compositions. It is now documented that Genesis samples suffered surface contamination both during flight and during the breach of the Sample Return Capsule when it crashed. Since accurate quantitative analysis is compromised by sample contamination, several features have been built into the new LPI SNMS instrument to mitigate this difficulty. A normally-incident, low-energy (<500 eV) ion beam combined with a keV energy ion beam and a desorbing laser beam (both microfocused) enables dual beam analyses. The low-energy ion beam can be used to remove surface contaminant by sputtering with minimum ion beam mixing. This low-energy beam also will be used to perform ion beam milling, while either the microfocused ion or laser beam probes the solar wind elemental compositions as a function of sample depth. Because of the high depth resolution of dual beam analyses, such depth profiles clearly distinguish between surface contaminants and solar wind implanted atoms. In addition, in-situ optical and electron beam imaging for observing and avoiding particulates and scratches on solar wind sample surfaces is incorporated in the new LPI SNMS instrument to further reduce quantification problems. The current status of instrument tests and analyses will be presented. This work is supported by the U. S. Department of Energy, BES-Materials Sciences, under Contract W-31-109-ENG-38, and by NASA under Work Orders W-19,895 and W-10,091.

The velocity structure of the lunar crust.

NASA Technical Reports Server (NTRS)

Kovach, R. L.; Watkins, J. S.

1973-01-01

Seismic refraction data, obtained at the Apollo 14 and 16 sites, when combined with other lunar seismic data, allow a compressional wave velocity profile of the lunar near-surface and crust to be derived. The regolith, although variable in thickness over the lunar surface, possesses surprisingly similar seismic properties. Underlying the regolith at both the Apollo 14 Fra Mauro site and the Apollo 16 Descartes site is low-velocity brecciated material or impact derived debris. Key features of the lunar seismic velocity profile are: (1) velocity increases from 100 to 300 m/sec in the upper 100 m to about 4 km/sec at 5 km depth, (2) a more gradual increase from about 4 km/sec to about 6 km/sec at 25 km depth,(3) a discontinuity at a depth of 25 km, and (4) a constant value of about 7 km/sec at depths from 25 km to about 60 km.

Clinical spectrum of lamellar macular defects including pseudoholes and pseudocysts defined by optical coherence tomography

PubMed Central

Chen, J C; Lee, L R

2008-01-01

Objective: To present the clinical spectrum of lamellar macular defects and describe the different subtypes based on their optical coherence tomography (OCT) configuration and visual prognosis. Methods: The retrospective observational case series reviewed OCT scans of 92 eyes with lamellar macular defects. Lamellar macular defects were categorised into subtypes of macular pseudohole (MPH), lamellar macular hole (LMH) and foveal pseudocyst (FP) according to their OCT morphology. The defects were quantitatively characterised in terms of base diameter, depth and central foveal thickness, and examined for the presence of associated epiretinal membranes (ERM). Results: Visual acuity (VA) was significantly correlated with the central foveal thickness and depth of the lamellar defect. MPH was associated with better VA compared with LMH and FP. MPH was of a smaller base diameter and had a greater central foveal thickness than that of LMH and FP. Fifty-per cent of all lamellar defects had an associated ERM. Conclusions: Different profiles of lamellar macular defects were characterised and quantified by OCT. Deeper and wider lamellar defects were associated with poorer visual outcome. Such objective parameters lamellar macular defects are of value when explaining to patients regarding their decreased acuity. Future prospective investigations are required to study the natural history of lamellar defects of different aetiology and surgical indications. PMID:18684752

Application of Raman Spectroscopy for the Detection of Acetone Dissolved in Transformer Oil

NASA Astrophysics Data System (ADS)

Gu, Z.; Chen, W.; Du, L.; Shi, H.; Wan, F.

2018-05-01

The CLRS detection characteristics of acetone dissolved in transformer oil were analyzed. Raman spectral peak at 780 cm-1 was used as the characteristic spectral peak for qualitative and quantitative analyses. The effect of the detection depth and the temperature was investigated in order to obtain good Raman signals. The optimal detection depth and temperature were set as 3 mm and room temperature. A quantitative model relation between concentration and the Raman peak intensity ratio I 780/I 893 was constructed via the least-squares method. The results demonstrated that CLRS can quantitatively detect the concentration of acetone in transformer oil and CLRS has potential as a useful alternative for accelerating the in-situ analysis of the concentration of acetone in transformer oil.

Application of Raman Spectroscopy for the Detection of Acetone Dissolved in Transformer Oil

NASA Astrophysics Data System (ADS)

Gu, Z.; Chen, W.; Du, L.; Shi, H.; Wan, F.

2018-05-01

The CLRS detection characteristics of acetone dissolved in transformer oil were analyzed. Raman spectral peak at 780 cm-1 was used as the characteristic spectral peak for qualitative and quantitative analyses. The effect of the detection depth and the temperature was investigated in order to obtain good Raman signals. The optimal detection depth and temperature were set as 3 mm and room temperature. A quantitative model relation between concentration and the Raman peak intensity ratio I 780/ I 893 was constructed via the least-squares method. The results demonstrated that CLRS can quantitatively detect the concentration of acetone in transformer oil and CLRS has potential as a useful alternative for accelerating the in-situ analysis of the concentration of acetone in transformer oil.

Complex N-S variations in Moho depth and Vp/Vs ratio beneath the western Tibetan Plateau as revealed by receiver function analysis

NASA Astrophysics Data System (ADS)

Murodov, Davlatkhudzha; Zhao, Junmeng; Xu, Qiang; Liu, Hongbing; Pei, Shunping

2018-04-01

We present herein detailed images of the Moho depth and Vp/Vs ratio along ANTILOPE-1 profile beneath the western Tibetan Plateau derived from receiver function analysis. Along the ANTILOPE -1 profile, a rapidly northward dipping Moho extends from ˜50 km below the Himalaya to ˜80 km across the Indus-Yarlung suture (IYS), shallowing to ˜66 km under the central Lhasa terrane. The Moho depth shows a dramatic increase from ˜66 km north of the Bangong-Nujiang suture (BNS) to ˜93 km beneath central Qiangtang terrane where it reaches the maximum depth observed along this profile before steeply rising to ˜73 km. We interpret both the 15 km and 20 km offsets of Moho depth occurring beneath the central Lhasa and central Qiangtang terranes as being related to the northern frontiers of the decoupled underthrusting Indian lower crust and lithospheric mantle, respectively. The Moho remains at a depth of ˜70 km with a slight undulation beneath the northern Qiangtang and Songpan-Ganzi terranes, and then abruptly shallows to ˜45 km near the Altyn Tagh Fault. The ˜25 km Moho offset observed at the conjunction of the Tarim Basin and the Altyn Tagh mountain range suggests that the crustal shortening is achieved by pure shear thickening without much underthrusting. The average crustal Vp/Vs ratio changes from 1.66 to 1.80 beneath the Himalaya, the Lhasa terrane and the Tarim Basin indicating a felsic-to-intermediate composition. However, higher Vp/Vs ratios between 1.76 and 1.83 (except for a few outlying low values) are found beneath the Qiangtang and Songpan-Ganzi terranes, which could be attributed to the joint effects of the more mafic composition and partial melt within the crust. The Moho depth and Vp/Vs ratio exhibit complex N-S variations along this profile, which can be attributed to the joint effects of Indian lower crust underthrusting, the low velocity zone of the mid-upper crust, crustal shortening and thickening and other involved dynamic mechanisms.

Understanding University Students' Thoughts and Practices about Digital Citizenship: A Mixed Methods Study

ERIC Educational Resources Information Center

Kara, Nuri

2018-01-01

The purpose of this study was to investigate university students' thoughts and practices concerning digital citizenship. An explanatory mixed methods design was used, and it involved collecting qualitative data after a quantitative phase in order to follow up on the quantitative data in more depth. In the first quantitative phase of the study, a…

Clay mineralogy of weathering profiles from the Carolina Piedmont.

USGS Publications Warehouse

Loferski, P.J.

1981-01-01

Saprolite profiles (12) that formed over various crystalline rocks from the Charlotte 1o X 2o quadrangle showed overall similarity in their clay mineralogy to depths of 6 to 45 m indicating control by weathering processes rather than by rock type. Most saprolite contained 10-25% clay, and ranged 3 to 70%. Kaolinite and halloysite composed = or >75% of the clay fraction of most samples. The ratio kaolinite:halloysite ranged widely, from 95% kaolinite to 90% halloysite, independent of depth. Clay-size mica was present in all profiles, and ranged 5-75% over a sericite schist. Mixed-layer mica-smectite and mica-vermiculite were subordinate; discrete smectite and vermiculite were rare. The abundance of halloysite indicates a continuously humid environment since the time of profile formation, because of the rapidity with which halloysite dehydrates irreversibly. -R.S.M.

Using High Frequency Focused Water-Coupled Ultrasound for 3-D Surface Depression Profiling

NASA Technical Reports Server (NTRS)

Roth, Don J.; Whalen, Mike F.; Hendricks, J. Lynne; Bodis, James R.

1999-01-01

Surface topography is an important variable in the performance of many industrial components and is normally measured with diamond-tip profilometry over a small area or using optical scattering methods for larger area measurement. A prior study was performed demonstrating that focused air-coupled ultrasound at 1 MHz was capable of profiling surfaces with 25 micron depth resolution and 400 micron lateral resolution over a 1.4 mm depth range. In this article, the question of whether higher-frequency focused water-coupled ultrasound can improve on these specifications is addressed. 10 and 25 MHz focused ultrasonic transducers were employed in the water-coupled mode. Time-of-flight images of the sample surface were acquired and converted to depth / surface profile images using the simple relation (d = V*t/2) between distance (d), time-of-flight (t), and the velocity of sound in water (V). Results are compared for the two frequencies used and with those from the 1 MHz air-coupled configuration.

Effect of water table fluctuations on phreatophytic root distribution.

PubMed

Tron, Stefania; Laio, Francesco; Ridolfi, Luca

2014-11-07

The vertical root distribution of riparian vegetation plays a relevant role in soil water balance, in the partition of water fluxes into evaporation and transpiration, in the biogeochemistry of hyporheic corridors, in river morphodynamics evolution, and in bioengineering applications. The aim of this work is to assess the effect of the stochastic variability of the river level on the root distribution of phreatophytic plants. A function describing the vertical root profile has been analytically obtained by coupling a white shot noise representation of the river level variability to a description of the dynamics of root growth and decay. The root profile depends on easily determined parameters, linked to stream dynamics, vegetation and soil characteristics. The riparian vegetation of a river characterized by a high variability turns out to have a rooting system spread over larger depths, but with shallower mean root depths. In contrast, a lower river variability determines root profiles with higher mean root depths. Copyright © 2014 Elsevier Ltd. All rights reserved.

