Secondary ion mass spectrometry study of ex situ annealing of epitaxial GaAs grown on Si substrates

NASA Technical Reports Server (NTRS)

Radhakrishnan, G.; Mccullough, O.; Cser, J.; Katz, J.

1988-01-01

Samples of epitaxial GaAs grown on (100) Si substrates using molecular beam epitaxy were annealed at four different temperatures, from 800 to 950 C. Following annealing, the samples were analyzed using secondary ion mass spectrometry. Depth profiles of Ga, As, and Si reveal optimum conditions for annealing, and place a lower limit on a damage threshold for GaAs/Si substrates.

High-throughput and targeted in-depth mass spectrometry-based approaches for biofluid profiling and biomarker discovery.

PubMed

Jimenez, Connie R; Piersma, Sander; Pham, Thang V

2007-12-01

Proteomics aims to create a link between genomic information, biological function and disease through global studies of protein expression, modification and protein-protein interactions. Recent advances in key proteomics tools, such as mass spectrometry (MS) and (bio)informatics, provide tremendous opportunities for biomarker-related clinical applications. In this review, we focus on two complementary MS-based approaches with high potential for the discovery of biomarker patterns and low-abundant candidate biomarkers in biofluids: high-throughput matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy-based methods for peptidome profiling and label-free liquid chromatography-based methods coupled to MS for in-depth profiling of biofluids with a focus on subproteomes, including the low-molecular-weight proteome, carrier-bound proteome and N-linked glycoproteome. The two approaches differ in their aims, throughput and sensitivity. We discuss recent progress and challenges in the analysis of plasma/serum and proximal fluids using these strategies and highlight the potential of liquid chromatography-MS-based proteomics of cancer cell and tumor secretomes for the discovery of candidate blood-based biomarkers. Strategies for candidate validation are also described.

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.

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.

Theoretical study of depth profiling with gamma- and X-ray spectrometry based on measurements of intensity ratios

NASA Astrophysics Data System (ADS)

Bártová, H.; Trojek, T.; Johnová, K.

2017-11-01

This article describes the method for the estimation of depth distribution of radionuclides in a material with gamma-ray spectrometry, and the identification of a layered structure of a material with X-ray fluorescence analysis. This method is based on the measurement of a ratio of two gamma or X-ray lines of a radionuclide or a chemical element, respectively. Its principle consists in different attenuation coefficient for these two lines in a measured material. The main aim of this investigation was to show how the detected ratio of these two lines depends on depth distribution of an analyte and mainly how this ratio depends on density and chemical composition of measured materials. Several different calculation arrangements were made and a lot of Monte Carlo simulation with the code MCNP - Monte Carlo N-Particle (Briesmeister, 2000) was performed to answer these questions. For X-ray spectrometry, the calculated Kα/Kβ diagrams were found to be almost independent upon matrix density and composition. Thanks to this phenomenon it would be possible to draw only one Kα/Kβ diagram for an element whose depth distribution is examined.

Secondary ion mass spectrometry: The application in the analysis of atmospheric particulate matter

DOE PAGES

Huang, Di; Hua, Xin; Xiu, Guang-Li; ...

2017-07-24

Currently, considerable attention has been paid to atmospheric particulate matter (PM) investigation due to its importance in human health and global climate change. Surface characterization, single particle analysis and depth profiling of PM is important for a better understanding of its formation processes and predicting its impact on the environment and human being. Secondary ion mass spectrometry (SIMS) is a surface technique with high surface sensitivity, high spatial resolution chemical imaging and unique depth profiling capabilities. Recent research shows that SIMS has great potential in analyzing both surface and bulk chemical information of PM. In this review, we give amore » brief introduction of SIMS working principle and survey recent applications of SIMS in PM characterization. In particular, analyses from different types of PM sources by various SIMS techniques were discussed concerning their advantages and limitations. Finally, we propose, the future development and needs of SIMS in atmospheric aerosol measurement with a perspective in broader environmental sciences.« less

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

Donald, Scott B.; Siekhaus, Wigbert J.; Nelson, Art J.

X-ray photoelectron spectroscopy in combination with secondary ion mass spectrometry depth profiling were used to investigate the surface and interfacial chemistry of C + ion implanted polycrystalline uranium subsequently oxidized in air for over 10 years at ambient temperature. The original implantation of 33 keV C + ions into U 238 with a dose of 4.3 × 10 17 cm –3 produced a physically and chemically modified surface layer that was characterized and shown to initially prevent air oxidation and corrosion of the uranium after 1 year in air at ambient temperature. The aging of the surface and interfacial layersmore » were examined by using the chemical shift of the U 4f, C 1s, and O 1s photoelectron lines. In addition, valence band spectra were used to explore the electronic structure of the aged carbide surface and interface layer. Moreover, the time-of-flight secondary ion mass spectrometry depth profiling results for the aged sample confirmed an oxidized uranium carbide layer over the carbide layer/U metal interface.« less

Secondary ion mass spectrometry: The application in the analysis of atmospheric particulate matter

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

Huang, Di; Hua, Xin; Xiu, Guang-Li

Currently, considerable attention has been paid to atmospheric particulate matter (PM) investigation due to its importance in human health and global climate change. Surface characterization, single particle analysis and depth profiling of PM is important for a better understanding of its formation processes and predicting its impact on the environment and human being. Secondary ion mass spectrometry (SIMS) is a surface technique with high surface sensitivity, high spatial resolution chemical imaging and unique depth profiling capabilities. Recent research shows that SIMS has great potential in analyzing both surface and bulk chemical information of PM. In this review, we give amore » brief introduction of SIMS working principle and survey recent applications of SIMS in PM characterization. In particular, analyses from different types of PM sources by various SIMS techniques were discussed concerning their advantages and limitations. Finally, we propose, the future development and needs of SIMS in atmospheric aerosol measurement with a perspective in broader environmental sciences.« less

Deuterium depth profile quantification in a ASDEX Upgrade divertor tile using secondary ion mass spectrometry

NASA Astrophysics Data System (ADS)

Ghezzi, F.; Caniello, R.; Giubertoni, D.; Bersani, M.; Hakola, A.; Mayer, M.; Rohde, V.; Anderle, M.; ASDEX Upgrade Team

2014-10-01

We present the results of a study where secondary ion mass spectrometry (SIMS) has been used to obtain depth profiles of deuterium concentration on plasma facing components of the first wall of the ASDEX Upgrade tokamak. The method uses primary and secondary standards to quantify the amount of deuterium retained. Samples of bulk graphite coated with tungsten or tantalum-doped tungsten are independently profiled with three different SIMS instruments. Their deuterium concentration profiles are compared showing good agreement. In order to assess the validity of the method, the integrated deuterium concentrations in the coatings given by one of the SIMS devices is compared with nuclear reaction analysis (NRA) data. Although in the case of tungsten the agreement between NRA and SIMS is satisfactory, for tantalum-doped tungsten samples the discrepancy is significant because of matrix effect induced by tantalum and differently eroded surface (W + Ta always exposed to plasma, W largely shadowed). A further comparison where the SIMS deuterium concentration is obtained by calibrating the measurements against NRA values is also presented. For the tungsten samples, where no Ta induced matrix effects are present, the two methods are almost equivalent.The results presented show the potential of the method provided that the standards used for the calibration reproduce faithfully the matrix nature of the samples.

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

Nanoscale Investigation of the Impact of pH and Orthophosphate on the Corrosion of Copper Surfaces in Water

EPA Science Inventory

Advanced surface characterization techniques were used to systematically investigate the passivation of copper during corrosion in water as impacted by pH and orthophosphate. Atomic force microscopy, depth profiling with time-of-flight secondary ion mass spectrometry and X-ray d...

Kim Magrini | NREL

Science.gov Websites

Developing char-based soil amendments Soil carbon and char analysis via molecular beam mass spectrometry depth profiling, Fourier transform infrared [FTIR]) Rapid soil carbon analysis using analytical DRIFTS, 13C NMR, and py-MBMS to Characterize the Effects of Soil Science Oxidation Assays on Soil Organic

Quantitative secondary ion mass spectrometric analysis of secondary ion polarity in GaN films implanted with oxygen

NASA Astrophysics Data System (ADS)

Hashiguchi, Minako; Sakaguchi, Isao; Adachi, Yutaka; Ohashi, Naoki

2016-10-01

Quantitative analyses of N and O ions in GaN thin films implanted with oxygen ions (16O+) were conducted by secondary ion mass spectrometry (SIMS). Positive (CsM+) and negative secondary ions extracted by Cs+ primary ion bombardment were analyzed for oxygen quantitative analysis. The oxygen depth profiles were obtained using two types of primary ion beams: a Gaussian-type beam and a broad spot beam. The oxygen peak concentrations in GaN samples were from 3.2 × 1019 to 7.0 × 1021 atoms/cm3. The depth profiles show equivalent depth resolutions in the two analyses. The intensity of negative oxygen ions was approximately two orders of magnitude higher than that of positive ions. In contrast, the O/N intensity ratio measured using CsM+ molecular ions was close to the calculated atomic density ratio, indicating that the SIMS depth profiling using CsM+ ions is much more effective for the measurements of O and N ions in heavy O-implanted GaN than that using negative ions.

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

XPS and SIMS study of the surface and interface of aged C + implanted uranium

DOE PAGES

Donald, Scott B.; Siekhaus, Wigbert J.; Nelson, Art J.

2016-09-08

X-ray photoelectron spectroscopy in combination with secondary ion mass spectrometry depth profiling were used to investigate the surface and interfacial chemistry of C + ion implanted polycrystalline uranium subsequently oxidized in air for over 10 years at ambient temperature. The original implantation of 33 keV C + ions into U 238 with a dose of 4.3 × 10 17 cm –3 produced a physically and chemically modified surface layer that was characterized and shown to initially prevent air oxidation and corrosion of the uranium after 1 year in air at ambient temperature. The aging of the surface and interfacial layersmore » were examined by using the chemical shift of the U 4f, C 1s, and O 1s photoelectron lines. In addition, valence band spectra were used to explore the electronic structure of the aged carbide surface and interface layer. Moreover, the time-of-flight secondary ion mass spectrometry depth profiling results for the aged sample confirmed an oxidized uranium carbide layer over the carbide layer/U metal interface.« less

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.

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.

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.

Studies on cosmogenic nuclides in meteorites with regard to an application as potential depth indicators

NASA Technical Reports Server (NTRS)

Sarafin, R.; Herpers, U.; Englert, P.; Wieler, R.; Signer, P.; Bonani, G.; Hofmann, H. J.; Morenzoni, E.; Nessi, M.; Suter, M.

1986-01-01

Measurements of stable and radioactive spallation products in meteorites allow to investigate their histories, especially with respect to the exposure to galactic cosmic ray particles and the pre-atmospheric size of the object. While the concentrations of spallation products lead to the determination of exposure and terrestrial ages, production rate ratios are characteristic for the location of the sample in the meteorite. So, one of the aims of this investigation on meteorites is to obtain depth indicators from suitable pairs of cosmogenic nuclides. Because of the different depth profiles for nuclide productions it is necessary to determine the concentrations of a larger number of spallation products in aliquots of a single small sample. Such same sample measurements of Be-10 and light noble gases were performed on 15 ordinary chondrites (7 H- and 8 L-chondrites. Be-10 was determined by accelerator mass spectrometry and the noble gases were measured by static mass spectrometry. The results are summarized and discussed.

Suppression of self-organized surface nanopatterning on GaSb/InAs multilayers induced by low energy oxygen ion bombardment by using simultaneously sample rotation and oxygen flooding

NASA Astrophysics Data System (ADS)

Beainy, Georges; Cerba, Tiphaine; Bassani, Franck; Martin, Mickaël; Baron, Thierry; Barnes, Jean-Paul

2018-05-01

Time of flight secondary ion mass spectrometry (ToF-SIMS) is a well-adapted analytical method for the chemical characterization of concentration profiles in layered or multilayered materials. However, under ion beam bombardment, initially smooth material surface becomes morphologically unstable. This leads to abnormal secondary ion yields and depth profile distortions. In this contribution, we explore the surface topography and roughening evolution induced by O2+ ion bombardment on GaSb/InAs multilayers. We demonstrate the formation of nanodots and ripples patterning according to the ion beam energy. Since the latter are undesirable for ToF-SIMS analysis, we managed to totally stop their growth by using simultaneously sample rotation and oxygen flooding. This unprecedented coupling between these two latter mechanisms leads to a significant enhancement in depth profiles resolution.

New Cs sputter ion source with polyatomic ion beams for secondary ion mass spectrometry applications

NASA Astrophysics Data System (ADS)

Belykh, S. F.; Palitsin, V. V.; Veryovkin, I. V.; Kovarsky, A. P.; Chang, R. J. H.; Adriaens, A.; Dowsett, M. G.; Adams, F.

2007-08-01

A simple design for a cesium sputter ion source compatible with vacuum and ion-optical systems as well as with electronics of the commercially available Cameca IMS-4f instrument is reported. This ion source has been tested with the cluster primary ions of Sin- and Cun-. Our experiments with surface characterization and depth profiling conducted to date demonstrate improvements of the analytical capabilities of the secondary ion mass spectrometry instrument due to the nonadditive enhancement of secondary ion emission and shorter ion ranges of polyatomic projectiles compared to atomic ones with the same impact energy.

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.

Depth profiling of inks in authentic and counterfeit banknotes by electrospray laser desorption ionization/mass spectrometry.

PubMed

Kao, Yi-Ying; Cheng, Sy-Chyi; Cheng, Chu-Nian; Shiea, Jentaie

2016-01-01

Electrospray laser desorption ionization is an ambient ionization technique that generates neutrals via laser desorption and ionizes those neutrals in an electrospray plume and was utilized to characterize inks in different layers of copy paper and banknotes of various currencies. Depth profiling of inks was performed on overlapping color bands on copy paper by repeatedly scanning the line with a pulsed laser beam operated at a fixed energy. The molecules in the ink on a banknote were desorbed by irradiating the banknote surface with a laser beam operated at different energies, with results indicating that different ions were detected at different depths. The analysis of authentic $US100, $100 RMB and $1000 NTD banknotes indicated that ions detected in 'color-shifting' and 'typography' regions were significantly different. Additionally, the abundances of some ions dramatically changed with the depth of the aforementioned regions. This approach was used to distinguish authentic $1000 NTD banknotes from counterfeits. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

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

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

Xue, Haizhou; Zhang, Yanwen; Zhu, Zihua

Single crystalline 6H-SiC samples were irradiated at 150 K with 2 MeV Pt ions. The local volume swelling was determined by electron energy loss spectroscopy (EELS), and a nearly sigmoidal dependence on irradiation dose is observed. The disorder profiles and ion distribution were determined by Rutherford backscattering spectrometry (RBS), transmission electron microscopy, and secondary ion mass spectrometry. Since the volume swelling reaches 12% over the damage region at high ion fluence, the effect of lattice expansion is considered and corrected for in the analysis of RBS spectra to obtain depth profiles. Projectile and damage profiles are estimated by SRIM (Stoppingmore » and Range of Ions in Matter).When compared with the measured profiles, the SRIM code predictions of ion distribution and the damage profiles are underestimated due to significant overestimation of the electronic stopping power for the slow heavy Pt ions. By utilizing the reciprocity method, which is based on the invariance of the inelastic energy loss in ion-solid collisions against interchange of projectile and target atom, a much lower electronic stopping power is deduced. A simple approach, based on reducing the density of SiC target in SRIM simulation, is proposed to compensate the overestimated SRIM electronic stopping power values, which results in improved agreement between predicted and measured damage profiles and ion ranges.« less

Simulation of RBS spectra with known 3D sample surface roughness

NASA Astrophysics Data System (ADS)

Malinský, Petr; Siegel, Jakub; Hnatowicz, Vladimir; Macková, Anna; Švorčík, Václav

2017-09-01

The Rutherford Backscattering Spectrometry (RBS) is a technique for elemental depth profiling with a nanometer depth resolution. Possible surface roughness of analysed samples can deteriorate the RBS spectra and makes their interpretation more difficult and ambiguous. This work describes the simulation of RBS spectra which takes into account real 3D morphology of the sample surface obtained by AFM method. The RBS spectrum is calculated as a sum of the many particular spectra obtained for randomly chosen particle trajectories over sample 3D landscape. The spectra, simulated for different ion beam incidence angles, are compared to the experimental ones measured with 2.0 MeV 4He+ ions. The main aim of this work is to obtain more definite information on how a particular surface morphology and measuring geometry affects the RBS spectra and derived elemental depth profiles. A reasonable agreement between the measured and simulated spectra was found and the results indicate that the AFM data on the sample surface can be used for the simulation of RBS spectra.

{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

Development of an ion time-of-flight spectrometer for neutron depth profiling

NASA Astrophysics Data System (ADS)

Cetiner, Mustafa Sacit

Ion time-of-flight spectrometry techniques are investigated for applicability to neutron depth profiling. Time-of-flight techniques are used extensively in a wide range of scientific and technological applications including energy and mass spectroscopy. Neutron depth profiling is a near-surface analysis technique that gives concentration distribution versus depth for certain technologically important light elements. The technique uses thermal or sub-thermal neutrons to initiate (n, p) or (n, alpha) reactions. Concentration versus depth distribution is obtained by the transformation of the energy spectrum into depth distribution by using stopping force tables of the projectiles in the substrate, and by converting the number of counts into concentration using a standard sample of known dose value. Conventionally, neutron depth profiling measurements are based on charged particle spectrometry, which employs semiconductor detectors such as a surface barrier detector (SBD) and the associated electronics. Measurements with semiconductor detectors are affected by a number of broadening mechanisms, which result from the interactions between the projectile ion and the detector material as well as fluctuations in the signal generation process. These are inherent features of the detection mechanism that involve the semiconductor detectors and cannot be avoided. Ion time-of-flight spectrometry offers highly precise measurement capabilities, particularly for slow particles. For high-energy low-mass particles, measurement resolution tends to degrade with all other parameters fixed. The threshold for more precise ion energy measurements with respect to conventional techniques, such as direct energy measurement by a surface barrier detector, is directly related to the design and operating parameters of the device. Time-of-flight spectrometry involves correlated detection of two signals by a coincidence unit. In ion time-of-flight spectroscopy, the ion generates the primary input signal. Without loss of generality, the secondary signal is obtained by the passage of the ion through a thin carbon foil, which produces ion-induced secondary electron emission (IISEE). The time-of-flight spectrometer physically acts as an ion/electron separator. The electrons that enter the active volume of the spectrometer are transported onto the microchannel plate detector to generate the secondary signal. The electron optics can be designed in variety of ways depending on the nature of the measurement and physical requirements. Two ion time-of-flight spectrometer designs are introduced: the parallel electric and magnetic (PEM) field spectrometer and the cross electric and magnetic (CEM) field spectrometer. The CEM field spectrometers have been extensively used in a wide range of applications where precise mass differentiation is required. The PEM field spectrometers have lately found interest in mass spectroscopy applications. The application of the PEM field spectrometer for energy measurements is a novel approach. The PEM field spectrometer used in the measurements employs axial electric and magnetic fields along the nominal direction of the incident ion. The secondary electrons are created by a thin carbon foil on the entrance disk and transported on the microchannel plate that faces the carbon foil. The initial angular distribution of the secondary electrons has virtually no effect on the transport time of the secondary electrons from the surface of the carbon foil to the electron microchannel plate detector. Therefore, the PEM field spectrometer can offer high-resolution energy measurement for relatively lower electric fields. The measurements with the PEM field spectrometer were made with the Tandem linear particle accelerator at the IBM T. J. Watson Research Center at Yorktown Heights, NY. The CEM field spectrometer developed for the thesis employs axial electric field along the nominal direction of the ion, and has perpendicular magnetic field. As the electric field accelerates and then decelerates the emitted secondary electron beam, the magnetic field steers the beam away from the source and focuses it onto the electron microchannel plate detector. The initial momentum distribution of the electron beam is observed to have profound effect on the electron transport time. Hence, the CEM field spectrometer measurements suffer more from spectral broadening at similar operating parameters. The CEM field spectrometer measurements were obtained with a 210Po alpha source at the Penn State Radiation Science and Engineering Center, University Park, PA. Although the PEM field spectrometer suffers less from electron transport time dispersion, the CEM field spectrometer is more suited for application to neutron depth profiling. The multiple small-diameter apertures used in the PEM field configuration considerably reduces the geometric efficiency of the spectrometer. Most of the neutron depth profiling measurements, where isotropic emission of charged particles is observed, have relatively low count rates; hence, high detection efficiency is essential.

Characterisation of nickel silicide thin films by spectroscopy and microscopy techniques.

PubMed

Bhaskaran, M; Sriram, S; Holland, A S; Evans, P J

2009-01-01

This article discusses the formation and detailed materials characterisation of nickel silicide thin films. Nickel silicide thin films have been formed by thermally reacting electron beam evaporated thin films of nickel with silicon. The nickel silicide thin films have been analysed using Auger electron spectroscopy (AES) depth profiles, secondary ion mass spectrometry (SIMS), and Rutherford backscattering spectroscopy (RBS). The AES depth profile shows a uniform NiSi film, with a composition of 49-50% nickel and 51-50% silicon. No oxygen contamination either on the surface or at the silicide-silicon interface was observed. The SIMS depth profile confirms the existence of a uniform film, with no traces of oxygen contamination. RBS results indicate a nickel silicide layer of 114 nm, with the simulated spectra in close agreement with the experimental data. Atomic force microscopy and transmission electron microscopy have been used to study the morphology of the nickel silicide thin films. The average grain size and average surface roughness of these films was found to be 30-50 and 0.67 nm, respectively. The film surface has also been studied using Kikuchi patterns obtained by electron backscatter detection.

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.

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.

Mass spectrometry techniques in the survey of steroid metabolites as potential disease biomarkers: a review.

PubMed

Gouveia, Maria João; Brindley, Paul J; Santos, Lúcio Lara; Correia da Costa, José Manuel; Gomes, Paula; Vale, Nuno

2013-09-01

Mass spectrometric approaches have been fundamental to the identification of metabolites associated with steroid hormones, yet this topic has not been reviewed in depth in recent years. To this end, and given the increasing relevance of liquid chromatography-mass spectrometry (LC-MS) studies on steroid hormones and their metabolites, the present review addresses this subject. This review provides a timely summary of the use of various mass spectrometry-based analytical techniques during the evaluation of steroidal biomarkers in a range of human disease settings. The sensitivity and specificity of these technologies are clearly providing valuable new insights into breast cancer and cardiovascular disease. We aim to contribute to an enhanced understanding of steroid metabolism and how it can be profiled by LC-MS techniques. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

Two-dimensional and three-dimensional dynamic imaging of live biofilms in a microchannel by time-of-flight secondary ion mass spectrometry

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

Hua, Xin; Marshall, Matthew J.; Xiong, Yijia

2015-05-01

A vacuum compatible microfluidic reactor, SALVI (System for Analysis at the Liquid Vacuum Interface) was employed for in situ chemical imaging of live biofilms using time-of-flight secondary ion mass spectrometry (ToF-SIMS). Depth profiling by sputtering materials in sequential layers resulted in live biofilm spatial chemical mapping. 2D images were reconstructed to report the first 3D images of hydrated biofilm elucidating spatial and chemical heterogeneity. 2D image principal component analysis (PCA) was conducted among biofilms at different locations in the microchannel. Our approach directly visualized spatial and chemical heterogeneity within the living biofilm by dynamic liquid ToF-SIMS.

Investigation of Damage with Cluster Ion Beam Irradiation Using HR-RBS

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

Seki, Toshio; Aoki, Takaaki; Matsuo, Jiro

2008-11-03

Cluster ion beam can process targets with shallow damage because of the very low irradiation energy per atom. However, it is needed to investigate the damage with cluster ion beam irradiation, because recent applications demand process targets with ultra low damage. The shallow damage can be investigated from depth profiles of specific species before and after ion irradiation. They can be measured with secondary ion mass spectrometry (SIMS) and Rutherford backscattering spectroscopy (RBS). High resolution Rutherford backscattering spectroscopy (HR-RBS) is a non destructive measurement method and depth profiles can be measured with nano-resolution. The cluster ion beam mixing of thinmore » Ni layer in carbon targets can be investigated with HR-RBS. The mixing depth with cluster ion irradiation at 10 keV was about 10 nm. The mixing depth with cluster ion irradiation at 1 keV and 5 keV were less than 1 nm and 5 nm, respectively. The number of displaced Ni atoms with cluster ion irradiation was very larger than that with monomer ion irradiation of same energy. This result shows that violent mixing occurs with single cluster impact.« less

Study of the Au-Cr bilayer system using X-ray reflectivity, GDOES, and ToF-SIMS

DOE PAGES

Jonnard, Philippe; Modi, Mohammed H.; Le Guen, Karine; ...

2018-04-17

Here, we study a Au (25 nm)/Cr (10 nm) bilayer system as a model of mirror for the soft X–ray energy range. The Au and Cr thin films are a few nanometer thick and are deposited on a float glass substrate. The sample is characterized by using 3 complementary techniques: soft X–ray reflectivity, glow discharge optical emission spectrometry (GDOES), and time–of–flight secondary ion mass spectroscopy (ToF–SIMS). Soft X–ray reflectivity provides information about the thickness and roughness of the different layers, while GDOES is used to obtain the elemental depth profile of the stack and ToF–SIMS to obtain the elemental andmore » chemical depth profiles. GDOES and ToF–SIMS have both a nanometer depth resolution. A coherent description of the bilayer stack is obtained through the combination of these techniques. It consists in 5 layers namely a surface contamination layer, a principal gold layer, a Au–Cr mixed layer, a Cr layer, and another contamination layer at the top of the substrate.« less

Study of the Au-Cr bilayer system using X-ray reflectivity, GDOES, and ToF-SIMS

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

Jonnard, Philippe; Modi, Mohammed H.; Le Guen, Karine

Here, we study a Au (25 nm)/Cr (10 nm) bilayer system as a model of mirror for the soft X–ray energy range. The Au and Cr thin films are a few nanometer thick and are deposited on a float glass substrate. The sample is characterized by using 3 complementary techniques: soft X–ray reflectivity, glow discharge optical emission spectrometry (GDOES), and time–of–flight secondary ion mass spectroscopy (ToF–SIMS). Soft X–ray reflectivity provides information about the thickness and roughness of the different layers, while GDOES is used to obtain the elemental depth profile of the stack and ToF–SIMS to obtain the elemental andmore » chemical depth profiles. GDOES and ToF–SIMS have both a nanometer depth resolution. A coherent description of the bilayer stack is obtained through the combination of these techniques. It consists in 5 layers namely a surface contamination layer, a principal gold layer, a Au–Cr mixed layer, a Cr layer, and another contamination layer at the top of the substrate.« less

SIMS of Organic Materials—Interface Location in Argon Gas Cluster Depth Profiles Using Negative Secondary Ions

NASA Astrophysics Data System (ADS)

Havelund, R.; Seah, M. P.; Tiddia, M.; Gilmore, I. S.

2018-02-01

A procedure has been established to define the interface position in depth profiles accurately when using secondary ion mass spectrometry and the negative secondary ions. The interface position varies strongly with the extent of the matrix effect and so depends on the secondary ion measured. Intensity profiles have been measured at both fluorenylmethyloxycarbonyl-uc(l)-pentafluorophenylalanine (FMOC) to Irganox 1010 and Irganox 1010 to FMOC interfaces for many secondary ions. These profiles show separations of the two interfaces that vary over some 10 nm depending on the secondary ion selected. The shapes of these profiles are strongly governed by matrix effects, slightly weakened by a long wavelength roughening. The matrix effects are separately measured using homogeneous, known mixtures of these two materials. Removal of the matrix and roughening effects give consistent compositional profiles for all ions that are described by an integrated exponentially modified Gaussian (EMG) profile. Use of a simple integrated Gaussian may lead to significant errors. The average interface positions in the compositional profiles are determined to standard uncertainties of 0.19 and 0.14 nm, respectively, using the integrated EMG function. Alternatively, and more simply, it is shown that interface positions and profiles may be deduced from data for several secondary ions with measured matrix factors by simply extrapolating the result to Ξ = 0. Care must be taken in quoting interface resolutions since those measured for predominantly Gaussian interfaces with Ξ above or below zero, without correction, appear significantly better than the true resolution.

Mass spectrometry-based proteomics: from cancer biology to protein biomarkers, drug targets, and clinical applications.

PubMed

Jimenez, Connie R; Verheul, Henk M W

2014-01-01

Proteomics is optimally suited to bridge the gap between genomic information on the one hand and biologic functions and disease phenotypes at the other, since it studies the expression and/or post-translational modification (especially phosphorylation) of proteins--the major cellular players bringing about cellular functions--at a global level in biologic specimens. Mass spectrometry technology and (bio)informatic tools have matured to the extent that they can provide high-throughput, comprehensive, and quantitative protein inventories of cells, tissues, and biofluids in clinical samples at low level. In this article, we focus on next-generation proteomics employing nanoliquid chromatography coupled to high-resolution tandem mass spectrometry for in-depth (phospho)protein profiling of tumor tissues and (proximal) biofluids, with a focus on studies employing clinical material. In addition, we highlight emerging proteogenomic approaches for the identification of tumor-specific protein variants, and targeted multiplex mass spectrometry strategies for large-scale biomarker validation. Below we provide a discussion of recent progress, some research highlights, and challenges that remain for clinical translation of proteomic discoveries.

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.

Quantitative analysis of Si1-xGex alloy films by SIMS and XPS depth profiling using a reference material

NASA Astrophysics Data System (ADS)

Oh, Won Jin; Jang, Jong Shik; Lee, Youn Seoung; Kim, Ansoon; Kim, Kyung Joong

2018-02-01

Quantitative analysis methods of multi-element alloy films were compared. The atomic fractions of Si1-xGex alloy films were measured by depth profiling analysis with secondary ion mass spectrometry (SIMS) and X-ray Photoelectron Spectroscopy (XPS). Intensity-to-composition conversion factor (ICF) was used as a mean to convert the intensities to compositions instead of the relative sensitivity factors. The ICFs were determined from a reference Si1-xGex alloy film by the conventional method, average intensity (AI) method and total number counting (TNC) method. In the case of SIMS, although the atomic fractions measured by oxygen ion beams were not quantitative due to severe matrix effect, the results by cesium ion beam were very quantitative. The quantitative analysis results by SIMS using MCs2+ ions are comparable to the results by XPS. In the case of XPS, the measurement uncertainty was highly improved by the AI method and TNC method.

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.

Characterization and application of automated in-vacuum PIXE/EBS system for direct analysis of chloride and sulfate ions attack in cementitious materials

NASA Astrophysics Data System (ADS)

Rihawy, M. S.; Alwazzeh, M.; Abbas, K.

2018-01-01

Ion beam analysis (IBA) techniques (Particle Induced X-ray Emission, PIXE and Elastic Backscattering Spectrometry, EBS), were applied to investigate chloride and sulfate ions diffusion into laboratory prepared mortar samples. Development and characterization of an automated in-vacuum macro PIXE/EBS system is thoroughly discussed. Depth profile information of both chloride and sulfate ions in laboratory prepared mortar samples, after immersion in sea water for nine months, was rapidly and easily obtained at fairly low cost and with standardless analysis, demonstrating the value of the application of IBA to elemental depth profiling in cementitious materials. Chloride and sulfate depth profiles were obtained for two sets of mortar samples, one prepared with different water/cement (W/C) ratios and the other with different sand/cement (S/C) ratios. Results showed higher diffusion rates of both chloride and sulfate ions when both ratios are increased. Additionally, the W/C ratio has a stronger influence in both sulfate and chloride penetration than the S/C ratio, and chloride ions penetrate faster than sulfates. Advantages and limitations of applying IBA techniques in this investigation are discussed. The comparison between PIXE and other X-ray based analytical techniques, namely X-ray fluorescence (XRF) and energy and wavelength dispersive X-rays (EDX/WDX), as well as other traditional wet chemical methods is reviewed, and industrial applications are discussed.

Effects of oxygen-inserted layers on diffusion of boron, phosphorus, and arsenic in silicon for ultra-shallow junction formation

NASA Astrophysics Data System (ADS)

Zhang, X.; Connelly, D.; Takeuchi, H.; Hytha, M.; Mears, R. J.; Rubin, L. M.; Liu, T.-J. K.

2018-03-01

The effects of oxygen-inserted (OI) layers on the diffusion of boron (B), phosphorus (P), and arsenic (As) in silicon (Si) are investigated, for ultra-shallow junction formation by high-dose ion implantation followed by rapid thermal annealing. The projected range (Rp) of the implanted dopants is shallower than the depth of the OI layers. Secondary ion mass spectrometry is used to compare the dopant profiles in silicon samples that have OI layers against the dopant profiles in control samples that do not have OI layers. Diffusion is found to be substantially retarded by the OI layers for B and P, and less for As, providing shallower junction depth. The experimental results suggest that the OI layers serve to block the diffusion of Si self-interstitials and thereby effectively reduce interstitial-aided diffusion beyond the depth of the OI layers. The OI layers also help to retain more dopants within the Si, which technology computer-aided design simulations indicate to be beneficial for achieving shallower junctions with lower sheet resistance to enable further miniaturization of planar metal-oxide-semiconductor field-effect transistors for improved integrated-circuit performance and cost per function.

Development of a quadrupole-based Secondary-Ion Mass Spectrometry (SIMS) system at Lewis Research Center

NASA Technical Reports Server (NTRS)

Vargas-Aburto, Carlos; Aron, Paul R.; Liff, Dale R.

1990-01-01

The design, construction, and initial use of an ion microprobe to carry out secondary ion mass spectrometry (SIMS) of solid samples is reported. The system is composed of a differentially pumped custom-made UHV (Ultra High Vacuum) chamber, a quadrupole mass spectrometer and a telefocus A-DIDA ion gun with the capability of producing beams of Cesium, as well as inert and reactive gases. The computer control and acquisition of the data were designed and implemented using a personal computer with plug-in boards, and external circuitry built as required to suit the system needs. The software is being developed by using a FORTH-like language. Initial tests aimed at characterizing the system, as well as preliminary surface and depth-profiling studies are presently underway.

Evidence of adipocere in a burial pit from the foot and mouth epidemic of 1967 using gas chromatography-mass spectrometry.

PubMed

Vane, Christopher H; Trick, Julian K

2005-11-10

Gas-chromatography-mass spectrometry was used to characterise the fatty acids from soils and associated tissues excavated from a 1967 Foot and Mouth burial pit. Subcutaneous fats were mainly comprised of 55-75% palmitic acid, 17-22% stearic acid and 3-16% oleic acid as well as 5-7% myristic acid. The distribution of fatty acids confirmed that the tissues were decayed to adipocere. The loss of oleic acid to <3% in two of the decayed fats suggested advanced stages of adipocere. However, adipocere formation was limited in a third tissue sample recovered from greater depth. Inductively coupled plasma atomic emission spectrometry of the pore waters revealed a decrease in Ca concentration and concurrent increase in Na concentrations this suggested that insoluble calcium salt had formed through displacement of sodium. The use of fatty acid profiles from soils and soil interstitial pore waters provide complementary evidence of adipocere formation in foot and mouth burial pits.

Uranium passivation by C + implantation: A photoemission and secondary ion mass spectrometry study

NASA Astrophysics Data System (ADS)

Nelson, A. J.; Felter, T. E.; Wu, K. J.; Evans, C.; Ferreira, J. L.; Siekhaus, W. J.; McLean, W.

2006-03-01

Implantation of 33 keV C + ions into polycrystalline U 238 with a dose of 4.3 × 10 17 cm -2 produces a physically and chemically modified surface layer that prevents further air oxidation and corrosion. X-ray photoelectron spectroscopy and secondary ion mass spectrometry were used to investigate the surface chemistry and electronic structure of this C + ion implanted polycrystalline uranium and a non-implanted region of the sample, both regions exposed to air for more than a year. In addition, scanning electron microscopy was used to examine and compare the surface morphology of the two regions. The U 4f, O 1s and C 1s core-level and valence band spectra clearly indicate carbide formation in the modified surface layer. The time-of-flight secondary ion mass spectrometry depth profiling results reveal an oxy-carbide surface layer over an approximately 200 nm thick UC layer with little or no residual oxidation at the carbide layer/U metal transitional interface.

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

Dynamic Reactive Ionization with Cluster Secondary Ion Mass Spectrometry

NASA Astrophysics Data System (ADS)

Tian, Hua; Wucher, Andreas; Winograd, Nicholas

2016-02-01

Gas cluster ion beams (GCIB) have been tuned to enhance secondary ion yields by doping small gas molecules such as CH4, CO2, and O2 into an Ar cluster projectile, Arn + ( n = 1000-10,000) to form a mixed cluster. The `tailored beam' has the potential to expand the application of secondary ion mass spectrometry for two- and three-dimensional molecular specific imaging. Here, we examine the possibility of further enhancing the ionization by doping HCl into the Ar cluster. Water deposited on the target surface facilitates the dissociation of HCl. This concerted effect, occurring only at the impact site of the cluster, arises since the HCl is chemically induced to ionize to H+ and Cl- , allowing improved protonation of neutral molecular species. This hypothesis is confirmed by depth profiling through a trehalose thin film exposed to D2O vapor, resulting in ~20-fold increase in protonated molecules. The results show that it is possible to dynamically maintain optimum ionization conditions during depth profiling by proper adjustment of the water vapor pressure. H-D exchange in the trehalose molecule M was monitored upon deposition of D2O on the target surface, leading to the observation of [Mn* + H]+ or [Mn* + D]+ ions, where n = 1-8 hydrogen atoms in the trehalose molecule M have been replaced by deuterium. In general, we discuss the role of surface chemistry and dynamic reactive ionization of organic molecules in increasing the secondary ion yield.

Metabolic profile of esculin in rats by ultra high performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Wang, Yinan; Zhao, Min; Ou, Yingfu; Zeng, Bowen; Lou, Xinyu; Wang, Miao; Zhao, Chunjie

2016-05-01

Esculin, a coumarin derivative found in Fraxinus rhynchophylla, has been reported to possess multiple biological activities. This present study is designed to investigate the metabolic profile of esculin in vivo based on ultra high performance liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (UHPLC-FT-ICR-MS) for the first time. After oral administration of esculin (100 mg/kg) for rats, plasma, urine, feces and bile samples were collected to screen metabolites. As a result, a total of 19 metabolites (10 phase I metabolites and 9 phase II metabolites) were found and identified. Results showed that metabolic pathways of esculin included hydrolysis, dehydrogenation, hydroxylation, methylation, dehydrogenation, glucuronidation, sulfation, and glycine conjugation. It was also found that after oral administration of esculin, the esculin could be metabolized to esculetin in vivo via deglycosylation, and esculetin was found in all biological samples. This study also laid solid basis for in-depth development of esculin and provided important information for clarifying the biotransformation process of esculin in vivo. Copyright © 2016 Elsevier B.V. All rights reserved.

A Generic Multiple Reaction Monitoring Based Approach for Plant Flavonoids Profiling Using a Triple Quadrupole Linear Ion Trap Mass Spectrometry

NASA Astrophysics Data System (ADS)

Yan, Zhixiang; Lin, Ge; Ye, Yang; Wang, Yitao; Yan, Ru

2014-06-01

Flavonoids are one of the largest classes of plant secondary metabolites serving a variety of functions in plants and associating with a number of health benefits for humans. Typically, they are co-identified with many other secondary metabolites using untargeted metabolomics. The limited data quality of untargeted workflow calls for a shift from the breadth-first to the depth-first screening strategy when a specific biosynthetic pathway is focused on. Here we introduce a generic multiple reaction monitoring (MRM)-based approach for flavonoids profiling in plants using a hybrid triple quadrupole linear ion trap (QTrap) mass spectrometer. The approach includes four steps: (1) preliminary profiling of major aglycones by multiple ion monitoring triggered enhanced product ion scan (MIM-EPI); (2) glycones profiling by precursor ion triggered EPI scan (PI-EPI) of major aglycones; (3) comprehensive aglycones profiling by combining MIM-EPI and neutral loss triggered EPI scan (NL-EPI) of major glycone; (4) in-depth flavonoids profiling by MRM-EPI with elaborated MRM transitions. Particularly, incorporation of the NH3 loss and sugar elimination proved to be very informative and confirmative for flavonoids screening. This approach was applied for profiling flavonoids in Astragali radix ( Huangqi), a famous herb widely used for medicinal and nutritional purposes in China. In total, 421 flavonoids were tentatively characterized, among which less than 40 have been previously reported in this medicinal plant. This MRM-based approach provides versatility and sensitivity that required for flavonoids profiling in plants and serves as a useful tool for plant metabolomics.

Numerical investigation of depth profiling capabilities of helium and neon ions in ion microscopy

PubMed Central

Rzeznik, Lukasz; Wirtz, Tom

2016-01-01

The analysis of polymers by secondary ion mass spectrometry (SIMS) has been a topic of interest for many years. In recent years, the primary ion species evolved from heavy monatomic ions to cluster and massive cluster primary ions in order to preserve a maximum of organic information. The progress in less-damaging sputtering goes along with a loss in lateral resolution for 2D and 3D imaging. By contrast the development of a mass spectrometer as an add-on tool for the helium ion microscope (HIM), which uses finely focussed He+ or Ne+ beams, allows for the analysis of secondary ions and small secondary cluster ions with unprecedented lateral resolution. Irradiation induced damage and depth profiling capabilities obtained with these light rare gas species have been far less investigated than ion species used classically in SIMS. In this paper we simulated the sputtering of multi-layered polymer samples using the BCA (binary collision approximation) code SD_TRIM_SP to study preferential sputtering and atomic mixing in such samples up to a fluence of 1018 ions/cm2. Results show that helium primary ions are completely inappropriate for depth profiling applications with this kind of sample materials while results for neon are similar to argon. The latter is commonly used as primary ion species in SIMS. For the two heavier species, layers separated by 10 nm can be distinguished for impact energies of a few keV. These results are encouraging for 3D imaging applications where lateral and depth information are of importance. PMID:28144525

MALDI imaging mass spectrometry analysis-A new approach for protein mapping in multiple sclerosis brain lesions.

PubMed

Maccarrone, Giuseppina; Nischwitz, Sandra; Deininger, Sören-Oliver; Hornung, Joachim; König, Fatima Barbara; Stadelmann, Christine; Turck, Christoph W; Weber, Frank

2017-03-15

Multiple sclerosis is a disease of the central nervous system characterized by recurrent inflammatory demyelinating lesions in the early disease stage. Lesion formation and mechanisms leading to lesion remyelination are not fully understood. Matrix Assisted Laser Desorption Ionisation Mass Spectrometry imaging (MALDI-IMS) is a technology which analyses proteins and peptides in tissue, preserves their spatial localization, and generates molecular maps within the tissue section. In a pilot study we employed MALDI imaging mass spectrometry to profile and identify peptides and proteins expressed in normal-appearing white matter, grey matter and multiple sclerosis brain lesions with different extents of remyelination. The unsupervised clustering analysis of the mass spectra generated images which reflected the tissue section morphology in luxol fast blue stain and in myelin basic protein immunohistochemistry. Lesions with low remyelination extent were defined by compounds with molecular weight smaller than 5300Da, while more completely remyelinated lesions showed compounds with molecular weights greater than 15,200Da. An in-depth analysis of the mass spectra enabled the detection of cortical lesions which were not seen by routine luxol fast blue histology. An ion mass, mainly distributed at the rim of multiple sclerosis lesions, was identified by liquid chromatography and tandem mass spectrometry as thymosin beta-4, a protein known to be involved in cell migration and in restorative processes. The ion mass of thymosin beta-4 was profiled by MALDI imaging mass spectrometry in brain slides of 12 multiple sclerosis patients and validated by immunohistochemical analysis. In summary, our results demonstrate the ability of the MALDI-IMS technology to map proteins within the brain parenchyma and multiple sclerosis lesions and to identify potential markers involved in multiple sclerosis pathogenesis and/or remyelination. Copyright © 2016 Elsevier B.V. All rights reserved.

Metabolic profile of naringenin in the stomach and colon using liquid chromatography/electrospray ionization linear ion trap quadrupole-Orbitrap-mass spectrometry (LC-ESI-LTQ-Orbitrap-MS) and LC-ESI-MS/MS.

PubMed

Orrego-Lagarón, Naiara; Vallverdú-Queralt, Anna; Martínez-Huélamo, Miriam; Lamuela-Raventos, Rosa M; Escribano-Ferrer, Elvira

2016-02-20

Several biological activities (antioxidant, anti-inflammatory, anticarcinogenic) are attributed to naringenin (NAR)-a predominant flavonoid of citrus fruit and tomato-despite its low bioavailability after ingestion. NAR undergoes extensive metabolism when crossing the gastrointestinal tract, resulting in enteric, hepatic and microbial metabolites, some of them with recognized beneficial effects on human health. This study sought to provide new insights into the metabolism of NAR in regions of the gastrointestinal tract where it has been less studied: the stomach and colon. With this purpose, liquid chromatography coupled with an electrospray ionization hybrid linear ion trap quadrupole Orbitrap mass spectrometry technique (LC-ESI-LTQ-Orbitrap-MS) was used for an accurate identification of NAR metabolites, and liquid chromatography/electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) on a triple quadrupole was used for their identification and quantification. The combination of both analytical techniques provided a broader metabolic profile of NAR. As far as we know, this is the first in-depth metabolic profiling study of NAR in the stomach of mice. Three of the metabolites determined using the LC-LTQ-Orbitrap could not be identified by LC-ESI-MS/MS in stomach perfusion samples: apigenin, 3-(4-hydroxyphenyl) propionic acid and phloroglucinol. The number of colonic metabolites determined using the LTQ-Orbitrap-MS was more than twice the number identified by LC-ESI-MS/MS. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

Secondary ion mass spectrometry: The application in the analysis of atmospheric particulate matter

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

Huang, Di; Hua, Xin; Xiu, Guang-Li

Currently, considerable attention has been paid to atmospheric particulate matter (PM) investigation due to its importance in human health and global climate change. Surface characterization of PM is important since the chemical heterogeneity between the surface and bulk may vary its impact on the environment and human being. Secondary ion mass spectrometry (SIMS) is a surface technique with high surface sensitivity, capable of high spatial chemical imaging and depth profiling. Recent research shows that SIMS holds great potential in analyzing both surface and bulk chemical information of PM. In this review, we presented the working principal of SIMS in PMmore » characterization, summarized recent applications in PM analysis from different sources, discussed its advantages and limitations, and proposed the future development of this technique with a perspective in environmental sciences.« less

Oxygen isotopic distribution along the otolith growth axis by secondary ion mass spectrometry: Applications for studying ontogenetic change in the depth inhabited by deep-sea fishes

NASA Astrophysics Data System (ADS)

Shiao, Jen-Chieh; Itoh, Shoichi; Yurimoto, Hisayoshi; Iizuka, Yoshiyuki; Liao, Yun-Chih

2014-02-01

This study using tuna otoliths as working standards established a high lateral resolution and precision analysis to measure δ18Ootolith by secondary ion mass spectrometry. This analytical approach of the ion probe was applied to deep-sea fishes to reconstruct the likely depths inhabited by the fishes at different life history stages based on the measured δ18Ootolith values as a proxy of water temperature. Dramatic increases up to 5-6‰ in δ18Ootolith, representing a temperature decrease of approximately 20 °C, were detected in a blind cusk eel (Barathronus maculatus) otolith and in the otoliths of Synaphobranchus kaupii during leptocephalus metamorphosis to glass eel, inferred from the drop of otolith Sr/Ca ratios and increase of otolith growth increment width. δ18Ootolith profiles clearly divided the fish's life history into a planktonic stage in the mixed layer of the ocean and a benthic stage on the deep-sea ocean bottom. The habitat shift signal was recorded within a 150 μm width of otolith growth zone, which was too narrow to be clearly detected by mechanical drilling and conventional isotopic ratio mass spectrometry. However, variations down to -7‰ were found in δ18Ootolith profiles as the result of Cs2+ beam sputter in the core and larval portions of the otoliths. Carbon mapping by electron probe microanalyzer and staining by toluidine blue suggested abundant proteins existed in the areas with anomaly negative δ18Ootolith values, which cannot be interpreted as a habitat change but due to the isotopic fractionation by O emission from the proteins. These results implied that careful design and understanding of the chemical composition of the analytical areas or tracks on the heterogeneous otolith was essential for highly accurate and precise analysis.