Pilot study of facial soft tissue thickness differences among three skeletal classes in Japanese females.

PubMed

Utsuno, Hajime; Kageyama, Toru; Uchida, Keiichi; Yoshino, Mineo; Oohigashi, Shina; Miyazawa, Hiroo; Inoue, Katsuhiro

2010-02-25

Facial reconstruction is a technique used in forensic anthropology to estimate the appearance of the antemortem face from unknown human skeletal remains. This requires accurate skull assessment (for variables such as age, sex, and race) and soft tissue thickness data. However, the skull can provide only limited information, and further data are needed to reconstruct the face. The authors herein obtained further information from the skull in order to reconstruct the face more accurately. Skulls can be classified into three facial types on the basis of orthodontic skeletal classes (namely, straight facial profile, type I, convex facial profile, type II, and concave facial profile, type III). This concept was applied to facial tissue measurement and soft tissue depth was compared in each skeletal class in a Japanese female population. Differences of soft tissue depth between skeletal classes were observed, and this information may enable more accurate reconstruction than sex-specific depth alone. 2009 Elsevier Ireland Ltd. All rights reserved.

Identification of Chinese medicinal fungus Cordyceps sinensis by depth-profiling mid-infrared photoacoustic spectroscopy.

PubMed

Du, Changwen; Zhou, Jianmin; Liu, Jianfeng

2017-02-15

With increased demand for Cordyceps sinensis it needs rapid methods to meet the challenge of identification raised in quality control. In this study Cordyceps sinensis from four typical natural habitats in China was characterized by depth-profiling Fourier transform infrared photoacoustic spectroscopy. Results demonstrated that Cordyceps sinensis samples resulted in typical photoacoustic spectral appearance, but heterogeneity was sensed in the whole sample; due to the heterogeneity Cordyceps sinensis was represented by spectra of four groups including head, body, tail and leaf under a moving mirror velocity of 0.30cms -1 . The spectra of the four groups were used as input of a probabilistic neural network (PNN) to identify the source of Cordyceps sinensis, and all the samples were correctly identified by the PNN model. Therefore, depth-profiling Fourier transform infrared photoacoustic spectroscopy provides novel and unique technique to identify Cordyceps sinensis, which shows great potential in quality control of Cordyceps sinensis. Copyright © 2016 Elsevier B.V. All rights reserved.

Continual in situ monitoring of pore water stable isotopes in the subsurface

NASA Astrophysics Data System (ADS)

Volkmann, T. H. M.; Weiler, M.

2014-05-01

Stable isotope signatures provide an integral fingerprint of origin, flow paths, transport processes, and residence times of water in the environment. However, the full potential of stable isotopes to quantitatively characterize subsurface water dynamics is yet unfolded due to the difficulty in obtaining extensive, detailed, and repeated measurements of pore water in the unsaturated and saturated zone. This paper presents a functional and cost-efficient system for non-destructive continual in situ monitoring of pore water stable isotope signatures with high resolution. Automatic controllable valve arrays are used to continuously extract diluted water vapor in soil air via a branching network of small microporous probes into a commercial laser-based isotope analyzer. Normalized liquid-phase isotope signatures are then obtained based on a specific on-site calibration approach along with basic corrections for instrument bias and temperature dependent isotopic fractionation. The system was applied to sample depth profiles on three experimental plots with varied vegetation cover in southwest Germany. Two methods (i.e., based on advective versus diffusive vapor extraction) and two modes of sampling (i.e., using multiple permanently installed probes versus a single repeatedly inserted probe) were tested and compared. The results show that the isotope distribution along natural profiles could be resolved with sufficiently high accuracy and precision at sampling intervals of less than four minutes. The presented in situ approaches may thereby be used interchangeably with each other and with concurrent laboratory-based direct equilibration measurements of destructively collected samples. It is thus found that the introduced sampling techniques provide powerful tools towards a detailed quantitative understanding of dynamic and heterogeneous shallow subsurface and vadose zone processes.

Spatial and temporal variation of moisture content in the soil profiles of two different agricultural fields of semi-arid region.

PubMed

Baskan, Oguz; Kosker, Yakup; Erpul, Gunay

2013-12-01

Modeling spatio-temporal variation of soil moisture with depth in the soil profile plays an important role for semi-arid crop production from an agro-hydrological perspective. This study was performed in Guvenc Catchment. Two soil series that were called Tabyabayir (TaS) and Kervanpinari (KeS) and classified as Leptosol and Vertisol Soil Groups were used in this research. The TeS has a much shallower (0-34 cm) than the KeS (0-134 cm). At every sampling time, a total of geo-referenced 100 soil moisture samples were taken based on horizon depths. The results indicated that soil moisture content changed spatially and temporally with soil texture and profile depth significantly. In addition, land use was to be important factor when soil was shallow. When the soil conditions were towards to dry, higher values for the coefficient of variation (CV) were observed for TaS (58 and 43% for A and C horizons, respectively); however, the profile CV values were rather stable at the KeS. Spatial variability range of TaS was always higher at both dry and wet soil conditions when compared to that of KeS. Excessive drying of soil prevented to describe any spatial model for surface horizon, additionally resulting in a high nugget variance in the subsurface horizon for the TaS. On the contrary to TaS, distribution maps were formed all horizons for the KeS at any measurement times. These maps, depicting both dry and wet soil conditions through the profile depth, are highly expected to reduce the uncertainty associated with spatially and temporally determining the hydraulic responses of the catchment soils.

Identification of copy number variants in whole-genome data using Reference Coverage Profiles

PubMed Central

Glusman, Gustavo; Severson, Alissa; Dhankani, Varsha; Robinson, Max; Farrah, Terry; Mauldin, Denise E.; Stittrich, Anna B.; Ament, Seth A.; Roach, Jared C.; Brunkow, Mary E.; Bodian, Dale L.; Vockley, Joseph G.; Shmulevich, Ilya; Niederhuber, John E.; Hood, Leroy

2015-01-01

The identification of DNA copy numbers from short-read sequencing data remains a challenge for both technical and algorithmic reasons. The raw data for these analyses are measured in tens to hundreds of gigabytes per genome; transmitting, storing, and analyzing such large files is cumbersome, particularly for methods that analyze several samples simultaneously. We developed a very efficient representation of depth of coverage (150–1000× compression) that enables such analyses. Current methods for analyzing variants in whole-genome sequencing (WGS) data frequently miss copy number variants (CNVs), particularly hemizygous deletions in the 1–100 kb range. To fill this gap, we developed a method to identify CNVs in individual genomes, based on comparison to joint profiles pre-computed from a large set of genomes. We analyzed depth of coverage in over 6000 high quality (>40×) genomes. The depth of coverage has strong sequence-specific fluctuations only partially explained by global parameters like %GC. To account for these fluctuations, we constructed multi-genome profiles representing the observed or inferred diploid depth of coverage at each position along the genome. These Reference Coverage Profiles (RCPs) take into account the diverse technologies and pipeline versions used. Normalization of the scaled coverage to the RCP followed by hidden Markov model (HMM) segmentation enables efficient detection of CNVs and large deletions in individual genomes. Use of pre-computed multi-genome coverage profiles improves our ability to analyze each individual genome. We make available RCPs and tools for performing these analyses on personal genomes. We expect the increased sensitivity and specificity for individual genome analysis to be critical for achieving clinical-grade genome interpretation. PMID:25741365

Effects of immersion depth on super-resolution properties of index-different microsphere-assisted nanoimaging

NASA Astrophysics Data System (ADS)

Zhou, Yi; Tang, Yan; He, Yu; Liu, Xi; Hu, Song

2018-03-01

In related applications of microsphere-assisted super-resolution imaging in biomedical visualization and microfluidic detection, liquids are widely used as background media. For the first time, we quantitatively demonstrate that the maximum irradiances, focal lengths, and waists of photonic nanojets (PNJs) will logically vary with different immersion depths (IMDs). The experimental observations also numerically illustrate the trends of the lateral magnification and field of view (FOV) with the gradual evaporation of ethyl alcohol. This work can provide exact quantitative information for the proper selection of microspheres and IMD for the high-quality discernment of nanostructures.

In situ monitoring of powder blending by non-invasive Raman spectrometry with wide area illumination.

PubMed

Allan, Pamela; Bellamy, Luke J; Nordon, Alison; Littlejohn, David; Andrews, John; Dallin, Paul

2013-03-25

A 785nm diode laser and probe with a 6mm spot size were used to obtain spectra of stationary powders and powders mixing at 50rpm in a high shear convective blender. Two methods of assessing the effect of particle characteristics on the Raman sampling depth for microcrystalline cellulose (Avicel), aspirin or sodium nitrate were compared: (i) the information depth, based on the diminishing Raman signal of TiO(2) in a reference plate as the depth of powder prior to the plate was increased, and (ii) the depth at which a sample became infinitely thick, based on the depth of powder at which the Raman signal of the compound became constant. The particle size, shape, density and/or light absorption capability of the compounds were shown to affect the "information" and "infinitely thick" depths of individual compounds. However, when different sized fractions of aspirin were added to Avicel as the main component, the depth values of aspirin were the same and matched that of the Avicel: 1.7mm for the "information" depth and 3.5mm for the "infinitely thick" depth. This latter value was considered to be the minimum Raman sampling depth when monitoring the addition of aspirin to Avicel in the blender. Mixing profiles for aspirin were obtained non-invasively through the glass wall of the vessel and could be used to assess how the aspirin blended into the main component, identify the end point of the mixing process (which varied with the particle size of the aspirin), and determine the concentration of aspirin in real time. The Raman procedure was compared to two other non-invasive monitoring techniques, near infrared (NIR) spectrometry and broadband acoustic emission spectrometry. The features of the mixing profiles generated by the three techniques were similar for addition of aspirin to Avicel. Although Raman was less sensitive than NIR spectrometry, Raman allowed compound specific mixing profiles to be generated by studying the mixing behaviour of an aspirin-aspartame-Avicel mixture. Copyright © 2013 Elsevier B.V. All rights reserved.

Quantifying small-scale spatio-temporal variability of snow stratigraphy in forests based on high-resolution snow penetrometry

NASA Astrophysics Data System (ADS)

Teich, M.; Hagenmuller, P.; Bebi, P.; Jenkins, M. J.; Giunta, A. D.; Schneebeli, M.