Structural analysis of the outermost hair surface using TOF-SIMS with gas cluster ion beam sputtering.

PubMed

Lshikawa, Kazutaka; Okamoto, Masayuki; Aoyagi, Satoka

2016-06-28

A hair cuticle, which consists of flat overlapping scales that surround the hair fiber, protects inner tissues against external stimuli. The outermost surface of the cuticle is covered with a thin membrane containing proteins and lipids called the epicuticle. In a previous study, the authors conducted a depth profile analysis of a hair cuticle's amino acid composition to characterize its multilayer structure. Time-of-flight secondary ion mass spectrometry with a bismuth primary ion source was used in combination with the C60 sputtering technique for the analysis. It was confirmed that the lipids and cysteine-rich layer exist on the outermost cuticle surface, which is considered to be the epicuticle, though the detailed structure of the epicuticle has not been clarified. In this study, depth profile analysis of the cuticle surface was conducted using the argon gas cluster ion beam (Ar-GCIB) sputtering technique, in order to characterize the structure of the epicuticle. The shallow depth profile of the cuticle surface was investigated using an Ar-GCIB impact energy of 5 keV. Compared to the other amino acid peaks rich in the epicuticle, the decay of 18-methyleicosanic acid (18-MEA) thiolate peak was the fastest. This result suggests that the outermost surface of the hair is rich in 18-MEA. In conclusion, our results indicate that the outermost surfaces of cuticles have a multilayer (lipid and protein layers), which is consistent with the previously proposed structure.

Investigation of anodic TiO2 nanotube composition with high spatial resolution AES and ToF SIMS

NASA Astrophysics Data System (ADS)

Dronov, Alexey; Gavrilin, Ilya; Kirilenko, Elena; Dronova, Daria; Gavrilov, Sergey

2018-03-01

High resolution Scanning Auger Electron Spectroscopy (AES) and Time-of-Flight Secondary Ion Mass-Spectrometry (ToF SIMS) were used to investigate structure and elemental composition variation of both across an array of TiO2 nanotubes (NTs) and single tube of an array. The TiO2 NT array was grown by anodic oxidation of Ti foil in fluorine-containing ethylene glycol electrolyte. It was found that the studied anodic TiO2 nanotubes have a layered structure with rather sharp interfaces. The differences in AES depth profiling results of a single tube with the focused primary electron beam (point analysis) and over an area of 75 μm in diameter of a nanotube array with the defocused primary electron beam are discussed. Depth profiling by ToF SIMS was carried out over approximately the same size of a nanotube array to determine possible ionic fragments in the structure. The analysis results show that the combination of both mentioned methods is useful for a detailed analysis of nanostructures with complex morphology and multi-layered nature.

SIMS study of oxygen diffusion in monoclinic HfO2

NASA Astrophysics Data System (ADS)

Mueller, Michael P.; De Souza, Roger A.

2018-01-01

The diffusion of oxygen in dense ceramics of monoclinic HfO2 was studied by means of (18O/16O) isotope exchange annealing and subsequent determination of isotope depth profiles by Secondary Ion Mass Spectrometry. Anneals were performed in the temperature range of 573 ≤T /K ≤ 973 at an oxygen partial pressure of p O2=200 mbar . All measured isotope profiles exhibited two features: the first feature, closer to the surface, was attributed mainly to slow oxygen diffusion in an impurity silicate phase; the second feature, deeper in the sample, was attributed to oxygen diffusion in bulk monoclinic HfO2 . The activation enthalpy of oxygen tracer diffusion in bulk HfO2 was found to be ΔHD∗≈0.5 eV .

Fluorine-doping in titanium dioxide by ion implantation technique

NASA Astrophysics Data System (ADS)

Yamaki, T.; Umebayashi, T.; Sumita, T.; Yamamoto, S.; Maekawa, M.; Kawasuso, A.; Itoh, H.

2003-05-01

We implanted 200 keV F + in single crystalline titanium dioxide (TiO 2) rutile at a nominal fluence of 1 × 10 16 to 1 × 10 17 ions cm -2 and then thermally annealed the implanted sample in air. The radiation damage and its recovery process during the annealing were analyzed by Rutherford backscattering spectrometry in channeling geometry and variable-energy positron annihilation spectroscopy. The lattice disorder was completely recovered at 1200 °C by the migration of point defects to the surface. According to secondary ion mass spectrometry analysis, the F depth profile was shifted to a shallower region along with the damage recovery and this resulted in the formation of an F-doped layer where the impurity concentration steadily increased toward the surface. The F doping proved to provide a modification to the conduction-band edge of TiO 2, as assessed by theoretical band calculations.

SRF niobium characterization using SIMS and FIB-TEM

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

Stevie, F. A.

2015-12-04

Our understanding of superconducting radio frequency (SRF) accelerator cavities has been improved by elemental analysis at high depth resolution and by high magnification microscopy. This paper summarizes the technique development and the results obtained on poly-crystalline, large grain, and single crystal SRF niobium. Focused ion beam made possible sample preparation using transmission electron microscopy and the images obtained showed a very uniform oxide layer for all samples analyzed. Secondary ion mass spectrometry indicated the presence of a high concentration of hydrogen and the hydrogen content exhibited a relationship with improvement in performance. Depth profiles of carbon, nitrogen, and oxygen didmore » not show major differences with heat treatment. Niobium oxide less than 10 nm thick was shown to be an effective hydrogen barrier. Niobium with titanium contamination showed unexpected performance improvement.« less

Atomic transport during solid-phase epitaxial recrystallization of amorphous germanium

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

Radek, M.; Bracht, H., E-mail: bracht@uni-muenster.de; Johnson, B. C.

2015-08-24

The atomic mixing of matrix atoms during solid-phase epitaxy (SPE) is studied by means of isotopically enriched germanium (Ge) multilayer structures that were amorphized by Ge ion implantation up to a depth of 1.5 μm. Recrystallization of the amorphous structure is performed at temperatures between 350 °C and 450 °C. Secondary-ion-mass-spectrometry is used to determine the concentration-depth profiles of the Ge isotope before and after SPE. An upper limit of 0.5 nm is deduced for the displacement length of the Ge matrix atoms by the SPE process. This small displacement length is consistent with theoretical models and atomistic simulations of SPE, indicating that themore » SPE mechanism consists of bond-switching with nearest-neighbours across the amorphous-crystalline (a/c) interface.« less

Pulsed glow discharge enables direct mass spectrometric measurement of fluorine in crystal materials - Fluorine quantification and depth profiling in fluorine doped potassium titanyl phosphate

NASA Astrophysics Data System (ADS)

Bodnar, Victoria; Ganeev, Alexander; Gubal, Anna; Solovyev, Nikolay; Glumov, Oleg; Yakobson, Viktor; Murin, Igor

2018-07-01

A pulsed direct current glow discharge time-of-flight mass spectrometry (GD TOF MS) method for the quantification of fluorine in insoluble crystal materials with fluorine doped potassium titanyl phosphate (KTP) KTiOPO4:KF as an example has been proposed. The following parameters were optimized: repelling pulse delay, discharge duration, discharge voltage, and pressure in the discharge cell. Effective ionization of fluorine in the space between sampler and skimmer under short repelling pulse delay, related to the high-energy electron impact at the discharge front, has been demonstrated. A combination of instrumental and mathematical correction approaches was used to cope for the interferences of 38Ar2+ and 1H316O + on 19F+. To maintain surface conductivity in the dielectric KTP crystals and insure its effective sputtering in combined hollow cathode cell, silver suspension applied by the dip-coating method was employed. Fluorine quantification was performed using relative sensitivity factors. The analysis of a reference material and scanning electron microscope-energy dispersive X-ray spectroscopy was used for validation. Fluorine limit of detection by pulsed direct current GD TOF MS was 0.01 mass%. Real sample analysis showed that fluorine seems to be inhomogeneously distributed in the crystals. That is why depth profiling of F, K, O, and P was performed to evaluate the crystals' non-stoichiometry. The approaches designed allow for fluorine quantification in insoluble dielectric materials with minimal sample preparation and destructivity as well as performing depth profiling to assess crystal non-stoichiometry.

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

Xue, Haizhou; Zhang, Yanwen; Zhu, Zihua

Single crystalline 6H-SiC samples were irradiated at 150 K using 2MeV Pt ions. Local volume swelling is determined by electron energy loss spectroscopy (EELS), a nearly sigmoidal dependence with irradiation dose is observed. The disorder profiles and ion distribution are determined by Rutherford backscattering spectrometry (RBS), transmission electron microscopy and secondary ion mass spectrum. Since the volume swelling reaches 12% over the damage region under high ion fluence, lattice expansion is considered and corrected during the data analysis of RBS spectra to obtain depth profiles. Projectile and damage profiles are estimated by SRIM (Stopping and Range of Ions in Matter).more » Comparing with the measured profiles, SRIM code significantly overestimates the electronic stopping power for the slow heavy Pt ions, and large derivations are observed in the predicted ion distribution and the damage profiles. Utilizing the reciprocity method that is based on the invariance of the inelastic excitation in ion atom collisions against interchange of projectile and target, much lower electronic stopping is deduced. A simple approach based on reducing the density of SiC target in SRIM simulation is proposed to compensate the overestimated SRIM electronic stopping power values. Better damage profile and ion range are predicted.« less

Fundamental Studies of Molecular Secondary Ion Mass Spectrometry Ionization Probability Measured With Femtosecond, Infrared Laser Post-Ionization

NASA Astrophysics Data System (ADS)

Popczun, Nicholas James

The work presented in this dissertation is focused on increasing the fundamental understanding of molecular secondary ion mass spectrometry (SIMS) ionization probability by measuring neutral molecule behavior with femtosecond, mid-infrared laser post-ionization (LPI). To accomplish this, a model system was designed with a homogeneous organic film comprised of coronene, a polycyclic hydrocarbon which provides substantial LPI signal. Careful consideration was given to signal lost to photofragmentation and undersampling of the sputtered plume that is contained within the extraction volume of the mass spectrometer. This study provided the first ionization probability for an organic compound measured directly by the relative secondary ions and sputtered neutral molecules using a strong-field ionization (SFI) ionization method. The measured value of ˜10-3 is near the upper limit of previous estimations of ionization probability for organic molecules. The measurement method was refined, and then applied to a homogeneous guanine film, which produces protonated secondary ions. This measurement found the probability of protonation to occur to be on the order of 10-3, although with less uncertainty than that of the coronene. Finally, molecular depth profiles were obtained for SIMS and LPI signals as a function of primary ion fluence to determine the effect of ionization probability on the depth resolution of chemical interfaces. The interfaces chosen were organic/inorganic interfaces to limit chemical mixing. It is shown that approaching the inorganic chemical interface can enhance or suppress the ionization probability for the organic molecule, which can lead to artificially sharpened or broadened depths, respectively. Overall, the research described in this dissertation provides new methods for measuring ionization efficiency in SIMS in both absolute and relative terms, and will inform both innovation in the technique, as well as increase understanding of depth-dependent experiments.

Depth-Resolved Cathodoluminescence of Thorium Dioxide

DTIC Science & Technology

2013-03-01

exhibited more of an energy dependency than the cut and polished sample. However, in a companion study, ime of flight secondary ion mass spectrometry...Ion Mass Spectrometry (TOF SIMS) ......................17 2.7 Atomic Force Microscope (AFM...1 TOF SIMS……….Time of Flight Secondary Ion Mass Spectroscopy……………….62 1 DEPTH

Direct mass spectrometric measurement of gases in soil monoliths.

PubMed

Sheppard, S K; Lloyd, D

2002-07-01

An integrated approach to gas analysis in soil cores was conducted to provide a novel method for observing the gas dynamics associated with upland soil ecosystems. Depth profiles of the O(2), Ar, CO(2), CH(4), N(2) and NO(x) concentrations in intact soil monoliths were obtained simultaneously using membrane inlet mass spectrometry (MIMS). This technique enables the direct measurement of multiple gas species throughout the soil core with minimal disturbance. Depth profiles provided data on the vertical heterogeneity of gas concentrations, while horizontal heterogeneity was monitored by comparison between profiles. Detailed descriptions of the modifications to current MIMS methods for in situ environmental monitoring of terrestrial soils are provided. These included a thorough examination of calibration of the MIMS probe in gas phase, stirred and unstirred H(2)O, or between glass beads immersed in H(2)O. Calibration was also carried out in sterile (autoclaved) soil. The mean concentrations of CO(2) and CH(4) in the soil monoliths increased from 27 microM and undetectable levels respectively at the surface, to maximum values of 3.6 mM and 4.3 microM at 12-cm depth. These changes corresponded with decreases in mean O(2), Ar and N(2) concentration from 300, 20 and 720 microM respectively to 0-6, 10 and 574 microM at 12-cm depth. These data indicated the presence of a gradient within the core from an aerobic environment to an O(2)-depleted, but not in all cases a completely anaerobic, one. This transition corresponded, to some extent, with that between the upper and lower soil horizons. The increased methane and CO(2) concentrations observed at depth are indicative of anaerobic environments. General trends associated with the gradually changing vertical heterogeneity of these gas profiles and the transition towards anaerobiosis did not provide evidence for the existence of localised microsites. Some evidence for microsite-specific microbial communities was however, provided by observation of broad zones of accumulation of NO(x) species, but only at concentrations close to the limit of detection of the method. The ratio of each gas, to argon was calculated at each depth. This was done to correct for physical parameters, which influence inert and biologically active gases, equally. The amount of di-nitrogen as a ratio to Ar was seen to increase with depth. This could be evidence for denitrification in the lower horizon. An example of the dynamic 'online' data collection capabilities is provided for diurnal oscillations in subsurface (5 cm) soil gas concentrations.

Double perovskite cathodes for proton-conducting ceramic fuel cells: are they triple mixed ionic electronic conductors?

NASA Astrophysics Data System (ADS)

Téllez Lozano, Helena; Druce, John; Cooper, Samuel J.; Kilner, John A.

2017-12-01

18O and 2H diffusion has been investigated at a temperature of 300 °C in the double perovskite material PrBaCo2O5+δ (PBCO) in flowing air containing 200 mbar of 2H216O. Secondary ion mass spectrometry (SIMS) depth profiling of exchanged ceramics has shown PBCO still retains significant oxygen diffusivity ( 1.3 × 10-11 cm2s-1) at this temperature and that the presence of water (2H216O), gives rise to an enhancement of the surface exchange rate over that in pure oxygen by a factor of 3. The 2H distribution, as inferred from the 2H216O- SIMS signal, shows an apparent depth profile which could be interpreted as 2H diffusion. However, examination of the 3-D distribution of the signal shows it to be nonhomogeneous and probably related to the presence of hydrated layers in the interior walls of pores and is not due to proton diffusion. This suggests that PBCO acts mainly as an oxygen ion mixed conductor when used in PCFC devices, although the presence of a small amount of protonic conductivity cannot be discounted in these materials.

Long-Term (4 mo) Oxygen Isotope Exchange Experiment between Zircon and Hydrothermal Fluid

NASA Astrophysics Data System (ADS)

Bindeman, I. N.; Schmitt, A. K.; Lundstrom, C.; Golledge, S.

2013-12-01

Knowing oxygen diffusivity in zircon has several critical applications: 1) establishing zircon stability and solubility in hot silica-saturated hydrothermal solutions; 2) deriving metamorphic and magmatic heating timescales from intra-crystal oxygen isotopic gradients; 3) assessing the survivability of oxygen isotopic signatures in Hadean zircons. We report results of a microanalytical investigation of an isotope exchange experiment using a cold-seal pressure apparatus at 850°C and 500 MPa over 4 months duration. Natural zircon, quartz and rutile were sealed with a silica-rich solution doped with 18-O, D, 7-Li and 10-B in a gold capsule. The diffusion length-scales were examined by depth profiling using time-of-flight (TOF) and high-sensitivity dynamic secondary ionization mass spectrometry (SIMS). Starting materials had distinct and homogeneous δ18O: zircon from Mesa Falls tuff of Yellowstone (+3.6‰), rutile from Karelia (-29‰), Bishop Tuff Quartz (+8.4‰), and δ18O doped water (+400‰). Starting material zircon showed invariant 18O/16O during depth profiling. After the 4 month experiment, rutile crystal surfaces displayed etching (100's of nm), while zircon exteriors lacked visible change. Quartz was completely dissolved and reprecipitated in a minor residue. Rutile developed ~2 μm long Fickian diffusion profiles largely consistent with the wet diffusion coefficients for rutile previously reported [1]. Surface U-Pb dating of zircon detected no significant Pb loss from the outermost ~300 nm of the crystal face and returned identical core-face ages. We performed δ18O depth profiling of zircon in two directions. First, forward profiles (crystal rim inwards) by dynamic SIMS (no surface treatment besides Au-coating; Cs+ beam of 20 kV impact energy) showed initially high and decreasing 18O/16O over ~130 nm; TOF-SIMS forward profiles using a 2 kV Cs+ sputter beam and 25 kV Bi3+ primary ions on uncoated zircon surfaces (cleaned for 2 min with HF) yielded decreasing 18O/16O over a similar length scale. These profile lengths are largely consistent with wet diffusion coefficient for zircon reported by [2]. In contrast, back-side depth profiling was conducted by dynamic SIMS on a 1 μm thick wafer cut from the zircon by FIB. No significant elevation in 18O/16O was detected when the surface layer was penetrated, consistent with dry diffusion coefficients of [2]. The results suggest that nm-scale SIMS surface analysis of isotope ratios is challenging. We are investigating if they can be critically affected by knock-on effects and/or continuous mixing of a very thin enriched surface layer during depth profiling in our and previous experiments. [1] Moore et al., 1998, Am. Min. 83, 700-711 [2] Watson and Cherniak, 1997, EPSL 148, 537-544

Chemometrics comparison of gas chromatography with mass spectrometry and comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry Daphnia magna metabolic profiles exposed to salinity.

PubMed

Parastar, Hadi; Garreta-Lara, Elba; Campos, Bruno; Barata, Carlos; Lacorte, Silvia; Tauler, Roma

2018-06-01

The performances of gas chromatography with mass spectrometry and of comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry are examined through the comparison of Daphnia magna metabolic profiles. Gas chromatography with mass spectrometry and comprehensive two-dimensional gas chromatography with mass spectrometry were used to compare the concentration changes of metabolites under saline conditions. In this regard, a chemometric strategy based on wavelet compression and multivariate curve resolution-alternating least squares is used to compare the performances of gas chromatography with mass spectrometry and comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry for the untargeted metabolic profiling of Daphnia magna in control and salinity-exposed samples. Examination of the results confirmed the outperformance of comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry over gas chromatography with mass spectrometry for the detection of metabolites in D. magna samples. The peak areas of multivariate curve resolution-alternating least squares resolved elution profiles in every sample analyzed by comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry were arranged in a new data matrix that was then modeled by partial least squares discriminant analysis. The control and salt-exposed daphnids samples were discriminated and the most relevant metabolites were estimated using variable importance in projection and selectivity ratio values. Salinity de-regulated 18 metabolites from metabolic pathways involved in protein translation, transmembrane cell transport, carbon metabolism, secondary metabolism, glycolysis, and osmoregulation. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomics meets blue biotechnology: a wealth of novelties and opportunities.

PubMed

Hartmann, Erica M; Durighello, Emie; Pible, Olivier; Nogales, Balbina; Beltrametti, Fabrizio; Bosch, Rafael; Christie-Oleza, Joseph A; Armengaud, Jean

2014-10-01

Blue biotechnology, in which aquatic environments provide the inspiration for various products such as food additives, aquaculture, biosensors, green chemistry, bioenergy, and pharmaceuticals, holds enormous promise. Large-scale efforts to sequence aquatic genomes and metagenomes, as well as campaigns to isolate new organisms and culture-based screenings, are helping to push the boundaries of known organisms. Mass spectrometry-based proteomics can complement 16S gene sequencing in the effort to discover new organisms of potential relevance to blue biotechnology by facilitating the rapid screening of microbial isolates and by providing in depth profiles of the proteomes and metaproteomes of marine organisms, both model cultivable isolates and, more recently, exotic non-cultivable species and communities. Proteomics has already contributed to blue biotechnology by identifying aquatic proteins with potential applications to food fermentation, the textile industry, and biomedical drug development. In this review, we discuss historical developments in blue biotechnology, the current limitations to the known marine biosphere, and the ways in which mass spectrometry can expand that knowledge. We further speculate about directions that research in blue biotechnology will take given current and near-future technological advancements in mass spectrometry. Copyright © 2014 Elsevier B.V. All rights reserved.

Electronic stopping powers for heavy ions in SiC and SiO{sub 2}

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

Jin, K.; Xue, H.; Zhang, Y., E-mail: Zhangy1@ornl.gov

2014-01-28

Accurate information on electronic stopping power is fundamental for broad advances in materials science, electronic industry, space exploration, and sustainable energy technologies. In the case of slow heavy ions in light targets, current codes and models provide significantly inconsistent predictions, among which the Stopping and Range of Ions in Matter (SRIM) code is the most commonly used one. Experimental evidence, however, has demonstrated considerable errors in the predicted ion and damage profiles based on SRIM stopping powers. In this work, electronic stopping powers for Cl, Br, I, and Au ions are experimentally determined in two important functional materials, SiC andmore » SiO{sub 2}, based on a single ion technique, and new electronic stopping power values are derived over the energy regime from 0 to 15 MeV, where large deviations from the SRIM predictions are observed. As an experimental validation, Rutherford backscattering spectrometry (RBS) and secondary ion mass spectrometry (SIMS) are utilized to measure the depth profiles of implanted Au ions in SiC for energies from 700 keV to 15 MeV. The measured ion distributions by both RBS and SIMS are considerably deeper than the SRIM predictions, but agree well with predictions based on our derived stopping powers.« less

Electronic Stopping Powers For Heavy Ions In SiC And SiO2

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

Jin, Ke; Zhang, Y.; Zhu, Zihua

2014-01-24

Accurate information on electronic stopping power is fundamental for broad advances in materials science, electronic industry, space exploration, and sustainable energy technologies. In the case of slow heavy ions in light targets, current codes and models provide significantly inconsistent predictions, among which the Stopping and Range of Ions in Matter (SRIM) code is the most commonly used one. Experimental evidence, however, has demonstrated considerable errors in the predicted ion and damage profiles based on SRIM stopping powers. In this work, electronic stopping powers for Cl, Br, I, and Au ions are experimentally determined in two important functional materials, SiC andmore » SiO2, based on a single ion technique, and new electronic stopping power values are derived over the energy regime from 0 to 15 MeV, where large deviations from the SRIM predictions are observed. As an experimental validation, Rutherford backscattering spectrometry (RBS) and secondary ion mass spectrometry (SIMS) are utilized to measure the depth profiles of implanted Au ions in SiC for energies from 700 keV to 15MeV. The measured ion distributions by both RBS and SIMS are considerably deeper than the SRIM predictions, but agree well with predictions based on our derived stopping powers.« less

Characterization of inertial confinement fusion (ICF) targets using PIXE, RBS, and STIM analysis.

PubMed

Li, Yongqiang; Liu, Xue; Li, Xinyi; Liu, Yiyang; Zheng, Yi; Wang, Min; Shen, Hao

2013-08-01

Quality control of the inertial confinement fusion (ICF) target in the laser fusion program is vital to ensure that energy deposition from the lasers results in uniform compression and minimization of Rayleigh-Taylor instabilities. The technique of nuclear microscopy with ion beam analysis is a powerful method to provide characterization of ICF targets. Distribution of elements, depth profile, and density image of ICF targets can be identified by particle-induced X-ray emission, Rutherford backscattering spectrometry, and scanning transmission ion microscopy. We present examples of ICF target characterization by nuclear microscopy at Fudan University in order to demonstrate their potential impact in assessing target fabrication processes.

Combined evaluation of grazing incidence X-ray fluorescence and X-ray reflectivity data for improved profiling of ultra-shallow depth distributions☆

PubMed Central

Ingerle, D.; Meirer, F.; Pepponi, G.; Demenev, E.; Giubertoni, D.; Wobrauschek, P.; Streli, C.

2014-01-01

The continuous downscaling of the process size for semiconductor devices pushes the junction depths and consequentially the implantation depths to the top few nanometers of the Si substrate. This motivates the need for sensitive methods capable of analyzing dopant distribution, total dose and possible impurities. X-ray techniques utilizing the external reflection of X-rays are very surface sensitive, hence providing a non-destructive tool for process analysis and control. X-ray reflectometry (XRR) is an established technique for the characterization of single- and multi-layered thin film structures with layer thicknesses in the nanometer range. XRR spectra are acquired by varying the incident angle in the grazing incidence regime while measuring the specular reflected X-ray beam. The shape of the resulting angle-dependent curve is correlated to changes of the electron density in the sample, but does not provide direct information on the presence or distribution of chemical elements in the sample. Grazing Incidence XRF (GIXRF) measures the X-ray fluorescence induced by an X-ray beam incident under grazing angles. The resulting angle dependent intensity curves are correlated to the depth distribution and mass density of the elements in the sample. GIXRF provides information on contaminations, total implanted dose and to some extent on the depth of the dopant distribution, but is ambiguous with regard to the exact distribution function. Both techniques use similar measurement procedures and data evaluation strategies, i.e. optimization of a sample model by fitting measured and calculated angle curves. Moreover, the applied sample models can be derived from the same physical properties, like atomic scattering/form factors and elemental concentrations; a simultaneous analysis is therefore a straightforward approach. This combined analysis in turn reduces the uncertainties of the individual techniques, allowing a determination of dose and depth profile of the implanted elements with drastically increased confidence level. Silicon wafers implanted with Arsenic at different implantation energies were measured by XRR and GIXRF using a combined, simultaneous measurement and data evaluation procedure. The data were processed using a self-developed software package (JGIXA), designed for simultaneous fitting of GIXRF and XRR data. The results were compared with depth profiles obtained by Secondary Ion Mass Spectrometry (SIMS). PMID:25202165

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.

Hyperfine and radiological characterization of soils of the province of Buenos Aires, Argentina

NASA Astrophysics Data System (ADS)

Montes, M. L.; Taylor, M. A.; Mercader, R. C.; Sives, F. R.; Desimoni, J.

2010-03-01

The depth profile concentration of both natural and anthropogenic gamma-ray-emitter nuclides were determined in soil samples collected in an area located at 34° 54.452' S, 58° 8.365' W, down to 50 cm in depth, using an hyper-pure Ge spectrometer. The soil samples were also characterized by means of Mössbauer spectrometry and X-ray diffraction. The activities of 238U and 232Th natural chains remain constant in depth at 41 Bq/kg and 46 Bq/kg, respectively, while the 40K activity increases from 531 Bq/kg to 618 Bq/kg between 2.5 cm y 25.5 cm of depth. The only anthropogenic detected nuclide is 137Cs, whose activity changes form 1.4 Bq/kg to values lower than the detection limit (LD) for depths below 25 cm, exhibiting a maximum at 10 cm beneath the surface. The Mössbauer spectra show two magnetic sextets associated with α-Fe2O3 and Fe3O4, as well as two Fe+3 Fe+2 doublets, probably originated in octahedral and tetrahedral sites of paramagnetic phases. The Fe3+ paramagnetic signal relative fraction increases up to 82% at the expense of the α-Fe2O3 one when de depth increases. No correlation between Fe3O4 and the 137Cs was identificated.

Measuring Compositions in Organic Depth Profiling: Results from a VAMAS Interlaboratory Study.

PubMed

Shard, Alexander G; Havelund, Rasmus; Spencer, Steve J; Gilmore, Ian S; Alexander, Morgan R; Angerer, Tina B; Aoyagi, Satoka; Barnes, Jean-Paul; Benayad, Anass; Bernasik, Andrzej; Ceccone, Giacomo; Counsell, Jonathan D P; Deeks, Christopher; Fletcher, John S; Graham, Daniel J; Heuser, Christian; Lee, Tae Geol; Marie, Camille; Marzec, Mateusz M; Mishra, Gautam; Rading, Derk; Renault, Olivier; Scurr, David J; Shon, Hyun Kyong; Spampinato, Valentina; Tian, Hua; Wang, Fuyi; Winograd, Nicholas; Wu, Kui; Wucher, Andreas; Zhou, Yufan; Zhu, Zihua; Cristaudo, Vanina; Poleunis, Claude

2015-08-20

We report the results of a VAMAS (Versailles Project on Advanced Materials and Standards) interlaboratory study on the measurement of composition in organic depth profiling. Layered samples with known binary compositions of Irganox 1010 and either Irganox 1098 or Fmoc-pentafluoro-l-phenylalanine in each layer were manufactured in a single batch and distributed to more than 20 participating laboratories. The samples were analyzed using argon cluster ion sputtering and either X-ray photoelectron spectroscopy (XPS) or time-of-flight secondary ion mass spectrometry (ToF-SIMS) to generate depth profiles. Participants were asked to estimate the volume fractions in two of the layers and were provided with the compositions of all other layers. Participants using XPS provided volume fractions within 0.03 of the nominal values. Participants using ToF-SIMS either made no attempt, or used various methods that gave results ranging in error from 0.02 to over 0.10 in volume fraction, the latter representing a 50% relative error for a nominal volume fraction of 0.2. Error was predominantly caused by inadequacy in the ability to compensate for primary ion intensity variations and the matrix effect in SIMS. Matrix effects in these materials appear to be more pronounced as the number of atoms in both the primary analytical ion and the secondary ion increase. Using the participants' data we show that organic SIMS matrix effects can be measured and are remarkably consistent between instruments. We provide recommendations for identifying and compensating for matrix effects. Finally, we demonstrate, using a simple normalization method, that virtually all ToF-SIMS participants could have obtained estimates of volume fraction that were at least as accurate and consistent as XPS.

Measuring Compositions in Organic Depth Profiling: Results from a VAMAS Interlaboratory Study

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

Shard, A. G.; Havelund, Rasmus; Spencer, Steve J.

We report the results of a VAMAS (Versailles Project on Advanced Materials and Standards) interlaboratory study on the measurement of composition in organic depth profiling. Layered samples with known binary compositions of Irganox 1010 and either Irganox 1098 or Fmoc-pentafluoro-L-phenylalanine in each layer were manufactured in a single batch and distributed to more than 20 participating laboratories. The samples were analyzed using argon cluster ion sputtering and either X-ray Photoelectron Spectroscopy (XPS) or Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) to generate depth profiles. Participants were asked to estimate the volume fractions in two of the layers and were provided withmore » the compositions of all other layers. Participants using XPS provided volume fractions within 0.03 of the nominal values. Participants using ToF-SIMS either made no attempt, or used various methods that gave results ranging in error from 0.02 to over 0.10 in volume fraction, the latter representing a 50% relative error for a nominal volume fraction of 0.2. Error was predominantly caused by inadequacy in the ability to compensate for primary ion intensity variations and the matrix effect in SIMS. Matrix effects in these materials appear to be more pronounced as the number of atoms in both the primary analytical ion and the secondary ion increase. Using the participants’ data we show that organic SIMS matrix effects can be measured and are remarkably consistent between instruments. We provide recommendations for identifying and compensating for matrix effects. Finally we demonstrate, using a simple normalization method, that virtually all ToF-SIMS participants could have obtained estimates of volume fraction that were at least as accurate and consistent as XPS.« less

SIMS of organics—Advances in 2D and 3D imaging and future outlook

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

Gilmore, Ian S.

Secondary ion mass spectrometry (SIMS) has become a powerful technique for the label-free analysis of organics from cells to electronic devices. The development of cluster ion sources has revolutionized the field, increasing the sensitivity for organics by two or three orders of magnitude and for large clusters, such as C{sub 60} and argon clusters, allowing depth profiling of organics. The latter has provided the capability to generate stunning three dimensional images with depth resolutions of around 5 nm, simply unavailable by other techniques. Current state-of-the-art allows molecular images with a spatial resolution of around 500 nm to be achieved andmore » future developments are likely to progress into the sub-100 nm regime. This review is intended to bring those with some familiarity with SIMS up-to-date with the latest developments for organics, the fundamental principles that underpin this and define the future progress. State-of-the-art examples are showcased and signposts to more in-depth reviews about specific topics given for the specialist.« less

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.

Comprehensive Lipidome-Wide Profiling Reveals Dynamic Changes of Tea Lipids during Manufacturing Process of Black Tea.

PubMed

Li, Jia; Hua, Jinjie; Zhou, Qinghua; Dong, Chunwang; Wang, Jinjin; Deng, Yuliang; Yuan, Haibo; Jiang, Yongwen

2017-11-22

As important biomolecules in Camellia sinensis L., lipids undergo substantial changes during black tea manufacture, which is considered to contribute to tea sensory quality. However, limited by analytical capacity, detailed lipid composition and its dynamic changes during black tea manufacture remain unclear. Herein, we performed tea lipidome profiling using high resolution liquid chromatography coupled to mass spectrometry (LC-MS), which allows simultaneous and robust analysis of 192 individual lipid species in black tea, covering 17 (sub)classes. Furthermore, dynamic changes of tea lipids during black tea manufacture were investigated. Significant alterations of lipid pattern were revealed, involved with chlorophyll degradation, metabolic pathways of glycoglycerolipids, and other extraplastidial membrane lipids. To our knowledge, this report presented most comprehensive coverage of lipid species in black tea. This study provides a global and in-depth metabolic map of tea lipidome during black tea manufacture.

In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS

PubMed Central

Yu, Jiachao; Zhu, Zihua; Yu, Xiao-Ying

2016-01-01

This work demonstrates in situ characterization of protein biomolecules in the aqueous solution using the System for Analysis at the Liquid Vacuum Interface (SALVI) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The fibronectin protein film was immobilized on the silicon nitride (SiN) membrane that forms the SALVI detection area. During ToF-SIMS analysis, three modes of analysis were conducted including high spatial resolution mass spectrometry, two-dimensional (2D) imaging, and depth profiling. Mass spectra were acquired in both positive and negative modes. Deionized water was also analyzed as a reference sample. Our results show that the fibronectin film in water has more distinct and stronger water cluster peaks compared to water alone. Characteristic peaks of amino acid fragments are also observable in the hydrated protein ToF-SIMS spectra. These results illustrate that protein molecule adsorption on a surface can be studied dynamically using SALVI and ToF-SIMS in the liquid environment for the first time. PMID:26966995

Determination of diffusion coefficients of hydrogen and deuterium in Zr-2.5%Nb pressure tube material using hot vacuum extraction-quadrupole mass spectrometry

NASA Astrophysics Data System (ADS)

Shrivastava, Komal Chandra; Kulkarni, A. S.; Ramanjaneyulu, P. S.; Sunil, Saurav; Saxena, M. K.; Singh, R. N.; Tomar, B. S.; Ramakumar, K. L.

2015-06-01

The diffusion coefficients of hydrogen and deuterium in Zr-2.5%Nb alloy were measured in the temperature range 523 to 673 K, employing hot vacuum extraction-quadrupole mass spectrometry (HVE-QMS). One end of the Zr-2.5%Nb alloy specimens was charged electrolytically with the desired hydrogen isotope. After annealing at different temperatures for a predetermined time, the specimens were cut into thin slices, which were analyzed for their H2/D2 content using the HVE-QMS technique. The depth profile data were fitted into the equation representing the solution of Fick's second law of diffusion. The activation energy of hydrogen/deuterium diffusion was obtained from the Arrhenius relation between the diffusion coefficient and temperature. The temperature dependent diffusion coefficient can be represented as DH = 1.41 × 10-7 exp(-36,000/RT) and DD = 6.16 × 10-8 exp(-35,262/RT) for hydrogen and deuterium, respectively.

Exploring ancient microbial community assemblages by creating complex lipid biomarker profiles for stromatolites and microbial mats in Hamelin Pool, Shark Bay, Australia

NASA Astrophysics Data System (ADS)

Myers, E.; Summons, R. E.; Schubotz, F.; Matys, E. D.

2015-12-01

Stromatolites that are biogenic in origin, a characteristic that can be determined by the coexistence of microbial mats (active microbial communities) and stromatolites (lithified structures) like in Hamelin Pool, comprise one of the best modern analogs to ancient microbial community assemblages. Comprehensive lipid biomarker profiles that include lipids of varying persistence in the rock record can help determine how previously living microbial communities are represented in lithified stromatolites. To create these profiles, the samples analyzed included non-lithified smooth, pustular, and colloform microbial mats, as well as smooth and colloform stromatolites. Select samples were separated into upper and lower layers of 5cm depth each. Intact polar lipids, glycerol dialkyl glycerol tetraethers, and bacteriohopanepolyols were analyzed via liquid chromatography-mass spectrometry (LC-MS) coupled to a Quadropole Time-of-Flight (QTOF) mass spectrometer; additionally, fatty acids from each sample were analyzed using gas chromatography-mass spectrometry (GC-MS) to prove consistent signatures with those determined by Allen et al. in 2010 for similar microbial mat samples. In accordance with those findings, 2-methylhopanoids were detected, as well as limited signals from higher (vascular) plants, the latter of which suggests terrestrial inputs, potentially from runoff. The rarely detected presence of 3-methylhopanoids appears in a significant portion of the samples, though further isolations of the molecule are needed to confirm. While all lipid profiles were relatively similar, certain differences in relative composition are likely attributable to morphological differences of the mats, some of which allow deeper oxygen and/or sunlight penetration, which influence the microbial community. However, overall similarities of transient and persistent lipids suggest that the microbial communities of both the non-lithified microbial mats and stromatolites are similar.

Mass spectrometry based proteomics profiling as diagnostic tool in oncology: current status and future perspective.

PubMed

Findeisen, Peter; Neumaier, Michael

2009-01-01

Proteomics analysis has been heralded as a novel tool for identifying new and specific biomarkers that may improve diagnosis and monitoring of various disease states. Recent years have brought a number of proteomics profiling technologies. Although proteomics profiling has resulted in the detection of disease-associated differences and modification of proteins, current proteomics technologies display certain limitations that are hampering the introduction of these new technologies into clinical laboratory diagnostics and routine applications. In this review, we summarize current advances in mass spectrometry based biomarker discovery. The promises and challenges of this new technology are discussed with particular emphasis on diagnostic perspectives of mass-spectrometry based proteomics profiling for malignant diseases.

Overview of SIMS-Based Experimental Studies of Tracer Diffusion in Solids and Application to Mg Self-Diffusion

DOE PAGES

Kulkarni, Nagraj S.; Bruce Warmack, Robert J.; Radhakrishnan, Bala; ...

2014-09-23

Tracer diffusivities provide the most fundamental information on diffusion in materials and are the foundation of robust diffusion databases. Compared to traditional radiotracer techniques that utilize radioactive isotopes, the secondary ion mass spectrometry (SIMS) based thin-film technique for tracer diffusion is based on the use of enriched stable isotopes that can be accurately profiled using SIMS. Experimental procedures & techniques that are utilized for the measurement of tracer diffusion coefficients are presented for pure magnesium, which presents some unique challenges due to the ease of oxidation. The development of a modified Shewmon-Rhines diffusion capsule for annealing Mg and an ultra-highmore » vacuum (UHV) system for sputter deposition of Mg isotopes are discussed. Optimized conditions for accurate SIMS depth profiling in polycrystalline Mg are provided. An automated procedure for the correction of heat-up and cool-down times during tracer diffusion annealing is discussed. The non-linear fitting of a SIMS depth profile data using the thin film Gaussian solution to obtain the tracer diffusivity along with the background tracer concentration and tracer film thickness is discussed. An Arrhenius fit of the Mg self-diffusion data obtained using the low-temperature SIMS measurements from this study and the high-temperature radiotracer measurements of Shewmon and Rhines (1954) was found to be a good representation of both types of diffusion data that cover a broad range of temperatures between 250 - 627° C (523 900 K).« less

Double perovskite cathodes for proton-conducting ceramic fuel cells: are they triple mixed ionic electronic conductors?

PubMed Central

Téllez Lozano, Helena; Druce, John; Cooper, Samuel J.; Kilner, John A.

2017-01-01

Abstract 18O and 2H diffusion has been investigated at a temperature of 300 °C in the double perovskite material PrBaCo2O5+δ (PBCO) in flowing air containing 200 mbar of 2H2 16O. Secondary ion mass spectrometry (SIMS) depth profiling of exchanged ceramics has shown PBCO still retains significant oxygen diffusivity (~1.3 × 10−11 cm2s−1) at this temperature and that the presence of water (2H2 16O), gives rise to an enhancement of the surface exchange rate over that in pure oxygen by a factor of ~3. The 2H distribution, as inferred from the 2H2 16O− SIMS signal, shows an apparent depth profile which could be interpreted as 2H diffusion. However, examination of the 3-D distribution of the signal shows it to be nonhomogeneous and probably related to the presence of hydrated layers in the interior walls of pores and is not due to proton diffusion. This suggests that PBCO acts mainly as an oxygen ion mixed conductor when used in PCFC devices, although the presence of a small amount of protonic conductivity cannot be discounted in these materials. PMID:29383047

Three-dimensional imaging of cholesterol and sphingolipids within a Madin-Darby canine kidney cell

DOE PAGES

Yeager, Ashley N.; Weber, Peter K.; Kraft, Mary L.

2016-01-08

Metabolic stable isotope incorporation and secondary ion mass spectrometry(SIMS) depth profiling performed on a Cameca NanoSIMS 50 were used to image the 18O-cholesterol and 15N-sphingolipid distributions within a portion of a Madin-Darby canine kidney (MDCK) cell. Three-dimensional representations of the component-specific isotope distributions show clearly defined regions of 18O-cholesterol and 15N-sphingolipid enrichment that seem to be separate subcellular compartments. Furthermore, the low levels of nitrogen-containing secondary ions detected at the 18O-enriched regions suggest that these 18O-cholesterol-rich structures may be lipiddroplets, which have a core consisting of cholesterol esters and triacylglycerides.

Three-dimensional imaging of cholesterol and sphingolipids within a Madin-Darby canine kidney cell

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

Yeager, Ashley N.; Weber, Peter K.; Kraft, Mary L.

Metabolic stable isotope incorporation and secondary ion mass spectrometry(SIMS) depth profiling performed on a Cameca NanoSIMS 50 were used to image the 18O-cholesterol and 15N-sphingolipid distributions within a portion of a Madin-Darby canine kidney (MDCK) cell. Three-dimensional representations of the component-specific isotope distributions show clearly defined regions of 18O-cholesterol and 15N-sphingolipid enrichment that seem to be separate subcellular compartments. Furthermore, the low levels of nitrogen-containing secondary ions detected at the 18O-enriched regions suggest that these 18O-cholesterol-rich structures may be lipiddroplets, which have a core consisting of cholesterol esters and triacylglycerides.

In-Depth Two-Year Study of Phenolic Profile Variability among Olive Oils from Autochthonous and Mediterranean Varieties in Morocco, as Revealed by a LC-MS Chemometric Profiling Approach.

PubMed

Bajoub, Aadil; Medina-Rodríguez, Santiago; Olmo-García, Lucía; Ajal, El Amine; Monasterio, Romina P; Hanine, Hafida; Fernández-Gutiérrez, Alberto; Carrasco-Pancorbo, Alegría

2016-12-28

Olive oil phenolic fraction considerably contributes to the sensory quality and nutritional value of this foodstuff. Herein, the phenolic fraction of 203 olive oil samples extracted from fruits of four autochthonous Moroccan cultivars ("Picholine Marocaine", "Dahbia", "Haouzia" and "Menara"), and nine Mediterranean varieties recently introduced in Morocco ("Arbequina", "Arbosana", "Cornicabra", "Frantoio", "Hojiblanca", "Koroneiki", "Manzanilla", "Picholine de Languedoc" and "Picual"), were explored over two consecutive crop seasons (2012/2013 and 2013/2014) by using liquid chromatography-mass spectrometry. A total of 32 phenolic compounds (and quinic acid), belonging to five chemical classes (secoiridoids, simple phenols, flavonoids, lignans and phenolic acids) were identified and quantified. Phenolic profiling revealed that the determined phenolic compounds showed variety-dependent levels, being, at the same time, significantly affected by the crop season. Moreover, based on the obtained phenolic composition and chemometric linear discriminant analysis, statistical models were obtained allowing a very satisfactory classification and prediction of the varietal origin of the studied oils.

228Ra and 226Ra Profiles from the Northern South China Sea

NASA Astrophysics Data System (ADS)

Lin, H.; Chung, Y.; Lin, C.

2005-05-01

We previously reported the distributions of 228Ra and 226Ra in the northern South China Sea (SCS) which showed that both nuclides in surface waters were much higher than those in the open oceans because the SCS was enclosed mostly by landmasses which are known as sources of these nuclides. Large temporal and spectial variations were also observed probably due to the monsoons and intrusion of the Kuroshio Current. During a recent cruise conducted in the northern SCS in February, 2004, three vertical 228Ra profiles were measured by gamma spectrometry on the Ra isotopes which were concentrated first by the MnO2-impregnated acrylic fiber and then acid-washed as sample solution for counting. The two deep water 228Ra profiles are remarkably similar, showing high values in the surface layer and fairly uniform at about 10 to 13 dpm/100L below 200m depth but with a clear increase toward the bottom due to input from the underlying sediments. The shallow water profile on the shelf shows higher 228Ra values due to both vertical and horizontal mixing of the shelf water with additional source from the shore zone. Additional 228Ra profiles measured on samples from earlier cruises show that the deep water values may differ significantly (up to 5 dpm/100L) at the same location in different seasons or cruises. The associated 226Ra profiles are also variable but quite comparable to those in the northwest Pacific in deep water. 226Ra activities in the shallow water (less than 1000m depth) are higher in the SCS than in the open oceans. The 228Ra/226Ra activity ratios vary mostly from about 0.3 to 0.5 in the deep water. These values are much higher than those in the open oceans which are generally less than 0.1.

Direct Observation of Ion Distributions near Electrodes in Ionic Polymer Actuators Containing Ionic Liquids

PubMed Central

Liu, Yang; Lu, Caiyan; Twigg, Stephen; Ghaffari, Mehdi; Lin, Junhong; Winograd, Nicholas; Zhang, Q. M.

2013-01-01

The recent boom of energy storage and conversion devices, exploiting ionic liquids (ILs) to enhance the performance, requires an in-depth understanding of this new class of electrolytes in device operation conditions. One central question critical to device performance is how the mobile ions accumulate near charged electrodes. Here, we present the excess ion depth profiles of ILs in ionomer membrane actuators (Aquivion/1-butyl-2,3-dimethylimidazolium chloride (BMMI-Cl), 27 μm thick), characterized directly by Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) at liquid nitrogen temperature. Experimental results reveal that for the IL studied, cations and anions are accumulated at both electrodes. The large difference in the total volume occupied by the excess ions between the two electrodes cause the observed large bending actuation of the actuator. Hence we demonstrate that ToF-SIMS experiment provides great insights on the physics nature of ionic devices. PMID:23512124

Depth-Resolved Nanospray Desorption Electrospray Ionization Mass Spectrometry in Biofilms

DTIC Science & Technology

2015-11-16

metabolites and possibly proteins from biofilms at different depth. A microcapillary system was developed and tested for this goal. The...demonstrated that a dual microcapillary system can be used to collect nanoliter sample from the biofilms at 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND...Spectrometry in Biofilms The views, opinions and/or findings contained in this report are those of the author(s) and should not contrued as an official

Impurity measurements in semiconductor materials using trace element accelerator mass spectrometry

NASA Astrophysics Data System (ADS)

McDaniel, F. D.; Datar, S. A.; Nigam, M.; Ravi Prasad, G. V.

2002-05-01

Accelerator mass spectrometry (AMS) is commonly used to determine the abundance ratios of long-lived isotopes such as 10B, 14C, 36Cl, 129I, etc. to their stable counterparts at levels as low as 10 -16. Secondary ion mass spectrometry (SIMS) is routinely used to determine impurity levels in materials by depth profiling techniques. Trace-element accelerator mass spectrometry (TEAMS) is a combination of AMS and SIMS, presently being used at the University of North Texas, for high-sensitivity (ppb) impurity analyses of stable isotopes in semiconductor materials. The molecular break-up characteristics of AMS are used with TEAMS to remove the molecular interferences present in SIMS. Measurements made with different substrate/impurity combinations demonstrate that TEAMS has higher sensitivity for many elements than other techniques such as SIMS and can assist with materials characterization issues. For example, measurements of implanted As in the presence of Ge in Ge xSi 1- x/Si is difficult with SIMS because of molecular interferences from 74GeH, 29Si 30Si 16O, etc. With TEAMS, the molecular interferences are removed and higher sensitivities are obtained. Measured substrates include Si, SiGe, CoSi 2, GaAs and GaN. Measured impurities include B, N, F, Mg, P, Cl, Cr, Fe, Ni, Co, Cu, Zn, Ge, As, Se, Mo, Sn and Sb. A number of measurements will be presented to illustrate the range and power of TEAMS.

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.

Quantitative evaluation of sputtering induced surface roughness and its influence on AES depth profiles of polycrystalline Ni/Cu multilayer thin films

NASA Astrophysics Data System (ADS)

Yan, X. L.; Coetsee, E.; Wang, J. Y.; Swart, H. C.; Terblans, J. J.

2017-07-01

The polycrystalline Ni/Cu multilayer thin films consisting of 8 alternating layers of Ni and Cu were deposited on a SiO2 substrate by means of electron beam evaporation in a high vacuum. Concentration-depth profiles of the as-deposited multilayered Ni/Cu thin films were determined with Auger electron spectroscopy (AES) in combination with Ar+ ion sputtering, under various bombardment conditions with the samples been stationary as well as rotating in some cases. The Mixing-Roughness-Information depth (MRI) model used for the fittings of the concentration-depth profiles accounts for the interface broadening of the experimental depth profiling. The interface broadening incorporates the effects of atomic mixing, surface roughness and information depth of the Auger electrons. The roughness values extracted from the MRI model fitting of the depth profiling data agrees well with those measured by atomic force microscopy (AFM). The ion sputtering induced surface roughness during the depth profiling was accordingly quantitatively evaluated from the fitted MRI parameters with sample rotation and stationary conditions. The depth resolutions of the AES depth profiles were derived directly from the values determined by the fitting parameters in the MRI model.

Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling

DOE PAGES

Benton, H. Paul; Ivanisevic, Julijana; Mahieu, Nathaniel G.; ...

2014-12-12

An autonomous metabolomic workflow combining mass spectrometry analysis with tandem mass spectrometry data acquisition was designed to allow for simultaneous data processing and metabolite characterization. Although previously tandem mass spectrometry data have been generated on the fly, the experiments described herein combine this technology with the bioinformatic resources of XCMS and METLIN. We can analyze large profiling datasets and simultaneously obtain structural identifications, as a result of this unique integration. Furthermore, validation of the workflow on bacterial samples allowed the profiling on the order of a thousand metabolite features with simultaneous tandem mass spectra data acquisition. The tandem mass spectrometrymore » data acquisition enabled automatic search and matching against the METLIN tandem mass spectrometry database, shortening the current workflow from days to hours. Overall, the autonomous approach to untargeted metabolomics provides an efficient means of metabolomic profiling, and will ultimately allow the more rapid integration of comparative analyses, metabolite identification, and data analysis at a systems biology level.« less

Model studies of diffusion-controlled (2-hydroxyethyl methacrylate) HEMA hydrogel membranes for controlled release of proteins

NASA Astrophysics Data System (ADS)

Appawu, Jennifer A. M.

This thesis project consisted of three main components that were connected by roots in chemical analysis for studies in tissue engineering. The first part focused on characterizing the structural parameters of synthetic cross-linked poly (2-hydroxyethyl methacrylate) (Poly(HEMA) hydrogel membranes to determine optimal formulations for clinical studies. Poly(HEMA) membranes were loaded with Keratincocyte Growth Factor (KGF) for controlled release studies. Protein loading and release kinetics were determined with fluorescence spectroscopy. The spatial distribution of a protein in the membrane was determined using Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS). The last part of the project focused on determining the biological effects of the polymer membranes in-vitro with a model cell line and a pilot in-vivo animal study. Based on the components completed in this project, five chapters are included in this dissertation document and are summarized below. A new protocol was developed using fluorescence spectroscopy that measured the rate of protein diffusion into cross-linked polymer membranes by measuring the change in the fluorescence intensity of the protein solution. This technique was also able to detect a conformational change that occurs within protein when KGF was imbibed within these cross-linked polymer membranes. ToF-SIMS chemical imaging and 3D depth profiling was used to determine the spatial distribution of KGF protein in frozen-hydrated HEMA hydrogel membranes. The 3D depth profiles showed that the KGF protein was aggregated in bright spots that indicated that KGF was not spatially homogenous on the surface and through the depth profiles. 3D depth profiles of the membranes studied at various times during release studies show that areas with aggregated proteins were retained during release, and at times with maximum release. The interpretation of the bright regions is that the KGf protein interacted with the cross-linked network of the hydrogel membranes, making it not available for release. The in-vitro biological experiments with the HaCaT cell line showed that the HEMA hydrogels were capable of sustaining cell viability, proliferation, and adhesion through cell adhesion and wounding experiments. The pilot in-vivo animal study also revealed that KGF protein had retained its pharmacological activity. The study also showed that the KGF protein enhanced the rate of wound closure.

One- and two-dimensional dopant/carrier profiling for ULSI

NASA Astrophysics Data System (ADS)

Vandervorst, W.; Clarysse, T.; De Wolf, P.; Trenkler, T.; Hantschel, T.; Stephenson, R.; Janssens, T.

1998-11-01

Dopant/carrier profiles constitute the basis of the operation of a semiconductor device and thus play a decisive role in the performance of a transistor and are subjected to the same scaling laws as the other constituents of a modern semiconductor device and continuously evolve towards shallower and more complex configurations. This evolution has increased the demands on the profiling techniques in particular in terms of resolution and quantification such that a constant reevaluation and improvement of the tools is required. As no single technique provides all the necessary information (dopant distribution, electrical activation,..) with the requested spatial and depth resolution, the present paper attempts to provide an assessment of those tools which can be considered as the main metrology technologies for ULSI-applications. For 1D-dopant profiling secondary ion mass spectrometry (SIMS) has progressed towards a generally accepted tool meeting the requirements. For 1D-carrier profiling spreading resistance profiling and microwave surface impedance profiling are envisaged as the best choices but extra developments are required to promote them to routinely applicable methods. As no main metrology tool exist for 2D-dopant profiling, main emphasis is on 2D-carrier profiling tools based on scanning probe microscopy. Scanning spreading resistance (SSRM) and scanning capacitance microscopy (SCM) are the preferred methods although neither of them already meets all the requirements. Complementary information can be extracted from Nanopotentiometry which samples the device operation in more detail. Concurrent use of carrier profiling tools, Nanopotentiometry, analysis of device characteristics and simulations is required to provide a complete characterization of deep submicron devices.

3D ToF-SIMS Analysis of Peptide Incorporation into MALDI Matrix Crystals with Sub-micrometer Resolution.

PubMed

Körsgen, Martin; Pelster, Andreas; Dreisewerd, Klaus; Arlinghaus, Heinrich F

2016-02-01

The analytical sensitivity in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is largely affected by the specific analyte-matrix interaction, in particular by the possible incorporation of the analytes into crystalline MALDI matrices. Here we used time-of-flight secondary ion mass spectrometry (ToF-SIMS) to visualize the incorporation of three peptides with different hydrophobicities, bradykinin, Substance P, and vasopressin, into two classic MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (HCCA). For depth profiling, an Ar cluster ion beam was used to gradually sputter through the matrix crystals without causing significant degradation of matrix or biomolecules. A pulsed Bi3 ion cluster beam was used to image the lateral analyte distribution in the center of the sputter crater. Using this dual beam technique, the 3D distribution of the analytes and spatial segregation effects within the matrix crystals were imaged with sub-μm resolution. The technique could in the future enable matrix-enhanced (ME)-ToF-SIMS imaging of peptides in tissue slices at ultra-high resolution. Graphical Abstract ᅟ.

3D ToF-SIMS Analysis of Peptide Incorporation into MALDI Matrix Crystals with Sub-micrometer Resolution

NASA Astrophysics Data System (ADS)

Körsgen, Martin; Pelster, Andreas; Dreisewerd, Klaus; Arlinghaus, Heinrich F.

2016-02-01

The analytical sensitivity in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is largely affected by the specific analyte-matrix interaction, in particular by the possible incorporation of the analytes into crystalline MALDI matrices. Here we used time-of-flight secondary ion mass spectrometry (ToF-SIMS) to visualize the incorporation of three peptides with different hydrophobicities, bradykinin, Substance P, and vasopressin, into two classic MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (HCCA). For depth profiling, an Ar cluster ion beam was used to gradually sputter through the matrix crystals without causing significant degradation of matrix or biomolecules. A pulsed Bi3 ion cluster beam was used to image the lateral analyte distribution in the center of the sputter crater. Using this dual beam technique, the 3D distribution of the analytes and spatial segregation effects within the matrix crystals were imaged with sub-μm resolution. The technique could in the future enable matrix-enhanced (ME)-ToF-SIMS imaging of peptides in tissue slices at ultra-high resolution.

Sugar nucleotide quantification by liquid chromatography tandem mass spectrometry reveals a distinct profile in Plasmodium falciparum sexual stage parasites

PubMed Central

López-Gutiérrez, Borja; Dinglasan, Rhoel R.

2017-01-01

The obligate intracellular lifestyle of Plasmodium falciparum and the difficulties in obtaining sufficient amounts of biological material have hampered the study of specific metabolic pathways in the malaria parasite. Thus, for example, the pools of sugar nucleotides required to fuel glycosylation reactions have never been studied in-depth in well-synchronized asexual parasites or in other stages of its life cycle. These metabolites are of critical importance, especially considering the renewed interest in the presence of N-, O-, and other glycans in key parasite proteins. In this work, we adapted a liquid chromatography tandem mass spectrometry (LC-MS/MS) method based on the use of porous graphitic carbon (PGC) columns and MS-friendly solvents to quantify sugar nucleotides in the malaria parasite. We report the thorough quantification of the pools of these metabolites throughout the intraerythrocytic cycle of P. falciparum. The sensitivity of the method enabled, for the first time, the targeted analysis of these glycosylation precursors in gametocytes, the parasite sexual stages that are transmissible to the mosquito vector. PMID:28104756

Glow discharge spectrometry for the characterization of nuclear and radioactively contaminated environmental samples

NASA Astrophysics Data System (ADS)

Betti, Maria; Aldave de las Heras, Laura

2004-09-01

Glow discharge (GD) spectrometry as applied to characterize nuclear samples as well as for the determination of radionuclides in environmental samples is reviewed. The use of instrumentation for direct current (d.c.) glow discharge mass spectrometry (GDMS) and radio frequency glow discharge optical emission spectrometry (rf GDOES), installed inside a glove-box for the handling of radioactive samples as well as the two installations and their analytical possibilities, is described in detail. The applications of GD techniques for the characterization of samples of nuclear concern both with respect to their major and trace elements, as well as to the matrix isotopic composition are presented. Procedures for quantitative determination of major, minor, and trace elements in conductive samples are reported. As for non-conductive samples three different approaches for their measurement can be followed. Namely, the use of rf sources, the mixing of the sample with a binder conducting host matrix, and the use of a secondary cathode. In the case of oxide-based samples, the employment of a tantalum secondary cathode, acting as an oxygen getter, reduces the availability of oxygen to form polyatomic species and to produce quenching. Considerations on the use of the relative sensitivity factors (RSFs) in different matrices are reported. The analytical capabilities of GDMS are compared with ICP-MS in terms of accuracy, precision, and detection limit for the determination of trace elements in uranium oxide specimens. As for the determination of isotopic composition, GDMS was found to be competitive with thermal ionisation mass spectrometry (TIMS) as well as for bulk determinations of major elements with titration methods. Applications of GDMS to the determination of radioisotopes in environmental samples, as well for depth profiling of trace elements in oxide layers, are discussed.

Plasma metabolic profiling analysis of nephrotoxicity induced by acyclovir using metabonomics coupled with multivariate data analysis.

PubMed

Zhang, Xiuxiu; Li, Yubo; Zhou, Huifang; Fan, Simiao; Zhang, Zhenzhu; Wang, Lei; Zhang, Yanjun

2014-08-01

Acyclovir (ACV) is an antiviral agent. However, its use is limited by adverse side effect, particularly by its nephrotoxicity. Metabonomics technology can provide essential information on the metabolic profiles of biofluids and organs upon drug administration. Therefore, in this study, mass spectrometry-based metabonomics coupled with multivariate data analysis was used to identify the plasma metabolites and metabolic pathways related to nephrotoxicity caused by intraperitoneal injection of low (50mg/kg) and high (100mg/kg) doses of acyclovir. Sixteen biomarkers were identified by metabonomics and nephrotoxicity results revealed the dose-dependent effect of acyclovir on kidney tissues. The present study showed that the top four metabolic pathways interrupted by acyclovir included the metabolisms of arachidonic acid, tryptophan, arginine and proline, and glycerophospholipid. This research proves the established metabonomic approach can provide information on changes in metabolites and metabolic pathways, which can be applied to in-depth research on the mechanism of acyclovir-induced kidney injury. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

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

Laser-ablation electrospray ionization mass spectrometry with ion mobility separation reveals metabolites in the symbiotic interactions of soybean roots and rhizobia.

PubMed

Stopka, Sylwia A; Agtuca, Beverly J; Koppenaal, David W; Paša-Tolić, Ljiljana; Stacey, Gary; Vertes, Akos; Anderton, Christopher R

2017-07-01

Technologies enabling in situ metabolic profiling of living plant systems are invaluable for understanding physiological processes and could be used for rapid phenotypic screening (e.g., to produce plants with superior biological nitrogen-fixing ability). The symbiotic interaction between legumes and nitrogen-fixing soil bacteria results in a specialized plant organ (i.e., root nodule) where the exchange of nutrients between host and endosymbiont occurs. Laser-ablation electrospray ionization mass spectrometry (LAESI-MS) is a method that can be performed under ambient conditions requiring minimal sample preparation. Here, we employed LAESI-MS to explore the well characterized symbiosis between soybean (Glycine max L. Merr.) and its compatible symbiont, Bradyrhizobium japonicum. The utilization of ion mobility separation (IMS) improved the molecular coverage, selectivity, and identification of the detected biomolecules. Specifically, incorporation of IMS resulted in an increase of 153 differentially abundant spectral features in the nodule samples. The data presented demonstrate the advantages of using LAESI-IMS-MS for the rapid analysis of intact root nodules, uninfected root segments, and free-living rhizobia. Untargeted pathway analysis revealed several metabolic processes within the nodule (e.g., zeatin, riboflavin, and purine synthesis). Compounds specific to the uninfected root and bacteria were also detected. Lastly, we performed depth profiling of intact nodules to reveal the location of metabolites to the cortex and inside the infected region, and lateral profiling of sectioned nodules confirmed these molecular distributions. Our results established the feasibility of LAESI-IMS-MS for the analysis and spatial mapping of plant tissues, with its specific demonstration to improve our understanding of the soybean-rhizobial symbiosis. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Laser-ablation electrospray ionization mass spectrometry with ion mobility separation reveals metabolites in the symbiotic interactions of soybean roots and rhizobia

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

Stopka, Sylwia A.; Agtuca, Beverly J.; Koppenaal, David W.

Technologies enabling in situ metabolic profiling of living plant systems are invaluable for understanding physiological processes and could be used for rapid phenotypic screening (e.g., to produce plants with superior biological nitrogen fixing ability). The symbiotic interaction between legumes and nitrogen-fixing soil bacteria results in a specialized plant organ (i.e., root nodule), where the exchange of nutrients between host and endosymbiont occurs. Laser ablation electrospray ionization mass spectrometry (LAESI-MS) is a method that can be performed under ambient conditions requiring minimal sample preparation. Here, we employed LAESI-MS to explore the well-characterized symbiosis between soybean (Glycine max L. Merr.) and itsmore » compatible symbiont, Bradyrhizobium japonicum. The utilization of ion mobility separation (IMS) improved the molecular coverage, selectivity, and identification of the detected biomolecules. Specifically, incorporation of IMS resulted in an increase of 153 detected metabolites in the nodule samples. The data presented demonstrates the advantages of using LAESI-IMS-MS for the rapid analysis of intact root nodules, uninfected root segments, and free-living rhizobia. Untargeted pathway analysis revealed several metabolic processes within the nodule (e.g., zeatin, riboflavin, and purine synthesis). Compounds specific to the uninfected root and bacteria were also detected. Lastly, we performed depth-profiling of intact nodules to reveal the location of metabolites to the cortex and inside the infected region, and lateral profiling of sectioned nodules confirmed these molecular distributions. Our results established the feasibility of LAESI-IMS-MS for the analysis and spatial mapping of plant tissues, with its specific demonstration to improve our understanding of the soybean-rhizobial symbiosis.« less

TOF-SIMS Analysis of Red Color Inks of Writing and Printing Tools on Questioned Documents.

PubMed

Lee, Jihye; Nam, Yun Sik; Min, Jisook; Lee, Kang-Bong; Lee, Yeonhee

2016-05-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a well-established surface technique that provides both elemental and molecular information from several monolayers of a sample surface while also allowing depth profiling or image mapping to be performed. Static TOF-SIMS with improved performances has expanded the application of TOF-SIMS to the study of a variety of organic, polymeric, biological, archaeological, and forensic materials. In forensic investigation, the use of a minimal sample for the analysis is preferable. Although the TOF-SIMS technique is destructive, the probing beams have microsized diameters so that only small portion of the questioned sample is necessary for the analysis, leaving the rest available for other analyses. In this study, TOF-SIMS and attenuated total reflectance Fourier transform infrared (ATR-FTIR) were applied to the analysis of several different pen inks, red sealing inks, and printed patterns on paper. The overlapping areas of ballpoint pen writing, red seal stamping, and laser printing in a document were investigated to identify the sequence of recording. The sequence relations for various cases were determined from the TOF-SIMS mapping image and the depth profile. TOF-SIMS images were also used to investigate numbers or characters altered with two different red pens. TOF-SIMS was successfully used to determine the sequence of intersecting lines and the forged numbers on the paper. © 2016 American Academy of Forensic Sciences.

Motion of W and He atoms during formation of W fuzz

NASA Astrophysics Data System (ADS)

Doerner, R. P.; Nishijima, D.; Krasheninnikov, S. I.; Schwarz-Selinger, T.; Zach, M.

2018-06-01

Measurements are conducted to identify the motion of tungsten and helium atoms during the formation of tungsten fuzz. In a first series of experiments the mobility of helium within the growing fuzz was measured by adding 3He to the different stages of plasma exposure under conditions that promoted tungsten fuzz growth. Ion beam analysis was used to quantify the amount of 3He remaining in the samples following the plasma exposure. The results indicate that the retention of helium in bubbles within tungsten is a dynamic process with direct implantation rather than diffusion into the bubbles, best describing the motion of the helium atoms. In the second experiment, an isotopically enriched layer of tungsten (~92.99% 182W) is deposited on the surface of a bulk tungsten sample with the natural abundance of the isotopes. This sample is then exposed to helium plasma at the conditions necessary to support the formation of tungsten ‘fuzz’. Depth profiles of the concentration of each of the tungsten isotopes are obtained using secondary ion mass spectrometry (SIMS) before and after the plasma exposure. The depth profiles clearly show mixing of tungsten atoms from the bulk sample toward the surface of the fuzz. This supports a physical picture of the dynamic behavior of helium bubbles which, also, causes an enhanced mixing of tungsten atoms.

Motion of W and He atoms during formation of W fuzz

DOE PAGES

Doerner, R. P.; Nishijima, D.; Krasheninnikov, S. I.; ...

2018-04-11

Measurements are conducted to identify the motion of tungsten and helium atoms during the formation of tungsten fuzz. In a first series of experiments the mobility of helium within the growing fuzz was measured by adding 3He to the different stages of plasma exposure under conditions that promoted tungsten fuzz growth. Ion beam analysis was used to quantify the amount of 3He remaining in the samples following the plasma exposure. The results indicate that the retention of helium in bubbles within tungsten is a dynamic process with direct implantation rather than diffusion into the bubbles, best describing the motion ofmore » the helium atoms. In the second experiment, an isotopically enriched layer of tungsten (~92.99% 182W) is deposited on the surface of a bulk tungsten sample with the natural abundance of the isotopes. This sample is then exposed to helium plasma at the conditions necessary to support the formation of tungsten 'fuzz'. Depth profiles of the concentration of each of the tungsten isotopes are obtained using secondary ion mass spectrometry (SIMS) before and after the plasma exposure. The depth profiles clearly show mixing of tungsten atoms from the bulk sample toward the surface of the fuzz. Lastly, this supports a physical picture of the dynamic behavior of helium bubbles which, also, causes an enhanced mixing of tungsten atoms.« less

Cerebrospinal Fluid Metabolomics After Natural Product Treatment in an Experimental Model of Cerebral Ischemia.

PubMed

Huan, Tao; Xian, Jia Wen; Leung, Wing Nang; Li, Liang; Chan, Chun Wai

2016-11-01

Cerebrospinal fluid (CSF) is an important biofluid for diagnosis of and research on neurological diseases. However, in-depth metabolomic profiling of CSF remains an analytical challenge due to the small volume of samples, particularly in small animal models. In this work, we report the application of a high-performance chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) workflow for CSF metabolomics in Gastrodia elata and Uncaria rhynchophylla water extract (GUW)-treated experimental cerebral ischemia model of rat. The GUW is a commonly used Traditional Chinese Medicine (TCM) for hypertension and brain disease. This study investigated the amine- and phenol-containing biomarkers in the CSF metabolome. After GUW treatment for 7 days, the neurological deficit score was significantly improved with infarct volume reduction, while the integrity of brain histological structure was preserved. Over 1957 metabolites were quantified in CSF by dansylation LC-MS. The analysis of this comprehensive list of metabolites suggests that metabolites associated with oxidative stress, inflammatory response, and excitotoxicity change during GUW-induced alleviation of ischemic injury. This work is significant in that (1) it shows CIL LC-MS can be used for in-depth profiling of the CSF metabolome in experimental ischemic stroke and (2) identifies several potential molecular targets (that might mediate the central nervous system) and associate with pharmacodynamic effects of some frequently used TCMs.

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.

In-depth analyses of native N-linked glycans facilitated by high-performance anion exchange chromatography-pulsed amperometric detection coupled to mass spectrometry.

PubMed

Szabo, Zoltan; Thayer, James R; Agroskin, Yury; Lin, Shanhua; Liu, Yan; Srinivasan, Kannan; Saba, Julian; Viner, Rosa; Huhmer, Andreas; Rohrer, Jeff; Reusch, Dietmar; Harfouche, Rania; Khan, Shaheer H; Pohl, Christopher

2017-05-01

Characterization of glycans present on glycoproteins has become of increasing importance due to their biological implications, such as protein folding, immunogenicity, cell-cell adhesion, clearance, receptor interactions, etc. In this study, the resolving power of high-performance anion exchange chromatography with pulsed amperometric detection (HPAE-PAD) was applied to glycan separations and coupled to mass spectrometry to characterize native glycans released from different glycoproteins. A new, rapid workflow generates glycans from 200 μg of glycoprotein supporting reliable and reproducible annotation by mass spectrometry (MS). With the relatively high flow rate of HPAE-PAD, post-column splitting diverted 60% of the flow to a novel desalter, then to the mass spectrometer. The delay between PAD and MS detectors is consistent, and salt removal after the column supports MS. HPAE resolves sialylated (charged) glycans and their linkage and positional isomers very well; separations of neutral glycans are sufficient for highly reproducible glycoprofiling. Data-dependent MS 2 in negative mode provides highly informative, mostly C- and Z-type glycosidic and cross-ring fragments, making software-assisted and manual annotation reliable. Fractionation of glycans followed by exoglycosidase digestion confirms MS-based annotations. Combining the isomer resolution of HPAE with MS 2 permitted thorough N-glycan annotation and led to characterization of 17 new structures from glycoproteins with challenging glycan profiles.

Profiling over 1500 lipids in induced lung sputum and the implications in studying lung diseases.

PubMed

t'Kindt, Ruben; Telenga, Eef D; Jorge, Lucie; Van Oosterhout, Antoon J M; Sandra, Pat; Ten Hacken, Nick H T; Sandra, Koen

2015-01-01

Induced lung sputum is a valuable matrix in the study of respiratory diseases. Although the methodology of sputum collection has evolved to a point where it is repeatable and responsive to inflammation, its use in molecular profiling studies is still limited. Here, an in-depth lipid profiling of induced lung sputum using high-resolution liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-Q-TOF MS) is described. An enormous complexity in lipid composition could be revealed. Over 1500 intact lipids, originating from 6 major lipid classes, have been accurately identified in 120 μL of induced sputum. By number and measured intensity, glycerophospholipids represent the largest lipid class, followed by sphingolipids, glycerolipids, fatty acyls, sterol lipids, and prenol lipids. Several prenol lipids, originating from tobacco, could be detected in the lung sputum of smokers. To illustrate the utility of the methodology in studying respiratory diseases, a comparative lipid screening was performed on lung sputum extracts in order to study the effect of Chronic Obstructive Pulmonary Disease (COPD) on the lung barrier lipidome. Results show that sphingolipid expression in induced sputum significantly differs between smokers with and without COPD.

In-Depth Two-Year Study of Phenolic Profile Variability among Olive Oils from Autochthonous and Mediterranean Varieties in Morocco, as Revealed by a LC-MS Chemometric Profiling Approach

PubMed Central

Bajoub, Aadil; Medina-Rodríguez, Santiago; Olmo-García, Lucía; Ajal, El Amine; Monasterio, Romina P.; Hanine, Hafida; Fernández-Gutiérrez, Alberto; Carrasco-Pancorbo, Alegría

2016-01-01

Olive oil phenolic fraction considerably contributes to the sensory quality and nutritional value of this foodstuff. Herein, the phenolic fraction of 203 olive oil samples extracted from fruits of four autochthonous Moroccan cultivars (“Picholine Marocaine”, “Dahbia”, “Haouzia” and “Menara”), and nine Mediterranean varieties recently introduced in Morocco (“Arbequina”, “Arbosana”, “Cornicabra”, “Frantoio”, “Hojiblanca”, “Koroneiki”, “Manzanilla”, “Picholine de Languedoc” and “Picual”), were explored over two consecutive crop seasons (2012/2013 and 2013/2014) by using liquid chromatography-mass spectrometry. A total of 32 phenolic compounds (and quinic acid), belonging to five chemical classes (secoiridoids, simple phenols, flavonoids, lignans and phenolic acids) were identified and quantified. Phenolic profiling revealed that the determined phenolic compounds showed variety-dependent levels, being, at the same time, significantly affected by the crop season. Moreover, based on the obtained phenolic composition and chemometric linear discriminant analysis, statistical models were obtained allowing a very satisfactory classification and prediction of the varietal origin of the studied oils. PMID:28036024

Profiling the indole alkaloids in yohimbe bark with ultra-performance liquid chromatography coupled with ion mobility quadrupole time-of-flight mass spectrometry

USDA-ARS?s Scientific Manuscript database

An ultra-high performance liquid chromatography-ion mobility- quadrupole time-of-flight mass spectrometry (UHPLC-IM-QTOF-MS) method was developed for profiling the indole alkaloids in yohimbe bark. Many indole alkaloids with the yohimbine core structure, plus methylated, oxidized, and reduced speci...

Characterization of Arsenic Contamination on Rust from Ton Containers

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

Gary S. Groenewold; Recep Avci; Robert V. Fox

The speciation and spatial distribution of arsenic on rusted steel surfaces affects both measurement and removal approaches. The chemistry of arsenic residing in the rust of ton containers that held the chemical warfare agents bis(2-chloroethyl)sulfide (sulfur mustard) and 2-chlorovinyldichloroarsine (Lewisite) is of particular interest, because while the agents have been decontaminated, residual arsenic could pose a health or environmental risk. The chemistry and distribution of arsenic in rust samples was probed using imaging secondary ion mass spectrometry (SIMS), X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy, and scanning electron microscopy/energy dispersive X-ray spectroscopy (SEM/EDX). Arsenic in the +3 and or +5more » oxidation state is homogeneously distributed at the very top-most layer of the rust samples, and is intimately associated with iron. Sputter depth profiling followed by SIMS and XPS shows As at a depth of several nm, in some cases in a reduced form. The SEM/EDX experiments show that As is present at a depth of several microns, but is inhomogeneously distributed; most locations contained oxidized As at concentrations of a few percent, however several locations showed very high As in a metallic form. These results indicate that the rust material must be removed if the steel containers are to be cleared of arsenic.« less

Fundamentals of Passive Oxidation In SiC and Si3N4

NASA Technical Reports Server (NTRS)

Thomas-Ogbuji, Linus U.

1998-01-01

The very slow oxidation kinetics of silicon carbide and silicon nitride, which derive from their adherent and passivating oxide films, has been explored at length in a broad series of studies utilizing thermogravimetric analysis, electron and optical micrography, energy dispersive spectrometry, x-ray diffractometry, micro-analytical depth profiling, etc. Some interesting microstructural phenomena accompanying the process of oxidation in the two materials will be presented. In Si3N4 the oxide is stratified, with an SiO2 topscale (which is relatively impervious to O2)underlain by a coherent subscale of silicon oxynitride which is even less permeable to O2- Such "defence in depth" endows Si3N4 with what is perhaps the highest oxidation resistance of any material, and results in a unique set of oxidation processes. In SiC the oxidation reactions are much simpler, yet new issues still emerge; for instance, studies involving controlled devitrification of the amorphous silica scale confirmed that the oxidation rate of SiC drops by more than an order of magnitude when the oxide scale fully crystallizes.

Rhenium in seawater - Confirmation of generally conservative behavior

NASA Technical Reports Server (NTRS)

Anbar, A. D.; Creaser, R. A.; Papanastassiou, D. A.; Wasserburg, G. J.

1992-01-01

A depth profile of the concentration of Re was measured in the Pacific Ocean using a technique developed for the clean chemical separation and the precise measurement of Re by isotope dilution and negative thermal ionization mass spectrometry (ID-NTIMS). We obtain a narrow range for Re from 7.20 +/- 0.03 to 7.38 +/- 0.03 ng/kg for depths between 45 m and 4700 m. This demonstrates that Re is relatively well mixed throughout the water column and confirms the theoretical prediction that the behavior of Re in the oceans is conservative. When examined in detail, both salinity and the concentration of Re increase by approximately 1.5 percent between 400 and 4700 m, a correlation consistent with conservative behavior. However, Re appears to be depleted relative to salinity by 1.0-1.5 percent at 100 m, and enriched by approximately 4 percent at the surface. These observations suggest a minor level of Re scavenging in near surface waters, and an input of Re to the ocean surface. This work demonstrates the utility of geochemical investigations of certain trace elements not previously been amenable to detailed study.

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.

Dendrimer pre-treatment enhances the skin permeation of chlorhexidine digluconate: Characterisation by in vitro percutaneous absorption studies and Time-of-Flight Secondary Ion Mass Spectrometry.

PubMed

Holmes, Amy M; Scurr, David J; Heylings, Jon R; Wan, Ka-Wai; Moss, Gary P

2017-06-15

Skin penetration and localisation of chlorhexidine digluconate (CHG) within the skin have been investigated in order to better understand and optimise the delivery using a nano polymeric delivery system of this topically-applied antimicrobial drug. Franz-type diffusion cell studies using in vitro porcine skin and tape stripping procedures were coupled with Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) to visualise the skin during various treatments with CHG and polyamidoamine dendrimers (PAMAM). Pre-treatment of the skin with PAMAM dendrimers significantly increased the amount and depth of permeation of CHG into the skin in vitro. The effect observed was not concentration dependant in the range 0.5-10mM PAMAM. This could be important in terms of the efficiency of treatment of bacterial infection in the skin. It appears that the mechanism of enhancement is due to the PAMAM dendrimer disrupting skin barrier lipid conformation or by occluding the skin surface. Franz-type diffusion cell experiments are complimented by the detailed visualisation offered by the semi-quantitative ToF-SIMS method which provides excellent benefits in terms of sensitivity and fragment ion specificity. This allows a more accurate depth profile of chlorhexidine permeation within the skin to be obtained and potentially affords the opportunity to map the co-localisation of permeants with skin structures, thus providing a greater ability to characterise skin absorption and to understand the mechanism of permeation, providing opportunities for new and more effective therapies. Copyright © 2017. Published by Elsevier B.V.

Substantial difference in target surface chemistry between reactive dc and high power impulse magnetron sputtering

NASA Astrophysics Data System (ADS)

Greczynski, G.; Mráz, S.; Schneider, J. M.; Hultman, L.

2018-02-01

The nitride layer formed in the target race track during the deposition of stoichiometric TiN thin films is a factor 2.5 thicker for high power impulse magnetron sputtering (HIPIMS), compared to conventional dc processing (DCMS). The phenomenon is explained using x-ray photoelectron spectroscopy analysis of the as-operated Ti target surface chemistry supported by sputter depth profiles, dynamic Monte Carlo simulations employing the TRIDYN code, and plasma chemical investigations by ion mass spectrometry. The target chemistry and the thickness of the nitride layer are found to be determined by the implantation of nitrogen ions, predominantly N+ and N2+ for HIPIMS and DCMS, respectively. Knowledge of this method-inherent difference enables robust processing of high quality functional coatings.

Trends in biochemical and biomedical applications of mass spectrometry

NASA Astrophysics Data System (ADS)

Gelpi, Emilio

1992-09-01

This review attempts an in-depth evaluation of progress and achievements made since the last 11th International Mass Spectrometry Conference in the application of mass spectrometric techniques to biochemistry and biomedicine. For this purpose, scientific contributions in this field at major international meetings have been monitored, together with an extensive appraisal of literature data covering the period from 1988 to 1991. A bibliometric evaluation of the MEDLINE database for this period provides a total of almost 4000 entries for mass spectrometry. This allows a detailed study of literature and geographical sources of the most frequent applications, of disciplines where mass spectrometry is most active and of types of sample and instrumentation most commonly used. In this regard major efforts according to number of publications (over 100 literature reports) are concentrated in countries like Canada, France, Germany, Italy, Japan, Sweden, UK and the USA. Also, most of the work using mass spectrometry in biochemistry and biomedicine is centred on studies on biotransformation, metabolism, pharmacology, pharmacokinetics and toxicology, which have been carried out on samples of blood, urine, plasma and tissue, by order of frequency of use. Human and animal studies appear to be evenly distributed in terms of the number of reports published in the literature in which the authors make use of experimental animals or describe work on human samples. Along these lines, special attention is given to the real usefulness of mass spectrometry (MS) technology in routine medical practice. Thus the review concentrates on evaluating the progress made in disease diagnosis and overall patient care. As regards prevailing techniques, GCMS continues to be the mainstay of the state of the art methods for multicomponent analysis, stable isotope tracer studies and metabolic profiling, while HPLC--MS and tandem MS are becoming increasingly important in biomedical research. However, despite the relatively large number of mass spectrometry reports in the biomedical sciences very few true routine applications are described, and recent technological innovations in instrumentation such as FABMS, electrospray, plasma or laser desorption have contributed relatively much more to structural biology, especially in biopolymer studies of macromolecules rather than to real life biomedical applications on patients and clinical problems.

Low-temperature lithium diffusion in simulated high-level boroaluminosilicate nuclear waste glasses

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

Neeway, James J.; Kerisit, Sebastien N.; Gin, Stephane

2014-12-01

Ion exchange is recognized as an integral, if underrepresented, mechanism influencing glass corrosion. However, due to the formation of various alteration layers in the presence of water, it is difficult to conclusively deconvolute the mechanisms of ion exchange from other processes occurring simultaneously during corrosion. In this work, an operationally inert non-aqueous solution was used as an alkali source material to isolate ion exchange and study the solid-state diffusion of lithium. Specifically, the experiments involved contacting glass coupons relevant to the immobilization of high-level nuclear waste, SON68 and CJ-6, which contained Li in natural isotope abundance, with a non-aqueous solutionmore » of 6LiCl dissolved in dimethyl sulfoxide at 90 °C for various time periods. The depth profiles of major elements in the glass coupons were measured using time-of-flight secondary ion mass spectrometry (ToF-SIMS). Lithium interdiffusion coefficients, D Li, were then calculated based on the measured depth profiles. The results indicate that the penetration of 6Li is rapid in both glasses with the simplified CJ-6 glass (D 6Li ≈ 4.0-8.0 × 10 -21 m 2/s) exhibiting faster exchange than the more complex SON68 glass (D Li ≈ 2.0-4.0 × 10 -21 m 2/s). Additionally, sodium ions present in the glass were observed to participate in ion exchange reactions; however, different diffusion coefficients were necessary to fit the diffusion profiles of the two alkali ions. Implications of the diffusion coefficients obtained in the absence of alteration layers to the long-term performance of nuclear waste glasses in a geological repository system are also discussed.« less

Defining Putative Glycan Cancer Biomarkers by Mass Spectrometry

PubMed Central

Mechref, Yehia; Hu, Yunli; Garcia, Aldo; Hussein, Ahmed

2013-01-01

Summary For decades, the association between aberrant glycosylation and many types of cancers has been shown. However, defining the changes of glycan structures has not been demonstrated until recently. This has been facilitated by the major advances in mass spectrometry and separation science which allowed the detailed characterization of glycan changes associated with cancer. Mass spectrometry glycomics methods have been successfully employed to compare the glycomic profiles of different human specimen collected from disease-free individuals and patients with cancer. Additionally, comparing the glycomic profiles of glycoproteins purified from specimen collected from disease-free individuals and patients with cancer has also been performed. These types of glycan analyses employing mass spectrometry or liquid-chromatography mass spectrometry allowed the characterization of native, labeled, and permethylated glycans. This review discusses the different glycomic and glycoproteomic methods employed for defining glycans as cancer biomarkers of different organs, including breast, colon, esophagus, liver, lung, ovarian, pancreas and prostate. PMID:23157355

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.

Detection of bio-signature by microscopy and mass spectrometry

NASA Astrophysics Data System (ADS)

Tulej, M.; Wiesendanger, R.; Neuland, M., B.; Meyer, S.; Wurz, P.; Neubeck, A.; Ivarsson, M.; Riedo, V.; Moreno-Garcia, P.; Riedo, A.; Knopp, G.

2017-09-01

We demonstrate detection of micro-sized fossilized bacteria by means of microscopy and mass spectrometry. The characteristic structures of lifelike forms are visualized with a micrometre spatial resolution and mass spectrometric analyses deliver elemental and isotope composition of host and fossilized materials. Our studies show that high selectivity in isolation of fossilized material from host phase can be achieved while applying a microscope visualization (location), a laser ablation ion source with sufficiently small laser spot size and applying depth profiling method. Our investigations shows that fossilized features can be well isolated from host phase. The mass spectrometric measurements can be conducted with sufficiently high accuracy and precision yielding quantitative elemental and isotope composition of micro-sized objects. The current performance of the instrument allows the measurement of the isotope fractionation in per mill level and yield exclusively definition of the origin of the investigated species by combining optical visualization of investigated samples (morphology and texture), chemical characterization of host and embedded in the host micro-sized structure. Our isotope analyses involved bio-relevant B, C, S, and Ni isotopes which could be measured with sufficiently accuracy to conclude about the nature of the micro-sized objects.

Chemical fingerprinting of naphthenic acids at an oil sands end pit lake by comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry (GC×GC/TOFMS)

NASA Astrophysics Data System (ADS)

Bowman, D. T.; Arriaga, D.; Morris, P.; Risacher, F.; Warren, L. A.; McCarry, B. E.; Slater, G.

2016-12-01

Naphthenic acids (NAs) are naturally occurring in Athabasca oil sands and accumulate in tailings as a result of water-based extraction processes. NAs contribute to the toxicity of tailings and oil sands process-affected water (OSPW). NAs exist as a complex mixture, so the development of an analytical technique to characterize them has been an on-going challenge. The monitoring of individual NAs and their associated isomers through multidimensional chromatography has the potential to provide greater insight into the behavior of NAs in the environment. For NAs whose proportions do not change during environmental processing, NA ratios may provide a means to develop fingerprints characteristic of specific sources. Alternatively, relative changes in the proportions of NAs may provide a tracer of their occurrence and extent of removal. As yet, only a few studies have begun to explore these possibilities. In this study, comprehensive two dimensional gas chromatography/time-of-flight mass spectrometry was used to monitor individual naphthenic acids in an end pit lake in Alberta, Canada. NA profiles from different depths and sampling locations were compared to evaluate the spatial variations at the site.

Full membrane spanning self-assembled monolayers as model systems for UHV-based studies of cell-penetrating peptides

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

Franz, Johannes; Graham, Daniel J.; Schmüser, Lars

2015-03-01

Biophysical studies of the interaction of peptides with model membranes provide a simple yet effective approach to understand the transport of peptides and peptide based drug carriers across the cell membrane. Therein, the authors discuss the use of self-assembled monolayers fabricated from the full membrane-spanning thiol (FMST) 3-((14-((4'-((5-methyl-1-phenyl-35-(phytanyl)oxy-6,9,12,15,18,21,24,27,30,33,37-undecaoxa-2,3-dithiahenpentacontan-51-yl)oxy)-[1,1'-biphenyl]-4-yl)oxy)tetradecyl)oxy)-2-(phytanyl)oxy glycerol for ultrahigh vacuum (UHV) based experiments. UHV-based methods such as electron spectroscopy and mass spectrometry can provide important information about how peptides bind and interact with membranes, especially with the hydrophobic core of a lipid bilayer. Moreover, near-edge x-ray absorption fine structure spectra and x-ray photoelectron spectroscopy (XPS) data showed thatmore » FMST forms UHV-stable and ordered films on gold. XPS and time of flight secondary ion mass spectrometry depth profiles indicated that a proline-rich amphipathic cell-penetrating peptide, known as sweet arrow peptide is located at the outer perimeter of the model membrane.« less

Study of runaway electrons with Hard X-ray spectrometry of tokamak plasmas

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

Shevelev, A.; Chugunov, I.; Khilkevitch, E.

2014-08-21

Hard-X-ray spectrometry is a tool widely used for diagnostic of runaway electrons in existing tokamaks. In future machines, ITER and DEMO, HXR spectrometry will be useful providing information on runaway electron energy, runaway beam current and its profile during disruption.

SPECIATION OF SUBSURFACE CONTAMINANTS BY CONE PENETROMETRY GAS CHROMATOGRAPHY/MASS SPECTROMETRY. (R826184)

EPA Science Inventory

A thermal extraction cone penetrometry gas chroma tography/mass spectrometry system (TECP GC/MS) has been developed to detect subsurface contaminants in situ. The TECP can collect soil-bound organics up to depths of 30 m. In contrast to traditional cone penetrometer sample collec...

Visualizing Antimicrobials in Bacterial Biofilms: Three-Dimensional Biochemical Imaging Using TOF-SIMS.

PubMed

Davies, Sarah K; Fearn, Sarah; Allsopp, Luke P; Harrison, Freya; Ware, Ecaterina; Diggle, Stephen P; Filloux, Alain; McPhail, David S; Bundy, Jacob G

2017-01-01

Bacterial biofilms are groups of bacteria that exist within a self-produced extracellular matrix, adhering to each other and usually to a surface. They grow on medical equipment and inserts such as catheters and are responsible for many persistent infections throughout the body, as they can have high resistance to many antimicrobials. Pseudomonas aeruginosa is an opportunistic pathogen that can cause both acute and chronic infections and is used as a model for research into biofilms. Direct biochemical methods of imaging of molecules in bacterial biofilms are of high value in gaining a better understanding of the fundamental biology of biofilms and biochemical gradients within them. Time of flight-secondary-ion mass spectrometry (TOF-SIMS) is one approach, which combines relatively high spatial resolution and sensitivity and can perform depth profiling analysis. It has been used to analyze bacterial biofilms but has not yet been used to study the distribution of antimicrobials (including antibiotics and the antimicrobial metal gallium) within biofilms. Here we compared two methods of imaging of the interior structure of P. aeruginosa in biological samples using TOF-SIMS, looking at both antimicrobials and endogenous biochemicals: cryosectioning of tissue samples and depth profiling to give pseudo-three-dimensional (pseudo-3D) images. The sample types included both simple biofilms grown on glass slides and bacteria growing in tissues in an ex vivo pig lung model. The two techniques for the 3D imaging of biofilms are potentially valuable complementary tools for analyzing bacterial infection. IMPORTANCE Modern analytical techniques are becoming increasingly important in the life sciences; imaging mass spectrometry offers the opportunity to gain unprecedented amounts of information on the distribution of chemicals in samples-both xenobiotics and endogenous compounds. In particular, simultaneous imaging of antibiotics (and other antimicrobial compounds) and bacterium-derived metabolites in complex biological samples could be very important in the future for helping to understand how sample matrices impact the survival of bacteria under antibiotic challenge. We have shown that an imaging mass spectrometric technique, TOF-SIMS, will be potentially extremely valuable for this kind of research in the future.

Profiling of patterned metal layers by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS)

NASA Astrophysics Data System (ADS)

Bi, Melody; Ruiz, Antonio M.; Gornushkin, Igor; Smith, Ben W.; Winefordner, James D.

2000-02-01

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) was used for profiling patterned thin metal layers on a polymer/silicon substrate. The parameters of the laser and ICP-MS operating conditions have been studied and optimized for this purpose. A new laser ablation chamber was designed and built to achieve the best spatial resolution. The results of the profiling by LA-ICP-MS were compared to those obtained from a laser ablation optical emission spectrometry (LA-OES) instrument, which measured the emission of the plasma at the sample surface, and thus, eliminated the time delay caused by the sample transport into the ICP-MS system. Emission spectra gave better spatial resolution than mass spectra. However, LA-ICP-MS provided much better sensitivity and was able to profile thin metal layers (on the order of a few nanometers) on the silicon surface. A lateral spatial resolution of 45 μm was achieved.

Combining Raman and laser induced breakdown spectroscopy by double pulse lasing.

PubMed

Lednev, Vasily N; Pershin, Sergey M; Sdvizhenskii, Pavel A; Grishin, Mikhail Ya; Fedorov, Alexander N; Bukin, Vladimir V; Oshurko, Vadim B; Shchegolikhin, Alexander N

2018-01-01

A new approach combining Raman spectrometry and laser induced breakdown spectrometry (LIBS) within a single laser event was suggested. A pulsed solid state Nd:YAG laser running in double pulse mode (two frequency-doubled sequential nanosecond laser pulses with dozens microseconds delay) was used to combine two spectrometry methods within a single instrument (Raman/LIBS spectrometer). First, a low-energy laser pulse (power density far below ablation threshold) was used for Raman measurements while a second powerful laser pulse created the plasma suitable for LIBS analysis. A short time delay between two successive pulses allows measuring LIBS and Raman spectra at different moments but within a single laser flash-lamp pumping. Principal advantages of the developed instrument include high quality Raman/LIBS spectra acquisition (due to optimal gating for Raman/LIBS independently) and absence of target thermal alteration during Raman measurements. A series of high quality Raman and LIBS spectra were acquired for inorganic salts (gypsum, anhydrite) as well as for pharmaceutical samples (acetylsalicylic acid). To the best of our knowledge, the quantitative analysis feasibility by combined Raman/LIBS instrument was demonstrated for the first time by calibration curves construction for acetylsalicylic acid (Raman) and copper (LIBS) in gypsum matrix. Combining ablation pulses and Raman measurements (LIBS/Raman measurements) within a single instrument makes it an efficient tool for identification of samples hidden by non-transparent covering or performing depth profiling analysis including remote sensing. Graphical abstract Combining Raman and laser induced breakdown spectroscopy by double pulse lasing.