2017-12-01

Snow stratigraphy, the characteristic layering within a seasonal snowpack, has important implications for snow remote sensing, hydrology and avalanches. Forests modify snowpack properties through interception, wind speed reduction, and changes to the energy balance. The lack of snowpack observations in forests limits our ability to understand the evolution of snow stratigraphy and its spatio-temporal variability as a function of forest structure and to observe snowpack response to changes in forest cover. We examined the snowpack under canopies of a spruce forest in the central Rocky Mountains, USA, using the SnowMicroPen (SMP), a high resolution digital penetrometer. Weekly-repeated penetration force measurements were recorded along 10 m transects every 0.3 m in winter 2015 and bi-weekly along 20 m transects every 0.5 m in 2016 in three study plots beneath canopies of undisturbed, bark beetle-disturbed and harvested forest stands, and an open meadow. To disentangle information about layer hardness and depth variabilities, and to quantitatively compare the different SMP profiles, we applied a matching algorithm to our dataset, which combines several profiles by automatically adjusting their layer thicknesses. We linked spatial and temporal variabilities of penetration force and depth, and thus snow stratigraphy to forest and meteorological conditions. Throughout the season, snow stratigraphy was more heterogeneous in undisturbed but also beneath bark beetle-disturbed forests. In contrast, and despite remaining small diameter trees and woody debris, snow stratigraphy was rather homogenous at the harvested plot. As expected, layering at the non-forested plot varied only slightly over the small spatial extent sampled. At the open and harvested plots, persistent crusts and ice lenses were clearly present in the snowpack, while such hard layers barely occurred beneath undisturbed and disturbed canopies. Due to settling, hardness significantly increased with depth at open and harvested plots, which was less distinctive at the other two plots. Our results contribute to the general understanding of forest-snowpack interactions and, if combined with density and specific surface area estimates, can be used to validate snowpack and microwave models for avalanche formation and SWE retrieval in forests.

Oxygen Isotope Compositions of Meteoric Water Across an Elevation Gradient in Southern Peru

NASA Astrophysics Data System (ADS)

Xu, D. R.; White, E.; Cassel, E. J.; Lynch, B.; Yanites, B.; Breecker, D.

2017-12-01

The Central Andes is a prime example of elevated topography generated by oceanic plate subduction. Whereas previous stable isotope studies have investigated the paleoelevation of the Andean Eastern Cordillera, little is known about the paleoelevation of the Western Cordillera, where arc volcanism now occurs. As a first step towards studying the paleoelevation of this region, we investigated the change in δ18O values of modern soil waters across an elevation gradient from sea level to about 4725 meters in southern Peru. We sampled soil profiles from 5 to 80 cm in 15-20cm increments, and we sampled water from flowing natural streams at various elevations. We used cryogenic vacuum extraction to quantitatively remove non-structural water from soil samples. The δ18O values of water extracted from soil samples varies with the depth in the soil due to the diminishing effect of seasonality and evaporation. Every high elevation (>3500m) soil profile we measured had nearly constant δ18O values below 5cm and a total range of δ18O values between -12.8‰ and -17.1‰, apart from the Cusco profile. In the Cusco profile, the δ18O values ranged from -7.2 ‰ at 5 cm to -21.8 ‰ at 60 cm, defining a strong monotonic decrease not seen in other soil profiles. The δ18O trend in the Cusco profile may be different due to the impact of evaporation, soil hydrology, and/or seasonality in the δ18O values of precipitation. Further spatial analysis must be conducted to pinpoint a specific cause. Considering only the samples collected below 40cm, which are likely the best estimate of mean annual precipitation, the δ18O values decrease with increasing elevation at a rate higher than the global mean, suggesting that oxygen isotope paleoaltimetry can work in this study region.

A Non-Steady-State Condition in Sediments at the Gashydrate Stability Boundary off West Spitsbergen: Evidence for Gashydrate Dissociation or Just Dynamic Methane Transport?

NASA Astrophysics Data System (ADS)

Treude, T.; Krause, S.; Bertics, V. J.; Steinle, L.; Niemann, H.; Liebetrau, V.; Feseker, T.; Burwicz, E.; Krastel, S.; Berndt, C.

2014-12-01

In 2008, a large area with several hundred methane plumes was discovered along the West Spitsbergen continental margin at water depths between 150 and 400 m (Westbrook et al. 2009, GRL 36, doi:10.1029/2009GL039191). Many of the observed plumes were located at the boundary of gas hydrate stability (~400 m water depth). It was speculated that the methane escape at this depth was correlated with gas hydrate destabilization caused by recent increases in water temperatures recorded in this region. In a later study, geochemical analyses of authigenic carbonates and modeling of heat flow data combined with seasonal changes in water temperature demonstrated that the methane seeps were active already prior to industrial warming but that the gas hydrate system nevertheless reacts very sensitive to even seasonal temperature changes (Berndt et al. 2014, Science 343: 284-287). Here, we report about a methane seep site at the gas hydrate stability boundary (394 m water depth) that features unusual geochemical profiles indicative for non-steady state conditions. Sediment was recovered with a gravity corer (core length 210 cm) and samples were analyzed to study porewater geochemistry, methane concentration, authigenic carbonates, and microbial activity. Porewater profiles revealed two zones of sulfate-methane transition at 50 and 200 cm sediment depth. The twin zones were confirmed by a double peaking in sulfide, total alkalinity, anaerobic oxidation of methane, and sulfate reduction. δ18O values sharply increased from around -2.8 ‰ between 0 and 126 cm to -1.2 ‰ below 126 cm sediment depth. While U/Th isotope measurements of authigenic seep carbonates that were collected from different depths of the core illustrated that methane seepage must be occurring at this site since at least 3000 years, the biogeochemical profiles suggest that methane flux must have been altered recently. By applying a multi-phase reaction-transport model using known initial parameters from the study site (e.g. water depth, temperature profile, salinity, and sediment surface concentrations of CH4, SO4, DIC, and POC) were able to show that the observed twin sulfate-methane transition zones are an ephemeral phenomenon occurring during increase of methane production in the sediment, which can be introduced by, e.g., gas hydrate dissociation.

Soil depth mapping using seismic surface waves: Evaluation on eroded loess covered hillslopes

NASA Astrophysics Data System (ADS)

Bernardie, Severine; Samyn, Kevin; Cerdan, Olivier; Grandjean, Gilles

2010-05-01

The purposes of the multidisciplinary DIGISOIL project are the integration and improvement of in situ and proximal technologies for the assessment of soil properties and soil degradation indicators. Foreseen developments concern sensor technologies, data processing and their integration to applications of (digital) soil mapping (DSM). Among available techniques, the seismic one is, in this study, particularly tested for characterising soil vulnerability to erosion. The spectral analysis of surface waves (SASW) method is an in situ seismic technique used for evaluation of the stiffnesses (G) and associated depth in layered systems. A profile of Rayleigh wave velocity versus frequency, i.e., the dispersion curve, is calculated from each recorded seismogram before to be inverted to obtain the vertical profile of shear wave velocity Vs. Then, the soil stiffness can easily be calculated from the shear velocity if the material density is estimated, and the soil stiffness as a function of depth can be obtained. This last information can be a good indicator to identify the soil bedrock limit. SASW measurements adapted to soil characterisation is proposed in the DIGISOIL project, as it produces in an easy and quick way a 2D map of the soil. This system was tested for the digital mapping of the depth of loamy material in a catchment of the European loess belt. The validation of this methodology has been performed with the realisation of several acquisitions along the seismic profiles: - Several boreholes were drilled until the bedrock, permitting to get the geological features of the soil and the depth of the bedrock; - Several laboratory measurements of various parameters were done on samples taken from the boreholes at various depths, such as dry density, solid density, and water content; - Dynamic penetration tests were also conducted along the seismic profile, until the bedrock is attained. Some empirical correlations between the parameters measured with laboratory tests, the qc obtained from the dynamic penetration tests and the Vs acquired from the SASW measurements permit to assess the accuracy of the procedure and to evaluate its limitations. The depth to bedrock determined by this procedure can then be combined with the soil erosion susceptibility to produce a risk map. This methodology will help to target measures within areas that show a reduced soil depth associated with a high soil erosion susceptibility.

Marine Geophysical Investigation of Selected Sites in Bridgeport Harbor, Connecticut, 2006

USGS Publications Warehouse

Johnson, Carole D.; White, Eric A.

2007-01-01

A marine geophysical investigation was conducted in 2006 to help characterize the bottom and subbottom materials and extent of bedrock in selected areas of Bridgeport Harbor, Connecticut. The data will be used by the U.S. Army Corps of Engineers in the design of confined aquatic disposal (CAD) cells within the harbor to facilitate dredging of the harbor. Three water-based geophysical methods were used to evaluate the geometry and composition of subsurface materials: (1) continuous seismic profiling (CSP) methods provide the depth to water bottom, and when sufficient signal penetration can be achieved, delineate the depth to bedrock and subbottom materials; (2) continuous resistivity profiling (CRP) methods were used to define the electrical properties of the shallow subbottom, and to possibly determine the distribution of conductive materials, such as clay, and resistive materials, such as sand and bedrock; (3) and magnetometer data were used to identify conductive anomalies of anthropogenic sources, such as cables and metallic debris. All data points were located using global positioning systems (GPS), and the GPS data were used for real-time navigation. The results of the CRP, CSP, and magnetometer data are consistent with the conceptual site model of a bedrock channel incised beneath the present day harbor. The channel appears to follow a north-northwest to south-southeast trend and is parallel to the Pequannock River. The seismic record and boring data indicate that under the channel, the depth to bedrock is as much as 42.7 meters (m) below mean low-low water (MLLW) in the dredged part of the harbor. The bedrock channel becomes shallower towards the shore, where bedrock outcrops have been mapped at land surface. CSP and CRP data were able to provide a discontinuous, but reasonable, trace from the channel toward the west under the proposed southwestern CAD cell. The data indicate a high amount of relief on the bedrock surface, as well as along the water bottom. Under the southwestern CAD cell, the sediments are only marginally thick enough for a CAD cell, at about 8 to 15 m in depth. Some of the profiles show small diffractions in the unconsolidated sediments, but no large-scale boulders or boulder fields were identified. No bedrock reflectors were imaged under the southeastern CAD cell, where core logs indicate the rock is as much as 30 m below MLLW. The chirp frequency, tuned transducer, and boomer-plate CSP surveys were adversely affected by a highly reflective water bottom causing strong multiples in the seismic record and very limited depths of penetration. These multiples are attributed to entrapped gas (methane) in the sediments or to very hard bottom conditions. In a limited number of places, the bedrock surface was observed in the CSP record, creating a discontinuous and sporadic image of the bedrock surface. These interpretations generally matched core data at FP-03-10 and FB-06-1. Use of two analog CSP systems, the boomer plate and tuned transducer, did not overcome the reflections off the water bottom and did not improve the depth of penetration. In general, the CRP profiles were used to corroborate the results of the CSP profiles. Relatively resistive zones associated with the locations of seismic reflections were interpreted as bedrock. The shape of the bedrock surface generally was similar in the CRP and CSP profiles. Evaluation of the CRP profiles indicated that the inversions were adversely affected where the depth and (or) ionic concentration of the water column varied. Consequently, the CRP profiles were broken into short intervals that extended just over the area of interest, where the depth to water bottom was fairly constant. Over these short profiles, efforts were made to evaluate the resistivity of the very shallow sediments to determine if there were any large contrasts in the resistivity of the sediments that might indicate differences in the shallow subbottom materials. No conclusions abo

Seasonal changes in depth of water uptake for encroaching trees Juniperus virginiana and Pinus ponderosa and two dominant C4 grasses in a semiarid grassland.