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

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.

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.

Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry

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

Zhou, Mowei; Wu, Si; Stenoien, David L.

Top-down mass spectrometry is a valuable tool for charactering post-translational modifications on histones for understanding of gene control and expression. In this protocol, we describe a top-down workflow using liquid chromatography coupled to mass spectrometry for fast global profiling of changes in histone proteoforms between a wild-type and a mutant of a fungal species. The proteoforms exhibiting different abundances can be subjected to further targeted studies by other mass spectrometric or biochemical assays. This method can be generally adapted for preliminary screening for changes in histone modifications between samples such as wild-type vs. mutant, and control vs. disease.

Steroid Profiling by Gas Chromatography–Mass Spectrometry and High Performance Liquid Chromatography–Mass Spectrometry for Adrenal Diseases

PubMed Central

McDonald, Jeffrey G.; Matthew, Susan

2012-01-01

The ability to measure steroid hormone concentrations in blood and urine specimens is central to the diagnosis and proper treatment of adrenal diseases. The traditional approach has been to assay each steroid hormone, precursor, or metabolite using individual aliquots of serum, each with a separate immunoassay. For complex diseases, such as congenital adrenal hyperplasia and adrenocortical cancer, in which the assay of several steroids is essential for management, this approach is time consuming and costly, in addition to using large amounts of serum. Gas chromatography/mass spectrometry profiling of steroid metabolites in urine has been employed for many years but only in a small number of specialized laboratories and suffers from slow throughput. The advent of commercial high-performance liquid chromatography instruments coupled to tandem mass spectrometers offers the potential for medium- to high-throughput profiling of serum steroids using small quantities of sample. Here, we review the physical principles of mass spectrometry, the instrumentation used for these techniques, the terminology used in this field and applications to steroid analysis. PMID:22170384

Induced radioactivity of LDEF materials and structural components

NASA Technical Reports Server (NTRS)

Harmon, B. A.; Laird, C. E.; Fishman, G. J.; Parnell, T. A.; Camp, D. C.; Frederick, C. E.; Hurley, D. L.; Lindstrom, D. J.; Moss, C. E.; Reedy, R. C.;

Distribution of radionuclides in the environment in northern Italy after the Chernobyl accident.

PubMed

Berzero, A; Borroni, P A; Oddone, M; Crespi, V C; Genova, N; Meloni, S

1992-03-01

Soon after the Chernobyl nuclear accident, the air-pumping stations in Pavia (northern Italy) were alerted. In a few days, a rapid increase in radionuclide concentration in air particulates was observed. Consequently, an environmental radioactivity monitoring programme was started in which several matrices such as soil, grass, vegetables and cows' milk were subjected to direct gamma-ray spectrometry. The radioactivity distribution and its variation with time is presented, discussed and compared with other available data. Detection limits, precision and accuracy are also reported, and depth profiles in soils for 137Cs are presented and correlated with soil quality parameters. A survey of environmental radioactivity in soil, in a search for residual Chernobyl fallout, was carried out and a map of the 137Cs distribution over a large area in northern Italy is presented and discussed.

Gold-implanted shallow conducting layers in polymethylmethacrylate

NASA Astrophysics Data System (ADS)

Teixeira, F. S.; Salvadori, M. C.; Cattani, M.; Brown, I. G.

2009-03-01

PMMA (polymethylmethacrylate) was ion implanted with gold at very low energy and over a range of different doses using a filtered cathodic arc metal plasma system. A nanometer scale conducting layer was formed, fully buried below the polymer surface at low implantation dose, and evolving to include a gold surface layer as the dose was increased. Depth profiles of the implanted material were calculated using the Dynamic TRIM computer simulation program. The electrical conductivity of the gold-implanted PMMA was measured in situ as a function of dose. Samples formed at a number of different doses were subsequently characterized by Rutherford backscattering spectrometry, and test patterns were formed on the polymer by electron beam lithography. Lithographic patterns were imaged by atomic force microscopy and demonstrated that the contrast properties of the lithography were well maintained in the surface-modified PMMA.

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

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.

Mechanisms of enhanced lithium intercalation into thin film V2O5 in ionic liquids investigated by X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry

NASA Astrophysics Data System (ADS)

Santos, Luis; Światowska, Jolanta; Lair, Virginie; Zanna, Sandrine; Seyeux, Antoine; Melendez-Ceballos, Arturo; Tran-Van, Pierre; Cassir, Michel; Marcus, Philippe

2017-10-01

Room temperature ionic liquids (RTILs) attract much attention as a new type of environmentally benign electrolytes for Li-ion batteries due to their numerous interesting physicochemical properties. Here, in this paper, Li intercalation/deintercalation in presence of the N-butyl-N-methylpyrrolidinium bis(trifluoromethanesulfonyl) imide (PYR14TFSI) and N-methyl-N-propylpyrrolidinium bis(fluorosulfonyl)imide (PYR13FSI) containing 0.3 M LiTFSI, was evaluated in a thin 100 nm layer of V2O5 deposited on Al substrate by atomic layer deposition. Potentiodynamic tests performed in LiTFSI/Pyr14TFSI show a quasi-reversible Li intercalation during 10 cycles (between 2.4 and 5 V) with an average coulombic efficiency of 99%. The capacity, calculated from the 1st cycle, is found to be 182 mAh g-1, about 19% (±2%) higher than the theoretical capacity reported for V2O5 (147 mAh g-1). X-ray photoelectron spectroscopy analysis confirms that the intercalation of more than 1 mol of Li+ per V2O5 is achieved as also the possible presence of a solid permeable interface (SPI) layer on the V2O5 surface. Likewise, the Li+ in-depth distribution on the V2O5 layer after intercalation in RTILs measured by time-of-flight secondary ion mass spectrometry ion depth profiles, show small irreversible electrode modifications with the presence of lithium through the entire V2O5 layer with significant lithium trapping at the V2O5 layer/Al substrate interface.

Spatially resolved chemical imaging of individual atmospheric particles using nanoscale imaging mass spectrometry: insight into particle origin and chemistry

DOE PAGES

Ghosal, Sutapa; Weber, Peter K.; Laskin, Alexander

2014-01-14

Knowledge of the spatially resolved composition of atmospheric particles is essential for differentiating between their surface versus bulk chemistry and understanding particle reactivity and the potential environmental impact. Here, we demonstrate the application of nanometer-scale secondary ion mass spectrometry (CAMECA NanoSIMS 50 ion probe) for 3D chemical imaging of individual atmospheric particles without any sample pre-treatment, such as sectioning of particles. Use of NanoSIMS depth profile analysis enables elemental mapping of particles with nanometer spatial resolution over a broad range of particle sizes. We have used this technique to probe the spatially resolved composition of ambient particles collected during amore » field campaign in Mexico City. Particles collected during this campaign have been extensively characterized in the past using other particle analysis techniques and hence offer a unique opportunity for exploring the utility of depth-resolved chemical imaging in ambient particle research. The particles that we examined in our study include those collected during a pollution episode related to urban waste incineration as well as background particles from the same location before the episode. Particles from the pollution episode show substantial intra-particle compositional variability typical of particles resulting from multiple emission sources. In contrast, the background particles have relatively homogeneous compositions with enhanced presence of nitrogen, oxygen, and chlorine at the particle surface. We also observed the surface enhancement of nitrogen and oxygen species is consistent with the presence of surface nitrates resulting from gas–particle heterogeneous interactions and is indicative of atmospheric ageing of the particles. The results presented here illustrate 3D characterization of ambient particles for insight into their chemical history.« less

Spatially resolved chemical imaging of individual atmospheric particles using nanoscale imaging mass spectrometry: Insighs into particle origin and chemistry

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

Ghosal, Sutapa; Weber, Peter K.; Laskin, Alexander

2014-04-21

Knowledge of the spatially-resolved composition of atmospheric particles is essential for differentiating between their surface versus bulk chemistry, understanding particle reactivity and the potential environmental impact. We demonstrate the application of nanometer-scale secondary ion mass spectrometry (Cameca NanoSIMS 50 ion probe) for 3D chemical imaging of individual atmospheric particles without any sample pre-treatment, such as the sectioning of particles. Use of NanoSIMS depth profile analysis enables elemental mapping of particles with nanometer spatial resolution over a broad of range of particle sizes. We have used this technique to probe spatially resolved composition of ambient particles collected during a field campaignmore » in Mexico City. Particles collected during this campaign have been extensively characterized in the past using other particle analysis techniques and hence offer a unique opportunity for exploring the utility of depth resolved chemical imaging in ambient particle research. 1 Particles examined in this study include those collected during a pollution episode related to urban waste incineration as well as background particles from the same location prior to the episode. Particles from the pollution episode show substantial intra-particle compositional variability typical of particles resulting from multiple emission sources. In contrast, the background particles have relatively homogeneous compositions with enhanced presence of nitrogen, oxygen and chlorine at the particle surface. The observed surface enhancement of nitrogen and oxygen species is consistent with the presence of surface nitrates resulting from gas-particle heterogeneous interactions and is indicative of atmospheric ageing of the particles. The results presented here illustrate 3D characterization of ambient particles for insights into their chemical history.« less

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.

Thin film characterization by laser interferometry combined with SIMS

NASA Astrophysics Data System (ADS)

Kempf, J.; Nonnenmacher, M.; Wagner, H. H.

1988-10-01

Thin film properties of technologically important materials (Si, GaAs, SiO2, WSix) have been measured by using a novel technique that combines secondary ion mass spectrometry (SIMS) and laser interferometry. The simultaneous measurement of optical phase and reflectance as well as SIMS species during ion sputtering yielded optical constants, sputtering rates and composition of thin films with high depth resolution. A model based on the principle of multiple reflection within a multilayer structure, which considered also transformation of the film composition in depth and time during sputtering, was fitted to the reflectance and phase data. This model was applied to reveal the transformation of silicon by sputtering with O{2/+} ions. Special attention was paid to the preequilibrium phase of the sputter process (amorphization, oxidation, and volume expansion). To demonstrate the analytical potential of our method the multilayer system WSix/poly-Si/SiO2/Si was investigated. The physical parameters and the stoichiometry of tungsten suicide were determined for annealed as well as deposited films. A highly sensitive technique that makes use of a Fabry-Perot etalon integrated with a Michelson type interferometer is proposed. This two-stage interferometer has the potential to profile a sample surface with subangstroem resolution.

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.

CCQM Pilot Study CCQM-P140: Quantitative surface analysis of multi-element alloy films

NASA Astrophysics Data System (ADS)

Kim, Kyung Joong; Jang, Jong Shik; Kim, An Soon; Suh, Jung Ki; Chung, Yong-Duck; Hodoroaba, Vasile-Dan; Wirth, Thomas; Unger, Wolfgang; Kang, Hee Jae; Popov, Oleg; Popov, Inna; Kuselman, Ilya; Lee, Yeon Hee; Sykes, David E.; Wang, Meiling; Wang, Hai; Ogiwara, Toshiya; Nishio, Mitsuaki; Tanuma, Shigeo; Simons, David; Szakal, Christopher; Osborn, William; Terauchi, Shinya; Ito, Mika; Kurokawa, Akira; Fujimoto, Toshiyuki; Jordaan, Werner; Jeong, Chil Seong; Havelund, Rasmus; Spencer, Steve; Shard, Alex; Streeck, Cornelia; Beckhoff, Burkhard; Eicke, Axel; Terborg, Ralf

2015-01-01

A pilot study for a quantitative surface analysis of multi-element alloy films has been performed by the Surface Analysis Working Group (SAWG) of the Consultative Committee for Amount of Substance (CCQM). The aim of this pilot study is to evaluate a protocol for a key comparison to demonstrate the equivalence of measures by National Metrology Institutes (NMIs) and Designated Institutes (DI) for the mole fractions of multi-element alloy films. A Cu(In,Ga)Se2 (CIGS) film with non-uniform depth distribution was chosen as a representative multi-element alloy film. The mole fractions of the reference and the test CIGS films were certified by isotope dilution—inductively coupled plasma/mass spectrometry. A total number counting (TNC) method was used as a method to determine the signal intensities of the constituent elements acquired in SIMS, XPS and AES depth profiling. TNC method is comparable with the certification process because the certified mole fractions are the average values of the films. The mole fractions of the CIGS films were measured by Secondary Ion Mass Spectrometry (SIMS), Auger Electron Spectroscopy (AES), X-ray Photoelectron Spectroscopy (XPS), X-Ray Fluorescence (XRF) Analysis and Electron Probe Micro Analysis (EPMA) with Energy Dispersive X-ray Spectrometry (EDX). Fifteen laboratories from eight NMIs, one DI, and six non-NMIs participated in this pilot study. The average mole fractions of the reported data showed relative standard deviations from 5.5 % to 6.8 % and average relative expanded uncertainties in the range from 4.52 % to 4.86 % for the four test CIGS specimens. These values are smaller than those in the key comparison CCQM-K67 for the measurement of mole fractions of Fe-Ni alloy films. As one result it can be stated that SIMS, XPS and AES protocols relying on the quantification of CIGS films using the TNC method are mature to be used in a CCQM key comparison. Main text. To reach the main text of this paper, click on Final Report. The final report has been peer-reviewed and approved for publication by CCQM.

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.

Determination of red blood cell fatty acid profiles: Rapid and high-confident analysis by chemical ionization-gas chromatography-tandem mass spectrometry.

PubMed

Schober, Yvonne; Wahl, Hans Günther; Renz, Harald; Nockher, Wolfgang Andreas

2017-01-01

Cellular fatty acid (FA) profiles have been acknowledged as biomarkers in various human diseases. Nevertheless, common FA analysis by gas chromatography mass spectrometry (GC-MS) requires long analysis time. Hence, there is a need for feasible methods for high throughput analysis in clinical studies. FA was extracted from red blood cells (RBC) and derivatized to fatty acid methyl esters (FAME). A method using gas chromatography tandem mass spectrometry (GC-MS/MS) with ammonia-induced chemical ionization (CI) was developed for the analysis of FA profiles in human RBC. We compared this method with classical single GC-MS using electron impact ionization (EI). The FA profiles of 703 RBC samples were determined by GC-MS/MS. In contrast to EI ammonia-induced CI resulted in adequate amounts of molecular ions for further fragmentation of FAME. Specific fragments for confident quantification and fragmentation were determined for 45 FA. The GC-MS/MS method has a total run time of 9min compared to typical analysis times of up to 60min in conventional GC-MS. Intra and inter assay variations were <10% for all FA analyzed. Analysis of RBC FA composition revealed an age-dependent increase of the omega-3 eicosapentaenoic and docosahexaenoic acid, and a decline of the omega-6 linoleic acid with a corresponding rise of the omega-3 index. The combination of ammonia-induced CI and tandem mass spectrometry after GC separation allows for high-throughput, robust and confident analysis of FA profiles in the clinical laboratory. Copyright © 2016. Published by Elsevier B.V.

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

Stability of Fe-Cr alloy interconnects under CH 4-H 2O atmosphere for SOFCs

NASA Astrophysics Data System (ADS)

Horita, Teruhisa; Xiong, Yueping; Yamaji, Katsuhiko; Sakai, Natsuko; Yokokawa, Harumi

The chemical stability of Fe-Cr alloys (ZMG232 and SUS430) was examined under humidified CH 4 gases at 1073 K to simulate the real anode atmosphere in SOFC operation. Surface microstructure change and oxide scale layer formation were observed on the oxidized Fe-Cr alloy surfaces. The main reaction products were Mn-Cr-(Fe) spinels for both alloys. Secondary ion mass spectrometry (SIMS) was applied to measure the elemental distribution of minor and major elements around the oxide scale/alloy interface. A high concentration of Mn on the oxide scale surface suggested the fast diffusion of Mn in the oxide scale to form the spinels. Annealing in CH 4-H 2O made the oxide scale thicker with duration time on the alloy surface. The parabolic growth rates ( kp) of oxide scale layer were evaluated from the thickness of oxide scales by secondary ion mass spectrometry (SIMS) depth profiles, which were calculated to the following: kp=6.25×10 -6 μm 2/s for SUS430 and kp=4.42×10 -6 μm 2/s for ZMG232. The electrical conductivity of oxidized alloys showed the semi-conductor temperature dependence for both alloys. The electrical conductivity of oxidized ZMG232 alloy was higher than that of oxidized SUS430.

Hydrogen analysis for granite using proton-proton elastic recoil coincidence spectrometry.

PubMed

Komatsubara, T; Sasa, K; Ohshima, H; Kimura, H; Tajima, Y; Takahashi, T; Ishii, S; Yamato, Y; Kurosawa, M

2008-07-01

In an effort to develop DS02, a new radiation dosimetry system for the atomic bomb survivors of Hiroshima and Nagasaki, measurements of neutron-induced activities have provided valuable information to reconstruct the radiation situation at the time of the bombings. In Hiroshima, the depth profile of (152)Eu activity measured in a granite pillar of the Motoyasu Bridge (128 m from the hypocenter) was compared with that calculated using the DS02 methodology. For calculation of the (152)Eu production due to the thermal-neutron activation reaction, (151)Eu(n,gamma)(152)Eu, information on the hydrogen content in granite is important because the transport and slowing-down process of neutrons penetrating into the pillar is strongly affected by collisions with the protons of hydrogen. In this study, proton-proton elastic recoil coincidence spectrometry has been used to deduce the proton density in the Motoyasu pillar granite. Slices of granite samples were irradiated by a 20 MeV proton beam, and the energies of scattered and recoil protons were measured with a coincidence method. The water concentration in the pillar granite was evaluated to be 0.30 +/- 0.07%wt. This result is consistent with earlier data on adsorptive water (II) and bound water obtained by the Karl Fisher method.

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.

Structural and optical properties of vanadium ion-implanted GaN

NASA Astrophysics Data System (ADS)

Macková, A.; Malinský, P.; Jagerová, A.; Sofer, Z.; Klímová, K.; Sedmidubský, D.; Mikulics, M.; Lorinčík, J.; Veselá, D.; Böttger, R.; Akhmadaliev, S.

2017-09-01

The field of advanced electronic and optical devices searches for a new generation of transistors and lasers. The practical development of these novel devices depends on the availability of materials with the appropriate magnetic and optical properties, which is strongly connected to the internal morphology and the structural properties of the prepared doped structures. In this contribution, we present the characterisation of V ion-doped GaN epitaxial layers. GaN layers, oriented along the (0 0 0 1) crystallographic direction, grown by low-pressure metal-organic vapour-phase epitaxy (MOVPE) on c-plane sapphire substrates were implanted with 400 keV V+ ions at fluences of 5 × 1015 and 5 × 1016 cm-2. Elemental depth profiling was accomplished by Rutherford Backscattering Spectrometry (RBS) and Secondary Ion Mass Spectrometry (SIMS) to obtain precise information about the dopant distribution. Structural investigations are needed to understand the influence of defect distribution on the crystal-matrix recovery and the desired structural and optical properties. The structural properties of the ion-implanted layers were characterised by RBS-channelling and Raman spectroscopy to get a comprehensive insight into the structural modification of implanted GaN and to study the influence of subsequent annealing on the crystalline matrix reconstruction. Photoluminescence measurement was carried out to check the optical properties of the prepared structures.

Mid-Award Progress Report for Department of Energy Office of Science Graduate Student Research Program

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

Hoffman, M. K.

The purpose of the work proposed for this study is to investigate the behavior and transport mechanisms for cesium-137 in soils collected from contaminated sites with distinct source release scenarios. More specifically, this study aims to determine with which elements and minerals cesium-137 associates in these various environments to more reliably predict its migration in the subsurface. This will be achieved using a state-of-the-art analysis technique available at Lawrence Livermore National Laboratory (LLNL) known as NanoSIMS. Nano-scale secondary ion mass spectrometry, or NanoSIMS, is a destructive surface analysis technique in which positive secondary ions are generated from the surface ofmore » a sample and then quantified based on their mass-to-charge ratio (m/z) using mass spectrometry. The data collected about the secondary ions can then be used to create isotope-specific spatial maps with a resolution of a few hundred nanometers and depth profiles that show the variation of the secondary ion intensity with sputtering time. This should be an ideal technique for locating cesium-137 in a sample, as cesium is an easily ionized element, meaning the yield of secondary cesium (Cs) ions produced should be high and making the identification of cesium-137 straight forward.« less

Rare earth elements profile in a cultivated and non-cultivated soil determined by laser ablation-inductively coupled plasma mass spectrometry.

PubMed

Neves, Vinicius M; Heidrich, Graciela M; Hanzel, Flavia B; Muller, Edson I; Dressler, Valderi L

2018-05-01

Rare earth elements (REEs) have several applications but the effects on environment are not well known. Therefore, the aim of this work is to establish a method for direct solid sample analysis by laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS) to evaluate the concentration and distribution of REEs in cultivated and non-cultivated soil. Samples were collected in two areas to 40 cm of depth. The LA-ICP-MS method is easy to be implemented and the sample treatment is very fast comprising only its drying, grounding and pressing as a pellet. The accuracy of the method was evaluated by using a certified reference material (BCR 667 - Estuarine Sediment, Institute for Reference Materials and Measurements (IRMM)) where good agreement with the certified values was obtained. Analyte recovery at two levels of concentration (2.5 and 15.0 μg g -1 ) was also performed and recoveries in the range of 85%-120% were achieved, values that are acceptable for LA-ICP-MS analysis. In general, the concentration of the REEs is higher in the cultivated soil and increased from the surface to deeper layers, which can be a consequence of fertilizer application. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Proteomics: from hypothesis to quantitative assay on a single platform. Guidelines for developing MRM assays using ion trap mass spectrometers.

PubMed

Han, Bomie; Higgs, Richard E

2008-09-01

High-throughput HPLC-mass spectrometry (HPLC-MS) is routinely used to profile biological samples for potential protein markers of disease, drug efficacy and toxicity. The discovery technology has advanced to the point where translating hypotheses from proteomic profiling studies into clinical use is the bottleneck to realizing the full potential of these approaches. The first step in this translation is the development and analytical validation of a higher throughput assay with improved sensitivity and selectivity relative to typical profiling assays. Multiple reaction monitoring (MRM) assays are an attractive approach for this stage of biomarker development given their improved sensitivity and specificity, the speed at which the assays can be developed and the quantitative nature of the assay. While the profiling assays are performed with ion trap mass spectrometers, MRM assays are traditionally developed in quadrupole-based mass spectrometers. Development of MRM assays from the same instrument used in the profiling analysis enables a seamless and rapid transition from hypothesis generation to validation. This report provides guidelines for rapidly developing an MRM assay using the same mass spectrometry platform used for profiling experiments (typically ion traps) and reviews methodological and analytical validation considerations. The analytical validation guidelines presented are drawn from existing practices on immunological assays and are applicable to any mass spectrometry platform technology.

Influence of fermentable carbohydrates or protein on large intestinal and urinary metabolomic profiles in piglets.

PubMed

Pieper, R; Neumann, K; Kröger, S; Richter, J F; Wang, J; Martin, L; Bindelle, J; Htoo, J K; Vahjen, V; Van Kessel, A G; Zentek, J

2012-12-01

It was recently shown that variations in the ratio of dietary fermentable carbohydrates (fCHO) and fermentable protein (fCP) differentially affect large intestinal microbial ecology and the mucosal response. Here we investigated the use of mass spectrometry to profile changes in metabolite composition in colon and urine associated with variation in dietary fCHO and fCP composition and mucosal physiology. Thirty-two weaned piglets were fed 4 diets in a 2 × 2 factorial design with low fCP and low fCHO, low fCP and high fCHO, high fCP and low fCHO, and high fCP and high fCHO. After 21 to 23 d, all pigs were euthanized and colon digesta and urine metabolite profiles were obtained by mass spectrometry. Analysis of mass spectra by partial least squares approach indicated a clustering of both colonic and urinary profiles for each pig by feeding group. Metabolite identification and annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed increased abundance of metabolites associated with arachidonic acid metabolism in colon of pigs fed a high concentration of fCP irrespective of dietary fCHO. Urinary metabolites did not show as clear patterns. Mass spectrometry can effectively differentiate metabolite profiles in colon contents and urine associated with changes in dietary composition. Whether metabolite profiling is an effective tool to identify specific metabolites (biomarkers) or metabolite profiles associated with gut function and integrity needs further elucidation.

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

Effect of thermal annealing on the redistribution of alkali metals in Cu(In,Ga)Se2 solar cells on glass substrate

NASA Astrophysics Data System (ADS)

Kamikawa, Yukiko; Nishinaga, Jiro; Ishizuka, Shogo; Tayagaki, Takeshi; Guthrey, Harvey; Shibata, Hajime; Matsubara, Koji; Niki, Shigeru

2018-03-01

The precise control of alkali-metal concentrations in Cu(In,Ga)Se2 (CIGS) solar cells via post deposition treatment (PDT) has recently attracted attention. When PDT is performed at an elevated temperature, an accompanying annealing effect is expected. Here, we investigate how thermal annealing affects the redistribution of alkali metals in CIGS solar cells on glass substrates and the properties of the solar cells. In addition, we investigate the origin of non-homogeneous alkali-metal depth profiles that are typical of CIGS grown using a three-stage process. In particular, we use secondary-ion mass spectrometry measurements of the ion concentration as a function of distance from the CIGS surface to investigate the impact of thermal annealing on the distribution of alkali metals (Na, Ka, and Rb) and constituent elements (Ga and In) in the CIGS absorbers. We find that the depth profiles of the alkali metals strongly reflect the density of sites that tend to accommodate alkali metals, i.e., vacancies. Annealing at elevated temperature caused a redistribution of the alkali metals. The thermal-diffusion kinetics of alkali metals depends strongly on the species involved. We introduced low flux potassium fluoride (KF) to study a side effect of KF-PDT, i.e., Na removal from CIGS, separately from its predominant effects such as surface modification. When sufficient amounts of Na are supplied from the soda lime glass via annealing at an elevated temperature, the negative effect was not apparent. Conversely, when the Na supply was not sufficient, it caused a deterioration of the photovoltaic properties.

Molecular Depth Profiling of Sucrose Films: A Comparative Study of C₆₀n⁺ Ions and Traditional Cs⁺ and O₂⁺ Ions

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

Zhu, Zihua; Nachimuthu, Ponnusamy; Lea, Alan S.

2009-10-15

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling of sucrose thin films were investigated using 10 keV C60+, 20 keV C602+, 30 keV C603+, 250 eV, 500 eV and 1000 eV Cs+ and O2+ as sputtering ions. With C60n+ ions, the molecular ion signal initially decreases, and reaches a steady-state that is about 38-51% of its original intensity, depending on the energy of the C60n+ ions. On the contrary, with Cs+ and O2+ sputtering, molecular ion signals decrease quickly to the noise level, even using low energy (250 eV) sputtering ions. In addition, the sucrose/Si interface by C60+ sputtering ismore » much narrower than that of Cs+ and O2+ sputtering. To understand the mechanisms of sputtering-induced damage by these ions, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) were used to characterize the bottoms of these sputter craters. XPS data show very little chemical change in the C60+ sputter crater, while considerable amorphous carbon was found in the O2+ and Cs+ sputter craters, indicating extensive decomposition of the sucrose molecules. AFM images show a very flat bottom in the C60+ sputter crater, while the Cs+ and O2+ sputter crater bottoms are significantly rougher than that of the C60+ sputter crater. Based on above data, we developed a simple model to explain different damage mechanisms during sputtering process.« less

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

Nanolaminated FeCoB/FeCo and FeCoB/NiFe soft magnetic thin films with tailored magnetic properties deposited by magnetron sputtering

NASA Astrophysics Data System (ADS)

Hida, Rachid; Falub, Claudiu V.; Perraudeau, Sandrine; Morin, Christine; Favier, Sylvie; Mazel, Yann; Saghi, Zineb; Michel, Jean-Philippe

2018-05-01

Thin films based on layers of Fe52Co28B20 (at%), Fe65Co35 (at%), and Ni80Fe20 (at%) were deposited by sputtering on 8″ bare Si and Si/200 nm-thermal-SiO2 wafers by simultaneous use of two or more cathodes. Due to the continuous rotation of the substrate cage, such that the substrates faced different targets alternately, the multilayers consisted of stacks of alternating, nanometer-thick regular layers. The composition of the films was determined by Rutherford Backscattering Spectrometry (RBS) and Nuclear Reactive Analysis (NRA), whereas Plasma Profiling Time of Flight Mass Spectrometry (PP-TOFMS) analysis gave depth profile information about the chemical elements. The structural and magnetic properties of the films were investigated by X-ray Diffraction and by TEM analysis, B-H loop tracer and high frequency single coil technique permeametry, respectively. The linear dependence of the coercivity of these thin films versus the grain size can be explained by the random anisotropy model. These novel, composite soft magnetic multilayers, with tunable in-plane anisotropy, allow operation at tunable frequencies, as shown by broadband (between 100 MHz and 10 GHz) RF measurements that exhibit a classical Landau-Lifschitz-Gilbert (LLG) behavior and, combine the magnetic properties of the individual materials in an advantageous way. This article presents a method to produce nanostructured soft magnetic multilayers, the properties of which can easily be tuned by choosing the ratio of the individual nanolayers. In this way it's possible to combine soft magnetic materials with complementary properties, e.g. high saturation magnetization, low coercivity, high specific resistivity and low magnetostriction

Secondary Ion Mass Spectrometry Imaging of Tissues, Cells, and Microbial Systems

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

Anderton, Christopher R.; Gamble, Lara J.

2016-03-01

Mass spectrometry imaging (MSI) techniques are increasingly being utilized within many biological fields, including medicine, pathology, microbial ecology, and more. Of the MSI methods available, secondary ion mass spectrometry (SIMS) offers the highest lateral resolution of any technique. Moreover, SIMS versatility in the number of different operating modes and types of mass spectrometers available has made it an increasing popular method for bio-related measurements. Here, we discuss SIMS ability to image tissues, single cells, and microbes with a particular emphasis on the types chemical and spatial information that can be ascertained by the different types of SIMS instruments and methods.more » The recently developed Fourier transform ion cyclotron resonance (FTICR) SIMS located at PNNL is capable of generating molecular maps of tissues with an unprecedented mass resolving power and mass accuracy, with respect to SIMS measurements. ToF-SIMS can generate chemical maps, where detection of small molecules and fragments can be acquired with an order of magnitude better lateral resolution than the FTICR-SIMS. Furthermore, many of commercially available ToF-SIMS instruments are capable of depth profiling measurements, offering the ability to attain three-dimensional information of one’s sample. The NanoSIMS instrument offers the highest lateral resolution of any MSI method available. In practice, NanoSIMS regularly achieves sub-100 nm resolution of atomic and diatomic secondary ions within biological samples. The strengths of the different SIMS methods are more and more being leveraged in both multimodal-imaging endeavors that use complementary MSI techniques as well with optical, fluorescence, and force microscopy methods.« less

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.

Insight into metabolic potential of carbon-poor pelagic sediments derived from the abundance and composition of organic carbon

NASA Astrophysics Data System (ADS)

Estes, E. R.; Hansel, C. M.; Orsi, W. D.; Anderson, C. H.; Murray, R. W.; Wankel, S. D.; Johnson, D.; Nordlund, D.; Spivack, A. J.; Sauvage, J.; McKinley, C. C.; Homola, K.; Present, T. M.; Pockalny, R. A.; D'Hondt, S.

2016-02-01

Pelagic marine sediments are often carbon-limited, with oxic sediments bearing exceedingly small concentrations of metabolizable organic carbon (OC) and anoxic sediments lacking electron acceptors to drive heterotrophy. This OC is typically considered recalcitrant and presumed to be of limited bioavailability as much of it is difficult to characterize molecularly. Here, we utilize a combination of spectrometry, spectroscopy, and fluorescent assays to characterize the OC content and composition of sediment cores from the western subtropical North Atlantic collected during R/V Knorr expedition 223 in November 2014. We find that OC concentrations decrease linearly over 15m burial depth from 0.15 to 0.075 mol OC/kg sediment, beyond which this lower OC level persists to depths approaching 30m. The ratio of organic carbon to nitrogen (C/N) varies but is consistently close to Redfield values of 6. Further, protein concentrations within the suboxic sediments are 1.75 to 4.90 μg protein/mg sediment, values in excess of predicted cell abundance in subsurface sediments. After an initial decrease in concentration between 0-3 meters below core top, protein content increases and stabilizes at 4 μg protein/mg sediment. RNA is detectable throughout the core and profiles (as μg cDNA amplified/g sediment) generally correlate with the shape of protein profiles. Combined, these results imply a small but active microbial community and the potential for these proteins to fuel heterotrophy at depth. Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy finds that amide and carboxyl C functionalities comprise 25% of total spectral area, with the remainder dominated by aromatic C and O-alkyl-C groups. These findings suggest that sedimentary OC contain identifiable components, including a substantial concentration of intact proteins that may fuel heterotrophic microbial communities.

Profiling and Quantification of Regioisomeric Caffeoyl Glucoses in Berry Fruits.

PubMed

Patras, Maria A; Jaiswal, Rakesh; McDougall, Gordon J; Kuhnert, Nikolai

2018-02-07

On the basis of a recently developed tandem mass spectrometry-based hierarchical scheme for the identification of regioisomeric caffeoyl glucoses, selected berry fruits were profiled for their caffeoyl glucose ester content. Fresh edible berries profiled, including strawberries, raspberries, blueberries, blackberries, red currant, black currant, lingonberries, gooseberries, and juices of elderberries, goji berries, chokeberries, cranberries, açai berries, sea buckthorn berries, Montmorency sour cherries, and pomegranates, were investigated. 1-Caffeoyl glucose was found to be the predominant isomer in the majority of samples, with further profiling revealing the presence of additional hydroxycinnamoyl glucose esters and O-glycosides with p-coumaroyl, feruloyl, and sinapoyl substituents. A quantitative liquid chromatography-mass spectrometry-based method was developed and validated, and all caffeoyl glucose isomers were quantified for the first time in edible berries.

A modified Girard derivatizing reagent for universal profiling and trace analysis of aldehydes and ketones by electrospray ionization tandem mass spectrometry.

PubMed

Johnson, David W

2007-01-01

4-Hydrazino-N,N,N-trimethyl-4-oxobutanaminium iodide (HTMOB) is a modified Girard derivatizing reagent synthesized to improve the sensitivity of analysis of aldehydes and ketones with electrospray ionization tandem mass spectrometry. Compared with Girard T reagent the measured signal intensity increase is between 3.3 times (succinylacetone) and 7.0 times (17-hydroxyprogesterone). HTMOB is a universal profiling reagent for aldehydes and ketones. A neutral loss of 59 Da scan detects all aldehydes and ketones from acetone to corticosteroids. Applications described include the profiling of ketones, ketoacids and ketodiacids in the urine of children with ketosis and the profiling of long-chain aldehydes incorporated in plasma plasmalogens. Copyright (c) 2007 John Wiley & Sons, Ltd.

Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry.

PubMed

Zhou, Mowei; Wu, Si; Stenoien, David L; Zhang, Zhaorui; Connolly, Lanelle; Freitag, Michael; Paša-Tolić, Ljiljana

2017-01-01

Top-down mass spectrometry is a valuable tool for understanding gene expression through characterization of combinatorial histone post-translational modifications (i.e., histone code). In this protocol, we describe a top-down workflow that employs liquid chromatography (LC) coupled to mass spectrometry (MS), for fast global profiling of changes in histone proteoforms, and apply LCMS top-down approach for comparative analysis of a wild-type and a mutant fungal species. The proteoforms exhibiting differential abundances can be subjected to further targeted studies by other MS or orthogonal (e.g., biochemical) assays. This method can be generally adapted for screening of changes in histone modifications between samples such as wild type vs. mutant or healthy vs. diseased.

Nanomanipulation-coupled nanospray mass spectrometry as an approach for single cell analysis

NASA Astrophysics Data System (ADS)

Phelps, Mandy; Hamilton, Jason; Verbeck, Guido F.

2014-12-01

Electrospray mass spectrometry is now a widely used technique for observing cell content of various biological tissues. However, electrospray techniques (liquid chromatography and direct infusion) often involve lysing a group of cells and extracting the biomolecules of interest, rather than a sensitive, individual cell method to observe local chemistry. Presented here is an approach of combining a nanomanipulator workstation with nanospray mass spectrometry, which allows for extraction of a single cell, followed by rapid mass analysis that can provide a detailed metabolic profile. Triacylglycerol content was profiled with this tool coupled to mass spectrometry to investigate heterogeneity between healthy and tumorous tissues as well as lipid droplet containing adipocytes in vitro as proof of concept. This selective approach provides cellular resolution and complements existing bioanalytical techniques with minimal invasion to samples. In addition, the coupling of nanomanipulation and mass spectrometry holds the potential to be used in a great number of applications for individual organelles, diseased tissues, and in vitro cell cultures for observing heterogeneity even amongst cells and organelles of the same tissue.

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

Yu, Jiachao; Zhou, Yufan; Hua, Xin

We demonstrate in situ chemical imaging of protein biomolecules in the aqueous solution using System for Analysis at the Liquid Vacuum Interface (SALVI) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The fibronectin protein film was immobilized on the silicon nitride (SiN) membrane forming the SALVI detection area. During ToF-SIMS analysis, three modes of analysis were conducted including high spatial resolution mass spectra, two-dimensional (2D) imaging, and depth profiling. Mass spectra were acquired in both positive and negative modes. Deionized water was also analyzed as a reference sample. Our results show that fibronectin film in water has more distinct and strongermore » water cluster peaks compared to water alone. Characteristic peaks of amino acid fragments are also observable in the hydrated protein ToF-SIMS spectra. These results illustrate that protein molecule adsorption on a surface can be studied dynamically using SALVI and ToF-SIMS in the liquid environment.« less

Concentration transient analysis of antimony surface segregation during Si(100) molecular beam epitaxy

NASA Technical Reports Server (NTRS)

Markert, L. C.; Greene, J. E.; Ni, W.-X.; Hansson, G. V.; Sundgren, J.-E.

1991-01-01

Antimony surface segregation during Si(100) molecular beam epitaxy (MBE) was investigated at temperatures T(sub s) = 515 - 800 C using concentration transient analysis (CTA). The dopant surface coverage Theta, bulk fraction gamma, and incorporation probability sigma during MBE were determined from secondary-ion mass spectrometry depth profiles of modulation-doped films. Programmed T(sub s) changes during growth were used to trap the surface-segregated dopant overlayer, producing concentration spikes whose integrated area corresponds to Theta. Thermal antimony doping by coevaporation was found to result in segregation strongly dependent on T(sub s) with Theta(sub Sb) values up to 0.9 monolayers (ML): in films doped with Sb(+) ions accelerated by 100 V, Theta(sub Sb) was less than or equal to 4 x 10(exp -3) ML. Surface segregation of coevaporated antimony was kinematically limited for the film growth conditions in these experiments.

SIMS depth profiling of working environment nanoparticles

NASA Astrophysics Data System (ADS)

Konarski, P.; Iwanejko, I.; Mierzejewska, A.

2003-01-01

Morphology of working environment nanoparticles was analyzed using sample rotation technique in secondary ion mass spectrometry (SIMS). The particles were collected with nine-stage vacuum impactor during gas tungsten arc welding (GTAW) process of stainless steel and shielded metal arc welding (SMAW) of mild steel. Ion erosion of 300-400 nm diameter nanoparticles attached to indium substrate was performed with 2 keV, 100 μm diameter, Ar + ion beam at 45° ion incidence and 1 rpm sample rotation. The results show that both types of particles have core-shell morphology. A layer of fluorine, chlorine and carbon containing compounds covers stainless steel welding fume particles. The cores of these particles are enriched in iron, manganese and chromium. Outer shell of mild steel welding fume particles is enriched in carbon, potassium, chlorine and fluorine, while the deeper layers of these nanoparticles are richer in main steel components.

A study to investigate the chemical stability of gallium phosphate oxide/gallium arsenide phosphide

NASA Technical Reports Server (NTRS)

Kuhlman, G. J.

1979-01-01

The elemental composition with depth into the oxide films was examined using secondary ion mass spectrometry. Results indicate that the layers are arsenic-deficient through the bulk of the oxide and arsenic-rich near both the oxide surface and the oxide-semiconductor interface region. Phosphorus is incorporated into the oxide in an approximately uniform manner. The MIS capacitor structures exhibited deep-depletion characteristics and hysteresis indicative of electron trapping at the oxide-semiconductor interface. Post-oxidation annealing of the films in argon or nitrogen generally results in slightly increased dielectric leakage currents and decreased C-V hysteresis effects, and is associated with arsenic loss at the oxide surface. The results of bias-temperature stress experiments indicate that the major instability effects are due to changes in the electron trapping behavior. No changes were observed in the elemental profiles following electrical stressing, indicating that the grown films are chemically stable under device operating conditions.

Examining the sources of variability in cell culture media used for biopharmaceutical production.

PubMed

McGillicuddy, Nicola; Floris, Patrick; Albrecht, Simone; Bones, Jonathan

2018-01-01

Raw materials, in particular cell culture media, represent a significant source of variability to biopharmaceutical manufacturing processes that can detrimentally affect cellular growth, viability and specific productivity or alter the quality profile of the expressed therapeutic protein. The continual expansion of the biopharmaceutical industry is creating an increasing demand on the production and supply chain consistency for cell culture media, especially as companies embrace intensive continuous processing. Here, we provide a historical perspective regarding the transition from serum containing to serum-free media, the development of chemically-defined cell culture media for biopharmaceutical production using industrial scale bioprocesses and review production mechanisms for liquid and powder culture media. An overview and critique of analytical approaches used for the characterisation of cell culture media and the identification of root causes of variability are also provided, including in-depth liquid phase separations, mass spectrometry and spectroscopic methods.

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

Exudate Chemical Profiles Derived from Lespedeza and Other Tallgrass Prairie Plant Species

DTIC Science & Technology

2017-05-01

assayed by liquid chromatography–tandem mass spec- trometry (LC-MS/MS) and gas chromatography/mass spectrometry (GC/MS). The objective was to elucidate...molecular weight compounds were identified via gas chromatography/mass spectrometry (GC/MS) and tentatively identified as benzophenone and 1,4...diacetylbenzene. Three higher molecular weight compounds were identified by liquid chromatography-electrospray ionization- mass spectrometry (LC-ESI-MS

Complementary use of ion beam elastic backscattering and recoil detection analysis for the precise determination of the composition of thin films made of light elements

NASA Astrophysics Data System (ADS)

Climent-Font, A.; Cervera, M.; Hernández, M. J.; Muñoz-Martín, A.; Piqueras, J.

2008-04-01

Rutherford backscattering spectrometry (RBS) is a well known powerful technique to obtain depth profiles of the constituent elements in a thin film deposited on a substrate made of lighter elements. In its standard use the probing beam is typically 2 MeV He. Its capabilities to obtain precise composition profiles are severely diminished when the overlaying film is made of elements lighter than the substrate. In this situation the analysis of the energy of the recoiled element from the sample in the elastic scattering event, the ERDA technique may be advantageous. For the detection of light elements it is also possible to use beams at specific energies producing elastic resonances with these light elements to be analyzed, with a much higher scattering cross sections than the Rutherford values. This technique may be called non-RBS. In this work we report on the complementary use of ERDA with a 30 MeV Cl beam and non-RBS with 1756 keV H ions to characterize thin films made of boron, carbon and nitrogen (BCN) deposited on Si substrates.

Ion Beam Analysis of Iridium-Based TES for Microcalorimeter Detectors

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

Gomes, M. Ribeiro; Galeazzi, M.; Bogorin, D.

2009-12-16

The physical properties of thin multilayer structures are deeply related to the crystalline quality and stoichiometry of the films. The interface roughness/mixing require a detailed study to determine its influence on the growth processes and surface topography. This is an important aspect when we have lattice mismatch between the superconducting thin-films and the substrates, and a high reliability/reproducibility is required as for large array microcalorimeter applications, as in the case of the MARE experiment, designed to measure the mass of the neutrino with sub-eV sensitivity by measuring the beta decay of {sup 187}Re with cryogenic microcalorimeters. Ion beam analysis techniquesmore » are ideal to determine the thickness and concentration profiles of the chemical species in ultra-thin films. Here we present the results on the Ir-based superconducting films deposited on Si-substrates based on systematic investigations of the concentration depth profiles of the multilayer structure using 2.0 MeV {sup 4}He{sup +} ions for high resolution Rutherford Backscattering Spectrometry combined with X-Ray Reflectrometry to evaluate the interface/roughness mixing and the crystalline quality in the TES prototypes.« less

Radiation effects on interface reactions of U/Fe, U/(Fe+Cr), and U/(Fe+Cr+Ni)

DOE PAGES

Shao, Lin; Chen, Di; Wei, Chaochen; ...

2014-10-01

We study the effects of radiation damage on interdiffusion and intermetallic phase formation at the interfaces of U/Fe, U/(Fe + Cr), and U/(Fe + Cr + Ni) diffusion couples. Magnetron sputtering is used to deposit thin films of Fe, Fe + Cr, or Fe + Cr + Ni on U substrates to form the diffusion couples. One set of samples are thermally annealed under high vacuum at 450 C or 550 C for one hour. A second set of samples are annealed identically but with concurrent 3.5 MeV Fe++ ion irradiation. The Fe++ ion penetration depth is sufficient to reachmore » the original interfaces. Rutherford backscattering spectrometry analysis with high fidelity spectral simulations is used to obtain interdiffusion profiles, which are used to examine differences in U diffusion and intermetallic phase formation at the buried interfaces. For all three diffusion systems, Fe++ ion irradiations enhance U diffusion. Furthermore, the irradiations accelerate the formation of intermetallic phases. In U/Fe couples, for example, the unirradiated samples show typical interdiffusion governed by Fick’s laws, while the irradiated ones show step-like profiles influenced by Gibbs phase rules.« less

Spatial variability of soil 137Cs in the South Caspian region.

PubMed

Khoshbinfar, Soheil; Vahabi Moghaddam, Masoud

2012-05-01

In a comprehensive program of environmental radioactivity survey in South Caspian region, (137)Cs inventories in soil has been measured at more than 50 sites in the Iranian northern province of Guilan. This has been the first wide-range survey of soil radionuclide inventories in the narrow band sensitive ecosystem of south Caspian shore. Radioactivity measurements were carried out using HPGe gamma-spectrometry system. The activity concentration of (137)Cs in surface soil exhibits a mean value of 17.6 ± 9.4 Bq kg(-1), with a range of 2.3-41.7 Bq kg(-1). In many sites, split-level sampling method has been applied down to a depth of 20 cm. There were found generally two profiles. Most profiles exhibit a negative exponential distribution, while others revealed a clear subsurface peak in 5-10-cm layer. Cesium deposition in the study area has been estimated to be in the range of 0.38-2.9 kBq m(-2) with a mean value of 1.7 kBq m(-2). Distribution patterns of (137)Cs concentration levels and deposition values have been estimated using Kriging interpolation method. Observed hotspots in deposition pattern coincide with areas of higher precipitation.

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.