PubMed

Eggemeyer, Kathleen D; Awada, Tala; Harvey, F Edwin; Wedin, David A; Zhou, Xinhua; Zanner, C William

2009-02-01

We used the natural abundance of stable isotopic ratios of hydrogen and oxygen in soil (0.05-3 m depth), plant xylem and precipitation to determine the seasonal changes in sources of soil water uptake by two native encroaching woody species (Pinus ponderosa P. & C. Lawson, Juniperus virginiana L.), and two C(4) grasses (Schizachyrium scoparium (Michx.) Nash, Panicum virgatum L.), in the semiarid Sandhills grasslands of Nebraska. Grass species extracted most of their water from the upper soil profile (0.05-0.5 m). Soil water uptake from below 0.5 m depth increased under drought, but appeared to be minimal in relation to the total water use of these species. The grasses senesced in late August in response to drought conditions. In contrast to grasses, P. ponderosa and J. virginiana trees exhibited significant plasticity in sources of water uptake. In winter, tree species extracted a large fraction of their soil water from below 0.9 m depth. In spring when shallow soil water was available, tree species used water from the upper soil profile (0.05-0.5 m) and relied little on water from below 0.5 m depth. During the growing season (May-August) significant differences between the patterns of tree species water uptake emerged. Pinus ponderosa acquired a large fraction of its water from the 0.05-0.5 and 0.5-0.9 m soil profiles. Compared with P. ponderosa, J. virginiana acquired water from the 0.05-0.5 m profile during the early growing season but the amount extracted from this profile progressively declined between May and August and was mirrored by a progressive increase in the fraction taken up from 0.5-0.9 m depth, showing plasticity in tracking the general increase in soil water content within the 0.5-0.9 m profile, and being less responsive to growing season precipitation events. In September, soil water content declined to its minimum, and both tree species shifted soil water uptake to below 0.9 m. Tree transpiration rates (E) and water potentials (Psi) indicated that deep water sources did not maintain E which sharply declined in September, but played an important role in the recovery of tree Psi. Differences in sources of water uptake among these species and their ecological implications on tree-grass dynamics and soil water in semiarid environments are discussed.

Intravital microscopy of biosensor activities and intrinsic metabolic states

PubMed Central

Winfree, Seth; Hato, Takashi; Day, Richard N.

2018-01-01

Intravital microscopy (IVM) is an imaging tool that is capable of detecting subcellular signaling or metabolic events as they occur in tissues in the living animal. Imaging in highly scattering biological tissues, however, is challenging because of the attenuation of signal in images acquired at increasing depths. Depth-dependent signal attenuation is the major impediment to IVM, limiting the depth from which significant data can be obtained. Therefore, making quantitative measurements by IVM requires methods that use internal calibration, or alternatively, a completely different way of evaluating the signals. Here, we describe how ratiometric imaging of genetically encoded biosensor probes can be used to make quantitative measurements of changes in the activity of cell signaling pathways. Then, we describe how fluorescence lifetime imaging can be used for label-free measurements of the metabolic states of cells within the living animal. PMID:28434902

Temperature and electrical conductivity of the lunar interior from magnetic transient measurements in the geomagnetic tail

NASA Technical Reports Server (NTRS)

Dyal, P.; Parkin, C. W.; Daily, W. D.

1974-01-01

Magnetometers were deployed at four Apollo sites on the moon to measure remanent and induced lunar magnetic fields. Measurements from this network of instruments were used to calculate the electrical conductivity, temperature, magnetic permeability, and iron abundance of the lunar interior. Global lunar fields due to eddy currents, induced in the lunar interior by magnetic transients in the geomagnetic tail field, were analyzed to calculate an electrical conductivity profile for the moon: the conductivity increases rapidly with depth from 10 to the minus 9 power mhos/meter at the lunar surface to .0001 mhos/meter at 200 km depth, then less rapidly to .02 mhos/meter at 1000 km depth. A temperature profile is calculated from conductivity: temperature rises rapidly with depth to 1100 K at 200 km depth, then less rapidly to 1800 K at 1000 km depth. Velocities and thicknesses of the earth's magnetopause and bow shock are estimated from simultaneous magnetometer measurements. Average speeds are determined to be about 50 km/sec for the magnetopause and 70 km/sec for the bow shock, although there are large variations in the measurements for any particular boundary crossing.

Assessment of vertical soil solid phase transport (pedoturbations) in different types of land use by magnetic tracer method (Belgorod region, Russia)

NASA Astrophysics Data System (ADS)

Zhidkin, Andrey

2015-04-01

New method of quantitative assessments of vertical soil solid phase transport (pedoturbations) is based on redistribution of spherical magnetic particles (SMP) in soil profiles. SMP - are fly ash components, which mainly produce during coal burning. The main sources of SMP on studied object were locomotives on the railroads, which used coal at the turn of the XIX century. SMP income into the soil only from the atmosphere, very stable for destructions, can be preserved in soils for centuries, and have the same size and weight as the soil matter. So SMP redistribution reflects soil solid phase transport. SMP used as tracers of soil erosion (Olson et.al., 2013), but for the first time applied for quantitative assessments of pedoturbations. In Belgorod region of Russia studied vertical distribution of SMP in soils in different types of land use: a) arable chernozem about 160-year plowing, b) arable chernozem 120-year plowing, c) dark-gray forest soil, which didn't plow at least last 150 years. All three sites are located nearby for the same physical-geography conditions. Distribution of SMP studied layer by layer (thickness of the layer 7 cm) from the top to 70 cm depth, in triplicate soil columns in every land use type (totally 90 soil samples). The period of SMP kept in studied soils is about 115 years. Revealed the different depth of SMP penetration (burial) in soil profiles for this period: 49 cm in the soil of 160-year arable land, 58 cm in the soil of 120-year arable land and 68 cm in the virgin forest soil. Different depth of SMP penetration is connected with different activity of pedoturbations, which differs according to the composition of soil flora and fauna, root activity, and animal mixing work. It is supposed that in the arable land single cropping can reduce the thickness of the active layer and as a result the zone of active pedoturbation depth. Based on SMP distribution counted rates of vertical soil solid phase transport, which are equaled: 31 t/ha/year in the soil of 160-year arable land, 28 t/ha/year in the soil of 120-year arable land, 24 t/ha/year in the virgin forest soil. Certainly raised rates of vertical transport in arable land relative to forest is connected with agricultural plowing. Revealed the connection between the period of plowing and rates of vertical soil transport. Also worth noting is that the rates of pedoturbation in virgin forest soils are rather high and only 1,2-1,3 times less than on arable land uses. This research is funded by Russian Foundation for Basic Research - Project 14-05-31141. 1. Olson K.R., Gennadiyev A.N., Zhidkin A.P., Markelov M.V., Golosov V.N., Lang J.M. Use of magnetic tracer and radio-cesium methods to determine past cropland soil erosion amounts and rates // Catena. - 2013. - V. 104 - P. 103-110.

Oral and endotracheal tubes colonization by periodontal bacteria: a case-control ICU study.

PubMed

Porto, A N; Cortelli, S C; Borges, A H; Matos, F Z; Aquino, D R; Miranda, T B; Oliveira Costa, F; Aranha, A F; Cortelli, J R

2016-03-01

Periodontal infection is a possible risk factor for respiratory disorders; however, no studies have assessed the colonization of periodontal pathogens in endotracheal tubes (ET). This case-control study analyzed whether periodontal pathogens are able to colonize ET of dentate and edentulous patients in intensive care units (ICU) and whether oral and ET periodontal pathogen profiles have any correlation between these patients. We selected 18 dentate and 18 edentulous patients from 78 eligible ICU patients. Oral clinical examination including probing depth, clinical attachment level, gingival index , and plaque index was performed by a single examiner, followed by oral and ET sampling and processing by quantitative polymerase chain reaction (total bacterial load, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and Tannerella forsythia). Data were statistically analyzed by Mann-Whitney U, two-way analysis of variance (p < 0.05). Among dentate, there was no correlation between clinical parameters and ET bacterial levels. Both dentate and edentulous patients showed similar ET bacterial levels. Dentate patients showed no correlation between oral and ET bacterial levels, while edentulous patients showed positive correlations between oral and ET levels of A. actinomycetemcomitans, P. gingivalis, and T. forsythia. Periodontal pathogens can colonize ET and the oral cavity of ICU patients. Periodontal pathogen profiles tend to be similar between dentate and edentulous ICU patients. In ICU patients, oral cavity represents a source of ET contamination. Although accompanied by higher oral bacterial levels, teeth do not seem to influence ET bacterial profiles.

Local and profile soil water content monitoring: A comparison of methods in terms of apparent and actual spatial variation

USDA-ARS?s Scientific Manuscript database

Although many soil water sensors are now available, questions about their accuracy, precision, and representativeness still abound. This study examined down-hole (access tube profiling type) and insertion or burial (local) type sensors for their ability to assess soil profile water content (depth of...

Sea surface cooling in the Northern South China Sea observed using Chinese sea-wing underwater glider measurements

NASA Astrophysics Data System (ADS)

Qiu, Chunhua; Mao, Huabin; Yu, Jiancheng; Xie, Qiang; Wu, Jiaxue; Lian, Shumin; Liu, Qinyan

2015-11-01

Based on 26 days of Chinese Sea-wing underwater glider measurements and satellite microwave data, we documented cooling of the upper mixed layer of the ocean in response to changes in the wind in the Northern South China Sea (NSCS) from September 19, 2014, to October 15, 2014. The Sea-wing underwater glider measured 177 profiles of temperature, salinity, and pressure within a 55 km×55 km area, and reached a depth of 1000 m at a temporal resolution of ∼4 h. The study area experienced two cooling events, Cooling I and Cooling II, according to their timing. During Cooling I, water temperature at 1-m depth (T1) decreased by ∼1.0 °C, and the corresponding satellite-derived surface winds increased locally by 4.2 m/s. During Cooling II, T1 decreased sharply by 1.7 °C within a period of 4 days; sea surface winds increased by 7 m/s and covered the entire NSCS. The corresponding mixed layer depth (MLD) deepened sharply from 30 m to 60 m during Cooling II, and remained steady during Cooling I. We estimated temperature tendencies using a ML model. High resolution Sea-wing underwater glider measurements provided an estimation of MLD migration, allowing us to obtain the temporal entrainment rate of cool sub-thermocline water. Quantitative analysis confirmed that the entrainment rate and latent heat flux were the two major components that regulated cooling of the ML, and that the Ekman advection and sensible heat flux were small.

Frictional strength and heat flow of southern San Andreas Fault

NASA Astrophysics Data System (ADS)

Zhu, P. P.

2016-01-01

Frictional strength and heat flow of faults are two related subjects in geophysics and seismology. To date, the investigation on regional frictional strength and heat flow still stays at the stage of qualitative estimation. This paper is concentrated on the regional frictional strength and heat flow of the southern San Andreas Fault (SAF). Based on the in situ borehole measured stress data, using the method of 3D dynamic faulting analysis, we quantitatively determine the regional normal stress, shear stress, and friction coefficient at various seismogenic depths. These new data indicate that the southern SAF is a weak fault within the depth of 15 km. As depth increases, all the regional normal and shear stresses and friction coefficient increase. The former two increase faster than the latter. Regional shear stress increment per kilometer equals 5.75 ± 0.05 MPa/km for depth ≤15 km; regional normal stress increment per kilometer is equal to 25.3 ± 0.1 MPa/km for depth ≤15 km. As depth increases, regional friction coefficient increment per kilometer decreases rapidly from 0.08 to 0.01/km at depths less than ~3 km. As depth increases from ~3 to ~5 km, it is 0.01/km and then from ~5 to 15 km, and it is 0.002/km. Previously, frictional strength could be qualitatively determined by heat flow measurements. It is difficult to obtain the quantitative heat flow data for the SAF because the measured heat flow data exhibit large scatter. However, our quantitative results of frictional strength can be employed to investigate the heat flow in the southern SAF. We use a physical quantity P f to describe heat flow. It represents the dissipative friction heat power per unit area generated by the relative motion of two tectonic plates accommodated by off-fault deformation. P f is called "fault friction heat." On the basis of our determined frictional strength data, utilizing the method of 3D dynamic faulting analysis, we quantitatively determine the regional long-term fault friction heat at various seismogenic depths in the southern SAF. The new data show that as depth increases, regional friction stress increases within the depth of 15 km; its increment per kilometer equals 5.75 ± 0.05 MPa/km. As depth increases, regional long-term fault friction heat increases; its increment per kilometer is equal to 3.68 ± 0.03 mW/m2/km. The values of regional long-term fault friction heat provided by this study are always lower than those from heat flow measurements. The difference between them and the scatter existing in the measured heat flow data are mainly caused by the following processes: (i) heat convection, (ii) heat advection, (iii) stress accumulation, (iv) seismic bursts between short-term lull periods in a long-term period, and (v) influence of seismicity in short-term periods upon long-term slip rate and heat flow. Fault friction heat is a fundamental parameter in research on heat flow.

GC-FID coupled with chemometrics for quantitative and chemical fingerprinting analysis of Alpinia oxyphylla oil.

PubMed

Miao, Qing; Kong, Weijun; Zhao, Xiangsheng; Yang, Shihai; Yang, Meihua

2015-01-01

Analytical methods for quantitative analysis and chemical fingerprinting of volatile oils from Alpinia oxyphylla were established. The volatile oils were prepared by hydrodistillation, and the yields were between 0.82% and 1.33%. The developed gas chromatography-flame ionization detection (GC-FID) method showed good specificity, linearity, reproducibility, stability and recovery, and could be used satisfactorily for quantitative analysis. The results showed that the volatile oils contained 2.31-77.30 μL/mL p-cymene and 12.38-99.34 mg/mL nootkatone. A GC-FID fingerprinting method was established, and the profiles were analyzed using chemometrics. GC-MS was used to identify the principal compounds in the GC-FID profiles. The profiles of almost all the samples were consistent and stable. The harvesting time and source were major factors that affected the profile, while the volatile oil yield and the nootkatone content had minor secondary effects. Copyright © 2014 Elsevier B.V. All rights reserved.

Depth of penetration of a 785nm wavelength laser in food powders

NASA Astrophysics Data System (ADS)

Chao, Kuanglin; Dhakal, Sagar; Qin, Jianwei; Kim, Moon S.; Peng, Yankun; Schmidt, Walter F.

2015-05-01

Raman spectroscopy is a useful, rapid, and non-destructive method for both qualitative and quantitative evaluation of chemical composition. However it is important to measure the depth of penetration of the laser light to ensure that chemical particles at the very bottom of a sample volume is detected by Raman system. The aim of this study was to investigate the penetration depth of a 785nm laser (maximum power output 400mw) into three different food powders, namely dry milk powder, corn starch, and wheat flour. The food powders were layered in 5 depths between 1 and 5 mm overtop a Petri dish packed with melamine. Melamine was used as the subsurface reference material for measurement because melamine exhibits known and identifiable Raman spectral peaks. Analysis of the sample spectra for characteristics of melamine and characteristics of milk, starch and flour allowed determination of the effective penetration depth of the laser light in the samples. Three laser intensities (100, 200 and 300mw) were used to study the effect of laser intensity to depth of penetration. It was observed that 785nm laser source was able to easily penetrate through every point in all three food samples types at 1mm depth. However, the number of points that the laser could penetrate decreased with increasing depth of the food powder. ANOVA test was carried out to study the significant effect of laser intensity to depth of penetration. It was observed that laser intensity significantly influences the depth of penetration. The outcome of this study will be used in our next phase of study to detect different chemical contaminants in food powders and develop quantitative analysis models for detection of chemical contaminants.

Distortion of depth perception in virtual environments using stereoscopic displays: quantitative assessment and corrective measures

NASA Astrophysics Data System (ADS)

Kleiber, Michael; Winkelholz, Carsten

2008-02-01

The aim of the presented research was to quantify the distortion of depth perception when using stereoscopic displays. The visualization parameters of the used virtual reality system such as perspective, haploscopic separation and width of stereoscopic separation were varied. The experiment was designed to measure distortion in depth perception according to allocentric frames of reference. The results of the experiments indicate that some of the parameters have an antithetic effect which allows to compensate the distortion of depth perception for a range of depths. In contrast to earlier research which reported underestimation of depth perception we found that depth was overestimated when using true projection parameters according to the position of the eyes of the user and display geometry.

Glycoproteins Enrichment and LC-MS/MS Glycoproteomics in Central Nervous System Applications.

PubMed

Zhu, Rui; Song, Ehwang; Hussein, Ahmed; Kobeissy, Firas H; Mechref, Yehia

2017-01-01

Proteins and glycoproteins play important biological roles in central nervous systems (CNS). Qualitative and quantitative evaluation of proteins and glycoproteins expression in CNS is critical to reveal the inherent biomolecular mechanism of CNS diseases. This chapter describes proteomic and glycoproteomic approaches based on liquid chromatography/tandem mass spectrometry (LC-MS or LC-MS/MS) for the qualitative and quantitative assessment of proteins and glycoproteins expressed in CNS. Proteins and glycoproteins, extracted by a mass spectrometry friendly surfactant from CNS samples, were subjected to enzymatic (tryptic) digestion and three down-stream analyses: (1) a nano LC system coupled with a high-resolution MS instrument to achieve qualitative proteomic profile, (2) a nano LC system combined with a triple quadrupole MS to quantify identified proteins, and (3) glycoprotein enrichment prior to LC-MS/MS analysis. Enrichment techniques can be applied to improve coverage of low abundant glycopeptides/glycoproteins. An example described in this chapter is hydrophilic interaction liquid chromatographic (HILIC) enrichment to capture glycopeptides, allowing efficient removal of peptides. The combination of three LC-MS/MS-based approaches is capable of the investigation of large-scale proteins and glycoproteins from CNS with an in-depth coverage, thus offering a full view of proteins and glycoproteins changes in CNS.

Compositional and quantitative microtextural characterization of historic paintings by micro-X-ray diffraction and Raman microscopy.

PubMed

Romero-Pastor, Julia; Duran, Adrian; Rodríguez-Navarro, Alejandro Basilio; Van Grieken, René; Cardell, Carolina

2011-11-15

This work shows the benefits of characterizing historic paintings via compositional and microtextural data from micro-X-ray diffraction (μ-XRD) combined with molecular information acquired with Raman microscopy (RM) along depth profiles in paint stratigraphies. The novel approach was applied to identify inorganic and organic components from paintings placed at the 14th century Islamic University-Madrasah Yusufiyya-in Granada (Spain), the only Islamic University still standing from the time of Al-Andalus (Islamic Spain). The use of μ-XRD to obtain quantitative microtextural information of crystalline phases provided by two-dimensional diffraction patterns to recognize pigments nature and manufacture, and decay processes in complex paint cross sections, has not been reported yet. A simple Nasrid (14th century) palette made of gypsum, vermilion, and azurite mixed with glue was identified in polychromed stuccos. Here also a Christian intervention was found via the use of smalt, barite, hematite, Brunswick green and gold; oil was the binding media employed. On mural paintings and wood ceilings, more complex palettes dated to the 19th century were found, made of gypsum, anhydrite, barite, dolomite, calcite, lead white, hematite, minium, synthetic ultramarine blue, and black carbon. The identified binders were glue, egg yolk, and oil.

Levels of Processing: A Reply to Eysenck

ERIC Educational Resources Information Center

Lockhart, Robert S.; Craik, Fergus I. M.

1978-01-01

These comments take up the major issues raised in Eyseck's (1978) critique (AA 528 584) of Craik & Lockhart (1972): the problem of circularity in the definition of "depth", the distinction between qualitative and quantitative differences in encoding, and the relationships between the concepts of depth, strength and elaboration. (Editor/RK)

210Pb and 137Cs as tracers of recent sedimentary processes in two water reservoirs in Cuba.