Chemical analysis of solid materials by a LIMS instrument designed for space research: 2D elemental imaging, sub-nm depth profiling and molecular surface analysis

NASA Astrophysics Data System (ADS)

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

2016-04-01

Direct quantitative chemical analysis with high lateral and vertical resolution of solid materials is of prime importance for the development of a wide variety of research fields, including e.g., astrobiology, archeology, mineralogy, electronics, among many others. Nowadays, studies carried out by complementary state-of-the-art analytical techniques such as Auger Electron Spectroscopy (AES), X-ray Photoelectron Spectroscopy (XPS), Secondary Ion Mass Spectrometry (SIMS), Glow Discharge Time-of-Flight Mass Spectrometry (GD-TOF-MS) or Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) provide extensive insight into the chemical composition and allow for a deep understanding of processes that might have fashioned the outmost layers of an analyte due to its interaction with the surrounding environment. Nonetheless, these investigations typically employ equipment that is not suitable for implementation on spacecraft, where requirements concerning weight, size and power consumption are very strict. In recent years Laser Ablation/Ionization Mass Spectrometry (LIMS) has re-emerged as a powerful analytical technique suitable not only for laboratory but also for space applications.[1-3] Its improved performance and measurement capabilities result from the use of cutting edge ultra-short femtosecond laser sources, improved vacuum technology and fast electronics. Because of its ultimate compactness, simplicity and robustness it has already proven to be a very suitable analytical tool for elemental and isotope investigations in space research.[4] In this contribution we demonstrate extended capabilities of our LMS instrument by means of three case studies: i) 2D chemical imaging performed on an Allende meteorite sample,[5] ii) depth profiling with unprecedented sub-nm vertical resolution on Cu electrodeposited interconnects[6,7] and iii) preliminary molecular desorption of polymers without assistance of matrix or functionalized substrates.[8] On the whole, these results prove the adequacy of LMS as a powerful analytical tool able to address a great variety of topics in in situ space research. References: [1] U. Rohner, J. A. Whitby, P. Wurz, Meas. Sci. Technol. 2003, 14, 2159. [2] W. B. Brinckerhoff, G. G. Managadze, R. W. McEntire, A. F. Cheng, W. J. Green, Rev. Sci. Instrum. 2000, 71, 536. [3] G. G. Managadze, P. Wurz, R. Z. Sagdeev, A. E. Chumikov, M. Tuley, M. Yakovleva, N. G. Managadze, A. L. Bondarenko, Sol. Syst. Res. 2010, 44, 376. [4] A. Riedo, M. Neuland, S. Meyer, M. Tulej, P. Wurz, J. Anal. At. Spectrom. 2013, 28, 1256. [5] M.B. Neuland, S. Meyer, K. Mezger, A. Riedo, M. Tulej, P. Wurz, Planet. Space Sci. 2014, 101, 196. [6] V. Grimaudo, P. Moreno-García, A. Riedo, M. B. Neuland, M. Tulej, P. Broekmann, P. Wurz, Anal. Chem. 2015, 87, 2037. [7] A. Riedo, V. Grimaudo, P. Moreno-García, M. B. Neuland, M. Tulej, P. Wurz, P. Broekmann, J. Anal. At. Spectrom. 2015, 30, 2371. [8] P. Moreno-García, V. Grimaudo, A. Riedo, M. Tulej, P. Wurz, P. Broekmann, submitted to Rapid. Commun. Mass Spectrom., 2016.

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.

Mass Spectrometry Based Ultrasensitive DNA Methylation Profiling Using Target Fragmentation Assay.

PubMed

Lin, Xiang-Cheng; Zhang, Ting; Liu, Lan; Tang, Hao; Yu, Ru-Qin; Jiang, Jian-Hui

2016-01-19

Efficient tools for profiling DNA methylation in specific genes are essential for epigenetics and clinical diagnostics. Current DNA methylation profiling techniques have been limited by inconvenient implementation, requirements of specific reagents, and inferior accuracy in quantifying methylation degree. We develop a novel mass spectrometry method, target fragmentation assay (TFA), which enable to profile methylation in specific sequences. This method combines selective capture of DNA target from restricted cleavage of genomic DNA using magnetic separation with MS detection of the nonenzymatic hydrolysates of target DNA. This method is shown to be highly sensitive with a detection limit as low as 0.056 amol, allowing direct profiling of methylation using genome DNA without preamplification. Moreover, this method offers a unique advantage in accurately determining DNA methylation level. The clinical applicability was demonstrated by DNA methylation analysis using prostate tissue samples, implying the potential of this method as a useful tool for DNA methylation profiling in early detection of related diseases.

Assessment of the vertical distribution of natural radionuclides in a mineralized uranium area in south-west Spain.

PubMed

Blanco Rodríguez, P; Vera Tomé, F; Lozano, J C

2014-01-01

Low-level alpha spectrometry techniques using semiconductor detectors (PIPS) and liquid scintillation (LKB Quantulus 1220™) were used to determine the activity concentration of (238)U, (234)U, (230)Th, (226)Ra, (232)Th, and (210)Pb in soil samples. The soils were collected from an old disused uranium mine located in southwest Spain. The soils were sampled from areas with different levels of influence from the installation and hence had different levels of contamination. The vertical profiles of the soils (down to 40 cm depth) were studied in order to evaluate the vertical distribution of the natural radionuclides. To determine the origin of these natural radionuclides the Enrichment Factor was used. Also, study of the activity ratios between radionuclides belonging to the same radioactive series allowed us to assess the different types of behaviors of the radionuclides involved. The vertical profiles for the radionuclide members of the (238)U series were different at each sampling point, depending on the level of influence of the installation. However, the profiles of each point were similar for the long-lived radionuclides of the (238)U series ((238)U, (234)U, (230)Th, and (226)Ra). Moreover, a major imbalance was observed between (210)Pb and (226)Ra in the surface layer, due to (222)Rn exhalation and the subsequent surface deposition of (210)Pb. Copyright © 2013 Elsevier Ltd. All rights reserved.

Advanced Mass Spectrometry Technologies for the Study of Microbial Pathogenesis

PubMed Central

Moore, Jessica L.; Caprioli, Richard M.; Skaar, Eric P.

2014-01-01

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has been successfully applied to the field of microbial pathogenesis with promising results, principally in diagnostic microbiology to rapidly identify bacteria based on the molecular profiles of small cell populations. Direct profiling of molecules from serum and tissue samples by MALDI MS providesa means to study the pathogen-host interaction and to discover potential markers of infection. Systematic molecular profiling across tissue sections represents a new imaging modality, enabling regiospecific molecular measurements to be made in situ, in both two- and three-dimensional analyses. Herein, we briefly summarize work that employs MALDI MS to study the pathogenesis of microbial infection. PMID:24997399

Profiling analysis of low molecular weight heparins by multiple heart-cutting two dimensional chromatography with quadruple time-of-flight mass spectrometry.

PubMed

Ouyang, Yilan; Zeng, Yangyang; Rong, Yinxiu; Song, Yue; Shi, Lv; Chen, Bo; Yang, Xinlei; Xu, Naiyu; Linhardt, Robert J; Zhang, Zhenqing

2015-09-01

Low molecular weight heparins (LMWHs) are polydisperse and microheterogenous mixtures of polysaccharides used as anticoagulant drugs. Profiling analysis is important for obtaining deeper insights into the structure of LMWHs. Previous oligosaccharide mapping methods are relatively low resolution and are unable to show an entire picture of the structural complexity of LMWHs. In the current study a profiling method was developed relying on multiple heart-cutting, two-dimensional, ultrahigh performance liquid chromatography with quadruple time-of-flight mass spectrometry. This represents an efficient, automated, and robust approach for profiling LMWHs. Using size-exclusion chromatography and ion-pairing reversed-phase chromatography in a two-dimensional separation, LMW components of different sizes and LMW components of the same size but with different charges and polarities can be resolved, providing a more complete picture of a LMWH. Structural information on each component was then obtained with quadrupole time-of-flight mass spectrometry. More than 80 and 120 oligosaccharides were observed and unambiguously assigned from the LMWHs, nadroparin and enoxaparin, respectively. This method might be useful for quality control of LMWHs and as a powerful tool for heparin-related glycomics.

microMS: A Python Platform for Image-Guided Mass Spectrometry Profiling

NASA Astrophysics Data System (ADS)

Comi, Troy J.; Neumann, Elizabeth K.; Do, Thanh D.; Sweedler, Jonathan V.

2017-09-01

Image-guided mass spectrometry (MS) profiling provides a facile framework for analyzing samples ranging from single cells to tissue sections. The fundamental workflow utilizes a whole-slide microscopy image to select targets of interest, determine their spatial locations, and subsequently perform MS analysis at those locations. Improving upon prior reported methodology, a software package was developed for working with microscopy images. microMS, for microscopy-guided mass spectrometry, allows the user to select and profile diverse samples using a variety of target patterns and mass analyzers. Written in Python, the program provides an intuitive graphical user interface to simplify image-guided MS for novice users. The class hierarchy of instrument interactions permits integration of new MS systems while retaining the feature-rich image analysis framework. microMS is a versatile platform for performing targeted profiling experiments using a series of mass spectrometers. The flexibility in mass analyzers greatly simplifies serial analyses of the same targets by different instruments. The current capabilities of microMS are presented, and its application for off-line analysis of single cells on three distinct instruments is demonstrated. The software has been made freely available for research purposes. [Figure not available: see fulltext.

microMS: A Python Platform for Image-Guided Mass Spectrometry Profiling.

PubMed

Comi, Troy J; Neumann, Elizabeth K; Do, Thanh D; Sweedler, Jonathan V

2017-09-01

Image-guided mass spectrometry (MS) profiling provides a facile framework for analyzing samples ranging from single cells to tissue sections. The fundamental workflow utilizes a whole-slide microscopy image to select targets of interest, determine their spatial locations, and subsequently perform MS analysis at those locations. Improving upon prior reported methodology, a software package was developed for working with microscopy images. microMS, for microscopy-guided mass spectrometry, allows the user to select and profile diverse samples using a variety of target patterns and mass analyzers. Written in Python, the program provides an intuitive graphical user interface to simplify image-guided MS for novice users. The class hierarchy of instrument interactions permits integration of new MS systems while retaining the feature-rich image analysis framework. microMS is a versatile platform for performing targeted profiling experiments using a series of mass spectrometers. The flexibility in mass analyzers greatly simplifies serial analyses of the same targets by different instruments. The current capabilities of microMS are presented, and its application for off-line analysis of single cells on three distinct instruments is demonstrated. The software has been made freely available for research purposes. Graphical Abstract ᅟ.

Advances in imaging secondary ion mass spectrometry for biological samples

DOE PAGES

Boxer, Steven G.; Kraft, Mary L.; Weber, Peter K.

2008-12-16

Imaging mass spectrometry combines the power of mass spectrometry to identify complex molecules based on mass with sample imaging. Recent advances in secondary ion mass spectrometry have improved sensitivity and spatial resolution, so that these methods have the potential to bridge between high-resolution structures obtained by X-ray crystallography and cyro-electron microscopy and ultrastructure visualized by conventional light microscopy. Following background information on the method and instrumentation, we address the key issue of sample preparation. Because mass spectrometry is performed in high vacuum, it is essential to preserve the lateral organization of the sample while removing bulk water, and this hasmore » been a major barrier for applications to biological systems. Furthermore, recent applications of imaging mass spectrometry to cell biology, microbial communities, and biosynthetic pathways are summarized briefly, and studies of biological membrane organization are described in greater depth.« less

Rapid Identification and Subtyping of Helicobacter cinaedi Strains by Intact-Cell Mass Spectrometry Profiling with the Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Taniguchi, Takako; Sekiya, Ayumi; Higa, Mariko; Saeki, Yuji; Umeki, Kazumi; Okayama, Akihiko; Hayashi, Tetsuya

2014-01-01

Helicobacter cinaedi infection is recognized as an increasingly important emerging disease in humans. Although H. cinaedi-like strains have been isolated from a variety of animals, it is difficult to identify particular isolates due to their unusual phenotypic profiles and the limited number of biochemical tests for detecting helicobacters. Moreover, analyses of the 16S rRNA gene sequences are also limited due to the high levels of similarity among closely related helicobacters. This study was conducted to evaluate intact-cell mass spectrometry (ICMS) profiling using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) as a tool for the identification of H. cinaedi. A total of 68 strains of H. cinaedi isolated from humans, dogs, a cat, and hamsters were examined in addition to other Helicobacter species. The major ICMS profiles of H. cinaedi were identical and differed from those of Helicobacter bilis, which show >98% sequence similarity at the 16S rRNA sequence level. A phyloproteomic analysis of the H. cinaedi strains examined in this work revealed that human isolates formed a single cluster that was distinct from that of the animal isolates, with the exception of two strains from dogs. These phyloproteomic results agreed with those of the phylogenetic analysis based on the nucleotide sequences of the hsp60 gene. Because they formed a distinct cluster in both analyses, our data suggest that animal strains may not be a major source of infection in humans. In conclusion, the ICMS profiles obtained using a MALDI-TOF MS approach may be useful for the identification and subtyping of H. cinaedi. PMID:24153128

Discovery of safety biomarkers for atorvastatin in rat urine using mass spectrometry based metabolomics combined with global and targeted approach.

PubMed

Kumar, Bhowmik Salil; Lee, Young-Joo; Yi, Hong Jae; Chung, Bong Chul; Jung, Byung Hwa

2010-02-19

In order to develop a safety biomarker for atorvastatin, this drug was orally administrated to hyperlipidemic rats, and a metabolomic study was performed. Atorvastatin was given in doses of either 70 mg kg(-1) day(-1) or 250 mg kg(-1) day(-1) for a period of 7 days (n=4 for each group). To evaluate any abnormal effects of the drug, physiological and plasma biochemical parameters were measured and histopathological tests were carried out. Safety biomarkers were derived by comparing these parameters and using both global and targeted metabolic profiling. Global metabolic profiling was performed using liquid chromatography/time of flight/mass spectrometry (LC/TOF/MS) with multivariate data analysis. Several safety biomarker candidates that included various steroids and amino acids were discovered as a result of global metabolic profiling, and they were also confirmed by targeted metabolic profiling using gas chromatography/mass spectrometry (GC/MS) and capillary electrophoresis/mass spectrometry (CE/MS). Serum biochemical and histopathological tests were used to detect abnormal drug reactions in the liver after repeating oral administration of atorvastatin. The metabolic differences between control and the drug-treated groups were compared using PLS-DA score plots. These results were compared with the physiological and plasma biochemical parameters and the results of a histopathological test. Estrone, cortisone, proline, cystine, 3-ureidopropionic acid and histidine were proposed as potential safety biomarkers related with the liver toxicity of atorvastatin. These results indicate that the combined application of global and targeted metabolic profiling could be a useful tool for the discovery of drug safety biomarkers. Copyright 2009 Elsevier B.V. All rights reserved.

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.

Digging a Little Deeper: Microbial Communities, Molecular Composition and Soil Organic Matter Turnover along Tropical Forest Soil Depth Profiles

NASA Astrophysics Data System (ADS)

Pett-Ridge, J.; McFarlane, K. J.; Heckman, K. A.; Reed, S.; Green, E. A.; Nico, P. S.; Tfaily, M. M.; Wood, T. E.; Plante, A. F.

2016-12-01

Tropical forest soils store more carbon (C) than any other terrestrial ecosystem and exchange vast amounts of CO2, water, and energy with the atmosphere. Much of this C is leached and stored in deep soil layers where we know little about its fate or the microbial communities that drive deep soil biogeochemistry. Organic matter (OM) in tropical soils appears to be associated with mineral particles, suggesting deep soils may provide greater C stabilization. However, few studies have evaluated sub-surface soils in tropical ecosystems, including estimates of the turnover times of deep soil C, the sensitivity of this C to global environmental change, and the microorganisms involved. We quantified bulk C pools, microbial communities, molecular composition of soil organic matter, and soil radiocarbon turnover times from surface soils to 1.5m depths in multiple soil pits across the Luquillo Experimental Forest, Puerto Rico. Soil C, nitrogen, and root and microbial biomass all declined exponentially with depth; total C concentrations dropped from 5.5% at the surface to <0.5% at 140cm depth. High-throughput sequencing highlighted distinct microbial communities in surface soils (Acidobacteria and Proteobacteria) versus those below the active rooting zone (Verrucomicrobia and Thaumarchaea). High resolution mass spectrometry (FTICR-MS) analyses suggest a shift in the composition of OM with depth (especially in the water soluble fraction), an increase in oxidation, and decreasing H/C with depth (indicating higher aromaticity). Additionally, surface samples were rich in lignin-like compounds of plant origin that were absent with depth. Soil OM 14C and mean turnover times were variable across replicate horizons, ranging from 3-1500 years at the surface, to 5000-40,000 years at depth. In comparison to temperate deciduous forests, these 14C values reflect far older soil C. Particulate organic matter (free light fraction), with a relatively modern 14C was found in low but measureable concentration in even the deepest soil horizons. Our results indicate these tropical subsoils contain small but metabolically active microbial communities that are highly OM limited and may persist via degradation of recent inputs.

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.

Quantitative detection of caffeine in human skin by confocal Raman spectroscopy--A systematic in vitro validation study.

PubMed

Franzen, Lutz; Anderski, Juliane; Windbergs, Maike

2015-09-01

For rational development and evaluation of dermal drug delivery, the knowledge of rate and extent of substance penetration into the human skin is essential. However, current analytical procedures are destructive, labor intense and lack a defined spatial resolution. In this context, confocal Raman microscopy bares the potential to overcome current limitations in drug depth profiling. Confocal Raman microscopy already proved its suitability for the acquisition of qualitative penetration profiles, but a comprehensive investigation regarding its suitability for quantitative measurements inside the human skin is still missing. In this work, we present a systematic validation study to deploy confocal Raman microscopy for quantitative drug depth profiling in human skin. After we validated our Raman microscopic setup, we successfully established an experimental procedure that allows correlating the Raman signal of a model drug with its controlled concentration in human skin. To overcome current drawbacks in drug depth profiling, we evaluated different modes of peak correlation for quantitative Raman measurements and offer a suitable operating procedure for quantitative drug depth profiling in human skin. In conclusion, we successfully demonstrate the potential of confocal Raman microscopy for quantitative drug depth profiling in human skin as valuable alternative to destructive state-of-the-art techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

Iodine-129 in soils from Northern Ukraine and the retrospective dosimetry of the iodine-131 exposure after the Chernobyl accident.

PubMed

Michel, R; Handl, J; Ernst, T; Botsch, W; Szidat, S; Schmidt, A; Jakob, D; Beltz, D; Romantschuk, L D; Synal, H-A; Schnabel, C; López-Gutiérrez, J M

2005-03-20

Forty-eight soil profiles down to a depth of 40 cm were taken in Russia and Ukraine in 1995 and 1997, respectively, in order to investigate the feasibility of retrospective dosimetry of the 131I exposure after the Chernobyl accident via the long-lived 129I. The sampling sites covered areas almost not affected by fallout from the Chernobyl accident such as Moscow/Russia and the Zhitomir district in Ukraine as well as the highly contaminated Korosten and Narodici districts in Ukraine. 129I was analyzed by radiochemical neutron activation analysis (RNAA) and accelerator mass spectrometry (AMS). 127I was measured for some profiles by RNAA or ion chromatography (IC). The results for 127I demonstrated large differences in the capabilities of the soils to store iodine over long time spans. The depth profiles of 129I and of 137Cs showed large differences in the migration behavior between the two nuclides but also for each nuclide among the different sampling sites. Though it cannot be quantified how much 129I and 137Cs was lost out of the soil columns into deeper depths, the inventories in the columns were taken as proxies for the total inventories. For 129I, these inventories were at least three orders of magnitude higher than a pre-nuclear value of 0.084+/-0.017 mBq m(-2) derived from a soil profile taken in 1939 in Lutovinovo/Russia. From the samples from Moscow and Zhitomir, a pre-Chernobyl 129I inventory of (44+/-24) mBq m(-2) was determined, limiting the feasibility of 129I retrospective dosimetry to areas where the 129I inventories exceed 100 mBq m(-2). Higher average 129I inventories in the Korosten and Narodici districts of 130 and 848 mBq m(-2), respectively, allowed determination of the 129I fallout due to the Chernobyl accident. Based on the total 129I inventories and on literature data for the atomic ratio of 129I/131I=13.6+/-2.8 for the Chernobyl emissions and on aggregated dose coefficients for 131I, the thyroid exposure due to 131I after the Chernobyl accident was estimated for the inhabitants of four villages in the Korosten and of three villages in the Narodici districts. The limitations and uncertainties of the 129I retrospective dosimetry are discussed.

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.

Quantitative operando visualization of the energy band depth profile in solar cells.

PubMed

Chen, Qi; Mao, Lin; Li, Yaowen; Kong, Tao; Wu, Na; Ma, Changqi; Bai, Sai; Jin, Yizheng; Wu, Dan; Lu, Wei; Wang, Bing; Chen, Liwei

2015-07-13

The energy band alignment in solar cell devices is critically important because it largely governs elementary photovoltaic processes, such as the generation, separation, transport, recombination and collection of charge carriers. Despite the expenditure of considerable effort, the measurement of energy band depth profiles across multiple layers has been extremely challenging, especially for operando devices. Here we present direct visualization of the surface potential depth profile over the cross-sections of operando organic photovoltaic devices using scanning Kelvin probe microscopy. The convolution effect due to finite tip size and cantilever beam crosstalk has previously prohibited quantitative interpretation of scanning Kelvin probe microscopy-measured surface potential depth profiles. We develop a bias voltage-compensation method to address this critical problem and obtain quantitatively accurate measurements of the open-circuit voltage, built-in potential and electrode potential difference.

Quantitative operando visualization of the energy band depth profile in solar cells

PubMed Central

Chen, Qi; Mao, Lin; Li, Yaowen; Kong, Tao; Wu, Na; Ma, Changqi; Bai, Sai; Jin, Yizheng; Wu, Dan; Lu, Wei; Wang, Bing; Chen, Liwei

2015-01-01

The energy band alignment in solar cell devices is critically important because it largely governs elementary photovoltaic processes, such as the generation, separation, transport, recombination and collection of charge carriers. Despite the expenditure of considerable effort, the measurement of energy band depth profiles across multiple layers has been extremely challenging, especially for operando devices. Here we present direct visualization of the surface potential depth profile over the cross-sections of operando organic photovoltaic devices using scanning Kelvin probe microscopy. The convolution effect due to finite tip size and cantilever beam crosstalk has previously prohibited quantitative interpretation of scanning Kelvin probe microscopy-measured surface potential depth profiles. We develop a bias voltage-compensation method to address this critical problem and obtain quantitatively accurate measurements of the open-circuit voltage, built-in potential and electrode potential difference. PMID:26166580

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.

Global gas chromatography/time-of-flight mass spectrometry (GC/TOFMS)-based metabonomic profiling of lyophilized human feces.

PubMed

Phua, Lee Cheng; Koh, Poh Koon; Cheah, Peh Yean; Ho, Han Kiat; Chan, Eric Chun Yong

2013-10-15

Gas chromatography mass spectrometry (GC/MS)-based fecal metabonomics represents a powerful systems biology approach for elucidating metabolic biomarkers of lower gastrointestinal tract (GIT) diseases. Unlike metabolic profiling of fecal water, the profiling of complete fecal material remains under-explored. Here, a gas chromatography/time-of-flight mass spectrometry (GC/TOFMS) method was developed and validated for the global metabonomic profiling of human feces. Fecal and fecal water metabotypes were also profiled and compared. Additionally, the unclear influence of blood in stool on the fecal metabotype was investigated unprecedentedly. Eighty milligram of lyophilized feces was ultrasonicated with 1mL of methanol:water (8:2) for 30min, followed by centrifugation, drying of supernatant, oximation and trimethylsilylation for 45min. Lyophilized feces demonstrated a more comprehensive metabolic coverage than fecal water, based on the number of chromatographic peaks. Principal component analysis (PCA) indicated occult blood (1mgHb/g feces) exerted a negligible effect on the fecal metabotype. Conversely, a unique metabotype related to feces spiked with gross blood (100mgHb/g feces) was revealed (PCA, R(2)X=0.837, Q(2)=0.794), confirming the potential confounding effect of gross GIT bleeding on the fecal metabotype. This pertinent finding highlights the importance of prudent interpretation of fecal metabonomic data, particularly in GIT diseases where bleeding is prevalent. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

First study on 236U in the Northeast Pacific Ocean using a new target preparation procedure for AMS measurements.

PubMed

Eigl, R; Steier, P; Winkler, S R; Sakata, K; Sakaguchi, A

2016-10-01

We succeeded in obtaining the depth profile of 236 U for a sampling station in the Northeast Pacific Ocean using only one litre of seawater sample from each depth. For this purpose, a new procedure was developed that allowed for the preparation of accelerator mass spectrometry targets for trace uranium using only 100 μg of iron carrier material. The 236 U concentrations in water samples from the Northeast Pacific Ocean showed large variations from (9.26 ± 0.42) × 10 6 atoms/kg at 60 m depth to (0.08 ± 0.02) × 10 6 atoms/kg at a depth of 3000 m. The high 236 U concentrations in surface water reflect the input of 236 U by global and local fallout from nuclear weapons tests. The low 236 U concentrations in seawater from 1500 m and below are an indicator for the low vertical diffusion of surface water to deeper layers in the North Pacific Ocean. The total inventory of 236 U on the water column was (8.35 ± 0.23) × 10 12 atoms/m 2 , which is lower compared to those of other ocean regions solely affected by global fallout on comparable latitudes. This study represents the first dataset for 236 U in the Pacific Ocean and shows the possibility of downsizing sample volumes which may help in future applications of 236 U as tracer for large ocean areas. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mercury in the Black Sea - results of the 2013 GEOTRACES MEDBlack cruise

NASA Astrophysics Data System (ADS)

Heimbürger, L. E.; Sonke, J.; Rijkenberg, M. J. A.; Gerringa, L. J.; De Baar, H. J. W.

2014-12-01

Inorganic mercury (Hg), whether of natural or anthropogenic origin, can be converted into the neurotoxin methylmercury (MeHg). Today we believe this conversion occurs during the bacterial remineralization of sinking organic matter in the oceanic water column. The Black Sea with its high organic matter inputs and anoxic deep waters is an excellent study site to investigate in more detail the processes yielding MeHg. To date only one vertical profile of Hg species near the Western shelf and one vertical profile in the Western Gyre are published (Lamborg et al. 2008). We will present new results of the 2013 Dutch-led GEOTRACES MEDBlack cruise in the Black Sea. Research vessel "Pelagia" occupied 12 full depth stations along an east-west transect from 13 to 25 July 2013. High resolution vertical profiles were sampled using a titanium ultraclean CTD frame (de Baar et al., 2008) equipped with 24 x 24L PVDF samplers. Samples were filtered (0.2µm, Sartobran 300), drawn into pre-cleaned 250mL Savillex PFA bottles and acidified to 0.4% (v:v) with double-distilled HCl. Dissolved MeHg, as the sum of monomethylHg and dimethylHg, was analyzed via isotope dilution gas chromatography sector field inductively coupled mass spectrometry. Total dissolved Hg was determined following the US EPA 1631 method. We will present high resolution vertical Hg species profiles, including one ultra-high resolution profile (1 sample every 5m-depth) to understand the dynamics along the chemocline (Luther et al., 1991). We will also present the results of the GEOTRACES international intercalibration exercise for dissolved MeHg and dissolved total Hg in surface seawater that we organized during the same cruise. References De Baar HJW, Timmermans KR, Laan P, De Porto HH, Ober S, Blom JJ, Bakker MC, Schilling J, Sarthou G, Smit MG, Klunder M. Titan: A new facility for ultraclean sampling of trace elements and isotopes in the deep oceans in the international Geotraces program. Mar. Chem. 2008, 111(1-2): 4-21. Lamborg CH, Yiğiterhan O, Fitzgerald WF, Balcom PH, Hammerschmidt CR, Murray J.Vertical distribution of mercury species at two sites in the Western Black Sea. Mar.Chem. 2008, 111(1-2): 77-89. Luther III GW, Church TM, Powell D. Sulfur speciation and sulfide oxidation in the water column of the Black Sea. DSR I 1991, 38:1121-1137.

Soufrière Hills Plagioclase: Postcards From the Edge.

NASA Astrophysics Data System (ADS)

Genareau, K.; Clarke, A.; Hervig, R.

2005-12-01

Secondary Ion Mass Spectrometry (SIMS) can provide sub-micron depth resolution for analyzing products of volcanic eruptions. SIMS was used to examine the outer rims of plagioclase phenocrysts derived from both explosive and effusive eruptions of the Soufrière Hills Volcano (SHV), Montserrat. Phenocrysts were separated from the host igneous rock by crushing with a mortar and pestle and then cleaned with a Branson Sonifier. A 12.5 kV O2+ primary ion beam was used to examine the variation in ten elements (Ca, Na, Si, Al, Ti, Zr, K, Fe, Sr, Li) through a crystal depth of 5-9 microns. Plagioclase crystals separated from explosively produced pumice clasts show increasing anorthite (An) content with depth into the crystal surface, starting at ~10% An at the surface and reaching a constant composition of ~45% An at 2-4 microns depth. According to experimentally determined estimates of plagioclase growth rates for the SHV magma (Couch et al. 2003; J. Petrology 44, 1477-1502), the 2-4 microns depth over which An changes corresponds to 1-7 hours of growth. Sr also shows a general increase with depth into the crystal. K shows a rapid decrease in abundance with depth. Fe shows more complex patterns that may indicate late-stage crystallization of magnetite. Plagioclase derived from exogenous dome samples also have surface compositions of ~10% An increasing with depth to ~30% An, but rather than plateau, the values begin to decrease again at 2-5 microns depth. This fluctuating abundance of An may reveal the presence of micron-scale decompression-induced growth zones that have not been previously documented due to limitations in the spatial resolution of conventional analytical techniques. Explosive and effusive samples exhibit conflicting Li trends. The explosively derived plagioclase have elevated surface Li concentrations while the dome derived plagioclase have low surface Li concentrations. These differing trends may provide evidence of closed system vs. open system degassing as a function of eruptive style. Geochemical analyses of igneous phenocrysts using the SIMS depth-profiling technique can be used to constrain the style of magma decompression and eruption. Additional analyses are currently being performed on an expanded suite of samples in order to confirm these results and to relate crystal-edge chemistry to other parameters such as quench pressure and degree of magma degassing.

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.

Zn precipitation and Li depletion in Zn implanted ZnO

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

Chan, K. S.; Jagadish, C.; Wong-Leung, J., E-mail: jenny.wongleung@anu.edu.au

2016-07-11

Ion implantation of Zn substituting elements in ZnO has been shown to result in a dramatic Li depletion of several microns in hydrothermally grown ZnO. This has been ascribed to a burst of mobile Zn interstials. In this study, we seek to understand the reason behind this interstitial mediated transient enhanced diffusion in Li-containing ZnO samples after Zn implantation. ZnO wafers were implanted with Zn to two doses, 5 × 10{sup 15} cm{sup −2} and 1 × 10{sup 17} cm{sup −2}. Secondary ion mass spectrometry was carried out to profile the Li depletion depth for different annealing temperatures between 600 and 800 °C. The 800 °C annealing hadmore » the most significant Li depletion of close to 60 μm. Transmission electron microscopy (TEM) was carried out in selected samples to identify the reason behind the Li depletion. In particular, TEM investigations of samples annealed at 750 °C show significant Zn precipitation just below the depth of the projected range of the implanted ions. We propose that the Zn precipitation is indicative of Zn supersaturation. Both the Li depletion and Zn precipitation are competing synchronous processes aimed at reducing the excess Zn interstitials.« less

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.

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.

Authentication of organically and conventionally grown basils by gas chromatograpy/mass spectrometry chemical profiles

USDA-ARS?s Scientific Manuscript database

Basil plants cultivated by organic and conventional farming practices were differentiated using gas chromatography/mass spectrometry (GC/MS) and chemometric methods. The two-way GC/MS data sets were baseline-corrected and retention time-aligned prior to data processing. Two self-devised fuzzy clas...

Gas chromatography-mass spectrometry-based metabolic profiling of cerebrospinal fluid from epileptic dogs.

PubMed

Hasegawa, Tetsuya; Sumita, Maho; Horitani, Yusuke; Tamai, Reo; Tanaka, Katsuhiro; Komori, Masayuki; Takenaka, Shigeo

2014-04-01

Epilepsy is a common neurological disorder with seizures, but diagnostic approaches in veterinary clinics remain limited. Cerebrospinal fluid (CSF) is a body fluid used for diagnosis in veterinary medicine. In this study, we explored canine epilepsy diagnostic biomarkers using gas chromatography-mass spectrometry (GC-MS)-based metabolic profiling of CSF and multivariate data analysis. Profiles for subjects with idiopathic epilepsy differed significantly from those of healthy controls and subjects with symptomatic epilepsy. Among 60 identified metabolites, the levels of 20 differed significantly among the three groups. Glutamic acid was significantly increased in idiopathic epilepsy, and some metabolites including ascorbic acid were changed in both forms of epilepsy. These findings show that metabolic profiles of CSF differ between idiopathic and symptomatic epilepsy and that metabolites including glutamic acid and ascorbic acid in CSF may be useful for diagnosis of canine epilepsy.

Instantaneous characterization of vegetable oils via TAG and FFA profiles by easy ambient sonic-spray ionization mass spectrometry.

PubMed

Simas, Rosineide C; Catharino, Rodrigo R; Cunha, Ildenize B S; Cabral, Elaine C; Barrera-Arellano, Daniel; Eberlin, Marcos N; Alberici, Rosana M

2010-04-01

A fast and reliable method is presented for the analysis of vegetable oils. Easy ambient sonic-spray ionization mass spectrometry (EASI-MS) is shown to efficiently desorb and ionize the main oil constituents from an inert surface under ambient conditions and to provide comprehensive triacylglyceride (TAG) and free fatty acid (FFA) profiles detected mainly as either [TAG + Na](+) or [FFA-H](-) ions. EASI(+/-)-MS analysis is simple, easily implemented, requires just a tiny droplet of the oil and is performed without any pre-separation or chemical manipulation. It also causes no fragmentation of TAG ions hence diacylglyceride (DAG) and monoacylglyceride (MAG) profiles and contents can also be measured. The EASI(+/-)-MS profiles of TAG and FFA permit authentication and quality control and can be used, for instance, to access levels of adulteration, acidity, oxidation or hydrolysis of vegetable oils in general.

Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology.

PubMed

Aretz, Ina; Meierhofer, David

2016-04-27

Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

PubMed Central

Aretz, Ina; Meierhofer, David

2016-01-01

Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology. PMID:27128910

Effect of thermal annealing on the redistribution of alkali metals in Cu(In,Ga)Se 2 solar cells on glass substrate

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

Kamikawa, Yukiko; Nishinaga, Jiro; Ishizuka, Shogo

The precise control of alkali-metal concentrations in Cu(In,Ga)Se 2 (CIGS) solar cells via post deposition treatment (PDT) has recently attracted attention. When PDT is performed at an elevated temperature, an accompanying annealing effect is expected. Here, we investigate how thermal annealing affects the redistribution of alkali metals in CIGS solar cells on glass substrates and the properties of the solar cells. In addition, we investigate the origin of non-homogeneous alkali-metal depth profiles that are typical of CIGS grown using a three-stage process. In particular, we use secondary-ion mass spectrometry measurements of the ion concentration as a function of distance frommore » the CIGS surface to investigate the impact of thermal annealing on the distribution of alkali metals (Na, Ka, and Rb) and constituent elements (Ga and In) in the CIGS absorbers. We find that the depth profiles of the alkali metals strongly reflect the density of sites that tend to accommodate alkali metals, i.e., vacancies. Annealing at elevated temperature caused a redistribution of the alkali metals. The thermal-diffusion kinetics of alkali metals depends strongly on the species involved. We introduced low flux potassium fluoride (KF) to study a side effect of KF-PDT, i.e., Na removal from CIGS, separately from its predominant effects such as surface modification. When sufficient amounts of Na are supplied from the soda lime glass via annealing at an elevated temperature, the negative effect was not apparent. Conversely, when the Na supply was not sufficient, it caused a deterioration of the photovoltaic properties.« less

Effect of thermal annealing on the redistribution of alkali metals in Cu(In,Ga)Se 2 solar cells on glass substrate

DOE PAGES

Kamikawa, Yukiko; Nishinaga, Jiro; Ishizuka, Shogo; ...

2018-03-07

The precise control of alkali-metal concentrations in Cu(In,Ga)Se 2 (CIGS) solar cells via post deposition treatment (PDT) has recently attracted attention. When PDT is performed at an elevated temperature, an accompanying annealing effect is expected. Here, we investigate how thermal annealing affects the redistribution of alkali metals in CIGS solar cells on glass substrates and the properties of the solar cells. In addition, we investigate the origin of non-homogeneous alkali-metal depth profiles that are typical of CIGS grown using a three-stage process. In particular, we use secondary-ion mass spectrometry measurements of the ion concentration as a function of distance frommore » the CIGS surface to investigate the impact of thermal annealing on the distribution of alkali metals (Na, Ka, and Rb) and constituent elements (Ga and In) in the CIGS absorbers. We find that the depth profiles of the alkali metals strongly reflect the density of sites that tend to accommodate alkali metals, i.e., vacancies. Annealing at elevated temperature caused a redistribution of the alkali metals. The thermal-diffusion kinetics of alkali metals depends strongly on the species involved. We introduced low flux potassium fluoride (KF) to study a side effect of KF-PDT, i.e., Na removal from CIGS, separately from its predominant effects such as surface modification. When sufficient amounts of Na are supplied from the soda lime glass via annealing at an elevated temperature, the negative effect was not apparent. Conversely, when the Na supply was not sufficient, it caused a deterioration of the photovoltaic properties.« less

Single-cell RNA-sequencing reveals a distinct population of proglucagon-expressing cells specific to the mouse upper small intestine.

PubMed

Glass, Leslie L; Calero-Nieto, Fernando J; Jawaid, Wajid; Larraufie, Pierre; Kay, Richard G; Göttgens, Berthold; Reimann, Frank; Gribble, Fiona M

2017-10-01

To identify sub-populations of intestinal preproglucagon-expressing (PPG) cells producing Glucagon-like Peptide-1, and their associated expression profiles of sensory receptors, thereby enabling the discovery of therapeutic strategies that target these cell populations for the treatment of diabetes and obesity. We performed single cell RNA sequencing of PPG-cells purified by flow cytometry from the upper small intestine of 3 GLU-Venus mice. Cells from 2 mice were sequenced at low depth, and from the third mouse at high depth. High quality sequencing data from 234 PPG-cells were used to identify clusters by tSNE analysis. qPCR was performed to compare the longitudinal and crypt/villus locations of cluster-specific genes. Immunofluorescence and mass spectrometry were used to confirm protein expression. PPG-cells formed 3 major clusters: a group with typical characteristics of classical L-cells, including high expression of Gcg and Pyy (comprising 51% of all PPG-cells); a cell type overlapping with Gip-expressing K-cells (14%); and a unique cluster expressing Tph1 and Pzp that was predominantly located in proximal small intestine villi and co-produced 5-HT (35%). Expression of G-protein coupled receptors differed between clusters, suggesting the cell types are differentially regulated and would be differentially targetable. Our findings support the emerging concept that many enteroendocrine cell populations are highly overlapping, with individual cells producing a range of peptides previously assigned to distinct cell types. Different receptor expression profiles across the clusters highlight potential drug targets to increase gut hormone secretion for the treatment of diabetes and obesity. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

Simultaneous Quantification of Viral Antigen Expression Kinetics Using Data-Independent (DIA) Mass Spectrometry*

PubMed Central

Croft, Nathan P.; de Verteuil, Danielle A.; Smith, Stewart A.; Wong, Yik Chun; Schittenhelm, Ralf B.; Tscharke, David C.; Purcell, Anthony W.

2015-01-01

The generation of antigen-specific reagents is a significant bottleneck in the study of complex pathogens that express many hundreds to thousands of different proteins or to emerging or new strains of viruses that display potential pandemic qualities and therefore require rapid investigation. In these instances the development of antibodies for example can be prohibitively expensive to cover the full pathogen proteome, or the lead time may be unacceptably long in urgent cases where new highly pathogenic viral strains may emerge. Because genomic information on such pathogens can be rapidly acquired this opens up avenues using mass spectrometric approaches to study pathogen antigen expression, host responses and for screening the utility of therapeutics. In particular, data-independent acquisition (DIA) modalities on high-resolution mass spectrometers generate spectral information on all components of a complex sample providing depth of coverage hitherto only seen in genomic deep sequencing. The spectral information generated by DIA can be iteratively interrogated for potentially any protein of interest providing both evidence of protein expression and quantitation. Here we apply a solely DIA mass spectrometry based methodology to profile the viral antigen expression in cells infected with vaccinia virus up to 9 h post infection without the need for antigen specific antibodies or other reagents. We demonstrate deep coverage of the vaccinia virus proteome using a SWATH-MS acquisition approach, extracting quantitative kinetics of 100 virus proteins within a single experiment. The results highlight the complexity of vaccinia protein expression, complementing what is known at the transcriptomic level, and provide a valuable resource and technique for future studies of viral infection and replication kinetics. Furthermore, they highlight the utility of DIA and mass spectrometry in the dissection of host-pathogen interactions. PMID:25755296

Sediment budget for Murder Creek, Georgia, USA, from Pu239+240 - determined soil erosion rates

NASA Astrophysics Data System (ADS)

Stubblefield, A. P.; Matissoff, G.; Ketterer, M. E.; Whiting, P. J.

2005-12-01

Soil inventories of the radionuclides Cs137 and Pb210 have been used in a variety of environments as indicators for erosion and depositional processes. Development of sediment budgets for entire watersheds from radionuclide data has been somewhat constrained because limited sample numbers may not adequately characterize the wide range of geomorphic conditions and land uses found in heterogeneous environments. The measurement of Pu239+240 shows great potential for developing quantitative watershed sediment budgets. With inductively-coupled plasma mass spectrometry, hundreds of samples may be processed in dramatically shorter times than the gamma spectrometry method used for Cs137 or alpha spectrometry method used for Pb210. We collected surface soil samples from Murder Creek in the Piedmont region of Georgia, USA, to compare Pu239+240 inventories with Cs137 and Pb210 inventories for a range of land uses in a predominantly forested watershed. Excellent correlations were found for radionuclide inventories (r2 =0.88, n = 38) and high resolution (4 mm) depth profiles. The second objective was to generate a sediment budget using the full Pu239+240 dataset (n = 309). Average Pu239+240 inventories were 70.0 Bq/m2 for hardwood forest, 60.0 Bq/m2 for pine plantation, 65.1 Bq/m2 for pine forest, 66.7 Bq/m2 for row crop agriculture and 67.9 Bq/m2 for pasture. The sediment budget will be constructed by converting inventories into site-specific erosion rates. Erosion rates will be scaled up to the watershed scale using GIS coverages of land use, soil, slope, and slope position. Results will be compared with Murder Creek sediment budgets in the scientific literature generated from RUSLE erosion modeling, USGS monitoring networks and reservoir sedimentation.

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

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.

Characteristic component profiling and identification of different Uncaria species based on high-performance liquid chromatography-photodiode array detection tandem ion trap and time of flight mass spectrometry coupled with rDNA ITS sequence.

PubMed

Zhao, Bingqiang; Huang, Yanjun; Chen, Qiulan; Chen, Qizhao; Miao, Hui; Zhu, Shuang; Zeng, Changqing

2018-03-01

Uncaria is a multi-source herb and its species identification has become a bottleneck in quality control. To study the identification method of different Uncaria species herbs through HPLC-MS coupled with rDNA Internal Transcribed Spacer (rDNA ITS) sequence, both plant morphological traits and molecular identification were used to determine the species of every collected Uncaria herb. The genetic analysis of different Uncaria species was performed using their rDNA ITS sequence as a molecular marker. Meanwhile, the phylogenetic relationships of 22 samples from six Uncaria species were divided and classified clearly. By optimizing the chromatographic conditions, a practical HPLC method to differentiate various varieties of Uncaria herbs was set up based on a set of characteristic components across each species. A high-performance liquid chromatography-photodiode array detector tandem ion trap and time of flight mass spectrometry technique combined with reference substances was utilized to derive 21 characteristic compounds containing six groups of six Uncaria species in China. Thus, this study provides a feasible method to solve the current problem of confusion in Uncaria species, and makes a significant step forward in the appropriate clinical use, in-depth research and further utilization of different Uncaria species. Copyright © 2017 John Wiley & Sons, Ltd.

Characterization of Doped Amorphous Silicon Thin Films through the Investigation of Dopant Elements by Glow Discharge Spectrometry. A Correlation of Conductivity and Bandgap Energy Measurements

PubMed Central

Sánchez, Pascal; Lorenzo, Olaya; Menéndez, Armando; Menéndez, Jose Luis; Gomez, David; Pereiro, Rosario; Fernández, Beatriz

2011-01-01

The determination of optical parameters, such as absorption and extinction coefficients, refractive index and the bandgap energy, is crucial to understand the behavior and final efficiency of thin film solar cells based on hydrogenated amorphous silicon (a-Si:H). The influence of small variations of the gas flow rates used for the preparation of the p-a-SiC:H layer on the bandgap energy, as well as on the dopant elements concentration, thickness and conductivity of the p-layer, is investigated in this work using several complementary techniques. UV-NIR spectrophotometry and ellipsometry were used for the determination of bandgap energies of four p-a-SiC:H thin films, prepared by using different B2H6 and SiH4 fluxes (B2H6 from 12 sccm to 20 sccm and SiH4 from 6 sccm to 10 sccm). Moreover, radiofrequency glow discharge optical emission spectrometry technique was used for depth profiling characterization of p-a-SiC:H thin films and valuable information about dopant elements concentration and distribution throughout the coating was found. Finally, a direct relationship between the conductivity of p-a-SiC:H thin films and the dopant elements concentration, particularly boron and carbon, was observed for the four selected samples. PMID:21731436

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...

Optimum Waveforms for Differential Ion Mobility Spectrometry (FAIMS)

PubMed Central

Shvartsburg, Alexandre A.; Smith, Richard D.

2009-01-01

Differential mobility spectrometry or field asymmetric waveform ion mobility spectrometry (FAIMS) is a new tool for separation and identification of gas-phase ions, particularly in conjunction with mass-spectrometry. In FAIMS, ions are filtered by the difference between mobilities in gases (K) at high and low electric field intensity (E) using asymmetric waveforms. An infinite number of possible waveform profiles make maximizing the performance within engineering constraints a major issue for FAIMS technology refinement. Earlier optimizations assumed the non-constant component of mobility to scale as E2, producing the same result for all ions. Here we show that the optimum profiles are defined by the full series expansion of K(E) that includes terms beyond the 1st that is proportional to E2. For many ion/gas pairs, the first two terms have different signs, and the optimum profiles at sufficiently high E in FAIMS may differ substantially from those previously reported, improving the resolving power by up to 2.2 times. This situation arises for some ions in all FAIMS systems, but becomes more common in recent miniaturized devices that employ higher E. With realistic K(E) dependences, the maximum waveform amplitude is not necessarily optimum and reducing it by up to ∼20 – 30% is beneficial in some cases. The present findings are particularly relevant to targeted analyses where separation depends on the difference between K(E) functions for specific ions. PMID:18585054

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.

Thermal structure of the Martian atmosphere retrieved from the IR- spectrometry in the 15 mkm CO2 band

NASA Astrophysics Data System (ADS)

Zasova, L.; Formisano, V.; Grassi, D.; Igantiev, N.; Moroz, V.