PubMed

Díaz-Asencio, Misael; Corcho-Alvarado, José Antonio; Cartas-Aguila, Héctor; Pulido-Caraballé, Anabell; Betancourt, Carmen; Smoak, Joseph M; Alvarez-Padilla, Elizabeth; Labaut-Betancourt, Yeny; Alonso-Hernández, Carlos; Seisdedo-Losa, Mabel

2017-10-01

Hanabanilla and Paso Bonito Reservoirs are the main fresh water sources for about half a million inhabitants in central Cuba. Prior to this investigation precise information about the losses of storage capacity was not available. Sedimentation is the dominant process leading to reduction in water storage capacity. We investigated the sedimentation process in both reservoirs by analyzing environmental radionuclides (e.g. 210 Pb, 226 Ra and 137 Cs) in sediment cores. In the shallow Paso Bonito Reservoir (mean depth of 6.5 m; water volume of 8 × 10 6  m 3 ), we estimated a mean mass accumulation rate (MAR) of 0.4 ± 0.1 g cm -2 y -1 based on 210 Pb chronologies. 137 Cs was detected in the sediments, but due to the recent construction of this reservoir (1975), it was not possible to use it to validate the 210 Pb chronologies. The estimated MAR in this reservoir is higher than the typical values reported in similar shallow fresh water reservoirs worldwide. Our results highlight a significant loss of water storage capacity during the past 30 years. In the deeper and larger Hanabanilla Reservoir (mean depth of 15.5 m; water volume of 292 × 10 6  m 3 ), the MAR was investigated in three different sites of the reservoir. The mean MARs based on the 210 Pb chronologies varied between 0.15 and 0.24 g cm -2 y -1 . The MARs calculated based on the 137 Cs profiles further validated these values. We show that the sediment accumulation did not change significantly over the last 50 years. A simple empirical mixing and sedimentation model that assumes 137 Cs in the water originated from both, direct atmospheric fallout and the catchment area, was applied to interpret the 137 Cs depth profiles. The model consistently reproduced the measured 137 Cs profiles in the three cores (R 2  > 0.9). Mean residence times for 137 Cs in the water and in the catchment area of 1 y and 35-50 y, respectively were estimated. The model identified areas where the catchment component was higher, zones with higher erosion in the catchment, and sites where the fallout component was quantitatively recorded in the sediments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Stream bed temperature profiles as indicators of percolation characteristics beneath arroyos in the middle Rio Grande Basin, USA

USGS Publications Warehouse

Constantz, J.; Thomas, C.L.

1997-01-01

Stream bed temperature profiles were monitored continuously during water year 1990 and 1991 (WY90 and 91) in two New Mexico arroyos, similar in their meteorological features and dissimilar in their hydrological features. Stream bed temperature profiles between depths of 30 and 300 cm were examined to determine whether temporal changes in temperature profiles represent accurate indicators of the timing, depth and duration of percolation in each stream bed. These results were compared with stream flow, air temperature, and precipitation records for WY90 and 91, to evaluate the effect of changing surface conditions on temperature profiles. Temperature profiles indicate a persistently high thermal gradient with depth beneath Grantline Arroyo, except during a semi-annual thermal reversal in spring and autumn. This typifies the thermal response of dry sediments with low thermal conductivities. High thermal gradients were disrupted only during infrequent stream flows, followed by rapid re-establishment of high gradients. The stream bed temperature at 300 cm was unresponsive to individual precipitation or stream flow during WY90 and 91. This thermal pattern provides strong evidence that most seepage into Grantline Arroyo failed to percolate at a sufficient rate to reach 300 cm before being returned to the atmosphere. A distinctly different thermal pattern was recorded beneath Tijeras Arroyo. Low thermal gradients between 30 and 300 cm and large diurnal variations in temperature, suggest that stream flow created continuous, advection-dominated heat transport for over 300 days, annually. Beneath Tijeras Arroyo, low thermal gradients were interrupted only briefly during periodic, dry summer conditions. Comparisons of stream flow records for WY90 and 91 with stream bed temperature profiles indicate that independent analysis of thermal patterns provides accurate estimates of the timing, depth and duration of percolation beneath both arroyos. Stream flow loss estimates indicate that seepage rates were 15 times greater for Tijeras Arroyo than for Grantline Arroyo, which supports qualitative conclusions derived from analysis of stream bed temperature responses to surface conditions. ?? 1997 John Wiley & Sons, Ltd.

Seismic Images of the Non-Volcanic Tremor Region around Cholame, California, USA

NASA Astrophysics Data System (ADS)

Gutjahr, S.; Buske, S.

2012-04-01

We reprocessed the industry seismic reflection profile "WSJ-6" which is so far the only seismic profile crossing the San Andreas fault at the non-volcanic tremor region around Cholame. The profile "WSJ-6" runs from Morro Bay eastward to the foothills of the Sierra Nevada and crosses several prominent fault systems, e.g.the Rinconada fault as well as the San Juan fault and the San Andreas fault respectively. By applying the so-called Fresnel Volume migration to the data we produced seismic images of the lower crust and the upper mantle down to depths of approximately 40 km. A 3D tomographic velocity model derived from local earthquake data analysis (Thurber et al., 2006, Lin et al., 2010) was used for slowness analyses and traveltime calculations. The imaging technique was implemented in 3D taking into account the true shot and receiver locations on the crooked profile line. The imaged subsurface volume itself was divided into three separate parts to correctly account for the significant kink in the profile line near the San Andreas fault. The most prominent features in the resulting images are areas of high reflectivity down to 30 km depth in particular in the central western part of the profile corresponding to the Salinian Block between the Rinconada fault and the San Andreas fault. Southwest of the San Andreas fault surface trace a broad zone of high reflectivity is located at depths between 20 km to 35 km. In this region non-volcanic tremor has been located below the seismogenic zone down to 30 km depth. Tremor locations correlate with zones of high reflectivity. This correlation may be an indicator for high pore pressures and fluid content in that region as it is assumed by several authors. The images of the eastern part of the profile show slightly west dipping sedimentary layers in the area of the San Joaquin Valley that are folded and faulted below the Kettleman Hills. Our imaging results will be compared to existing interpretations of the same data.

Uplifting of palsa peatlands by permafrost identified by stable isotope depth profiles

NASA Astrophysics Data System (ADS)

Krüger, Jan Paul; Conen, Franz; Leifeld, Jens; Alewell, Christine

2015-04-01

Natural abundances of stable isotopes are a widespread tool to investigate biogeochemical processes in soils. Palsas are peatlands with an ice core and are common in the discontinuous permafrost region. Elevated parts of palsa peatlands, called hummocks, were uplifted by permafrost out of the influence of groundwater. Here we used the combination of δ15N values and C/N ratio along depth profiles to identify perturbation of these soils. In the years 2009 and 2012 we took in total 14 peat cores from hummocks in two palsa peatlands near Abisko, northern Sweden. Peat samples were analysed in 2 to 4 cm layers for stable isotope ratios and concentrations of C and N. The uplifting of the hummocks by permafrost could be detected by stable isotope depth patterns with the highest δ15N value at permafrost onset, a so-called turning point. Regression analyses indicated in 11 of 14 peat cores increasing δ15N values above and decreasing values below the turning point. This is in accordance with the depth patterns of δ13C values and C/N ratios in these palsa peatlands. Onset of permafrost aggradation identified by the highest δ15N value in the profile and calculated from peat accumulation rates show ages ranging from 80 to 545 years and indicate a mean (±SD) peat age at the turning points of 242 (±66) years for Stordalen and 365 (±53) years for Storflaket peatland. The mean peat ages at turning points are within the period of the Little Ice Age. Furthermore, we tested if the disturbance, in this case the uplifting of the peat material, can be displayed in the relation of δ15N and C/N ratio following the concept of Conen et al. (2013). In unperturbed sites soil δ15N values cover a relatively narrow range at any particular C/N ratio. Changes in N cycling, i.e. N loss or gain, results in the loss or gain of 15N depleted forms. This leads to larger or smaller δ15N values than usual at the observed C/N ratio. All, except one, turning point show a perturbation in the depth profile, with most of the adjacent sampling points also indicating perturbation. This perturbation shows the changes in N cycling, in this case N loss, from these depths due to permafrost aggradation. Deeper parts of some profiles at Stordalen peatland indicate with the same approach an N gain, maybe due to lateral N input to these nutrient poor ecosystems. Most of the uppermost samples in the δ15N depth profiles show no perturbation, potentially due to the adaptation of these soils to the new conditions. Both stable isotope (δ15N and δ13C) depth profiles are suitable to detect palsa uplifting by permafrost. The perturbation of the peat by uplifting as well as the potential nutrient input can be detected by δ15N when related to the C/N ratio. Conen, F., Yakutin, M. V., Carle, N., and Alewell, C. (2013): δ15N natural abundance may directly disclose perturbed soil when related to C:N ratio. Rapid Commun. Mass Spectrom. 27: 1101-1104.

Optoacoustic imaging of tissue blanching during photodynamic therapy of esophageal cancer

NASA Astrophysics Data System (ADS)

Jacques, Steven L.; Viator, John A.; Paltauf, Guenther

2000-05-01

Esophageal cancer patients often present a highly inflamed esophagus at the time of treatment by photodynamic therapy. Immediately after treatment, the inflamed vessels have been shut down and the esophagus presents a white surface. Optoacoustic imaging via an optical fiber device can provide a depth profile of the blanching of inflammation. Such a profile may be an indicator of the depth of treatment achieved by the PDT. Our progress toward developing this diagnostic for use in our clinical PDT treatments of esophageal cancer patients is presented.

Commissioning of a Varian Clinac iX 6 MV photon beam using Monte Carlo simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dirgayussa, I Gde Eka, E-mail: ekadirgayussa@gmail.com; Yani, Sitti; Haryanto, Freddy, E-mail: freddy@fi.itb.ac.id

2015-09-30

Monte Carlo modelling of a linear accelerator is the first and most important step in Monte Carlo dose calculations in radiotherapy. Monte Carlo is considered today to be the most accurate and detailed calculation method in different fields of medical physics. In this research, we developed a photon beam model for Varian Clinac iX 6 MV equipped with MilleniumMLC120 for dose calculation purposes using BEAMnrc/DOSXYZnrc Monte Carlo system based on the underlying EGSnrc particle transport code. Monte Carlo simulation for this commissioning head LINAC divided in two stages are design head Linac model using BEAMnrc, characterize this model using BEAMDPmore » and analyze the difference between simulation and measurement data using DOSXYZnrc. In the first step, to reduce simulation time, a virtual treatment head LINAC was built in two parts (patient-dependent component and patient-independent component). The incident electron energy varied 6.1 MeV, 6.2 MeV and 6.3 MeV, 6.4 MeV, and 6.6 MeV and the FWHM (full width at half maximum) of source is 1 mm. Phase-space file from the virtual model characterized using BEAMDP. The results of MC calculations using DOSXYZnrc in water phantom are percent depth doses (PDDs) and beam profiles at depths 10 cm were compared with measurements. This process has been completed if the dose difference of measured and calculated relative depth-dose data along the central-axis and dose profile at depths 10 cm is ≤ 5%. The effect of beam width on percentage depth doses and beam profiles was studied. Results of the virtual model were in close agreement with measurements in incident energy electron 6.4 MeV. Our results showed that photon beam width could be tuned using large field beam profile at the depth of maximum dose. The Monte Carlo model developed in this study accurately represents the Varian Clinac iX with millennium MLC 120 leaf and can be used for reliable patient dose calculations. In this commissioning process, the good criteria of dose difference in PDD and dose profiles were achieve using incident electron energy 6.4 MeV.« less

What are the associated parameters and temporal coverage?