Thermal IR spectrometry is one of the methods of the Martian atmosphere investigation below 55 km. The temperature profiles retrieved from the 15 μm CO2 band may be used for MIRA database. This approach gives the vertical resolution of several kilometers and accuracy of several Kelvins. An aerosol abundance, which influences the temperature profiles, is obtained from the continuum of the same spectrum. It is taken into account in the temperature retrieval procedure in a self- consistent way. Although this method has limited vertical resolution it possesses some advantages. For example, the radio occultation method gives the temperature profiles with higher spectral resolution, but the radio observations are sparse in space and local time. Direct measurements, which give the most accurate results, enable to obtain the temperature profiles only for some chosen points (landing places). Actually, the thermal IR-spectrometry is the only method, which allows to monitor the temperature profiles with good coverage both in space and local time. The first measurements of this kind were fulfilled by IRIS, installed on board of Mariner 9. This spectrometer was characterized by rather high spectral resolution (2.4 cm-1). The temperature profiles vs. local time dependencies for different latitudes and seasons were retrieved, including dust storm conditions, North polar night, Tharsis volcanoes. The obtained temperature profiles have been compared with the temperature profiles for the same conditions, taken from Climate Data Base (European GCM). The Planetary Fourier Spectrometer onboard Mars Express (which is planned to be launched in 2003) has the spectral range 1.2-45 μm and spectral resolution of 1.5 cm- 1. Temperature retrieval is one of the main scientific goals of the experiment. It opens a possibility to get a series of temperature profiles taken for different conditions, which can later be used in MIRA producing.

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.

Single Cell Profiling using Ionic Liquid Matrix-Enhanced Secondary Ion Mass Spectrometry for Neuronal Cell Type Differentiation

PubMed Central

Do, Thanh D.; Comi, Troy J.; Dunham, Sage J. B.; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

2017-01-01

A high-throughput single cell profiling method has been developed for matrix-enhanced secondary ion mass spectrometry (ME-SIMS) to investigate the lipid profiles of neuronal cells. Populations of cells are dispersed onto the substrate, their locations determined using optical microscopy, and the cell locations used to guide the acquisition of SIMS spectra from the cells. Up to 2,000 cells can be assayed in one experiment at a rate of 6 s per cell. Multiple saturated and unsaturated phosphatidylcholines (PCs) and their fragments are detected and verified with tandem mass spectrometry from individual cells when ionic liquids are employed as a matrix. Optically guided single cell profiling with ME-SIMS is suitable for a range of cell sizes, from Aplysia californica neurons larger than 75 μm to 7-μm rat cerebellar neurons. ME-SIMS analysis followed by t-distributed stochastic neighbor embedding of peaks in the lipid molecular mass range (m/z 700–850) distinguishes several cell types from the rat central nervous system, largely based on the relative proportions of the four dominant lipids, PC(32:0), PC(34:1), PC(36:1), and PC(38:5). Furthermore, subpopulations within each cell type are tentatively classified consistent with their endogenous lipid ratios. The results illustrate the efficacy of a new approach to classify single cell populations and subpopulations using SIMS profiling of lipid and metabolite contents. These methods are broadly applicable for high throughput single cell chemical analyses. PMID:28194949

Thermal structure of the Martian atmosphere retrieved from the IR spectrometry in the 15 μm CO2 band: input to MIRA

NASA Astrophysics Data System (ADS)

Zasova, L. V.; Formisano, V.; Grassi, D.; Igantiev, N. I.; Moroz, V. I.

This paper describes one of the sources of the data concerning the thermal structure of the Martian atmosphere, based on the thermal IR spectrometry method. It allows to investigate the Martian atmosphere below 55 km by retrieving the temperature profiles from the 15 μm CO2 band. This approach enables to reach the vertical resolution of several kilometers and the temperature accuracy of several Kelvins. An aerosol abundance, which influences the temperature profile, is obtained from the continuum of the same spectrum parallel with the temperature profile and is taken into account in the temperature retrieval procedure in a self consistent way. Although this method has the limited vertical resolution, it possesses a significant advantage: the thermal IR spectrometry allows to monitor the temperature profiles with a good coverage both in space and local time. The Planetary Fourier spectrometer on board of Mars Express has the spectral range from 250 to 8000 cm-1 and a high spectral resolution of about 2 cm-1. Vertical temperature profiles retrieval is one of the main scientific goals of the experiment. The important data are expected to be obtained on the vertical thermal structure of the atmosphere, and its dependence on latitude, longitude, season, local time, clouds and dust loadings. These results should give a significant input in the future MIRA, being included in the Chapter “Structure of the atmosphere from the surface to 100 km”.

PTR-MS volatile profiling of Pinot Noir wines for the investigation of differences based on vineyard site.

PubMed

Schueuermann, C; Bremer, P; Silcock, P

2017-09-01

This study investigated the effect of vineyard site on the volatile profiles of Pinot Noir wines using proton-transfer reaction mass spectrometry with prior headspace dilution. The ANOVA and PCA enabled discrimination of wine based on vineyard site. Sample separation was due to differences in the ratios of a mixture of compounds, including higher alcohols, ethyl, and acetate esters. Proton-transfer reaction mass spectrometry appears to be a useful technique for rapidly discriminating wines based on vineyard site. The similarities and differences expressed in the wines' volatile profiles may help winemakers to reveal the potential of individual vineyard sites to produce wines of certain character. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Imaging Mass Spectrometry on the Nanoscale with Cluster Ion Beams

PubMed Central

2015-01-01

Imaging with cluster secondary ion mass spectrometry (SIMS) is reaching a mature level of development. Using a variety of molecular ion projectiles to stimulate desorption, 3-dimensional imaging with the selectivity of mass spectrometry can now be achieved with submicrometer spatial resolution and <10 nm depth resolution. In this Perspective, stock is taken regarding what it will require to routinely achieve these remarkable properties. Issues include the chemical nature of the projectile, topography formation, differential erosion rates, and perhaps most importantly, ionization efficiency. Shortcomings of existing instrumentation are also noted. Speculation about how to successfully resolve these issues is a key part of the discussion. PMID:25458665

Association of Synergistetes and Cyclodipeptides with Periodontitis.

PubMed

Marchesan, J T; Morelli, T; Moss, K; Barros, S P; Ward, M; Jenkins, W; Aspiras, M B; Offenbacher, S

2015-10-01

The purpose of this study was to evaluate the microbial community (MC) composition as it relates to salivary metabolites and periodontal clinical parameters in a 21-d biofilm-overgrowth model. Subjects (N = 168) were enrolled equally into 5 categories of periodontal status per the biofilm-gingival interface classification. Microbial species within subgingival plaque samples were identified by human microbiome identification microarray. Whole saliva was analyzed by liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry for metabolite identification. Phylum was grouped into MCs according to principal component analysis. Generalized linear and regression models were used to examine the association among MC, species, periodontal clinical parameters, and salivary metabolome. Multiple comparisons were adjusted with the false discovery rate. The study population was distributed into 8 distinct MC profiles, designated MC-1 to MC-8. MC-2 explained 14% of the variance and was dominated by Synergistetes and Spirochaetes. It was the only community structure significantly associated with high probing depth (P = 0.02) and high bleeding on probing (P = 0.008). MC-2 was correlated with traditional periodontal pathogens and several newly identified putative periodontal pathogens: Fretibacterium fastidiosum, Fretibacterium sp. OT360/OT362, Filifactor alocis, Treponema lecithinolyticum, Eubacterium saphenum, Desulfobulbus sp./OT041, and Mogibacterium timidum. Synergistetes phylum was strongly associated with 2 novel metabolites-cyclo (-leu-pro) and cyclo (-phe-pro)-at 21 d of biofilm overgrowth (P = 0.02). In subjects with severe periodontitis (P2 and P3), cyclo (-leu-pro) and cyclo (-phe-pro) were significantly associated with increased changes in probing depth at 21 d of biofilm overgrowth (P ≤ 0.05). The analysis identified a MC dominated by Synergistetes, with classic and putative newly identified pathogens/pathobionts associated with clinical disease. The metabolomic discovery of 2 novel cyclodipeptides that have been reported to serve as quorum-sensing and/or bacteriocidal/bacteriostatic molecules, in association with Synergistetes, suggests a potential role in periodontal biofilm dysbiosis and periodontal disease that warrants further investigation. © International & American Associations for Dental Research 2015.

Lipid fatty acid profile analyses in liver and serum in rats with nonalcoholic steatohepatitis using improved gas chromatography-mass spectrometry methodology

USDA-ARS?s Scientific Manuscript database

Fatty acids (FA) are essential components of lipids and exhibit important biological functions. The analyses of FAs are routinely carried out by gas chromatography-mass spectrometry, after multi-step sample preparation. In this study, several key experimental factors were carefully examined, validat...

Comprehensive evaluation of direct injection mass spectrometry for the quantitative profiling of volatiles in food samples

PubMed Central

2016-01-01

Although qualitative strategies based on direct injection mass spectrometry (DIMS) have recently emerged as an alternative for the rapid classification of food samples, the potential of these approaches in quantitative tasks has scarcely been addressed to date. In this paper, the applicability of different multivariate regression procedures to data collected by DIMS from simulated mixtures has been evaluated. The most relevant factors affecting quantitation, such as random noise, the number of calibration samples, type of validation, mixture complexity and similarity of mass spectra, were also considered and comprehensively discussed. Based on the conclusions drawn from simulated data, and as an example of application, experimental mass spectral fingerprints collected by direct thermal desorption coupled to mass spectrometry were used for the quantitation of major volatiles in Thymus zygis subsp. zygis chemotypes. The results obtained, validated with the direct thermal desorption coupled to gas chromatography–mass spectrometry method here used as a reference, show the potential of DIMS approaches for the fast and precise quantitative profiling of volatiles in foods. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644978

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...

X-Ray Fluorescence Solvent Detection at the Substrate-Adhesive Interface

NASA Technical Reports Server (NTRS)

Wurth, Laura; Evans, Kurt; Weber, Bart; Headrick, Sarah

2005-01-01

With environmental regulations limiting the use of volatile organic compounds, low-vapor pressure solvents have replaced traditional degreasing solvents for bond substrate preparation. When used to clean and prepare porous bond substrates such as phenolic composites, low vapor pressure solvents can penetrate deep into substrate pore networks and remain there for extended periods. Trapped solvents can interact with applied adhesives either prior to or during cure, potentially compromising bond properties. Currently, methods for characterizing solvent time-depth profiles in bond substrates are limited to bulk gravimetric or sectioning techniques. While sectioning techniques such as microtome allow construction of solvent depth profiles, their depth resolution and reliability are limited by substrate type. Sectioning techniques are particularly limited near the adhesive-substrate interface where depth resolution is further limited by adhesive-substrate hardness and, in the case of a partially cured adhesive, mechanical properties differences. Additionally, sectioning techniques cannot provide information about lateral solvent diffusion. Cross-section component mapping is an alternative method for measuring solvent migration in porous substrates that eliminates the issues associated with sectioning techniques. With cross-section mapping, the solvent-wiped substrate is sectioned perpendicular rather than parallel to the wiped surface, and the sectioned surface is analyzed for the solvent or solvent components of interest using a two-dimensional mapping or imaging technique. Solvent mapping can be performed using either direct or indirect methods. With a direct method, one or more solvent components are mapped using red or Raman spectroscopy together with a moveable sample stage and/or focal plane array detector. With an indirect method, an elemental "tag" not present in the substrate is added to the solvent before the substrate is wiped. Following cross sectioning, the tag element can then be mapped by its characteristic x-ray emission using either x-ray fluorescence, or electron-beam energy-and wavelength-dispersive x-ray spectrometry. The direct mapping techniques avoid issues of different diffusion or migration rates of solvents and elemental tags, while the indirect techniques avoid spectral resolution issues in cases where solvents and substrates have adjacent or overlapping peaks. In this study, cross-section component indirect mapping is being evaluated as a method for measuring migration of d-limonene based solvents in glass-cloth phenolic composite (GCP) prior to and during subsequent bonding and epoxy adhesive cure.

HPLC-DAD-ESI/MS(n) profiling of phenolic compounds from Lathyrus cicera L. seeds.

PubMed

Ferreres, F; Magalhães, S C Q; Gil-Izquierdo, A; Valentão, P; Cabrita, A R J; Fonseca, A J M; Andrade, P B

2017-01-01

Lathyrus cicera L. seeds are of interest for food and feed purposes. Despite the recognized antioxidant activity of the seeds, arising from the phenolic fraction, their phenolic compounds have not been studied in depth yet. Therefore, to determine the phenolics profile of these seeds, a target analysis was performed using high-performance liquid chromatography coupled to photodiode-array detection and electrospray ionization/ion trap mass spectrometry (HPLC-DAD-ESI/MS(n)). Thirty-seven glycosylated flavonoids were identified for the first time in the seeds of this species and, according to their MS fragmentation, clustered in flavonol-3-O-di-/tri-glycosides-7-O-rhamnosides and other flavonol-glycosides, and flavonol-3-O-(cinnamoyl)glycoside-7-O-rhamnosides, flavonol-3-O-(dihydrophaseoyl, cinnamoyl)glycoside-7-O-rhamnosides and flavonol-3-O-(malonyl)glycoside-7-O-rhamnosides. Glycosides of kaempferol were the main flavonoids found (10 non-acylated and 21 acylated), followed by those of quercetin (3) and those of isorhamnetin, apigenin and luteolin (1). The most abundant flavonols were identified as kaempferol-3-O-(2-hexosyl)hexoside-7-O-rhamnosides. The methodology used allowed to increase the knowledge on a relevant phytochemical class of seeds from L. cicera. Copyright © 2016 Elsevier Ltd. All rights reserved.

High level active n+ doping of strained germanium through co-implantation and nanosecond pulsed laser melting

NASA Astrophysics Data System (ADS)

Pastor, David; Gandhi, Hemi H.; Monmeyran, Corentin P.; Akey, Austin J.; Milazzo, Ruggero; Cai, Yan; Napolitani, Enrico; Gwilliam, Russell M.; Crowe, Iain F.; Michel, Jurgen; Kimerling, L. C.; Agarwal, Anuradha; Mazur, Eric; Aziz, Michael J.

2018-04-01

Obtaining high level active n+ carrier concentrations in germanium (Ge) has been a significant challenge for further development of Ge devices. By ion implanting phosphorus (P) and fluorine (F) into Ge and restoring crystallinity using Nd:YAG nanosecond pulsed laser melting (PLM), we demonstrate 1020 cm-3 n+ carrier concentration in tensile-strained epitaxial germanium-on-silicon. Scanning electron microscopy shows that after laser treatment, samples implanted with P have an ablated surface, whereas P + F co-implanted samples have good crystallinity and a smooth surface topography. We characterize P and F concentration depth profiles using secondary ion mass spectrometry and spreading resistance profiling. The peak carrier concentration, 1020 cm-3 at 80 nm below the surface, coincides with the peak F concentration, illustrating the key role of F in increasing donor activation. Cross-sectional transmission electron microscopy of the co-implanted sample shows that the Ge epilayer region damaged during implantation is a single crystal after PLM. High-resolution X-ray diffraction and Raman spectroscopy measurements both indicate that the as-grown epitaxial layer strain is preserved after PLM. These results demonstrate that co-implantation and PLM can achieve the combination of n+ carrier concentration and strain in Ge epilayers necessary for next-generation, high-performance Ge-on-Si devices.

Early Prediction of Lupus Nephritis Using Advanced Proteomics

DTIC Science & Technology

2010-06-01

SELDI-TOF-MS. Additional proteomic profiling studies using NMR- and MS-based metabonomics have been completed, and LC/MS based protein profiling using...Flight mass spectrometry (SELDI-TOF-MS). Changes in proteomic profiles will be confirmed and enhanced using NMR- and MS-based metabonomics , by Dr...performed using NMR- and MS-based metabonomics at Miami University, in the laboratory of Dr. Michael Kennedy. Initial spectra and profiles obtained show

Development of Impurity Profiling Methods Using Modern Analytical Techniques.

PubMed

Ramachandra, Bondigalla

2017-01-02

This review gives a brief introduction about the process- and product-related impurities and emphasizes on the development of novel analytical methods for their determination. It describes the application of modern analytical techniques, particularly the ultra-performance liquid chromatography (UPLC), liquid chromatography-mass spectrometry (LC-MS), high-resolution mass spectrometry (HRMS), gas chromatography-mass spectrometry (GC-MS) and high-performance thin layer chromatography (HPTLC). In addition to that, the application of nuclear magnetic resonance (NMR) spectroscopy was also discussed for the characterization of impurities and degradation products. The significance of the quality, efficacy and safety of drug substances/products, including the source of impurities, kinds of impurities, adverse effects by the presence of impurities, quality control of impurities, necessity for the development of impurity profiling methods, identification of impurities and regulatory aspects has been discussed. Other important aspects that have been discussed are forced degradation studies and the development of stability indicating assay methods.

Analyses of moisture in polymers and composites

NASA Technical Reports Server (NTRS)

Ryan, L. E.; Vaughan, R. W.

1980-01-01

A suitable method for the direct measurement of moisture concentrations after humidity/thermal exposure on state of the art epoxy and polyimide resins and their graphite and glass fiber reinforcements was investigated. Methods for the determination of moisture concentration profiles, moisture diffusion modeling and moisture induced chemical changes were examined. Carefully fabricated, precharacterized epoxy and polyimide neat resins and their AS graphite and S glass reinforced composites were exposed to humid conditions using heavy water (D20), at ambient and elevated temperatures. These specimens were fixtured to theoretically limit the D20 permeation to a unidirectional penetration axis. The analytical techniques evaluated were: (1) laser pyrolysis gas chromatography mass spectrometry; (2) solids probe mass spectrometry; (3) laser pyrolysis conventional infrared spectroscopy; and (4) infrared imaging thermovision. The most reproducible and sensitive technique was solids probe mass spectrometry. The fabricated exposed specimens were analyzed for D20 profiling after humidity/thermal conditioning at three exposure time durations.

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.

High-mass-resolution MALDI mass spectrometry imaging reveals detailed spatial distribution of metabolites and lipids in roots of barley seedlings in response to salinity stress.

PubMed

Sarabia, Lenin D; Boughton, Berin A; Rupasinghe, Thusitha; van de Meene, Allison M L; Callahan, Damien L; Hill, Camilla B; Roessner, Ute

2018-01-01

Mass spectrometry imaging (MSI) is a technology that enables the visualization of the spatial distribution of hundreds to thousands of metabolites in the same tissue section simultaneously. Roots are below-ground plant organs that anchor plants to the soil, take up water and nutrients, and sense and respond to external stresses. Physiological responses to salinity are multifaceted and have predominantly been studied using whole plant tissues that cannot resolve plant salinity responses spatially. This study aimed to use a comprehensive approach to study the spatial distribution and profiles of metabolites, and to quantify the changes in the elemental content in young developing barley seminal roots before and after salinity stress. Here, we used a combination of liquid chromatography-mass spectrometry (LC-MS), inductively coupled plasma mass spectrometry (ICP-MS), and matrix-assisted laser desorption/ionization (MALDI-MSI) platforms to profile and analyze the spatial distribution of ions, metabolites and lipids across three anatomically different barley root zones before and after a short-term salinity stress (150 mM NaCl). We localized, visualized and discriminated compounds in fine detail along longitudinal root sections and compared ion, metabolite, and lipid composition before and after salt stress. Large changes in the phosphatidylcholine (PC) profiles were observed as a response to salt stress with PC 34:n showing an overall reduction in salt treated roots. ICP-MS analysis quantified changes in the elemental content of roots with increases of Na + and decreases of K + content. Our results established the suitability of combining three mass spectrometry platforms to analyze and map ionic and metabolic responses to salinity stress in plant roots and to elucidate tolerance mechanisms in response to abiotic stress, such as salinity stress.

A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls

PubMed Central

Titulaer, Mark K; Siccama, Ivar; Dekker, Lennard J; van Rijswijk, Angelique LCT; Heeren, Ron MA; Sillevis Smitt, Peter A; Luider, Theo M

2006-01-01

Background Statistical comparison of peptide profiles in biomarker discovery requires fast, user-friendly software for high throughput data analysis. Important features are flexibility in changing input variables and statistical analysis of peptides that are differentially expressed between patient and control groups. In addition, integration the mass spectrometry data with the results of other experiments, such as microarray analysis, and information from other databases requires a central storage of the profile matrix, where protein id's can be added to peptide masses of interest. Results A new database application is presented, to detect and identify significantly differentially expressed peptides in peptide profiles obtained from body fluids of patient and control groups. The presented modular software is capable of central storage of mass spectra and results in fast analysis. The software architecture consists of 4 pillars, 1) a Graphical User Interface written in Java, 2) a MySQL database, which contains all metadata, such as experiment numbers and sample codes, 3) a FTP (File Transport Protocol) server to store all raw mass spectrometry files and processed data, and 4) the software package R, which is used for modular statistical calculations, such as the Wilcoxon-Mann-Whitney rank sum test. Statistic analysis by the Wilcoxon-Mann-Whitney test in R demonstrates that peptide-profiles of two patient groups 1) breast cancer patients with leptomeningeal metastases and 2) prostate cancer patients in end stage disease can be distinguished from those of control groups. Conclusion The database application is capable to distinguish patient Matrix Assisted Laser Desorption Ionization (MALDI-TOF) peptide profiles from control groups using large size datasets. The modular architecture of the application makes it possible to adapt the application to handle also large sized data from MS/MS- and Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry experiments. It is expected that the higher resolution and mass accuracy of the FT-ICR mass spectrometry prevents the clustering of peaks of different peptides and allows the identification of differentially expressed proteins from the peptide profiles. PMID:16953879

A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls.

PubMed

Titulaer, Mark K; Siccama, Ivar; Dekker, Lennard J; van Rijswijk, Angelique L C T; Heeren, Ron M A; Sillevis Smitt, Peter A; Luider, Theo M

2006-09-05

Statistical comparison of peptide profiles in biomarker discovery requires fast, user-friendly software for high throughput data analysis. Important features are flexibility in changing input variables and statistical analysis of peptides that are differentially expressed between patient and control groups. In addition, integration the mass spectrometry data with the results of other experiments, such as microarray analysis, and information from other databases requires a central storage of the profile matrix, where protein id's can be added to peptide masses of interest. A new database application is presented, to detect and identify significantly differentially expressed peptides in peptide profiles obtained from body fluids of patient and control groups. The presented modular software is capable of central storage of mass spectra and results in fast analysis. The software architecture consists of 4 pillars, 1) a Graphical User Interface written in Java, 2) a MySQL database, which contains all metadata, such as experiment numbers and sample codes, 3) a FTP (File Transport Protocol) server to store all raw mass spectrometry files and processed data, and 4) the software package R, which is used for modular statistical calculations, such as the Wilcoxon-Mann-Whitney rank sum test. Statistic analysis by the Wilcoxon-Mann-Whitney test in R demonstrates that peptide-profiles of two patient groups 1) breast cancer patients with leptomeningeal metastases and 2) prostate cancer patients in end stage disease can be distinguished from those of control groups. The database application is capable to distinguish patient Matrix Assisted Laser Desorption Ionization (MALDI-TOF) peptide profiles from control groups using large size datasets. The modular architecture of the application makes it possible to adapt the application to handle also large sized data from MS/MS- and Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry experiments. It is expected that the higher resolution and mass accuracy of the FT-ICR mass spectrometry prevents the clustering of peaks of different peptides and allows the identification of differentially expressed proteins from the peptide profiles.

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.

Objective fitting of hemoglobin dynamics in traumatic bruises based on temperature depth profiling

NASA Astrophysics Data System (ADS)

Vidovič, Luka; Milanič, Matija; Majaron, Boris

2014-02-01

Pulsed photothermal radiometry (PPTR) allows noninvasive measurement of laser-induced temperature depth profiles. The obtained profiles provide information on depth distribution of absorbing chromophores, such as melanin and hemoglobin. We apply this technique to objectively characterize mass diffusion and decomposition rate of extravasated hemoglobin during the bruise healing process. In present study, we introduce objective fitting of PPTR data obtained over the course of the bruise healing process. By applying Monte Carlo simulation of laser energy deposition and simulation of the corresponding PPTR signal, quantitative analysis of underlying bruise healing processes is possible. Introduction of objective fitting enables an objective comparison between the simulated and experimental PPTR signals. In this manner, we avoid reconstruction of laser-induced depth profiles and thus inherent loss of information in the process. This approach enables us to determine the value of hemoglobin mass diffusivity, which is controversial in existing literature. Such information will be a valuable addition to existing bruise age determination techniques.

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

Wear-Induced Changes in FSW Tool Pin Profile: Effect of Process Parameters

NASA Astrophysics Data System (ADS)

Sahlot, Pankaj; Jha, Kaushal; Dey, G. K.; Arora, Amit

2018-06-01

Friction stir welding (FSW) of high melting point metallic (HMPM) materials has limited application due to tool wear and relatively short tool life. Tool wear changes the profile of the tool pin and adversely affects weld properties. A quantitative understanding of tool wear and tool pin profile is crucial to develop the process for joining of HMPM materials. Here we present a quantitative wear study of H13 steel tool pin profile for FSW of CuCrZr alloy. The tool pin profile is analyzed at multiple traverse distances for welding with various tool rotational and traverse speeds. The results indicate that measured wear depth is small near the pin root and significantly increases towards the tip. Near the pin tip, wear depth increases with increase in tool rotational speed. However, change in wear depth near the pin root is minimal. Wear depth also increases with decrease in tool traverse speeds. Tool pin wear from the bottom results in pin length reduction, which is greater for higher tool rotational speeds, and longer traverse distances. The pin profile changes due to wear and result in root defect for long traverse distance. This quantitative understanding of tool wear would be helpful to estimate tool wear, optimize process parameters, and tool pin shape during FSW of HMPM materials.

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.

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

Polycrystalline silicon on tungsten substrates

NASA Technical Reports Server (NTRS)

Bevolo, A. J.; Schmidt, F. A.; Shanks, H. R.; Campisi, G. J.

1979-01-01

Thin films of electron-beam-vaporized silicon were deposited on fine-grained tungsten substrates under a pressure of about 1 x 10 to the -10th torr. Mass spectra from a quadrupole residual-gas analyzer were used to determine the partial pressure of 13 residual gases during each processing step. During separate silicon depositions, the atomically clean substrates were maintained at various temperatures between 400 and 780 C, and deposition rates were between 20 and 630 A min. Surface contamination and interdiffusion were monitored by in situ Auger electron spectrometry before and after cleaning, deposition, and annealing. Auger depth profiling, X-ray analysis, and SEM in the topographic and channeling modes were utilized to characterize the samples with respect to silicon-metal interface, interdiffusion, silicide formation, and grain size of silicon. The onset of silicide formation was found to occur at approximately 625 C. Above this temperature tungsten silicides were formed at a rate faster than the silicon deposition. Fine-grain silicon films were obtained at lower temperatures.

Direct observation of conductive filament formation in Alq3 based organic resistive memories

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

Busby, Y., E-mail: yan.busby@unamur.be; Pireaux, J.-J.; Nau, S.

2015-08-21

This work explores resistive switching mechanisms in non-volatile organic memory devices based on tris(8-hydroxyquinolie)aluminum (Alq{sub 3}). Advanced characterization tools are applied to investigate metal diffusion in ITO/Alq{sub 3}/Ag memory device stacks leading to conductive filament formation. The morphology of Alq{sub 3}/Ag layers as a function of the metal evaporation conditions is studied by X-ray reflectivity, while depth profile analysis with X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry is applied to characterize operational memory elements displaying reliable bistable current-voltage characteristics. 3D images of the distribution of silver inside the organic layer clearly point towards the existence of conductive filamentsmore » and allow for the identification of the initial filament formation and inactivation mechanisms during switching of the device. Initial filament formation is suggested to be driven by field assisted diffusion of silver from abundant structures formed during the top electrode evaporation, whereas thermochemical effects lead to local filament inactivation.« less

Effect of V/III ratio on the surface morphology and electrical properties of m-plane (10 1 bar 0) GaN homoepitaxial layers

NASA Astrophysics Data System (ADS)

Barry, Ousmane I.; Tanaka, Atsushi; Nagamatsu, Kentaro; Bae, Si-Young; Lekhal, Kaddour; Matsushita, Junya; Deki, Manato; Nitta, Shugo; Honda, Yoshio; Amano, Hiroshi

2017-06-01

We have investigated the effect of V/III ratio on the surface morphology, impurity concentration and electrical properties of m-plane (10 1 bar 0) Gallium Nitride (GaN) homoepitaxial layers. Four-sided pyramidal hillocks are observed on the nominally on-axis m-plane GaN films. Hillocks sizes relatively increase by increasing the V/III ratio. All facets of pyramidal hillocks exhibit well-defined step-terrace features. Secondary ion mass spectrometry depth profiles reveal that carbon impurities decrease by increasing the V/III ratio while the lowest oxygen content is found at an optimized V/III ratio of 900. Vertical Schottky barrier diodes fabricated on the m-GaN samples were characterized. Low leakage current densities of the order of 10-10 A/cm2 at -5 V are obtained at the optimum V/III ratio. Oxygen impurities and screw-component dislocations around hillocks are found to have more detrimental impact on the leakage current mechanism.

Interfacial micropore defect formation in PEDOT:PSS-Si hybrid solar cells probed by TOF-SIMS 3D chemical imaging.

PubMed

Thomas, Joseph P; Zhao, Liyan; Abd-Ellah, Marwa; Heinig, Nina F; Leung, K T

2013-07-16

Conducting p-type polymer layers on n-type Si have been widely studied for the fabrication of cost-effective hybrid solar cells. In this work, time-of-flight secondary ion mass spectrometry (TOF-SIMS) is used to provide three-dimensional chemical imaging of the interface between poly(3,4-ethylene-dioxythiophene):polystyrenesulfonate (PEDOT:PSS) and SiOx/Si in a hybrid solar cell. To minimize structural damage to the polymer layer, an Ar cluster sputtering source is used for depth profiling. The present result shows the formation of micropore defects in the interface region of the PEDOT:PSS layer on the SiOx/Si substrate. This interfacial micropore defect formation becomes more prominent with increasing thickness of the native oxide layer, which is a key device parameter that greatly affects the hybrid solar cell performance. Three-dimensional chemical imaging coupled with Ar cluster ion sputtering has therefore been demonstrated as an emerging technique for probing the interface of this and other polymer-inorganic systems.

Comparison of two confocal micro-XRF spectrometers with different design aspects

PubMed Central

Smolek, S; Nakazawa, T; Tabe, A; Nakano, K; Tsuji, K; Streli, C; Wobrauschek, P

2014-01-01

Two different confocal micro X-ray fluorescence spectrometers have been developed and installed at Osaka City University and the Vienna University of Technology Atominstitut. The Osaka City University system is a high resolution spectrometer operating in air. The Vienna University of Technology Atominstitut spectrometer has a lower spatial resolution but is optimized for light element detection and operates under vacuum condition. The performance of both spectrometers was compared. In order to characterize the spatial resolution, a set of nine specially prepared single element thin film reference samples (500 nm in thickness, Al, Ti, Cr, Fe Ni, Cu, Zr, Mo, and Au) was used. Lower limits of detection were determined using the National Institute of Standards and Technology standard reference material glass standard 1412. A paint layer sample (cultural heritage application) and paint on automotive steel samples were analyzed with both instruments. The depth profile information was acquired by scanning the sample perpendicular to the surface. © 2013 The Authors. X-Ray Spectrometry published by John Wiley & Sons, Ltd. PMID:26430286

Comparison of two confocal micro-XRF spectrometers with different design aspects.

PubMed

Smolek, S; Nakazawa, T; Tabe, A; Nakano, K; Tsuji, K; Streli, C; Wobrauschek, P

2014-03-01

Two different confocal micro X-ray fluorescence spectrometers have been developed and installed at Osaka City University and the Vienna University of Technology Atominstitut. The Osaka City University system is a high resolution spectrometer operating in air. The Vienna University of Technology Atominstitut spectrometer has a lower spatial resolution but is optimized for light element detection and operates under vacuum condition. The performance of both spectrometers was compared. In order to characterize the spatial resolution, a set of nine specially prepared single element thin film reference samples (500 nm in thickness, Al, Ti, Cr, Fe Ni, Cu, Zr, Mo, and Au) was used. Lower limits of detection were determined using the National Institute of Standards and Technology standard reference material glass standard 1412. A paint layer sample (cultural heritage application) and paint on automotive steel samples were analyzed with both instruments. The depth profile information was acquired by scanning the sample perpendicular to the surface. © 2013 The Authors. X-Ray Spectrometry published by John Wiley & Sons, Ltd.

Chemical 3D-imaging of glass inclusions from allende (CV3) olivine via SIMS: A new insight on chondrule formation conditions

NASA Astrophysics Data System (ADS)

Florentin, L.; Deloule, E.; Faure, F.; Mangin, D.

2018-06-01

Natural glass inclusions - hosted in Mg-rich olivines from Allende (CV3) type I chondrules - and synthetic melt inclusions - trapped in forsterite crystallized from CMAS (CaO-MgO-Al2O3-SiO2) melts - were mapped by Secondary Ion Mass Spectrometry (SIMS) for CMAS major oxides. The first ever 3D chemical images of extra-terrestrial glass inclusions were obtained, along with chemical depth profiles for each oxide. Results show similar patterns for both synthetic glass inclusions (trapped in olivine formed by slow crystallization in a magmatic liquid) and natural inclusions from Allende's olivines. No incompatible-rich boundary layer or diffusion pattern was observed in either case. The absence of an incompatible-rich boundary layer suggests that the olivine overgrowth surrounding glass inclusions in Allende's olivines was formed during slow cooling of the host olivine and likely the surrounding chondrule. This provides new constraints on the cooling rates of type I chondrules.

Characterization of TiCN coatings deposited by magnetron sputter-ion plating process: RBS and GDOS complementary analyses

NASA Astrophysics Data System (ADS)

Freire, F. L., Jr.; Senna, L. F.; Achete, C. A.; Hirsch, T.

1998-03-01

Hard TiCN films were deposited by dc-magnetron sputter-ion plating technique onto high-speed carbon steel S-6-5-2 (M 2). For selected deposition conditions, TiCN films were also deposited onto Si substrates. A Ti target was sputtered in ArCH 4N 2 atmosphere. The argon flux (12 sccm) was fixed and corresponds to 90% of the total flux, whereas the N 2 flux ranged from 3% to 9% of the total flux. The total pressure in the chamber during film deposition was 8-9 × 10 -2Pa. The substrate bias, Vb, was between 0 and -140V and the substrate temperature, Ts, was 350°C. Film composition and depth profile of the elements were obtained by Rutherford backscattering spectrometry (RBS) and glow discharge optical spectroscopy (GDOS). Some limitations of both techniques in analysing TiCN films were presented. The effect of methane poisoing of the Ti target and how it influences the film composition was discussed.

Rapid Detection of Necrosis in Breast Cancer with Desorption Electrospray Ionization Mass Spectrometry

PubMed Central

Tata, Alessandra; Woolman, Michael; Ventura, Manuela; Bernards, Nicholas; Ganguly, Milan; Gribble, Adam; Shrestha, Bindesh; Bluemke, Emma; Ginsberg, Howard J.; Vitkin, Alex; Zheng, Jinzi; Zarrine-Afsar, Arash

2016-01-01

Identification of necrosis in tumors is of prognostic value in treatment planning, as necrosis is associated with aggressive forms of cancer and unfavourable outcomes. To facilitate rapid detection of necrosis with Mass Spectrometry (MS), we report the lipid MS profile of necrotic breast cancer with Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) imaging validated with statistical analysis and correlating pathology. This MS profile is characterized by (1) the presence of the ion of m/z 572.48 [Cer(d34:1) + Cl]− which is a ceramide absent from the viable cancer subregions; (2) the absence of the ion of m/z 391.25 which is present in small abundance only in viable cancer subregions; and (3) a slight increase in the relative intensity of known breast cancer biomarker ions of m/z 281.25 [FA(18:1)-H]− and 303.23 [FA(20:4)-H]−. Necrosis is accompanied by alterations in the tissue optical depolarization rate, allowing tissue polarimetry to guide DESI-MS analysis for rapid MS profiling or targeted MS imaging. This workflow, in combination with the MS profile of necrosis, may permit rapid characterization of necrotic tumors from tissue slices. Further, necrosis-specific biomarker ions are detected in seconds with single MS scans of necrotic tumor tissue smears, which further accelerates the identification workflow by avoiding tissue sectioning and slide preparation. PMID:27734938

Source identification of western Oregon Douglas-Fir wood cores using mass spectrometry and random forest Classification

Treesearch

Kristen Finch; Edgard Espinoza; F. Andrew Jones; Richard Cronn

2017-01-01

Premise of the study: We investigated whether wood metabolite profiles from direct analysis in real time (time-of-flight) mass spectrometry (DART-TOFMS) could be used to determine the geographic origin of Douglas-fir wood cores originating from two regions in western Oregon, USA. Methods: Three annual ring mass...

Monitoring single coffee bean roasting by direct volatile compound analysis with proton transfer reaction time-of-flight mass spectrometry.

PubMed

Yener, Sine; Navarini, Luciano; Lonzarich, Valentina; Cappellin, Luca; Märk, Tilmann D; Bonn, Günther K; Biasioli, Franco

2016-09-01

This study applies proton transfer reaction time-of-flight mass spectrometry for the rapid analysis of volatile compounds released from single coffee beans. The headspace volatile profiles of single coffee beans (Coffeea arabica) from different geographical origins (Brazil, Guatemala and Ethiopia) were analyzed via offline profiling at different stages of roasting. The effect of coffee geographical origin was reflected on volatile compound formation that was supported by one-way ANOVA. Clear origin signatures were observed in the formation of different coffee odorants. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Analytical Glycobiology at High Sensitivity: Current Approaches and Directions

PubMed Central

Novotny, Milos V.; Alley, William R.; Mann, Benjamin F.

2013-01-01

This review summarizes the analytical advances made during the last several years in the structural and quantitative determinations of glycoproteins in complex biological mixtures. The main analytical techniques used in the fields of glycomics and glycoproteomics involve different modes of mass spectrometry and their combinations with capillary separation methods such as microcolumn liquid chromatography and capillary electrophoresis. The needs for high-sensitivity measurements have been emphasized in the oligosaccharide profiling used in the field of biomarker discovery through MALDI mass spectrometry. High-sensitivity profiling of both glycans and glycopeptides from biological fluids and tissue extracts has been aided significantly through lectin preconcentration and the uses of affinity chromatography. PMID:22945852

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].

Advanced surface characterization of silver nanocluster segregation in Ag-TiCN bioactive coatings by RBS, GDOES, and ARXPS.

PubMed

Escobar Galindo, R; Manninen, N K; Palacio, C; Carvalho, S

2013-07-01

Surface modification by means of wear protective and antibacterial coatings represents, nowadays, a crucial challenge in the biomaterials field in order to enhance the lifetime of bio-devices. It is possible to tailor the properties of the material by using an appropriate combination of high wear resistance (e.g., nitride or carbide coatings) and biocide agents (e.g., noble metals as silver) to fulfill its final application. This behavior is controlled at last by the outmost surface of the coating. Therefore, the analytical characterization of these new materials requires high-resolution analytical techniques able to provide information about surface and depth composition down to the nanometric level. Among these techniques are Rutherford backscattering spectrometry (RBS), glow discharge optical emission spectroscopy (GDOES), and angle resolved X-ray photoelectron spectroscopy (ARXPS). In this work, we present a comparative RBS-GDOES-ARXPS study of the surface characterization of Ag-TiCN coatings with Ag/Ti atomic ratios varying from 0 to 1.49, deposited at room temperature and 200 °C. RBS analysis allowed a precise quantification of the silver content along the coating with a non-uniform Ag depth distribution for the samples with higher Ag content. GDOES surface profiling revealed that the samples with higher Ag content as well as the samples deposited at 200 °C showed an ultrathin (1-10 nm) Ag-rich layer on the coating surface followed by a silver depletion zone (20-30 nm), being the thickness of both layers enhanced with Ag content and deposition temperature. ARXPS analysis confirmed these observations after applying general algorithm involving regularization in addition to singular value decomposition techniques to obtain the concentration depth profiles. Finally, ARXPS measurements were used to provide further information on the surface morphology of the samples obtaining an excellent agreement with SEM observations when a growth model of silver islands with a height d = 1.5 nm and coverage θ = 0.20 was applied to the sample with Ag/Ti = 1.49 and deposited at room temperature.

Microbial Preference for Soil Organic Carbon Changes Along Redox Gradients as a Function of the Energetic Cost of Respiration

NASA Astrophysics Data System (ADS)

Naughton, H.; Keiluweit, M.; Fendorf, S. E.; Farrant, D. N.

2016-12-01

Soil organic carbon (SOC) chemistry is known to impact carbon preservation via mineral associations and physical protection, which chemically or physically block SOC from microbial enzymatic access for decomposition. However, SOC decay models that include these processes do not reliably predict SOC dynamics. We propose that the energetics of respiration additionally regulate SOC cycling. Specifically, organic carbon will only be respired if the available electron acceptors yield enough energy for microbial growth when metabolically coupled to the SOC. To test this hypothesis, we constructed dual pore domain reactors in which water flows normal to a column of packed soil, allowing oxygen to diffuse from the upper channel through the soil and establish a redox gradient. With increasing depth into the soil column, the soil experiences a typical redox profile indicative of anaerobic respiration processes: after oxygen is consumed, nitrate, Mn, Fe, and sulfate serve as electron acceptors. We measure porewater and effluent for nitrate, sulfate, Fe(II) and Mn(II) and take microsensor profiles of dissolved oxygen and H2S to characterize the redox gradient and respiration pathways. To this we couple incubations of solid material at each depth post-experiment and quantify CO2 and CH4 production to assess respiration potential along the redox gradient. Porewater SOC chemistry is analyzed via spectroscopy and mass spectrometry to interpret SOC oxidation state and composition and thus test thermodynamic predictions on SOC stability given the available redox acceptors at a given depth in the reactor. Within 0.5 cm of the soil surface, oxygen concentrations drop below detection and signs of anaerobic respiration (Fe(II) production, loss of nitrate) initiate while respiration rates drops precipitously. More oxidized SOC is preferentially utilized with progression along the redox gradient, supporting thermodynamic predictions. This work highlights the potential of SOC chemistry within specific redox metabolic zones of soils and sediments to drive carbon utilization. An improved understanding on organic carbon utliization is critical to predict SOC dynamics under changing hydrology (e.g. saltwater intrusion, permafrost melting), temperature, and other factors impacting microbial respiration energetics.

Identifying cancer biomarkers by mass spectrometry-based glycomics

PubMed Central

Mechref, Yehia; Hu, Yunli; Garcia, Aldo; Hussein, Ahmed

2013-01-01

Correlations between aberrant glycosylation and cancer have been established for decades. The major advances in mass spectrometry (MS) and separation science have rapidly advanced detailed characterization of the changes associated with cancer development and progression. Over the past 10 years, many reports have described MS-based glycomic methods directed toward comparing the glycomic profiles of different human specimens collected from disease-free individuals and patients with cancers. Glycomic profiling of glycoproteins isolated from human specimens originating from disease-free individuals and patients with cancers have also been performed. Profiling of native, labeled, and permethylated glycans has been acquired using MALDI-MS and LC-MS. This review focuses on describing, discussing, and evaluating the different glycomic methods employed to characterize and quantify glycomic changes associated with cancers of different organs, including breast, colon, esophagus, liver, ovarian, pancreas, and prostate. PMID:22740464

The lateritic profile of Balkouin, Burkina Faso: Geochemistry, mineralogy and genesis

NASA Astrophysics Data System (ADS)

Giorgis, Ilaria; Bonetto, Sabrina; Giustetto, Roberto; Lawane, Abdou; Pantet, Anne; Rossetti, Piergiorgio; Thomassin, Jean-Hugues; Vinai, Raffaele

2014-02-01

This study reports on the geochemical and mineralogical characterization of a lateritic profile cropping out in the Balkouin area, Central Burkina Faso, aimed at obtaining a better understanding of the processes responsible for the formation of the laterite itself and the constraints to its development. The lateritic profile rests on a Paleoproterozoic basement mostly composed of granodioritic rocks related to the Eburnean magmatic cycle passing upwards to saprolite and consists of four main composite horizons (bottom to top): kaolinite and clay-rich horizons, mottled laterite and iron-rich duricrust. In order to achieve such a goal, a multi-disciplinary analytical approach was adopted, which includes inductively coupled plasma (ICP) atomic emission and mass spectrometries (ICP-AES and ICP-MS respectively), X-ray powder diffraction (XRPD), scanning electron microscopy with energy dispersive spectrometry (SEM-EDS) and micro-Raman spectroscopy.

The future of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discovery

PubMed Central

Metz, Thomas O.; Zhang, Qibin; Page, Jason S.; Shen, Yufeng; Callister, Stephen J.; Jacobs, Jon M.; Smith, Richard D.

2008-01-01

SUMMARY The future utility of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discover will be discussed, beginning with a brief description of the evolution of metabolomics and the utilization of the three most popular analytical platforms in such studies: NMR, GC-MS, and LC-MS. Emphasis is placed on recent developments in high-efficiency LC separations, sensitive electrospray ionization approaches, and the benefits to incorporating both in LC-MS-based approaches. The advantages and disadvantages of various quantitative approaches are reviewed, followed by the current LC-MS-based tools available for candidate biomarker characterization and identification. Finally, a brief prediction on the future path of LC-MS-based methods in metabolic profiling and metabolomic studies is given. PMID:19177179

Alkaloid profiling of the traditional Chinese medicine Rhizoma corydalis using high performance liquid chromatography-tandem quadrupole time-of-flight mass spectrometry

PubMed Central

Sun, Mingqian; Liu, Jianxun; Lin, Chengren; Miao, Lan; Lin, Li

2014-01-01

Since alkaloids are the major active constituents of Rhizoma corydalis (RC), a convenient and accurate analytical method is needed for their identification and characterization. Here we report a method to profile the alkaloids in RC based on liquid chromatography-tandem quadrupole time-of-flight mass spectrometry (LC–Q-TOF-MS/MS). A total of 16 alkaloids belonging to four different classes were identified by comparison with authentic standards. The fragmentation pathway of each class of alkaloid was clarified and their differences were elucidated. Furthermore, based on an analysis of fragmentation pathways and alkaloid profiling, a rapid and accurate method for the identification of unknown alkaloids in RC is proposed. The method could also be useful for the quality control of RC. PMID:26579385

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.

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

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.

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.

Imaging Mass Spectrometry on the Nanoscale with Cluster Ion Beams

DOE PAGES

Winograd, Nicholas

2014-12-02

Imaging with cluster secondary ion mass spectrometry (SIMS) is reaching a mature level of development. When, using a variety of molecular ion projectiles to stimulate desorption, 3-dimensional imaging with the selectivity of mass spectrometry can now be achieved with submicrometer spatial resolution and <10 nm depth resolution. In this Perspective, stock is taken regarding what it will require to routinely achieve these remarkable properties. Some issues include the chemical nature of the projectile, topography formation, differential erosion rates, and perhaps most importantly, ionization efficiency. Shortcomings of existing instrumentation are also noted. One key part of this discussion involves speculation onmore » how best to resolve these issues.« less

Imaging Mass Spectrometry on the Nanoscale with Cluster Ion Beams

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

Winograd, Nicholas

Imaging with cluster secondary ion mass spectrometry (SIMS) is reaching a mature level of development. When, using a variety of molecular ion projectiles to stimulate desorption, 3-dimensional imaging with the selectivity of mass spectrometry can now be achieved with submicrometer spatial resolution and <10 nm depth resolution. In this Perspective, stock is taken regarding what it will require to routinely achieve these remarkable properties. Some issues include the chemical nature of the projectile, topography formation, differential erosion rates, and perhaps most importantly, ionization efficiency. Shortcomings of existing instrumentation are also noted. One key part of this discussion involves speculation onmore » how best to resolve these issues.« less

Analysis of human plasma lipids by using comprehensive two-dimensional gas chromatography with dual detection and with the support of high-resolution time-of-flight mass spectrometry for structural elucidation.