Atmospheric Science Data Center

2014-12-08

... Extinction Coefficient, Cloud Vertical Profile, Radar-only Liquid Water Content, Radar-only Liquid Ice Content, Vertical Flux Profile, ... ISCCP-D2like Cloud fraction, Effective Pressure, Temperature, optical depth, IWP/LWP, particle size, IR Emissivity in ...

Depth-resolved photo- and ionoluminescence of LiF and Al2O3

NASA Astrophysics Data System (ADS)

Skuratov, V. A.; Kirilkin, N. S.; Kovalev, Yu. S.; Strukova, T. S.; Havanscak, K.

2012-09-01

Microluminescence and laser confocal scanning microscopy techniques have been used to study spatial distribution of F-type color centers in LiF and mechanical stress profiles in Al2O3:Cr single crystals irradiated with 1.2 MeV/amu Ar, Kr, Xe and 3 MeV/amu Kr and Bi ions. It was found that F2 and F3+-center profiles at low ion fluences correlate with ionizing energy loss profiles. With increasing ion fluence, after ion track halo overlapping, the luminescence yield is defined by radiation defects formed in elastic collisions in the end-of-range area. Stress profiles and stress tensor components in ruby crystals across swift heavy ion irradiated layers have been deduced from depth-resolved photo-stimulated spectra using piezospectroscopic effect. Experimental data show that that stresses are compressive in basal plane and tensile in perpendicular direction in all samples irradiated with high energy ions.

Elemental profiling of laser cladded multilayer coatings by laser induced breakdown spectroscopy and energy dispersive X-ray spectroscopy

NASA Astrophysics Data System (ADS)

Lednev, V. N.; Sdvizhenskii, P. A.; Filippov, M. N.; Grishin, M. Ya.; Filichkina, V. A.; Stavertiy, A. Ya.; Tretyakov, R. S.; Bunkin, A. F.; Pershin, S. M.

2017-09-01

Multilayer tungsten carbide wear resistant coatings were analyzed by laser induced breakdown spectroscopy (LIBS) and energy dispersive X-ray (EDX) spectroscopy. Coaxial laser cladding technique was utilized to produce tungsten carbide coating deposited on low alloy steel substrate with additional inconel 625 interlayer. EDX and LIBS techniques were used for elemental profiling of major components (Ni, W, C, Fe, etc.) in the coating. A good correlation between EDX and LIBS data was observed while LIBS provided additional information on light element distribution (carbon). A non-uniform distribution of tungsten carbide grains along coating depth was detected by both LIBS and EDX. In contrast, horizontal elemental profiling showed a uniform tungsten carbide particles distribution. Depth elemental profiling by layer-by-layer LIBS analysis was demonstrated to be an effective method for studying tungsten carbide grains distribution in wear resistant coating without any sample preparation.

DNA Replication Profiling Using Deep Sequencing.

PubMed

Saayman, Xanita; Ramos-Pérez, Cristina; Brown, Grant W

2018-01-01

Profiling of DNA replication during progression through S phase allows a quantitative snap-shot of replication origin usage and DNA replication fork progression. We present a method for using deep sequencing data to profile DNA replication in S. cerevisiae.

Non-interferometric quantitative phase imaging of yeast cells

NASA Astrophysics Data System (ADS)

Poola, Praveen K.; Pandiyan, Vimal Prabhu; John, Renu

2015-12-01

Real-time imaging of live cells is quite difficult without the addition of external contrast agents. Various methods for quantitative phase imaging of living cells have been proposed like digital holographic microscopy and diffraction phase microscopy. In this paper, we report theoretical and experimental results of quantitative phase imaging of live yeast cells with nanometric precision using transport of intensity equations (TIE). We demonstrate nanometric depth sensitivity in imaging live yeast cells using this technique. This technique being noninterferometric, does not need any coherent light sources and images can be captured through a regular bright-field microscope. This real-time imaging technique would deliver the depth or 3-D volume information of cells and is highly promising in real-time digital pathology applications, screening of pathogens and staging of diseases like malaria as it does not need any preprocessing of samples.

Improvement of Depth Profiling into Biotissues Using Micro Electrical Impedance Spectroscopy on a Needle with Selective Passivation

PubMed Central

Yun, Joho; Kim, Hyeon Woo; Lee, Jong-Hyun

2016-01-01

A micro electrical impedance spectroscopy (EIS)-on-a-needle for depth profiling (μEoN-DP) with a selective passivation layer (SPL) on a hypodermic needle was recently fabricated to measure the electrical impedance of biotissues along with the penetration depths. The SPL of the μEoN-DP enabled the sensing interdigitated electrodes (IDEs) to contribute predominantly to the measurement by reducing the relative influence of the connection lines on the sensor output. The discrimination capability of the μEoN-DP was verified using phosphate-buffered saline (PBS) at various concentration levels. The resistance and capacitance extracted through curve fitting were similar to those theoretically estimated based on the mixing ratio of PBS and deionized water; the maximum discrepancies were 8.02% and 1.85%, respectively. Depth profiling was conducted using four-layered porcine tissue to verify the effectiveness of the discrimination capability of the μEoN-DP. The magnitude and phase between dissimilar porcine tissues (fat and muscle) were clearly discriminated at the optimal frequency of 1 MHz. Two kinds of simulations, one with SPL and the other with complete passivation layer (CPL), were performed, and it was verified that the SPL was advantageous over CPL in the discrimination of biotissues in terms of sensor output. PMID:28009845

Improvement of Depth Profiling into Biotissues Using Micro Electrical Impedance Spectroscopy on a Needle with Selective Passivation.

PubMed

Yun, Joho; Kim, Hyeon Woo; Lee, Jong-Hyun

2016-12-21

A micro electrical impedance spectroscopy (EIS)-on-a-needle for depth profiling (μEoN-DP) with a selective passivation layer (SPL) on a hypodermic needle was recently fabricated to measure the electrical impedance of biotissues along with the penetration depths. The SPL of the μEoN-DP enabled the sensing interdigitated electrodes (IDEs) to contribute predominantly to the measurement by reducing the relative influence of the connection lines on the sensor output. The discrimination capability of the μEoN-DP was verified using phosphate-buffered saline (PBS) at various concentration levels. The resistance and capacitance extracted through curve fitting were similar to those theoretically estimated based on the mixing ratio of PBS and deionized water; the maximum discrepancies were 8.02% and 1.85%, respectively. Depth profiling was conducted using four-layered porcine tissue to verify the effectiveness of the discrimination capability of the μEoN-DP. The magnitude and phase between dissimilar porcine tissues (fat and muscle) were clearly discriminated at the optimal frequency of 1 MHz. Two kinds of simulations, one with SPL and the other with complete passivation layer (CPL), were performed, and it was verified that the SPL was advantageous over CPL in the discrimination of biotissues in terms of sensor output.

Changes in dive profiles as an indicator of feeding success in king and Adélie penguins

NASA Astrophysics Data System (ADS)

Bost, C. A.; Handrich, Y.; Butler, P. J.; Fahlman, A.; Halsey, L. G.; Woakes, A. J.; Ropert-Coudert, Y.

2007-02-01

Determining when and how deep avian divers feed remains a challenge despite technical advances. Systems that record oesophageal temperature are able to determine rate of prey ingestion with a high level of accuracy but technical problems still remain to be solved. Here we examine the validity of using changes in depth profiles to infer feeding activity in free-ranging penguins, as more accessible proxies of their feeding success. We used oesophageal temperature loggers with fast temperature sensors, deployed in tandem with time-depth recorders, on king and Adélie penguins. In the king penguin, a high correspondence was found between the number of ingestions recorded per dive and the number of wiggles during the bottom and the ascent part of the dives. In the Adélie penguins, which feed on smaller prey, the number of large temperature drops was linearly related to the number of undulations per dive. The analysis of change in depth profiles from high-resolution time-depth recorders can provide key information to enhance the study of feeding rate and foraging success of these predators. Such potential is especially relevant in the context of using Southern marine top predators to study change in availability of marine resources.

Estimation of the optical errors on the luminescence imaging of water for proton beam

NASA Astrophysics Data System (ADS)

Yabe, Takuya; Komori, Masataka; Horita, Ryo; Toshito, Toshiyuki; Yamamoto, Seiichi

2018-04-01

Although luminescence imaging of water during proton-beam irradiation can be applied to range estimation, the height of the Bragg peak of the luminescence image was smaller than that measured with an ionization chamber. We hypothesized that the reasons of the difference were attributed to the optical phenomena; parallax errors of the optical system and the reflection of the luminescence from the water phantom. We estimated the errors cause by these optical phenomena affecting the luminescence image of water. To estimate the parallax error on the luminescence images, we measured the luminescence images during proton-beam irradiation using a cooled charge-coupled camera by changing the heights of the optical axis of the camera from those of the Bragg peak. When the heights of the optical axis matched to the depths of the Bragg peak, the Bragg peak heights in the depth profiles were the highest. The reflection of the luminescence of water with a black wall phantom was slightly smaller than that with a transparent phantom and changed the shapes of the depth profiles. We conclude that the parallax error significantly affects the heights of the Bragg peak and the reflection of the phantom affects the shapes of depth profiles of the luminescence images of water.

Geoelectrical investigation of oil contaminated soils in former underground fuel base: Borne Sulinowo, NW Poland

NASA Astrophysics Data System (ADS)

Zogala, B.; Dubiel, R.; Zuberek, W. M.; Rusin-Zogala, M.; Steininger, M.