PubMed

Salivo, Simona; Beccaria, Marco; Sullini, Giuseppe; Tranchida, Peter Q; Dugo, Paola; Mondello, Luigi

2015-01-01

The main focus of the present research is the analysis of the unsaponifiable lipid fraction of human plasma by using data derived from comprehensive two-dimensional gas chromatography with dual quadrupole mass spectrometry and flame ionization detection. This approach enabled us to attain both mass spectral information and analyte percentage data. Furthermore, gas chromatography coupled with high-resolution time-of-flight mass spectrometry was used to increase the reliability of identification of several unsaponifiable lipid constituents. The synergism between both the high-resolution gas chromatography and mass spectrometry processes enabled us to attain a more in-depth knowledge of the unsaponifiable fraction of human plasma. Additionally, information was attained on the fatty acid and triacylglycerol composition of the plasma samples, subjected to investigation by using comprehensive two-dimensional gas chromatography with dual quadrupole mass spectrometry and flame ionization detection and high-performance liquid chromatography with atmospheric pressure chemical ionization quadrupole mass spectrometry, respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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.

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.

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.

Neutron spectrometry for UF 6 enrichment verification in storage cylinders

DOE PAGES

Mengesha, Wondwosen; Kiff, Scott D.

2015-01-29

Verification of declared UF 6 enrichment and mass in storage cylinders is of great interest in nuclear material nonproliferation. Nondestructive assay (NDA) techniques are commonly used for safeguards inspections to ensure accountancy of declared nuclear materials. Common NDA techniques used include gamma-ray spectrometry and both passive and active neutron measurements. In the present study, neutron spectrometry was investigated for verification of UF 6 enrichment in 30B storage cylinders based on an unattended and passive measurement approach. MCNP5 and Geant4 simulated neutron spectra, for selected UF 6 enrichments and filling profiles, were used in the investigation. The simulated neutron spectra weremore » analyzed using principal component analysis (PCA). The PCA technique is a well-established technique and has a wide area of application including feature analysis, outlier detection, and gamma-ray spectral analysis. Results obtained demonstrate that neutron spectrometry supported by spectral feature analysis has potential for assaying UF 6 enrichment in storage cylinders. Thus the results from the present study also showed that difficulties associated with the UF 6 filling profile and observed in other unattended passive neutron measurements can possibly be overcome using the approach presented.« less

The expanding role of mass spectrometry in the field of vaccine development.

PubMed

Sharma, Vaneet Kumar; Sharma, Ity; Glick, James

2018-05-31

Biological mass spectrometry has evolved as a core analytical technology in the last decade mainly because of its unparalleled ability to perform qualitative as well as quantitative profiling of enormously complex biological samples with high mass accuracy, sensitivity, selectivity and specificity. Mass spectrometry-based techniques are also routinely used to assess glycosylation and other post-translational modifications, disulfide bond linkage, and scrambling as well as for the detection of host cell protein contaminants in the field of biopharmaceuticals. The role of mass spectrometry in vaccine development has been very limited but is now expanding as the landscape of global vaccine development is shifting towards the development of recombinant vaccines. In this review, the role of mass spectrometry in vaccine development is presented, some of the ongoing efforts to develop vaccines for diseases with global unmet medical need are discussed and the regulatory challenges of implementing mass spectrometry techniques in a quality control laboratory setting are highlighted. © 2018 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

Heavy doping of CdTe single crystals by Cr ion implantation

NASA Astrophysics Data System (ADS)

Popovych, Volodymyr D.; Böttger, Roman; Heller, Rene; Zhou, Shengqiang; Bester, Mariusz; Cieniek, Bogumil; Mroczka, Robert; Lopucki, Rafal; Sagan, Piotr; Kuzma, Marian

2018-03-01

Implantation of bulk CdTe single crystals with high fluences of 500 keV Cr+ ions was performed to achieve Cr concentration above the equilibrium solubility limit of this element in CdTe lattice. The structure and composition of the implanted samples were studied using secondary ion mass spectrometry (SIMS), scanning electron microscopy (SEM), energy dispersive X-ray (EDX) analysis, X-ray diffraction (XRD) and Rutherford backscattering spectrometry (RBS) to characterize the incorporation of chromium into the host lattice and to investigate irradiation-induced damage build-up. It was found that out-diffusion of Cr atoms and sputtering of the targets alter the depth distribution and limit concentration of the projectile ions in the as-implanted samples. Appearance of crystallographically oriented, metallic α-Cr nanoparticles inside CdTe matrix was found after implantation, as well as a strong disorder at the depth far beyond the projected range of the implanted ions.

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

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

Jin, Ke; Zhang, Yanwen; Zhu, Zihua

Accurate information of electronic stopping power is fundamental for broad advances in electronic industry, space exploration, national security, and sustainable energy technologies. The Stopping and Range of Ions in Matter (SRIM) code has been widely applied to predict stopping powers and ion distributions for decades. Recent experimental results have, however, shown considerable errors in the SRIM predictions for stopping of heavy ions in compounds containing light elements, indicating an urgent need to improve current stopping power models. The electronic stopping powers of 35Cl, 80Br, 127I, and 197Au ions are experimentally determined in two important functional materials, SiC and SiO2, frommore » tens to hundreds keV/u based on a single ion technique. By combining with the reciprocity theory, new electronic stopping powers are suggested in a region from 0 to 15 MeV, where large deviations from SRIM predictions are observed. For independent experimental validation of the electronic stopping powers we determined, Rutherford backscattering spectrometry (RBS) and secondary ion mass spectrometry (SIMS) are utilized to measure the depth profiles of implanted Au ions in SiC with energies from 700 keV to 15 MeV. The measured ion distributions from both RBS and SIMS are considerably deeper (up to ~30%) than the predictions from the commercial SRIM code. In comparison, the new electronic stopping power values are utilized in a modified TRIM-85 (the original version of the SRIM) code, M-TRIM, to predict ion distributions, and the results are in good agreement with the experimentally measured ion distributions.« less

Depth profile of 236U/238U in soil samples in La Palma, Canary Islands

PubMed Central

Srncik, M.; Steier, P.; Wallner, G.

2011-01-01

The vertical distribution of the 236U/238U isotopic ratio was investigated in soil samples from three different locations on La Palma (one of the seven Canary Islands, Spain). Additionally the 240Pu/239Pu atomic ratio, as it is a well establish tool for the source identification, was determined. The radiochemical procedure consisted of a U separation step by extraction chromatography using UTEVA® Resin (Eichrom Technologies, Inc.). Afterwards Pu was separated from Th and Np by anion exchange using Dowex 1x2 (Dow Chemical Co.). Furthermore a new chemical procedure with tandem columns to separate Pu and U from the matrix was tested. For the determination of the uranium and plutonium isotopes by alpha spectrometry thin sources were prepared by microprecipitation techniques. Additionally these fractions separated from the soil samples were measured by Accelerator Mass Spectrometry (AMS) to get information on the isotopic ratios 236U/238U, 240Pu/239Pu and 236U/239Pu, respectively. The 236U concentrations [atoms/g] in each surface layer (∼2 cm) were surprisingly high compared to deeper layers where values around two orders of magnitude smaller were found. Since the isotopic ratio 240Pu/239Pu indicated a global fallout signature we assume the same origin as the probable source for 236U. Our measured 236U/239Pu value of around 0.2 is within the expected range for this contamination source. PMID:21481502

Suppression effect of silicon (Si) on Er{sup 3+} 1.54μm excitation in ZnO thin films

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

Xu, Bo; Lu, Fei, E-mail: lufei@sdu.edu.cn; Fan, Ranran

2016-08-15

We have investigated the photoluminescence (PL) characteristics of ZnO:Er thin films on Si (100) single crystal and SiO{sub 2}-on-silicon (SiO{sub 2}) substrates, synthesized by radio frequency magnetron sputtering. Rutherford backscattering/channeling spectrometry (RBS), X-ray diffraction (XRD) and atomic force microscope (AFM) were used to analyze the properties of thin films. The diffusion depth profiles of Si were determined by second ion mass spectrometry (SIMS). Infrared spectra were obtained from the spectrometer and related instruments. Compared with the results at room temperature (RT), PL (1.54μm) intensity increased when samples were annealed at 250°C and decreased when at 550°C. A new peak atmore » 1.15μm from silicon (Si) appeared in 550°C samples. The Si dopants in ZnO film, either through the diffusion of Si from the substrate or ambient, directly absorbed the energy of pumping light and resulted in the suppression of Er{sup 3+} 1.54μm excitation. Furthermore, the energy transmission efficiency between Si and Er{sup 3+} was very low when compared with silicon nanocrystal (Si-NC). Both made the PL (1.54μm) intensity decrease. All the data in experiments proved the negative effects of Si dopants on PL at 1.54μm. And further research is going on.« less

A draft map of the human ovarian proteome for tissue engineering and clinical applications.

PubMed

Ouni, Emna; Vertommen, Didier; Chiti, Maria Costanza; Dolmans, Marie-Madeleine; Amorim, Christiani Andrade

2018-02-23

Fertility preservation research in women today is increasingly taking advantage of bioengineering techniques to develop new biomimetic materials and solutions to safeguard ovarian cell function and microenvironment in vitro and in vivo. However, available data on the human ovary are limited and fundamental differences between animal models and humans are hampering researchers in their quest for more extensive knowledge of human ovarian physiology and key reproductive proteins that need to be preserved. We therefore turned to multi-dimensional label-free mass spectrometry to analyze human ovarian cortex, as it is a high-throughput and conclusive technique providing information on the proteomic composition of complex tissues like the ovary. In-depth proteomic profiling through two-dimensional liquid chromatography-mass spectrometry, western blot, histological and immunohistochemical analyses, and data mining helped us to confidently identify 1,508 proteins. Moreover, our method allowed us to chart the most complete representation so far of the ovarian matrisome, defined as the ensemble of extracellular matrix proteins and associated factors, including more than 80 proteins. In conclusion, this study will provide a better understanding of ovarian proteomics, with a detailed characterization of the ovarian follicle microenvironment, in order to enable bioengineers to create biomimetic scaffolds for transplantation and three-dimensional in vitro culture. By publishing our proteomic data, we also hope to contribute to accelerating biomedical research into ovarian health and disease in general. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Evaluation of analytical performance and reliability of direct nanoLC-nanoESI-high resolution mass spectrometry for profiling the (xeno)metabolome.

PubMed

Chetwynd, Andrew J; David, Arthur; Hill, Elizabeth M; Abdul-Sada, Alaa

2014-10-01

Mass spectrometry (MS) profiling techniques are used for analysing metabolites and xenobiotics in biofluids; however, detection of low abundance compounds using conventional MS techniques is poor. To counter this, nanoflow ultra-high-pressure liquid chromatography-nanoelectrospray ionization-time-of-flight MS (nUHPLC-nESI-TOFMS), which has been used primarily for proteomics, offers an innovative prospect for profiling small molecules. Compared to conventional UHPLC-ESI-TOFMS, nUHPLC-nESI-TOFMS enhanced detection limits of a variety of (xeno)metabolites by between 2 and 2000-fold. In addition, this study demonstrates for the first time excellent repeatability and reproducibility for analysis of urine and plasma samples using nUHPLC-nESI-TOFMS, supporting implementation of this platform as a novel approach for high-throughput (xeno)metabolomics. Copyright © 2014 John Wiley & Sons, Ltd.

Direct characterization of commercial lecithins by easy ambient sonic-spray ionization mass spectrometry.

PubMed

Fernandes, Gabriel D; Alberici, Rosana M; Pereira, Gustavo G; Cabral, Elaine C; Eberlin, Marcos N; Barrera-Arellano, Daniel

2012-12-01

Commercial lecithins are composed mainly of phospholipids and triacylglycerols. The analysis of the commercial lecithins, including their fraction of phospholipids, normally involves laborious and expensive protocols. Easy ambient sonic-spray ionization mass spectrometry (EASI-MS) is shown to be an efficient technique for the analysis of lipids. Samples of commercial lecithins including standards, refined, deoiled and modified soy lecithin were tested. Characteristic profiles of phosphatidylcholines and triacylglycerols are detected by EASI(+)-MS, whereas EASI(-)-MS provided phosphatidylethanolamines, glycophospholipids and free fatty acids profiles. Acetylated lecithins also displayed characteristic acetylated derivatives. EASI-MS data was also compared to MALDI-MS, and found to display richer compositional information. The industrial process applied to lecithin fabrication was also characterised via typical EASI-MS profiles. EASI-MS both in its positive and negative ion modes offers a direct, fast and efficient technique able to characterise commercial lecithin. Copyright © 2012 Elsevier Ltd. All rights reserved.

Siderophile Element Profile Measurements in Iron Meteorites Using Laser Ablation ICP-MS

NASA Technical Reports Server (NTRS)

Watson, H. C.; Watson, E. B.; McDonough, W. F.

2005-01-01

Understanding the behaviour of siderophile elements during cooling of iron meteorites can lead to insight into the general thermal histories of the meteorites as well as their respective parent bodies. Traditionally trace element analyses in meteorites have been done using techniques that only measure the average concentration in each phase. With these methods, all of the spatial information with respect to the distribution of an element within one phase is lost. Measuring concentration profiles of trace elements in meteorites is now possible, with the advent of high-resolution analytical techniques such as laser ablation, inductively coupled plasma mass spectrometry (LA-ICP-MS) with spatial resolution <20 microns. [e.g. 1,2] and secondary ion mass spectrometry [3]. These profiles can give more insight into both the partitioning and diffusive behavior of siderophile elements in metal systems relevant to iron meteorites, as well as parent body cooling rates.

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.

Profiling of modified nucleosides from ribonucleic acid digestion by supercritical fluid chromatography coupled to high resolution mass spectrometry.

PubMed

Laboureur, Laurent; Guérineau, Vincent; Auxilien, Sylvie; Yoshizawa, Satoko; Touboul, David

2018-02-16

A method based on supercritical fluid chromatography coupled to high resolution mass spectrometry for the profiling of canonical and modified nucleosides was optimized, and compared to classical reverse-phase liquid chromatography in terms of separation, number of detected modified nucleosides and sensitivity. Limits of detection and quantification were measured using statistical method and quantifications of twelve nucleosides of a tRNA digest from E. coli are in good agreement with previously reported data. Results highlight the complementarity of both separation techniques to cover the largest view of nucleoside modifications for forthcoming epigenetic studies. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Profiling of Arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry.

PubMed

von Roepenack-Lahaye, Edda; Degenkolb, Thomas; Zerjeski, Michael; Franz, Mathias; Roth, Udo; Wessjohann, Ludger; Schmidt, Jürgen; Scheel, Dierk; Clemens, Stephan

2004-02-01

Large-scale metabolic profiling is expected to develop into an integral part of functional genomics and systems biology. The metabolome of a cell or an organism is chemically highly complex. Therefore, comprehensive biochemical phenotyping requires a multitude of analytical techniques. Here, we describe a profiling approach that combines separation by capillary liquid chromatography with the high resolution, high sensitivity, and high mass accuracy of quadrupole time-of-flight mass spectrometry. About 2000 different mass signals can be detected in extracts of Arabidopsis roots and leaves. Many of these originate from Arabidopsis secondary metabolites. Detection based on retention times and exact masses is robust and reproducible. The dynamic range is sufficient for the quantification of metabolites. Assessment of the reproducibility of the analysis showed that biological variability exceeds technical variability. Tools were optimized or established for the automatic data deconvolution and data processing. Subtle differences between samples can be detected as tested with the chalcone synthase deficient tt4 mutant. The accuracy of time-of-flight mass analysis allows to calculate elemental compositions and to tentatively identify metabolites. In-source fragmentation and tandem mass spectrometry can be used to gain structural information. This approach has the potential to significantly contribute to establishing the metabolome of Arabidopsis and other model systems. The principles of separation and mass analysis of this technique, together with its sensitivity and resolving power, greatly expand the range of metabolic profiling.

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.

A Phytochemical-Sensing Strategy Based on Mass Spectrometry Imaging and Metabolic Profiling for Understanding the Functionality of the Medicinal Herb Green Tea.

PubMed

Fujimura, Yoshinori; Miura, Daisuke; Tachibana, Hirofumi

2017-09-27

Low-molecular-weight phytochemicals have health benefits and reduce the risk of diseases, but the mechanisms underlying their activities have remained elusive because of the lack of a methodology that can easily visualize the exact behavior of such small molecules. Recently, we developed an in situ label-free imaging technique, called mass spectrometry imaging, for visualizing spatially-resolved biotransformations based on simultaneous mapping of the major bioactive green tea polyphenol and its phase II metabolites. In addition, we established a mass spectrometry-based metabolic profiling technique capable of evaluating the bioactivities of diverse green tea extracts, which contain multiple phytochemicals, by focusing on their compositional balances. This methodology allowed us to simultaneously evaluate the relative contributions of the multiple compounds present in a multicomponent system to its bioactivity. This review highlights small molecule-sensing techniques for visualizing the complex behaviors of herbal components and linking such information to an enhanced understanding of the functionalities of multicomponent medicinal herbs.

Profiling the indole alkaloids in yohimbe bark with ultra-performance liquid chromatography coupled with ion mobility quadrupole time-of-flight mass spectrometry.

PubMed

Sun, Jianghao; Baker, Andrew; Chen, Pei

2011-09-30

An ultra-performance liquid chromatography/ion mobility quadrupole time-of-flight mass spectrometry (UPLC/IM-QTOF-MS) method was developed for profiling the indole alkaloids in yohimbe bark. Many indole alkaloids with the yohimbine or ajmalicine core structure, plus methylated, oxidized and reduced species, were characterized. Common fragments and mass differences are described. It was shown that the use of IMS could provide another molecular descriptor, i.e. molecular shape by rotationally averaged collision cross-section; this is of great value for identification of constituents when reference materials are usually not available. Using the combination of high resolution (~40000) accurate mass measurement with time-aligned parallel (TAP) fragmentation, MS(E) (where E represents collision energy), ion mobility mass spectrometry (IMS) and UPLC chromatography, a total 55 indole alkaloids were characterized and a few new indole alkaloids are reported for the first time. Published in 2011 by John Wiley & Sons, Ltd.

Analytical considerations for mass spectrometry profiling in serum biomarker discovery.

PubMed

Whiteley, Gordon R; Colantonio, Simona; Sacconi, Andrea; Saul, Richard G

2009-03-01

The potential of using mass spectrometry profiling as a diagnostic tool has been demonstrated for a wide variety of diseases. Various cancers and cancer-related diseases have been the focus of much of this work because of both the paucity of good diagnostic markers and the knowledge that early diagnosis is the most powerful weapon in treating cancer. The implementation of mass spectrometry as a routine diagnostic tool has proved to be difficult, however, primarily because of the stringent controls that are required for the method to be reproducible. The method is evolving as a powerful guide to the discovery of biomarkers that could, in turn, be used either individually or in an array or panel of tests for early disease detection. Using proteomic patterns to guide biomarker discovery and the possibility of deployment in the clinical laboratory environment on current instrumentation or in a hybrid technology has the possibility of being the early diagnosis tool that is needed.

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.

Periodontal and serum protein profiles in patients with rheumatoid arthritis treated with tumor necrosis factor inhibitor adalimumab.

PubMed

Kobayashi, Tetsuo; Yokoyama, Tomoko; Ito, Satoshi; Kobayashi, Daisuke; Yamagata, Akira; Okada, Moe; Oofusa, Ken; Narita, Ichiei; Murasawa, Akira; Nakazono, Kiyoshi; Yoshie, Hiromasa

2014-11-01

Tumor necrosis factor (TNF)-α inhibitor has been shown to affect the periodontal condition of patients with rheumatoid arthritis (RA). The aim of the present study is to assess the effect of a fully humanized anti-TNF-α monoclonal antibody, adalimumab (ADA), on the periodontal condition of patients with RA and to compare serum protein profiles before and after ADA therapy. The study participants consisted of 20 patients with RA treated with ADA. Clinical periodontal and rheumatologic parameters and serum cytokine levels were evaluated at baseline and 3 months later. Serum protein spot volume was examined with two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis. Proteins with significant difference in abundance before and after ADA therapy were found and identified using mass spectrometry and protein databases. The patients showed a significant decrease in gingival index (P = 0.002), bleeding on probing (P = 0.003), probing depth (P = 0.002), disease activity score including 28 joints using C-reactive protein (P <0.001), and serum levels of TNF-α (P <0.001) and interleukin-6 (P <0.001) after ADA medication, although plaque levels were comparable. Among a total of 495 protein spots obtained, nine spots were significantly decreased in abundance at reassessment, corresponding to complement factor H, phospholipase D, serum amyloid A, complement component 4, and α-1-acid glycoprotein (P <0.01). These results suggest a beneficial effect of ADA therapy on the periodontal condition of patients with RA, which might be related to differences in serum protein profiles before and after ADA therapy.

Bile acid profiling and quantification in biofluids using ultra-performance liquid chromatography tandem mass spectrometry.

PubMed

Sarafian, Magali H; Lewis, Matthew R; Pechlivanis, Alexandros; Ralphs, Simon; McPhail, Mark J W; Patel, Vishal C; Dumas, Marc-Emmanuel; Holmes, Elaine; Nicholson, Jeremy K

2015-10-06

Bile acids are important end products of cholesterol metabolism. While they have been identified as key factors in lipid emulsification and absorption due to their detergent properties, bile acids have also been shown to act as signaling molecules and intermediates between the host and the gut microbiota. To further the investigation of bile acid functions in humans, an advanced platform for high throughput analysis is essential. Herein, we describe the development and application of a 15 min UPLC procedure for the separation of bile acid species from human biofluid samples requiring minimal sample preparation. High resolution time-of-flight mass spectrometry was applied for profiling applications, elucidating rich bile acid profiles in both normal and disease state plasma. In parallel, a second mode of detection was developed utilizing tandem mass spectrometry for sensitive and quantitative targeted analysis of 145 bile acid (BA) species including primary, secondary, and tertiary bile acids. The latter system was validated by testing the linearity (lower limit of quantification, LLOQ, 0.25-10 nM and upper limit of quantification, ULOQ, 2.5-5 μM), precision (≈6.5%), and accuracy (81.2-118.9%) on inter- and intraday analysis achieving good recovery of bile acids (serum/plasma 88% and urine 93%). The ultra performance liquid chromatography-mass spectrometry (UPLC-MS)/MS targeted method was successfully applied to plasma, serum, and urine samples in order to compare the bile acid pool compositional difference between preprandial and postprandial states, demonstrating the utility of such analysis on human biofluids.

Qualitative Profiling and Quantification of Neonicotinoid Metabolites in Human Urine by Liquid Chromatography Coupled with Mass Spectrometry

PubMed Central

Taira, Kumiko; Fujioka, Kazutoshi; Aoyama, Yoshiko

2013-01-01

Neonicotinoid pesticides have been widely applied for the production of fruits and vegetables, and occasionally detected in conventionally grown produce. Thus oral exposure to neonicotinoid pesticides may exist in the general population; however, neonicotinoid metabolites in human body fluids have not been investigated comprehensively. The purpose of this study is the qualitative profiling and quantitative analysis of neonicotinoid metabolites in the human spot urine by liquid chromatography coupled with mass spectrometry (LC/MS). Human urine samples were collected from three patients suspected of subacute exposure to neonicotinoid pesticides. A qualitative profiling of urinary metabolites was performed using liquid chromatography/time-of-flight mass spectrometry (LC/TOFMS) with a database of nominal molecular weights of 57 known metabolites of three neonicotinoid pesticides (acetamiprid, Imidacloprid, and clothianidin), as well as the parent compounds. Then a quantitative analysis of selected urinary metabolites was performed using liquid chromatography/tandem mass spectrometry (LC/MS/MS) with a standard pesticide and metabolite, which were detected by the qualitative profiling. The result of qualitative profiling showed that seven metabolites, i.e. an acetamiprid metabolite, N-desmethyl-acetamiprid; three Imidacloprid metabolites, 5-hydroxy-Imidacloprid, 4,5-dihydroxy-imidacloprid, 4,5-dehydro-Imidacloprid; a common metabolite of acetamiprid and Imidacloprid, N-(6-chloronicotinoyl)-glycine; and two clothianidin metabolites, N-desmethyl-clothianidin, N-(2-(methylsulfanyl)thiazole-5-carboxyl)-glycine, as well as acetamiprid, were detected in the urine of three cases. The result of the quantitative analysis showed N-desmethyl-acetamiprid was determined in the urine of one case, which had been collected on the first visit, at a concentration of 3.2 ng/mL. This is the first report on the qualitative and quantitative detection of N-desmethyl-acetamiprid in the human urine. The results suggest that the one case with detection of N-desmethyl-acetamiprid was exposed to acetamiprid through the consumption of contaminated foods. Urinary N-desmethyl-acetamiprid, as well as 5-hydroxy-Imidacloprid and N-desmethyl-clothianidin, may be a good biomarker for neonicotinoid exposure in humans and warrants further investigation. PMID:24265808

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

Cocoa content influences chocolate molecular profile investigated by MALDI-TOF mass spectrometry.

PubMed

Bonatto, Cínthia C; Silva, Luciano P

2015-06-01

Chocolate authentication is a key aspect of quality control and safety. Matrix-assisted laser desorption ionization time-of flight (MALDI-TOF) mass spectrometry (MS) has been demonstrated to be useful for molecular profiling of cells, tissues, and even food. The present study evaluated if MALDI-TOF MS analysis on low molecular mass profile may classify chocolate samples according to the cocoa content. The molecular profiles of seven processed commercial chocolate samples were compared by using MALDI-TOF MS. Some ions detected exclusively in chocolate samples corresponded to the metabolites of cocoa or other constituents. This method showed the presence of three distinct clusters according to confectionery and sensorial features of the chocolates and was used to establish a mass spectra database. Also, novel chocolate samples were evaluated in order to check the validity of the method and to challenge the database created with the mass spectra of the primary samples. Thus, the method was shown to be reliable for clustering unknown samples into the main chocolate categories. Simple sample preparation of the MALDI-TOF MS approach described will allow the surveillance and monitoring of constituents during the molecular profiling of chocolates. © 2014 Society of Chemical Industry.

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

Experimental analysis of bruises in human volunteers using radiometric depth profiling and diffuse reflectance spectroscopy

NASA Astrophysics Data System (ADS)

Vidovič, Luka; Milanič, Matija; Majaron, Boris

2015-07-01

We combine pulsed photothermal radiometry (PPTR) depth profiling with diffuse reflectance spectroscopy (DRS) measurements for a comprehensive analysis of bruise evolution in vivo. While PPTR enables extraction of detailed depth distribution and concentration profiles of selected absorbers (e.g. melanin, hemoglobin), DRS provides information in a wide range of visible wavelengths and thus offers an additional insight into dynamics of the hemoglobin degradation products. Combining the two approaches enables us to quantitatively characterize bruise evolution dynamics. Our results indicate temporal variations of the bruise evolution parameters in the course of bruise self-healing process. The obtained parameter values and trends represent a basis for a future development of an objective technique for bruise age determination.

Secondary metabolite profiling of Curcuma species grown at different locations using GC/TOF and UPLC/Q-TOF MS.

PubMed

Lee, Jueun; Jung, Youngae; Shin, Jeoung-Hwa; Kim, Ho Kyoung; Moon, Byeong Cheol; Ryu, Do Hyun; Hwang, Geum-Sook

2014-07-04

Curcuma, a genus of rhizomatous herbaceous species, has been used as a spice, traditional medicine, and natural dye. In this study, the metabolite profile of Curcuma extracts was determined using gas chromatography-time of flight mass spectrometry (GC/TOF MS) and ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS) to characterize differences between Curcuma aromatica and Curcuma longa grown on the Jeju-do or Jin-do islands, South Korea. Previous studies have performed primary metabolite profiling of Curcuma species grown in different regions using NMR-based metabolomics. This study focused on profiling of secondary metabolites from the hexane extract of Curcuma species. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) plots showed significant differences between the C. aromatica and C. longa metabolite profiles, whereas geographical location had little effect. A t-test was performed to identify statistically significant metabolites, such as terpenoids. Additionally, targeted profiling using UPLC/Q-TOF MS showed that the concentration of curcuminoids differed depending on the plant origin. Based on these results, a combination of GC- and LC-MS allowed us to analyze curcuminoids and terpenoids, the typical bioactive compounds of Curcuma, which can be used to discriminate Curcuma samples according to species or geographical origin.

Low-molecular weight protein profiling of genetically modified maize using fast liquid chromatography electrospray ionization and time-of-flight mass spectrometry.

PubMed

Koc, Anna; Cañuelo, Ana; Garcia-Reyes, Juan F; Molina-Diaz, Antonio; Trojanowicz, Marek

2012-06-01

In this work, the use of liquid chromatography coupled to electrospray time-of-flight mass spectrometry (LC-TOFMS) has been evaluated for the profiling of relatively low-molecular weight protein species in both genetically modified (GM) and non-GM maize. The proposed approach consisted of a straightforward sample fractionation with different water and ethanol-based buffer solutions followed by separation and detection of the protein species using liquid chromatography with a small particle size (1.8 μm) C(18) column and electrospray-time-of-flight mass spectrometry detection in the positive ionization mode. The fractionation of maize reference material containing different content of transgenic material (from 0 to 5% GM) led to five different fractions (albumins, globulins, zeins, zein-like glutelins, and glutelins), all of them containing different protein species (from 2 to 52 different species in each fraction). Some relevant differences in the quantity and types of protein species were observed in the different fractions of the reference material (with different GM contents) tested, thus revealing the potential use of the proposed approach for fast protein profiling and to detect tentative GMO markers in maize. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Profiling pneumococcal type 3-derived oligosaccharides by high resolution liquid chromatography-tandem mass spectrometry

PubMed Central

Li, Guoyun; Li, Lingyun; Xue, Changhu; Middleton, Dustin; Linhardt, Robert J.; Avci, Fikri Y.

2015-01-01

Pneumococcal type-3 polysaccharide (Pn3P) is considered a major target for the development of a human vaccine to protect against Streptococcus pneumonia infection. Thus, it is critical to develop methods for the preparation and analysis of Pn3P-derived oligosaccharides to better understand its immunological properties. In this paper, we profile oligosaccharides, generated by the free radical depolymerization of Pn3P, using liquid chromatography (LC)-tandem mass spectrometry (MS/MS). Hydrophilic liquid interaction chromatography (HILIC)-mass spectrometry (MS) revealed a series of oligosaccharides with an even- and odd-number of saccharide residues, ranging from monosaccharide, degree of polymerization (dp1) to large oligosaccharides up to dp 20, generated by free radical depolymerization. Isomers of oligosaccharides with an even number of sugar residues were easily separated on a HILIC column, and their sequences could be distinguished by comparing MS/MS of these oligosaccharides and their reduced alditols. Fluorescent labeling with 2-aminoacridone (AMAC) followed by reversed phase (RP)-LC-MS/MS was applied to analyze and sequence poorly separated product mixtures, as RP-LC affords higher resolution of AMAC-labeled oligosaccharides than does HILIC-based separation. The present methodology can be potentially applied to profiling other capsular polysaccharides. PMID:25913329

Profiling pneumococcal type 3-derived oligosaccharides by high resolution liquid chromatography-tandem mass spectrometry.

PubMed

Li, Guoyun; Li, Lingyun; Xue, Changhu; Middleton, Dustin; Linhardt, Robert J; Avci, Fikri Y

2015-06-05

Pneumococcal type-3 polysaccharide (Pn3P) is considered a major target for the development of a human vaccine to protect against Streptococcus pneumoniae infection. Thus, it is critical to develop methods for the preparation and analysis of Pn3P-derived oligosaccharides to better understand its immunological properties. In this paper, we profile oligosaccharides, generated by the free radical depolymerization of Pn3P, using liquid chromatography (LC)-tandem mass spectrometry (MS/MS). Hydrophilic liquid interaction chromatography (HILIC)-mass spectrometry (MS) revealed a series of oligosaccharides with an even- and odd-number of saccharide residues, ranging from monosaccharide, degree of polymerization (dp1) to large oligosaccharides up to dp 20, generated by free radical depolymerization. Isomers of oligosaccharides with an even number of sugar residues were easily separated on a HILIC column, and their sequences could be distinguished by comparing MS/MS of these oligosaccharides and their reduced alditols. Fluorescent labeling with 2-aminoacridone (AMAC) followed by reversed phase (RP)-LC-MS/MS was applied to analyze and sequence poorly separated product mixtures, as RP-LC affords higher resolution of AMAC-labeled oligosaccharides than does HILIC-based separation. The present methodology can be potentially applied to profiling other capsular polysaccharides. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

Classification of Ancient Mammal Individuals Using Dental Pulp MALDI-TOF MS Peptide Profiling

PubMed Central

Tran, Thi-Nguyen-Ny; Aboudharam, Gérard; Gardeisen, Armelle; Davoust, Bernard; Bocquet-Appel, Jean-Pierre; Flaudrops, Christophe; Belghazi, Maya; Raoult, Didier; Drancourt, Michel

2011-01-01

Background The classification of ancient animal corpses at the species level remains a challenging task for forensic scientists and anthropologists. Severe damage and mixed, tiny pieces originating from several skeletons may render morphological classification virtually impossible. Standard approaches are based on sequencing mitochondrial and nuclear targets. Methodology/Principal Findings We present a method that can accurately classify mammalian species using dental pulp and mass spectrometry peptide profiling. Our work was organized into three successive steps. First, after extracting proteins from the dental pulp collected from 37 modern individuals representing 13 mammalian species, trypsin-digested peptides were used for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard. Second, using a 279–modern spectrum database, we blindly classified 33 of 37 teeth collected in 37 modern individuals (89.1%). Third, we classified 10 of 18 teeth (56%) collected in 15 ancient individuals representing five mammal species including human, from five burial sites dating back 8,500 years. Further comparison with an upgraded database comprising ancient specimen profiles yielded 100% classification in ancient teeth. Peptide sequencing yield 4 and 16 different non-keratin proteins including collagen (alpha-1 type I and alpha-2 type I) in human ancient and modern dental pulp, respectively. Conclusions/Significance Mass spectrometry peptide profiling of the dental pulp is a new approach that can be added to the arsenal of species classification tools for forensics and anthropology as a complementary method to DNA sequencing. The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals. PMID:21364886

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.

Leveraging non-targeted metabolite profiling via statistical genomics

USDA-ARS?s Scientific Manuscript database

One of the challenges of systems biology is to integrate multiple sources of data in order to build a cohesive view of the system of study. Here we describe the mass spectrometry based profiling of maize kernels, a model system for genomic studies and a cornerstone of the agroeconomy. Using a networ...

Chemical profiling of two congeneric sea mat corals along the Brazilian coast: adaptive and functional patterns.

PubMed

Costa-Lotufo, L V; Carnevale-Neto, F; Trindade-Silva, A E; Silva, R R; Silva, G G Z; Wilke, D V; Pinto, F C L; Sahm, B D B; Jimenez, P C; Mendonça, J N; Lotufo, T M C; Pessoa, O D L; Lopes, N P

2018-02-20

Metabolomic profiles were explored to understand environmental and taxonomic influences on the metabolism of two congeneric zoanthids, Palythoa caribaeorum and P. variabilis, collected across distinct geographical ranges. Integrated mass spectrometry data suggested the major influence of geographical location on chemical divergence when compared to species differentiation.

DETECTING LOW-LEVEL SYNTHESIS IMPURITIES IN MODIFIED PHOSPHOROTHIOATE OLIGONUCLEOTIDES USING LIQUID CHROMATOGRAPHY – HIGH RESOLUTION MASS SPECTROMETRY

PubMed Central

Nikcevic, Irena; Wyrzykiewicz, Tadeusz K.; Limbach, Patrick A.

2010-01-01

Summary An LC-MS method based on the use of high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS) for profiling oligonucleotides synthesis impurities is described. Oligonucleotide phosphorothioatediesters (phosphorothioate oligonucleotides), in which one of the non-bridging oxygen atoms at each phosphorus center is replaced by a sulfur atom, are now one of the most popular oligonucleotide modifications due to their ease of chemical synthesis and advantageous pharmacokinetic properties. Despite significant progress in the solid-phase oligomerization chemistry used in the manufacturing of these oligonucleotides, multiple classes of low-level impurities always accompany synthetic oligonucleotides. Liquid chromatography-mass spectrometry has emerged as a powerful technique for the identification of these synthesis impurities. However, impurity profiling, where the entire complement of low-level synthetic impurities is identified in a single analysis, is more challenging. Here we present an LC-MS method based the use of high resolution-mass spectrometry, specifically Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS or FTMS). The optimal LC-FTMS conditions, including the stationary phase and mobile phases for the separation and identification of phosphorothioate oligonucleotides, were found. The characteristics of FTMS enable charge state determination from single m/z values of low-level impurities. Charge state information then enables more accurate modeling of the detected isotopic distribution for identification of the chemical composition of the detected impurity. Using this approach, a number of phosphorothioate impurities can be detected by LC-FTMS including failure sequences carrying 3′-terminal phosphate monoester and 3′-terminal phosphorothioate monoester, incomplete backbone sulfurization and desulfurization products, high molecular weight impurities, and chloral, isobutyryl, and N3 (2-cyanoethyl) adducts of the full length product. When compared with low resolution LC-MS, ~60% more impurities can be identified when charge state and isotopic distribution information is available and used for impurity profiling. PMID:21811394

A Comparison of DESI-MS and LC-MS for the Lipidomic Profiling of Human Cancer Tissue

NASA Astrophysics Data System (ADS)

Abbassi-Ghadi, Nima; Jones, Emrys A.; Gomez-Romero, Maria; Golf, Ottmar; Kumar, Sacheen; Huang, Juzheng; Kudo, Hiromi; Goldin, Rob D.; Hanna, George B.; Takats, Zoltan

2016-02-01

In this study, we make a direct comparison between desorption electrospray ionization-mass spectrometry (DESI-MS) and ultraperformance liquid chromatography-electrospray ionization-mass spectrometry (UPLC-ESI-MS) platforms for the profiling of glycerophospholipid (GPL) species in esophageal cancer tissue. In particular, we studied the similarities and differences in the range of GPLs detected and the congruency of their relative abundances as detected by each analytical platform. The main differences between mass spectra of the two modalities were found to be associated with the variance in adduct formation of common GPLs, rather than the presence of different GPL species. Phosphatidylcholines as formate adducts in UPLC-ESI-MS accounted for the majority of differences in negative ion mode and alkali metal adducts of phosphatidylcholines in DESI-MS for positive ion mode. Comparison of the relative abundance of GPLs, normalized to a common peak, revealed a correlation coefficient of 0.70 ( P < 0.001). The GPL profile detected by DESI-MS is congruent to UPLC-ESI-MS, which reaffirms the role of DESI-MS for lipidomic profiling and a potential premise for quantification.

Investigation of the aroma of commercial peach (Prunus persica L. Batsch) types by Proton Transfer Reaction-Mass Spectrometry (PTR-MS) and sensory analysis.

PubMed

Bianchi, Tiago; Weesepoel, Yannick; Koot, Alex; Iglesias, Ignasi; Eduardo, Iban; Gratacós-Cubarsí, Marta; Guerrero, Luis; Hortós, Maria; van Ruth, Saskia

2017-09-01

The aim of this study was to investigate the aroma and sensory profiles of various types of peaches (Prunus persica L. Batsch.). Forty-three commercial cultivars comprising peaches, flat peaches, nectarines, and canning peaches (pavías) were grown over two consecutive harvest years. Fruits were assessed for chemical aroma and sensory profiles. Chemical aroma profile was obtained by proton transfer reaction-mass spectrometry (PTR-MS) and spectral masses were tentatively identified with PTR-Time of Flight-MS (PTR-Tof-MS). Sensory analysis was performed at commercial maturity considering seven aroma/flavor attributes. The four types of peaches showed both distinct chemical aroma and sensory profiles. Flat peaches and canning peaches showed most distinct patterns according to discriminant analysis. The sensory data were related to the volatile compounds by partial least square regression. γ-Hexalactone, γ-octalactone, hotrienol, acetic acid and ethyl acetate correlated positively, and benzeneacetaldehyde, trimethylbenzene and acetaldehyde negatively to the intensities of aroma and ripe fruit sensory scores. Copyright © 2017 Elsevier Ltd. All rights reserved.

Detailed polyphenolic profiling of Annurca apple (M. pumila Miller cv Annurca) by a combination of RP-UHPLC and HILIC, both hyphenated to IT-TOF mass spectrometry.

PubMed

Sommella, Eduardo; Pepe, Giacomo; Pagano, Francesco; Ostacolo, Carmine; Tenore, Gian Carlo; Russo, Maria Teresa; Novellino, Ettore; Manfra, Michele; Campiglia, Pietro

2015-10-01

Annurca apple, a Southern Italian cultivar, possesses not only a particular taste and flavor, different from other types of apple, but also several healthy properties. With the aim to thoroughly elucidate the polyphenolic profile of this variety, listed as Protected Geographical Indication product, an extensive qualitative profiling of Annurca apple polyphenolic peel extract was carried out, by employing a combination of ultra high performance reversed phase (RP-UHPLC) and hydrophilic liquid chromatography (HILIC) coupled to ion trap-time of flight (IT-TOF) mass spectrometry. A total of 63 compounds were tentatively identified, 25 of which not reported in Annurca apple extract so far. Furthermore, thanks to the different selectivity obtained with the HILIC, in combination with accurate mass measurements, an improved separation and detection of procyanidins, was obtained. Moreover, the obtained profiles were compared with those of a conventional variety, such as Red Delicious (RD), highlighting their differences. This work contributes to increase the knowledge about the polyphenolic fingerprint of this typical apple variety. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

The distribution of mercury around the small-scale gold mining area along the Cikaniki river, Bogor, Indonesia.

PubMed

Tomiyasu, Takashi; Kono, Yuriko; Kodamatani, Hitoshi; Hidayati, Nuril; Rahajoe, Joeni Setijo

2013-08-01

The distribution of mercury in the soil, sediment and river water around the artisanal small-scale gold mining (ASGM) area along the Cikaniki River, West Java, Indonesia, was investigated. The total mercury concentration (T-Hg) in the forest soil ranged from 0.11 to 7.0mgkg(-1), and the highest value was observed at the ASGM village. In the vertical T-Hg profile around the villages, the highest value was observed at the soil surface, and the concentration decreased with depth. This result suggested that the mercury released by mining activity was dispersed through the atmosphere and deposited on the surface. The total organic carbon content (TOC) showed a similar vertical profile as the T-Hg, and a linear relationship was found between T-Hg and TOC. Mercury deposited on the surface can be absorbed by organic matter. The slope of the line was larger near the ASGM village, implying a higher rate of deposition of mercury. The T-Hg in the sediment ranged from 10 to 70mgkg(-1), decreasing gradually toward the lower reaches of the river. Mining waste can be transported with the river flow and deposited along the river. The distribution of the mining waste can be determined using the mineralogical composition measured by X-ray fluorescence spectrometry. Copyright © 2013 Elsevier Inc. All rights reserved.

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.

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.

Cosmogenic 10Be Depth Profile in top 560 m of West Antarctic Ice Sheet Divide Ice Core

NASA Astrophysics Data System (ADS)

Welten, K. C.; Woodruff, T. E.; Caffee, M. W.; Edwards, R.; McConnell, J. R.; Bisiaux, M. M.; Nishiizumi, K.

2009-12-01

Concentrations of cosmogenic 10Be in polar ice samples are a function of variations in solar activity, geomagnetic field strength, atmospheric mixing and annual snow accumulation rates. The 10Be depth profile in ice cores also provides independent chronological markers to tie Antarctic to Greenland ice cores and to tie Holocene ice cores to the 14C dendrochronology record. We measured 10Be concentrations in 187 samples from depths of 0-560 m of the main WAIS Divide core, WDC06A. The ice samples are typically 1-2 kg and represent 2-4 m of ice, equivalent to an average temporal resolution of ~12 years, based on the preliminary age-depth scale proposed for the WDC core, (McConnell et al., in prep). Be, Al and Cl were separated using ion exchange chromatography techniques and the 10Be concentrations were measured by accelerator mass spectrometry (AMS) at PRIME lab. The 10Be concentrations range from 8.1 to 19.1 x 10^3 at/g, yielding an average of (13.1±2.1) x 10^3 at/g. Adopting an average snow accumulation rate of 20.9 cm weq/yr, as derived from the age-depth scale, this value corresponds to an average 10Be flux of (2.7±0.5) x 10^5 atoms/yr/cm2. This flux is similar to that of the Holocene part of the Siple Dome (Nishiizumi and Finkel, 2007) and Dome Fuji (Horiuchi et al. 2008) ice cores, but ~30% lower than the value of 4.0 x 10^5 atoms/yr/cm2 for GISP2 (Finkel and Nishiizumi, 1997). The periods of low solar activity, known as Oort, Wolf, Spörer, Maunder and Dalton minima, show ~20% higher 10Be concentrations/fluxes than the periods of average solar activity in the last millennium. The maximum 10Be fluxes during some of these periods of low solar activity are up to ~50% higher than average 10Be fluxes, as seen in other polar ice cores, which makes these peaks suitable as chronologic markers. We will compare the 10Be record in the WAIS Divide ice core with that in other Antarctic as well as Greenland ice cores and with the 14C treering record. Acknowledgment. This work was supported by NSF grants ANT-0538427, 0636815, 0636964 and 0739780. Finkel R. C. and Nishiizumi K. 1997. J. Geophys. Res. 102, 26,699-26,706. Horiuchi K., et al. 2008. Quatern. Geochron. 3, 253-261. Nishiizumi K. and Finkel R. C. 2007. Boulder, Colorado USA: National Snow and Ice Data Center. Digital media.

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.

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.

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.

Reducing the Matrix Effect in Organic Cluster SIMS Using Dynamic Reactive Ionization

NASA Astrophysics Data System (ADS)

Tian, Hua; Wucher, Andreas; Winograd, Nicholas

2016-12-01

Dynamic reactive ionization (DRI) utilizes a reactive molecule, HCl, which is doped into an Ar cluster projectile and activated to produce protons at the bombardment site on the cold sample surface with the presence of water. The methodology has been shown to enhance the ionization of protonated molecular ions and to reduce salt suppression in complex biomatrices. In this study, we further examine the possibility of obtaining improved quantitation with DRI during depth profiling of thin films. Using a trehalose film as a model system, we are able to define optimal DRI conditions for depth profiling. Next, the strategy is applied to a multilayer system consisting of the polymer antioxidants Irganox 1098 and 1010. These binary mixtures have demonstrated large matrix effects, making quantitative SIMS measurement not feasible. Systematic comparisons of depth profiling of this multilayer film between directly using GCIB, and under DRI conditions, show that the latter enhances protonated ions for both components by 4- to 15-fold, resulting in uniform depth profiling in positive ion mode and almost no matrix effect in negative ion mode. The methodology offers a new strategy to tackle the matrix effect and should lead to improved quantitative measurement using SIMS.

Impact of comprehensive two-dimensional gas chromatography with mass spectrometry on food analysis.