2009-07-01

The survey has been carried out in the area of 0.23 km2 of the former military underground fuel base. The oil derivative products were observed in excavations and the laboratory tests confirmed the occurrence of hydrocarbons (>C12) in soils. The purpose of the survey was to determine the spatial extent of the contamination. The studied area is covered by postglacial sediments: sands, gravels and till. The first water table was observed at a depth of 10-12 m. The detailed electromagnetic measurements with Geonics EM31-MK2 conductivity meter were performed in the whole area of the former fuel base. Obtained results were elaborated statistically and the map of apparent electrical conductivity to a depth of 6 m was created. Many local low conductivity anomalies were observed. The measurements with Geonics EM34-3XL were performed along one A-A' profile and 1D electromagnetic modelling along with this profile was calculated to obtain the electrical conductivity cross-section to a depth of 30 m. Two-dimensional electrical resistivity imaging measurements were carried out along the same profile and the resistivity cross-section to a depth of 20 m was performed. Both conducivity and resistivity cross-sections show anomalous zones. The zones correlate with oil contaminated zones very well.

Differentiating Wheat Genotypes by Bayesian Hierarchical Nonlinear Mixed Modeling of Wheat Root Density.

PubMed

Wasson, Anton P; Chiu, Grace S; Zwart, Alexander B; Binns, Timothy R

2017-01-01

Ensuring future food security for a growing population while climate change and urban sprawl put pressure on agricultural land will require sustainable intensification of current farming practices. For the crop breeder this means producing higher crop yields with less resources due to greater environmental stresses. While easy gains in crop yield have been made mostly "above ground," little progress has been made "below ground"; and yet it is these root system traits that can improve productivity and resistance to drought stress. Wheat pre-breeders use soil coring and core-break counts to phenotype root architecture traits, with data collected on rooting density for hundreds of genotypes in small increments of depth. The measured densities are both large datasets and highly variable even within the same genotype, hence, any rigorous, comprehensive statistical analysis of such complex field data would be technically challenging. Traditionally, most attributes of the field data are therefore discarded in favor of simple numerical summary descriptors which retain much of the high variability exhibited by the raw data. This poses practical challenges: although plant scientists have established that root traits do drive resource capture in crops, traits that are more randomly (rather than genetically) determined are difficult to breed for. In this paper we develop a hierarchical nonlinear mixed modeling approach that utilizes the complete field data for wheat genotypes to fit, under the Bayesian paradigm, an "idealized" relative intensity function for the root distribution over depth. Our approach was used to determine heritability : how much of the variation between field samples was purely random vs. being mechanistically driven by the plant genetics? Based on the genotypic intensity functions, the overall heritability estimate was 0.62 (95% Bayesian confidence interval was 0.52 to 0.71). Despite root count profiles that were statistically very noisy, our approach led to denoised profiles which exhibited rigorously discernible phenotypic traits. Profile-specific traits could be representative of a genotype, and thus, used as a quantitative tool to associate phenotypic traits with specific genotypes. This would allow breeders to select for whole root system distributions appropriate for sustainable intensification, and inform policy for mitigating crop yield risk and food insecurity.

75 FR 13548 - Agency Information Collection Activities; Proposed Collection; Comment Request; Focus Groups...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-22

...-depth understanding of individuals' attitudes, beliefs, motivations, and feelings than do quantitative... and as a qualitative research tool have three major purposes: To obtain information that is useful for developing variables and measures for quantitative studies, To better understand people's attitudes and...

Sediment chronology in San Francisco Bay, California, defined by 210Pb, 234Th, 137Cs, and 239,340Pu

USGS Publications Warehouse

Fuller, C.C.; van Geen, Alexander; Baskaran, M.; Anima, R.

1999-01-01

Sediment chronologies based on radioisotope depth profiles were developed at two sites in the San Francisco Bay estuary to provide a framework for interpreting historical trends in organic compound and metal contaminant inputs. At Richardson Bay near the estuary mouth, sediments are highly mixed by biological and/or physical processes. Excess  penetration ranged from 2 to more than 10 cm at eight coring sites, yielding surface sediment mixing coefficients ranging from 12 to 170 cm2/year. At the site chosen for contaminant analyses, excess  activity was essentially constant over the upper 25 cm of the core with an exponential decrease below to the supported activity between 70 and 90 cm. Both  and  penetrated to 57-cm depth and have broad subsurface maxima between 33 and 41 cm. The best fit of the excess  profile to a steady state sediment accumulation and mixing model yielded an accumulation rate of 0.825 g/cm2/year (0.89 cm/year at sediment surface), surface mixing coefficient of 71 cm2/year, and 33-cm mixed zone with a half-Gaussian depth dependence parameter of 9 cm. Simulations of  and  profiles using these parameters successfully predicted the maximum depth of penetration and the depth of maximum  and  activity. Profiles of successive 1-year hypothetical contaminant pulses were generated using this parameter set to determine the age distribution of sediments at any depth horizon. Because of mixing, sediment particles with a wide range of deposition dates occur at each depth. A sediment chronology was derived from this age distribution to assign the minimum age of deposition and a date of maximum deposition to a depth horizon. The minimum age of sediments in a given horizon is used to estimate the date of first appearance of a contaminant from its maximum depth of penetration. The date of maximum deposition is used to estimate the peak year of input for a contaminant from the depth interval with the highest concentration of that contaminant. Because of the extensive mixing, sediment-bound constituents are rapidly diluted with older material after deposition. In addition, contaminants persist in the mixed zone for many years after deposition. More than 75 years are required to bury 90% of a deposited contaminant below the mixed zone. Reconstructing contaminant inputs is limited to changes occurring on a 20-year time scale. In contrast, mixing is much lower relative to accumulation at a site in San Pablo Bay. Instead, periods of rapid deposition and/or erosion occurred as indicated by frequent sand-silt laminae in the X-radiograph. , , and excess  activity all penetrated to about 120 cm. The distinct maxima in the fallout radionuclides at 105–110 cm yielded overall linear sedimentation rates of 3.9 to 4.1 cm/year, which are comparable to a rate of 4.5±1.5 cm/year derived from the excess  profile.

Biogenic VOC oxidation and organic aerosol formation in an urban nocturnal boundary layer: aircraft vertical profiles in Houston, TX

NASA Astrophysics Data System (ADS)

Brown, S. S.; Dubé, W. P.; Bahreini, R.; Middlebrook, A. M.; Brock, C. A.; Warneke, C.; de Gouw, J. A.; Washenfelder, R. A.; Atlas, E.; Peischl, J.; Ryerson, T. B.; Holloway, J. S.; Schwarz, J. P.; Spackman, R.; Trainer, M.; Parrish, D. D.; Fehshenfeld, F. C.; Ravishankara, A. R.

2013-11-01

Organic compounds are a large component of aerosol mass, but organic aerosol (OA) sources remain poorly characterized. Recent model studies have suggested nighttime oxidation of biogenic hydrocarbons as a potentially large OA source, but analysis of field measurements to test these predictions is sparse. We present nighttime vertical profiles of nitrogen oxides, ozone, VOCs and aerosol composition measured during low approaches of the NOAA P-3 aircraft to airfields in Houston, TX. This region has large emissions of both biogenic hydrocarbons and nitrogen oxides. The latter category serves as a source of the nitrate radical, NO3, a key nighttime oxidant. Biogenic VOCs (BVOC) and urban pollutants were concentrated within the nocturnal boundary layer (NBL), which varied in depth from 100-400 m. Despite concentrated NOx at low altitude, ozone was never titrated to zero, resulting in rapid NO3 radical production rates of 0.2-2.7 ppbv h-1 within the NBL. Monoterpenes and isoprene were frequently present within the NBL and underwent rapid oxidation (up to 1 ppbv h-1), mainly by NO3 and to a lesser extent O3. Concurrent enhancement in organic and nitrate aerosol on several profiles was consistent with primary emissions and with secondary production from nighttime BVOC oxidation, with the latter equivalent to or slightly larger than the former. Some profiles may have been influenced by biomass burning sources as well, making quantitative attribution of organic aerosol sources difficult. Ratios of organic aerosol to CO within the NBL ranged from 14 to 38 μg m-3 OA/ppmv CO. A box model simulation incorporating monoterpene emissions, oxidant formation rates and monoterpene SOA yields suggested overnight OA production of 0.5 to 9 μg m-3.

Novel Proximal Sensing for Monitoring Soil Organic C Stocks and Condition.

PubMed

Viscarra Rossel, Raphael A; Lobsey, Craig R; Sharman, Chris; Flick, Paul; McLachlan, Gordon

2017-05-16

Soil information is needed for environmental monitoring to address current concerns over food, water and energy securities, land degradation, and climate change. We developed the Soil Condition ANalysis System (SCANS) to help address these needs. It integrates an automated soil core sensing system (CSS) with statistical analytics and modeling to characterize soil at fine depth resolutions and across landscapes. The CSS's sensors include a γ-ray attenuation densitometer to measure bulk density, digital cameras to image the measured soil, and a visible-near-infrared (vis-NIR) spectrometer to measure iron oxides and clay mineralogy. The spectra are also modeled to estimate total soil organic carbon (C), particulate, humus, and resistant organic C (POC, HOC, and ROC, respectively), clay content, cation exchange capacity (CEC), pH, volumetric water content, available water capacity (AWC), and their uncertainties. Measurements of bulk density and organic C are combined to estimate C stocks. Kalman smoothing is used to derive complete soil property profiles with propagated uncertainties. The SCANS provides rapid, precise, quantitative, and spatially explicit information about the properties of soil profiles with a level of detail that is difficult to obtain with other approaches. The information gained effectively deepens our understanding of soil and calls attention to the central role soil plays in our environment.

Ultra-sensitive probe of spectral line structure and detection of isotopic oxygen

NASA Astrophysics Data System (ADS)

Garner, Richard M.; Dharamsi, A. N.; Khan, M. Amir

2018-01-01

We discuss a new method of investigating and obtaining quantitative behavior of higher harmonic (> 2f) wavelength modulation spectroscopy (WMS) based on the signal structure. It is shown that the spectral structure of higher harmonic WMS signals, quantified by the number of zero crossings and turnings points, can have increased sensitivity to ambient conditions or line-broadening effects from changes in temperature, pressure, or optical depth. The structure of WMS signals, characterized by combinations of signal magnitude and spectral locations of turning points and zero crossings, provides a unique scale that quantifies lineshape parameters and, thus, useful in optimization of measurements obtained from multi-harmonic WMS signals. We demonstrate this by detecting weaker rotational-vibrational transitions of isotopic atmospheric oxygen (16O18O) in the near-infrared region where higher harmonic WMS signals are more sensitive contrary to their signal-to-noise ratio considerations. The proposed approach based on spectral structure provides the ability to investigate and quantify signals not only at linecenter but also in the wing region of the absorption profile. This formulation is particularly useful in tunable diode laser spectroscopy and ultra-precision laser-based sensors where absorption signal profile carries information of quantities of interest, e.g., concentration, velocity, or gas collision dynamics, etc.