PubMed

Tranchida, Peter Q; Purcaro, Giorgia; Maimone, Mariarosa; Mondello, Luigi

2016-01-01

Comprehensive two-dimensional gas chromatography with mass spectrometry has been on the separation-science scene for about 15 years. This three-dimensional method has made a great positive impact on various fields of research, and among these that related to food analysis is certainly at the forefront. The present critical review is based on the use of comprehensive two-dimensional gas chromatography with mass spectrometry in the untargeted (general qualitative profiling and fingerprinting) and targeted analysis of food volatiles; attention is focused not only on its potential in such applications, but also on how recent advances in comprehensive two-dimensional gas chromatography with mass spectrometry will potentially be important for food analysis. Additionally, emphasis is devoted to the many instances in which straightforward gas chromatography with mass spectrometry is a sufficiently-powerful analytical tool. Finally, possible future scenarios in the comprehensive two-dimensional gas chromatography with mass spectrometry food analysis field are discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Peat in modern swamps mimics coal origins 300 M years ago

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

Given, P.H.; Ryan, N.J.; Rhoads, C.A.

1985-07-01

Peat swamps can provide excellent models of ancient coal-forming processes. Peats of differing salinity and vegetational cover exhibit different trends of chemistry with depth, which have been studied in order to clarify ideas of coal origins. Thus changes with depth of phenolic structures determined by pyrolysis/gas chromatography/mass spectrometry reflect changes in plant source and partial microbial degradation of lignin, which will be reflected in the structure of coals that may form later. 12 refs., 3 figs.

A new generation of x-ray spectrometry UHV instruments at the SR facilities BESSY II, ELETTRA and SOLEIL

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

Lubeck, J., E-mail: janin.lubeck@ptb.de; Fliegauf, R.; Holfelder, I.

A novel type of ultra-high vacuum instrument for X-ray reflectometry and spectrometry-related techniques for nanoanalytics by means of synchrotron radiation (SR) has been constructed and commissioned at BESSY II. This versa-tile instrument was developed by the PTB, Germany’s national metrology institute, and includes a 9-axis manipulator that allows for an independent alignment of the samples with respect to all degrees of freedom. In addition, it integrates a rotational and translational movement of several photodiodes as well as a translational movement of a beam-geometry-defining aperture system. Thus, the new instrument enables various analytical techniques based on energy dispersive X-ray detectors suchmore » as reference-free X-Ray Fluorescence (XRF) analysis, total-reflection XRF, grazing-incidence XRF, in addition to optional X-Ray Reflectometry (XRR) measurements or polarization-dependent X-ray absorption fine structure analyses (XAFS). Samples having a size of up to (100 × 100) mm{sup 2}; can be analyzed with respect to their mass deposition, elemental, spatial or species composition. Surface contamination, nanolayer composition and thickness, depth pro-file of matrix elements or implants, nanoparticles or buried interfaces as well as molecular orientation of bonds can be accessed. Three technology transfer projects of adapted instruments have enhanced X-Ray Spectrometry (XRS) research activities within Europe at the synchrotron radiation facilities ELETTRA (IAEA) and SOLEIL (CEA/LNE-LNHB) as well as at the X-ray innovation laboratory BLiX (TU Berlin) where different laboratory sources are used. Here, smaller chamber requirements led PTB in cooperation with TU Berlin to develop a modified instrument equipped with a 7-axis manipulator: reduced freedom in the choice of experimental geometry modifications (absence of out-of-SR-plane and reference-free XRS options) has been compensated by encoder-enhanced angular accuracy for GIXRF and XRR.« less

Direct tissue analysis by matrix-assisted laser desorption ionization mass spectrometry: application to kidney biology.

PubMed

Herring, Kristen D; Oppenheimer, Stacey R; Caprioli, Richard M

2007-11-01

Direct tissue analysis using matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) provides in situ molecular analysis of a wide variety of biological molecules including xenobiotics. This technology allows measurement of these species in their native biological environment without the use of target-specific reagents such as antibodies. It can be used to profile discrete cellular regions and obtain region-specific images, providing information on the relative abundance and spatial distribution of proteins, peptides, lipids, and drugs. In this article, we report the sample preparation, MS data acquisition and analysis, and protein identification methodologies used in our laboratory for profiling/imaging MS and how this has been applied to kidney disease and toxicity.

Metabolome analysis for discovering biomarkers of gastroenterological cancer.

PubMed

Suzuki, Makoto; Nishiumi, Shin; Matsubara, Atsuki; Azuma, Takeshi; Yoshida, Masaru

2014-09-01

Improvements in analytical technologies have made it possible to rapidly determine the concentrations of thousands of metabolites in any biological sample, which has resulted in metabolome analysis being applied to various types of research, such as clinical, cell biology, and plant/food science studies. The metabolome represents all of the end products and by-products of the numerous complex metabolic pathways operating in a biological system. Thus, metabolome analysis allows one to survey the global changes in an organism's metabolic profile and gain a holistic understanding of the changes that occur in organisms during various biological processes, e.g., during disease development. In clinical metabolomic studies, there is a strong possibility that differences in the metabolic profiles of human specimens reflect disease-specific states. Recently, metabolome analysis of biofluids, e.g., blood, urine, or saliva, has been increasingly used for biomarker discovery and disease diagnosis. Mass spectrometry-based techniques have been extensively used for metabolome analysis because they exhibit high selectivity and sensitivity during the identification and quantification of metabolites. Here, we describe metabolome analysis using liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and capillary electrophoresis-mass spectrometry. Furthermore, the findings of studies that attempted to discover biomarkers of gastroenterological cancer are also outlined. Finally, we discuss metabolome analysis-based disease diagnosis. Copyright © 2014 Elsevier B.V. All rights reserved.

Insights on the distribution of substitutions in spruce galactoglucomannan and its derivatives using integrated chemo-enzymatic deconstruction, chromatography and mass spectrometry.

PubMed

Liu, Jun; Leppänen, Ann-Sofie; Kisonen, Victor; Willför, Stefan; Xu, Chunlin; Vilaplana, Francisco

2018-06-01

Accurate determination of the distribution of substitutions in the primary molecular structure of heteropolysaccharides and their derivatives is a prerequisite for their increasing application in the pharmaceutical and biomedical fields, which is unfortunately hindered due to the lack of effective analytical techniques. Acetylated galactoglucomannan (GGM) is an abundant plant polysaccharide as the main hemicellulose in softwoods, and therefore constitutes an important renewable resource from lignocellulosic biomass for the development of bioactive and functional materials. Here we present a methodology for profiling the intramolecular structure of spruce GGM and its chemical derivatives (cationic, anionic, and benzoylated) by combining chemo-enzymatic hydrolysis, liquid chromatography, and mass spectrometry. Fast identification and qualitative mass profiling of GGM and its derivatives was conducted using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-MS) and electrospray ionization mass spectrometry (ESI-MS). Tandem mass fragmentation analysis and its hyphenation with hydrophilic interaction liquid chromatography (HILIC-ESI-MS/MS) provide further insights on the substitution placement of the GGM oligosaccharides and its derivatives. This method will be useful in understanding the structure-function relationships of native GGM and their derivatives, and therefore facilitate their potential application. Copyright © 2018 Elsevier B.V. All rights reserved.

Rapid profiling of polymeric phenolic acids in Salvia miltiorrhiza by hybrid data-dependent/targeted multistage mass spectrometry acquisition based on expected compounds prediction and fragment ion searching.

PubMed

Shen, Yao; Feng, Zijin; Yang, Min; Zhou, Zhe; Han, Sumei; Hou, Jinjun; Li, Zhenwei; Wu, Wanying; Guo, De-An

2018-04-01

Phenolic acids are the major water-soluble components in Salvia miltiorrhiza (>5%). According to previous studies, many of them contribute to the cardiovascular effects and antioxidant effects of S. miltiorrhiza. Polymeric phenolic acids can be considered as the tanshinol derived metabolites, e.g., dimmers, trimers, and tetramers. A strategy combined with tanshinol-based expected compounds prediction, total ion chromatogram filtering, fragment ion searching, and parent list-based multistage mass spectrometry acquisition by linear trap quadropole-orbitrap Velos mass spectrometry was proposed to rapid profile polymeric phenolic acids in S. miltiorrhiza. More than 480 potential polymeric phenolic acids could be screened out by this strategy. Based on the fragment information obtained by parent list-activated data dependent multistage mass spectrometry acquisition, 190 polymeric phenolic acids were characterized by comparing their mass information with literature data, and 18 of them were firstly detected from S. miltiorrhiza. Seven potential compounds were tentatively characterized as new polymeric phenolic acids from S. miltiorrhiza. This strategy facilitates identification of polymeric phenolic acids in complex matrix with both selectivity and sensitivity, which could be expanded for rapid discovery and identification of compounds from complex matrix. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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.

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.

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.

Resolving global versus local/regional Pu sources in the environment using sector ICP-MS

USGS Publications Warehouse

Ketterer, M.E.; Hafer, K.M.; Link, C.L.; Kolwaite, D.; Wilson, Jim; Mietelski, J.W.

2004-01-01

Sector inductively coupled plasma mass spectrometry is a versatile method for the determination of plutonium activities and isotopic compositions in samples containing this element at fallout levels. Typical detection limits for 239+240Pu are 0.1, 0.02 and 0.002 Bq kg -1Pu for samples sizes of 0.5 g, 3 g, and 50 g of soil, respectively. The application of sector ICP-MS-based Pu determinations is demonstrated in studies in sediment chronology, soil Pu inventory and depth distribution, and the provenance of global fallout versus local or regional Pu sources. A sediment core collected from Sloans Lake (Denver, Colorado, USA) exhibits very similar 137Cs and 239+240Pu activity profiles; 240Pu/239Pu atom ratios indicate possible small influences from the Nevada Test Site and/or the Rocky Flats Environmental Technology Site. An undisturbed soil profile from Lockett Meadow (Flagstaff, Arizona, USA) exhibits an exponential decrease in 239+240Pu activity versus depth; 240Pu/239Pu in the top 3 cm is slightly lower than the global fallout range of 0.180 ?? 0.014 due to possible regional influence of Nevada Test Site fallout. The 239??240Pu inventory at Lockett Meadow is 56 ?? 4 Bq m-2, consistent with Northern Hemisphere mid-latitude fallout. Archived NdF3 sources, prepared from Polish soils, demonstrate that substantial 239+240Pu from the 1986 Chernobyl disaster has been deposited in north eastern regions of Poland; compared to global fallout, Chernobyl Pu exhibits higher abundances of 240Pu and 241Pu. The ratios 240Pu/239pu and 241Pu/239Pu co-vary and range from 0.186-0.348 and 0.0029-0.0412, respectively, in forest soils (241Pu/239Pu = 0.2407??[240Pu/239Pu] - 0.0413; r2 = 0.9924). ?? The Royal Society of Chemistry 2004.

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.

The potential of on-line continuous leach ICP-MS analysis for linking trace elements to mineralogy

NASA Astrophysics Data System (ADS)

Roskam, Gerlinde; Verheul, Marc; Moraetis, Daniel; Giannakis, George; van Gaans, Pauline

2014-05-01

A set of five soil samples was subjected to an on-line continuous leach inductively coupled plasma mass spectrometry experiment, with progressively reactive solvents (0.01M CaCl2, 0.1 M HNO3, 1M HNO3, 4M HNO3) Each sample was packed in a quartz tube (Ø= 1 cm, length 2 cm) and diluted 1:1 with acid washed quartz to prevent clogging. The gas that was produced during the extraction was removed by leading the effluent into a small container, from where the sample was directly pumped into the ICP-MS. 115In was used as an internal standard. Continuous leach experiments have the advantage of real time (every 2 seconds) full elemental analysis. Mineral breakdown reactions can be monitored via the major elements. The trace elements associated with the minerals are monitored simultaneously, thus eliminating the uncertainties of host mineral-trace element combinations in traditional off-line sequential extractions. The continuous leach experimental data are correlated to XRD-results for mineralogy and total elemental concentrations. The soil samples used were collected from different sites in the Koiliaris River watershed, Crete, Greece 1). The selection of the sites was based on variability in bedrock (limestone, metamorphic and alluvial sediments) and current land use (grape farming, olive trees). Soils were sampled at two depths: at the surface and just above the bedrock. No large differences in the major elements between the two depths were measured. To provide background to the on-line sequential data, also total concentrations of the major elements were analysed by XRF and the mineralogy was analysed by XRD. The fraction <2mm was sieved and digested with HF, HClO4 and HNO3 for additional trace element analysis. 1) See related abstract Roskam et al., 2014: REE profiles in continuous leach ICP-MS (CL-ICP-MS) experiments in soil, linked to REE profiles in surface water in the Koiliaris River Critical Zone Observatory (CZO), Crete, Greece.

SALI chemical analysis of provided samples

NASA Technical Reports Server (NTRS)

Becker, Christopher H.

1993-01-01

SRI has completed the chemical analysis of all the samples supplied by NASA. The final batch of four samples consisted of: one inch diameter MgF2 mirror, control 1200-ID-FL3; one inch diameter neat resin, PMR-15, AO171-IV-55, half exposed and half unexposed; one inch diameter chromic acid anodized, EOIM-3 120-47 aluminum disc; and AO-exposed and unexposed samples of fullerene extract material in powdered form, pressed into In foil for analysis. Chemical analyses of the surfaces were performed by the surface analysis by laser ionization (SALI) method. The analyses emphasize surface contamination or general organic composition. SALI uses nonselective photoionization of sputtered or desorbed atoms and molecules above but close (approximately one mm) to the surface, followed by time-of-flight (TOF) mass spectrometry. In these studies, we used laser-induced desorption by 5-ns pulse-width 355-nm light (10-100 mJ/sq cm) and single-photon ionization (SPI) by coherent 118-nm radiation (at approximately 5 x 10(exp 5) W/sq cm). SPI was chosen primarily for its ability to obtain molecular information, whereas multiphoton ionization (not used in the present studies) is intended primarily for elemental and small molecule information. In addition to these four samples, the Au mirror (EOIM-3 200-11, sample four) was depth profiled again. Argon ion sputtering was used together with photoionization with intense 355-nm radiation (35-ps pulsewidths). Depth profiles are similar to those reported earlier, showing reproducibility. No chromium was found in the sample above noise level; its presence could at most be at the trace level. Somewhat more Ni appears to be present in the Au layer in the unexposed side, indicating thermal diffusion without chemical enhancement. The result of the presence of oxygen is apparently to tie-up/draw out the Ni as an oxide at the surface. The exposed region has a brownish tint appearance to the naked eye.

Serum amyloid beta peptides in patients with dementia and age-matched non-demented controls as detected by surface-enhanced laser desorption ionisation-time of flight mass spectrometry (SELDI-TOF MS).

PubMed

Frankfort, Suzanne V; van Campen, Jos P C M; Tulner, Linda R; Beijnen, Jos H

2008-09-01

By using surface enhanced laser desorption/ionisation- time of flight mass spectrometry (SELDI-TOF MS) an amyloid beta (Abeta) profile was shown in cerebrospinal fluid (CSF) of patients with dementia. To investigate the Abeta-profile in serum with SELDI-TOF MS, to evaluate if this profile resembles CSF profiles and to investigate the correlation between intensity of Abeta-peptide-peaks in serum and clinical, demographical and genetic variables. Duplicate profiling of Abeta by an SELDI-TOF MS immunocapture assay was performed in 106 patients, suffering from Alzheimer's Disease or Vascular Dementia and age-matched non-demented control patients. Linear regression analyses were performed to investigate the intensities of four selected Abeta peaks as dependent variables in relation to the independent clinical, demographic or genetic variables. Abeta37, Abeta38 and Abeta40 were found among additional unidentified Abeta peptides, with the most pronounced Abeta peak at a molecular mass of 7752. This profile partly resembled the CSF profile. The clinical diagnosis was not a predictive independent variable, however ABCB1 genotypes C1236T, G2677T/A, age and creatinine level showed to be related to Abeta peak intensities in multivariate analyses. We found an Abeta profile in serum that partly resembled the CSF profile in demented patients. Age, creatinine levels, presence of the APOE epsilon4 allele and ABCB1 genotypes (C1236T and G2677T/A) were correlated with the Abeta serum profile. The role of P-gp as an Abeta transporter and the role of ABCB1 genotypes deserves further research. The investigated serum Abeta profile is probably not useful in the diagnosis of dementia.

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.

Imaging mass spectrometry statistical analysis.

PubMed

Jones, Emrys A; Deininger, Sören-Oliver; Hogendoorn, Pancras C W; Deelder, André M; McDonnell, Liam A

2012-08-30

Imaging mass spectrometry is increasingly used to identify new candidate biomarkers. This clinical application of imaging mass spectrometry is highly multidisciplinary: expertise in mass spectrometry is necessary to acquire high quality data, histology is required to accurately label the origin of each pixel's mass spectrum, disease biology is necessary to understand the potential meaning of the imaging mass spectrometry results, and statistics to assess the confidence of any findings. Imaging mass spectrometry data analysis is further complicated because of the unique nature of the data (within the mass spectrometry field); several of the assumptions implicit in the analysis of LC-MS/profiling datasets are not applicable to imaging. The very large size of imaging datasets and the reporting of many data analysis routines, combined with inadequate training and accessible reviews, have exacerbated this problem. In this paper we provide an accessible review of the nature of imaging data and the different strategies by which the data may be analyzed. Particular attention is paid to the assumptions of the data analysis routines to ensure that the reader is apprised of their correct usage in imaging mass spectrometry research. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

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.

Analytical aspects of plant metabolite profiling platforms: current standings and future aims.

PubMed

Seger, Christoph; Sturm, Sonja

2007-02-01

Over the past years, metabolic profiling has been established as a comprehensive systems biology tool. Mass spectrometry or NMR spectroscopy-based technology platforms combined with unsupervised or supervised multivariate statistical methodologies allow a deep insight into the complex metabolite patterns of plant-derived samples. Within this review, we provide a thorough introduction to the analytical hard- and software requirements of metabolic profiling platforms. Methodological limitations are addressed, and the metabolic profiling workflow is exemplified by summarizing recent applications ranging from model systems to more applied topics.

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.

Metabolic profiling of Hoodia, Chamomile, Terminalia Species and evaluation of commercial preparations using Ultra-High Performance Quadrupole Time of Flight-Mass Spectrometry

USDA-ARS?s Scientific Manuscript database

Ultra-High Performance-Quadrupole Time of Flight Mass Spectrometr(UHPLC-QToF-MS)profiling has become an impattant tool for identification of marker compounds and generation of metabolic patterns that could be interrogated using chemometric modeling software. Chemometric approaches can be used to ana...

Software tool for mining liquid chromatography/multi-stage mass spectrometry data for comprehensive glycerophospholipid profiling.

PubMed

Hein, Eva-Maria; Bödeker, Bertram; Nolte, Jürgen; Hayen, Heiko

2010-07-30

Electrospray ionization mass spectrometry (ESI-MS) has emerged as an indispensable tool in the field of lipidomics. Despite the growing interest in lipid analysis, there are only a few software tools available for data evaluation, as compared for example to proteomics applications. This makes comprehensive lipid analysis a complex challenge. Thus, a computational tool for harnessing the raw data from liquid chromatography/mass spectrometry (LC/MS) experiments was developed in this study and is available from the authors on request. The Profiler-Merger-Viewer tool is a software package for automatic processing of raw-data from data-dependent experiments, measured by high-performance liquid chromatography hyphenated to electrospray ionization hybrid linear ion trap Fourier transform mass spectrometry (FTICR-MS and Orbitrap) in single and multi-stage mode. The software contains three parts: processing of the raw data by Profiler for lipid identification, summarizing of replicate measurements by Merger and visualization of all relevant data (chromatograms as well as mass spectra) for validation of the results by Viewer. The tool is easily accessible, since it is implemented in Java and uses Microsoft Excel (XLS) as output format. The motivation was to develop a tool which supports and accelerates the manual data evaluation (identification and relative quantification) significantly but does not make a complete data analysis within a black-box system. The software's mode of operation, usage and options will be demonstrated on the basis of a lipid extract of baker's yeast (S. cerevisiae). In this study, we focused on three important representatives of lipids: glycerophospholipids, lyso-glycerophospholipids and free fatty acids. Copyright 2010 John Wiley & Sons, Ltd.

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…

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.

Study of shallow junction formation by boron-containing cluster ion implantation of silicon and two-stage annealing

NASA Astrophysics Data System (ADS)

Lu, Xin-Ming

Shallow junction formation made by low energy ion implantation and rapid thermal annealing is facing a major challenge for ULSI (ultra large scale integration) as the line width decreases down to the sub micrometer region. The issues include low beam current, the channeling effect in low energy ion implantation and TED (transient enhanced diffusion) during annealing after ion implantation. In this work, boron containing small cluster ions, such as GeB, SiB and SiB2, was generated by using the SNICS (source of negative ion by cesium sputtering) ion source to implant into Si substrates to form shallow junctions. The use of boron containing cluster ions effectively reduces the boron energy while keeping the energy of the cluster ion beam at a high level. At the same time, it reduces the channeling effect due to amorphization by co-implanted heavy atoms like Ge and Si. Cluster ions have been used to produce 0.65--2keV boron for low energy ion implantation. Two stage annealing, which is a combination of low temperature (550°C) preannealing and high temperature annealing (1000°C), was carried out to anneal the Si sample implanted by GeB, SiBn clusters. The key concept of two-step annealing, that is, the separation of crystal regrowth, point defects removal with dopant activation from dopant diffusion, is discussed in detail. The advantages of the two stage annealing include better lattice structure, better dopant activation and retarded boron diffusion. The junction depth of the two stage annealed GeB sample was only half that of the one-step annealed sample, indicating that TED was suppressed by two stage annealing. Junction depths as small as 30 nm have been achieved by two stage annealing of sample implanted with 5 x 10-4/cm2 of 5 keV GeB at 1000°C for 1 second. The samples were evaluated by SIMS (secondary ion mass spectrometry) profiling, TEM (transmission electron microscopy) and RBS (Rutherford Backscattering Spectrometry)/channeling. Cluster ion implantation in combination with two-step annealing is effective in fabricating ultra-shallow junctions.

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.

Saliva analysis by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) in orthodontic treatment: first pilot study.

PubMed

Ciavarella, Domenico; Mastrovincenzo, Mario; D'Onofrio, Valentina; Chimenti, Claudio; Parziale, Vincenzo; Barbato, Ersilia; Lo Muzio, Lorenzo

2011-11-01

SELDI-TOF-MS (Surface-Enhanced Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry) allows the generation of an accurate protein profile from minimal amounts of biological samples and may executes proteomic profile of saliva. The aim of this work is to compare the proteomic profile of saliva of patients in orthodontic treatment to the beginning of treatment and after three months by using the surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) technology. Saliva was collected from 14 patients, between the 11 and 17 years, to the beginning of the orthodontic treatment and after three months. Specimens were centrifuged (10 min, 13000 x g); the Q10 ProteinChips were prepared according to the manufacturer's instructions and were loaded with the supernatants. A saturated solution of sinapinic acid was used as energy-absorbing matrix. The analysis was performed in a m/z range from 2500 to 25000 Da, and the proteomic profiles were compared by a specific data analysis software. Saliva (5 mL) was collected by spitting directly into a clean 15 mL conical tube. The samples were then aliquotted and stored at -80°C until use. Profile of saliva of patients before orthodontic treatment present a number of peaks different respect profile of saliva after three months of treatment. The average intensities of peaks at m/z 3372, 5232, 4045 and 10128 were significantly higher after three months then at beginning of treatment in the same patients and among these one. The Roc Plot has demonstrated high sensitivity and specificity. Many differences were noted in salivary proteomic profile obtained using the SELDI-TOF-MS technology in patients in orthodontic treatment to beginning and after three months. These data suggest that the proteomic analysis of saliva is a promising new tool for a non-invasive study of oral mucosa and bone changes. Copyright © 2011 Società Italiana di Ortodonzia SIDO. Published by Elsevier Srl. All rights reserved.

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.

Surface structure of imidazolium-based ionic liquids: Quantitative comparison between simulations and high-resolution RBS measurements.

PubMed

Nakajima, Kaoru; Nakanishi, Shunto; Lísal, Martin; Kimura, Kenji

2016-03-21

Elemental depth profiles of 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([CnMIM][TFSI], n = 4, 6, 8) are measured using high-resolution Rutherford backscattering spectroscopy (HRBS). The profiles are compared with the results of molecular dynamics (MD) simulations. Both MD simulations and HRBS measurements show that the depth profiles deviate from the uniform stoichiometric composition in the surface region, showing preferential orientations of ions at the surface. The MD simulations qualitatively reproduce the observed HRBS profiles but the agreement is not satisfactory. The observed discrepancy is ascribed to the capillary waves. By taking account of the surface roughness induced by the capillary waves, the agreement becomes almost perfect.

Surface structure of imidazolium-based ionic liquids: Quantitative comparison between simulations and high-resolution RBS measurements

NASA Astrophysics Data System (ADS)

Nakajima, Kaoru; Nakanishi, Shunto; Lísal, Martin; Kimura, Kenji

2016-03-01

Elemental depth profiles of 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([CnMIM][TFSI], n = 4, 6, 8) are measured using high-resolution Rutherford backscattering spectroscopy (HRBS). The profiles are compared with the results of molecular dynamics (MD) simulations. Both MD simulations and HRBS measurements show that the depth profiles deviate from the uniform stoichiometric composition in the surface region, showing preferential orientations of ions at the surface. The MD simulations qualitatively reproduce the observed HRBS profiles but the agreement is not satisfactory. The observed discrepancy is ascribed to the capillary waves. By taking account of the surface roughness induced by the capillary waves, the agreement becomes almost perfect.

Metabolite profiling of soy sauce using gas chromatography with time-of-flight mass spectrometry and analysis of correlation with quantitative descriptive analysis.

PubMed

Yamamoto, Shinya; Bamba, Takeshi; Sano, Atsushi; Kodama, Yukako; Imamura, Miho; Obata, Akio; Fukusaki, Eiichiro

2012-08-01

Soy sauces, produced from different ingredients and brewing processes, have variations in components and quality. Therefore, it is extremely important to comprehend the relationship between components and the sensory attributes of soy sauces. The current study sought to perform metabolite profiling in order to devise a method of assessing the attributes of soy sauces. Quantitative descriptive analysis (QDA) data for 24 soy sauce samples were obtained from well selected sensory panelists. Metabolite profiles primarily concerning low-molecular-weight hydrophilic components were based on gas chromatography with time-of-flightmass spectrometry (GC/TOFMS). QDA data for soy sauces were accurately predicted by projection to latent structure (PLS), with metabolite profiles serving as explanatory variables and QDA data set serving as a response variable. Moreover, analysis of correlation between matrices of metabolite profiles and QDA data indicated contributing compounds that were highly correlated with QDA data. Especially, it was indicated that sugars are important components of the tastes of soy sauces. This new approach which combines metabolite profiling with QDA is applicable to analysis of sensory attributes of food as a result of the complex interaction between its components. This approach is effective to search important compounds that contribute to the attributes. Copyright © 2012 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Profiling metals in Cordyceps sinensis by using inductively coupled plasma mass spectrometry.

PubMed

Wei, Xin; Hu, Hankun; Zheng, Baogeng; Arslan, Zikri; Huang, Hung-Chung; Mao, Weidong; Liu, Yi-Ming

2017-01-28

Cordyceps sinensis ( C. sinensis ) is a natural product that has diverse nutritional and medicinal values. Since the availability of natural C. sinensis becomes limited its authentication and quality control is of high significance. Herein we report on profiling of metals in C. sinensis by using inductively coupled plasma mass spectrometry (ICP-MS). The analysis reveals that C. sinensis contains a wide array of essential elements, including P, Mg, Zn, Cu, Fe, etc. Toxic metals detected are Cd, Pb, and As. In all five samples analyzed Pb contents are below 2.0 ppm. Arsenic level in C. sinensis caterpillar is significantly higher than that in its mycelium and varies from 3.0 to 32 ppm likely due to soil contamination. It's for the first time demonstrated in this work that clustering analysis on the proposed metal profiles consisting of 24 elements is very useful to identify "abnormal" C. sinensis samples, thus adding another dimension to the effective means for authentication and quality assessment of this highly demanded previous natural product.

Glycan profiling of monoclonal antibodies using zwitterionic-type hydrophilic interaction chromatography coupled with electrospray ionization mass spectrometry detection.

PubMed

Mauko, Lea; Nordborg, Anna; Hutchinson, Joseph P; Lacher, Nathan A; Hilder, Emily F; Haddad, Paul R

2011-01-15

We present a new method for the analysis of glycans enzymatically released from monoclonal antibodies (MAbs) employing a zwitterionic-type hydrophilic interaction chromatography (ZIC-HILIC) column coupled with electrospray ionization mass spectrometry (ESI-MS). Both native and reduced glycans were analyzed, and the developed procedure was compared with a standard HILIC procedure used in the pharmaceutical industry whereby fluorescent-labeled glycans are analyzed using a TSK Amide-80 column coupled with fluorescence detection. The separation of isobaric alditol oligosaccharides present in monoclonal antibodies and ribonuclease B is demonstrated, and ZIC-HILIC is shown to have good capability for structural recognition. Glycan profiles obtained with the ZIC-HILIC column and ESI-MS provided detailed information on MAb glycosylation, including identification of some less abundant glycan species, and are consistent with the profiles generated with the standard procedure. This new ZIC-HILIC method offers a simpler and faster approach for glycosylation analysis of therapeutic antibodies. Copyright © 2010 Elsevier Inc. All rights reserved.

Lipidomics profiling of goat milk, soymilk and bovine milk by UPLC-Q-Exactive Orbitrap Mass Spectrometry.

PubMed

Li, Qiangqiang; Zhao, Yan; Zhu, Dan; Pang, Xiumei; Liu, Yue; Frew, Russell; Chen, Gang

2017-06-01

Lipids are very important for human health and milk is a rich dietary source of lipids. In this study, the lipid content in three types of milk (goat, soy and bovine) were determined by using UPLC-Q-Exactive Orbitrap Mass Spectrometry. A total of 13 classes of lipids (including Cer, SM, LPC, PC, PE, DG, TG, PA, PG, PI, PS, LPE, FA) were measured. Moreover, lipid profiles differed significantly between the different milk types. Soymilk is rich in phospholipids including PC, PE, PS, PG, while goat milk is rich in medium chain triglycerides (MCT), USFA, ω-6 FA and ω-3 FA, especially EPA and DHA. Furthermore, a PLS model was established for differentiation of milk types based on the lipid profiles. A total of 14 lipids were identified as biomarkers for differentiation of milk types, thus providing a basis for milk authentication and detection of adulteration. Copyright © 2016 Elsevier Ltd. All rights reserved.

18O-tracer diffusion along nanoscaled Sc2O3/yttria stabilized zirconia (YSZ) multilayers: on the influence of strain.

PubMed

Aydin, Halit; Korte, Carsten; Janek, Jürgen

2013-06-01

The oxygen tracer diffusion coefficient describing transport along nano-/microscaled YSZ/Sc 2 O 3 multilayers as a function of the thick-ness of the ion-conducting YSZ layers has been measured by isotope exchange depth profiling (IEDP), using secondary ion mass spec-trometry (SIMS). The multilayer samples were prepared by pulsed laser deposition (PLD) on (0001) Al 2 O 3 single crystalline substrates. The values for the oxygen tracer diffusion coefficient were analyzed as a combination of contributions from bulk and interface contributions and compared with results from YSZ/Y 2 O 3 -multilayers with similar microstructure. Using the Nernst-Einstein equation as the relation between diffusivity and electrical conductivity we find very good agreement between conductivity and diffusion data, and we exclude substantial electronic conductivity in the multilayers. The effect of hetero-interface transport can be well explained by a simple interface strain model. As the multilayer samples consist of columnar film crystallites with a defined inter-face structure and texture, we also discuss the influence of this particular microstructure on the interfacial strain.

Comparison of monomode KTiOPO4 waveguide formed by C3+ ion implantation and Rb+ ion exchange

NASA Astrophysics Data System (ADS)

Cui, Xiao-Jun; Wang, Liang-Ling

2017-02-01

In this work, we report on the formation and characterization of monomode KTiOPO4 waveguide at 1539 nm by 6.0 MeV C3+ ion implantation with the dose of 2×1015 ions/cm2 and Rb+-K+ ion exchange, respectively. The relative intensity of light as a function of effective refractive index of TM modes at 633 nm and 1539 nm for KTiOPO4 waveguide formed by two different methods were compared with the prism coupling technique. The refractive index (nz) profile for the ion implanted waveguide was reconstructed by reflectivity calculation method, and one for the ion exchanged waveguide was by inverse Wentzel-Kramers-Brillouin. The nuclear energy loss versus penetration depth of the C3+ ions implantation into KTiOPO4 was simulated using the Stopping Range of Ions in Matter software. The Rutherford Backscattering Spectrometry spectrum of KTiOPO4 waveguide was analyzed after ions exchanged. The results showed that monomode waveguide at 1539 nm can be formed by ion implantation and Rb+ -K+ ion exchange, respectively.

Abundance, size and polymer composition of marine microplastics ≥10μm in the Atlantic Ocean and their modelled vertical distribution.

PubMed

Enders, Kristina; Lenz, Robin; Stedmon, Colin A; Nielsen, Torkel G

2015-11-15

We studied abundance, size and polymer type of microplastic down to 10μm along a transect from the European Coast to the North Atlantic Subtropical Gyre (NASG) using an underway intake filtration technique and Raman micro-spectrometry. Concentrations ranged from 13 to 501itemsm(-3). Highest concentrations were observed at the European coast, decreasing towards mid-Atlantic waters but elevated in the western NASG. We observed highest numbers among particles in the 10-20μm size fraction, whereas the total volume was highest in the 50-80μm range. Based on a numerical model size-dependent depth profiles of polyethylene microspheres in a range from 10-1000μm were calculated and show a strong dispersal throughout the surface mixed layer for sizes smaller than 200μm. From model and field study results we conclude that small microplastic is ubiquitously distributed over the ocean surface layer and has a lower residence time than larger plastic debris in this compartment. Copyright © 2015 Elsevier Ltd. All rights reserved.

ERDA at the 9 MV Tandem and at the 3 MV Tandetron of IFIN-HH

NASA Astrophysics Data System (ADS)

Petrascu, H.; Petrascu, M.; Pantelica, D.; Negoita, F.; Ionescu, P.; Mihai, M. D.; Acsente, T.; Statescu, M.; Scafes, A. C.

2017-09-01

Recoil spectrometry using heavy ions proposed in 1976 by L'Ecuyer has evolved into a universal IBA technique. Few years later an experimental setup for simultaneous light and medium heavy element detection including a compact ΔE(gas)-Er(solid) telescope, was developed at the Tandem accelerator of IFIN-HH. To increase the resolution, an integrated preamplifier was mounted close to the ionization chamber. The calibration procedure for the telescope and the software for the quantitative evaluation of the data are briefly presented. Recently, a 3 MV Tandetron accelerator has been installed and commissioned at the IFIN-HH. Among several ion-beam techniques for detection and depth profiling of hydrogen isotopes, Elastic Recoil Detection Analysis (ERDA) technique using a low energy 4He beam, proposed by Doyle and Peercy, is particularly advantageous. By measuring simultaneously both the H or D recoiling at a forward angle and backscattered 4He ions, a rather complete characterization of the sample can be achieved. Selected results from our investigations, obtained using these facilities, are presented.

Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression.

PubMed

Borirak, Orawan; Rolfe, Matthew D; de Koning, Leo J; Hoefsloot, Huub C J; Bekker, Martijn; Dekker, Henk L; Roseboom, Winfried; Green, Jeffrey; de Koster, Chris G; Hellingwerf, Klaas J

2015-10-01

Time-series transcript- and protein-profiles were measured upon initiation of carbon catabolite repression in Escherichia coli, in order to investigate the extent of post-transcriptional control in this prototypical response. A glucose-limited chemostat culture was used as the CCR-free reference condition. Stopping the pump and simultaneously adding a pulse of glucose, that saturated the cells for at least 1h, was used to initiate the glucose response. Samples were collected and subjected to quantitative time-series analysis of both the transcriptome (using microarray analysis) and the proteome (through a combination of 15N-metabolic labeling and mass spectrometry). Changes in the transcriptome and corresponding proteome were analyzed using statistical procedures designed specifically for time-series data. By comparison of the two sets of data, a total of 96 genes were identified that are post-transcriptionally regulated. This gene list provides candidates for future in-depth investigation of the molecular mechanisms involved in post-transcriptional regulation during carbon catabolite repression in E. coli, like the involvement of small RNAs. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

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

Varley, J. B.; Conway, A. M.; Voss, L. F.

Thallium bromide (TlBr) crystals subjected to hydrochloric acid (HCl) chemical treatments have been shown to advantageously affect device performance and longevity in TlBr-based room temperature radiation detectors, yet the exact mechanisms of the improvements remain poorly understood. Here in this paper, we investigate the influence of several HCl chemical treatments on device-grade TlBr and describe the changes in the composition and electronic structure of the surface. Composition analysis and depth profiles obtained from secondary ion mass spectrometry (SIMS) identify the extent to which each HCl etch condition affects the detector surface region and forms of a graded TlBr/TlBr 1-xCL xmore » surface heterojunction. Using a combination of X-ray photoemission spectroscopy (XPS) and hybrid density functional calculations, we are able to determine the valence band offsets, band gaps, and conduction band offsets as a function of Cl content over the entire composition range of TIBr 1-xC1 X. This study establishes a strong correlation between device process conditions, surface chemistry, and electronic structure with the goal of further optimizing the long-term stability and radiation response of TlBr-based detectors.« less

Electronic and Interfacial Properties of PD/6H-SiC Schottky Diode Gas Sensors

NASA Technical Reports Server (NTRS)

Chen, Liang-Yu; Hunter, Gary W.; Neudeck, Philip G.; Bansal, Gaurav; Petit, Jeremy B.; Knight, Dak; Liu, Chung-Chiun; Wu, Qinghai

1996-01-01

Pd/SiC Schottky diodes detect hydrogen and hydrocarbons with high sensitivity. Variation of the diode temperature from 100 C to 200 C shows that the diode sensitivity to propylene is temperature dependent. Long-term heat treating at 425 C up to 140 hours is carried out to determine the effect of extended heat treating on the diode properties and gas sensitivity. The heat treating significantly affects the diode's capacitive characteristics, but the diode's current carrying characteristics are much more stable with a large response to hydrogen. Scanning Electron Microscopy and X-ray Spectrometry studies of the Pd surface after the heating show cluster formation and background regions with grain structure observed in both regions. The Pd and Si concentrations vary between grains. Auger Electron Spectroscopy depth profiles revealed that the heat treating promoted interdiffusion and reaction between the Pd and SiC dw broadened the interface region. This work shows that Pd/SiC Schottky diodes have significant potential as high temperature gas sensors, but stabilization of the structure is necessary to insure their repeatability in long-term, high temperature applications.

Metabolic profiling of body fluids and multivariate data analysis.

PubMed

Trezzi, Jean-Pierre; Jäger, Christian; Galozzi, Sara; Barkovits, Katalin; Marcus, Katrin; Mollenhauer, Brit; Hiller, Karsten

2017-01-01

Metabolome analyses of body fluids are challenging due pre-analytical variations, such as pre-processing delay and temperature, and constant dynamical changes of biochemical processes within the samples. Therefore, proper sample handling starting from the time of collection up to the analysis is crucial to obtain high quality samples and reproducible results. A metabolomics analysis is divided into 4 main steps: 1) Sample collection, 2) Metabolite extraction, 3) Data acquisition and 4) Data analysis. Here, we describe a protocol for gas chromatography coupled to mass spectrometry (GC-MS) based metabolic analysis for biological matrices, especially body fluids. This protocol can be applied on blood serum/plasma, saliva and cerebrospinal fluid (CSF) samples of humans and other vertebrates. It covers sample collection, sample pre-processing, metabolite extraction, GC-MS measurement and guidelines for the subsequent data analysis. Advantages of this protocol include: •Robust and reproducible metabolomics results, taking into account pre-analytical variations that may occur during the sampling process•Small sample volume required•Rapid and cost-effective processing of biological samples•Logistic regression based determination of biomarker signatures for in-depth data analysis.

Diffusive gradients in thin films measurement of sulfur stable isotope variations in labile soil sulfate.

PubMed

Hanousek, Ondrej; Santner, Jakob; Mason, Sean; Berger, Torsten W; Wenzel, Walter W; Prohaska, Thomas

2016-11-01

A diffusive gradient in thin films (DGT) technique, based on a strongly basic anion exchange resin (Amberlite IRA-400), was successfully tested for 34 S/ 32 S analysis in labile soil sulfate. Separation of matrix elements (Na, K, and Ca) that potentially cause non-spectral interferences in 34 S/ 32 S analysis by MC ICP-MS (multi-collector inductively coupled plasma-mass spectrometry) during sampling of sulfate was demonstrated. No isotopic fractionation caused by diffusion or elution of sulfate was observed below a resin gel disc loading of ≤79 μg S. Above this threshold, fractionation towards 34 S was observed. The method was applied to 11 different topsoils and one mineral soil profile (0-100 cm depth) and compared with soil sulfate extraction by water. The S amount and isotopic ratio in DGT-S and water-extractable sulfate correlated significantly (r 2  = 0.89 and r 2  = 0.74 for the 11 topsoils, respectively). The systematically lower 34 S/ 32 S isotope ratios of the DGT-S were ascribed to mineralization of organic S.

Reactivity and biological properties of a series of cytotoxic PtI2(amine)2 complexes, either cis or trans configured.

PubMed

Messori, Luigi; Cubo, Leticia; Gabbiani, Chiara; Álvarez-Valdés, Amparo; Michelucci, Elena; Pieraccini, Giuseppe; Ríos-Luci, Carla; León, Leticia G; Padrón, José M; Navarro-Ranninger, Carmen; Casini, Angela; Quiroga, Adoración G

2012-02-06

Six diiodido-diamine platinum(II) complexes, either cis or trans configured, were prepared, differing only in the nature of the amine ligand (isopropylamine, dimethylamine, or methylamine), and their antiproliferative properties were evaluated against a panel of human tumor cell lines. Both series of complexes manifested pronounced cytotoxic effects, with the trans isomers being, generally, more effective than their cis counterparts. Cell cycle analysis revealed different modes of action for these new Pt(II) complexes with respect to cisplatin. The reactivity of these platinum compounds with a number of biomolecules, including cytochrome c, two sulfur containing modified amino acids, 9-ethylguanine, and a single strand oligonucleotide, was analyzed in depth by mass spectrometry and NMR spectroscopy. Interestingly, significant differences in the reactivity of the investigated compounds toward the various model biomolecules were observed: in particular we observed that trans complexes preferentially release their iodide ligands upon biomolecule binding, while the cis isomers may release the amine ligands with retention of iodides. Such differences in reactivity may have important mechanistic implications and a relevant impact on the respective pharmacological profiles.

High-mass heterogeneous cluster formation by ion bombardment of the ternary alloy Au 7Cu 5Al 4

DOE PAGES

Zinovev, Alexander V.; King, Bruce V.; Veryovkin, Igor V.; ...

2016-02-04

The ternary alloy Au 7Cu 5Al 4 was irradiated with 0.1–10 keV Ar + and the surface composition analyzed using laser sputter neutral mass spectrometry. Ejected clusters containing up to seven atoms, with masses up to 2000 amu, were observed. By monitoring the signals from sputtered clusters, the surface composition of the alloy was seen to change with 100 eV Ar + dose, reaching equilibrium after 10 nm of the surface was eroded, in agreement with TRIDYN simulation and indicating that the changes were due to preferential sputtering of Al and Cu. Ejected gold containing clusters were found to increasemore » markedly in intensity while aluminum containing clusters decreased in intensity as a result of Ar sputtering. Such an effect was most pronounced for low energy (<1 keV) Ar + sputtering and was consistent with TRIDYN simulations of the depth profiling. As a result, the component sputter yields from the ternary alloy were consistent with previous binary alloy measurements but showed greater Cu surface concentrations than expected from TRIDYN simulations.« less

Comparative study of the native oxide on 316L stainless steel by XPS and ToF-SIMS

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

Tardio, Sabrina, E-mail: s.tardio@surrey.ac.uk; Abel, Marie-Laure; Castle, James E.

2015-09-15

The very thin native oxide film on stainless steel, of the order of 2 nm, is known to be readily modified by immersion in aqueous media. In this paper, X-ray photoelectron spectroscopy (XPS) and time of flight secondary ions mass spectrometry are employed to investigate the nature of the air-formed film and modification after water emersion. The film is described in terms of oxide, hydroxide, and water content. The preferential dissolution of iron is shown to occur on immersion. It is shown that a water absorbed layer and a hydroxide layer are present above the oxide-like passive film. The concentrations ofmore » water and hydroxide appear to be higher in the case of exposure to water. A secure method for the peak fitting of Fe2p and Cr2p XPS spectra of such films on their metallic substrates is described. The importance of XPS survey spectra is underlined and the feasibility of C{sub 60}{sup +} SIMS depth profiling of a thin oxide layer is shown.« less

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...

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.

Characterization of the volatile profiles of beer using headspace solid-phase microextraction and gas chromatography-mass spectrometry.

PubMed

Rossi, Serena; Sileoni, Valeria; Perretti, Giuseppe; Marconi, Ombretta

2014-03-30

The objective of this study was a multivariate characterization of the volatile profile of beers. Such a characterization is timely considering the increasing worldwide consumption of beer, the continuous growth of microbreweries and the importance of volatile compounds to beer flavour. A method employing solid-phase microextraction and gas chromatography-mass spectrometry (SPME-GC-MS) was optimized and then applied to a sample set of 36 industrial and craft beers of various styles and fermentation types. The volatile profiles of different beer styles is described, with particular attention paid to the volatile compounds characteristic of a spontaneously fermented lambic raspberry framboise beer. Furthermore, it was also possible to identify which specific volatile compounds are principally responsible for the differences in the volatile profiles of top- and bottom-fermented beers. Moreover, a volatile fingerprint of the craft top-fermented Italian beers was defined, as they show a very similar volatile profile. Finally, the volatile compounds that are characteristic of the bock-style beers are described. The SPME-GC-MS analytical method optimized in this study is suitable for characterizing the volatile fingerprint of different beers, especially on the basis of the kind of fermentation (top, bottom or spontaneous), the method of production and the style of the beer. © 2013 Society of Chemical Industry.

Metabolic profile of salidroside in rats using high-performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Han, Fei; Li, Yan-ting; Mao, Xin-juan; Zhang, Xiao-shu; Guan, Jiao; Song, Ai-hua; Yin, Ran

2016-03-01

A high-performance liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (HPLC-FT-ICR MS) method was developed to study the in vivo metabolism of salidroside for the first time. Plasma, urine, bile, and feces samples were collected from male rats after a single intragastric gavage of salidroside at a dose of 50 mg/kg. Besides the parent drug, a total of seven metabolites (three phase I and four phase II metabolites) were detected and tentatively identified by comparing their mass spectrometry profiles with those of salidroside. Results indicated that metabolic pathways of salidroside in male rats included hydroxylation, dehydrogenation, glucuronidation, and sulfate conjugation. Among them, glucuronidation and sulfate conjugation were the major metabolic reactions. And most important, the detection of the sulfation metabolite of p-tyrosol provides a clue for whether the deglycosylation of salidroside occurs in vivo after intragastric gavage. In summary, results obtained in this study may contribute to the better understanding of the safety and mechanism of action of salidroside.

Evaluation of automated sample preparation, retention time locked gas chromatography-mass spectrometry and data analysis methods for the metabolomic study of Arabidopsis species.

PubMed

Gu, Qun; David, Frank; Lynen, Frédéric; Rumpel, Klaus; Dugardeyn, Jasper; Van Der Straeten, Dominique; Xu, Guowang; Sandra, Pat

2011-05-27

In this paper, automated sample preparation, retention time locked gas chromatography-mass spectrometry (GC-MS) and data analysis methods for the metabolomics study were evaluated. A miniaturized and automated derivatisation method using sequential oximation and silylation was applied to a polar extract of 4 types (2 types×2 ages) of Arabidopsis thaliana, a popular model organism often used in plant sciences and genetics. Automation of the derivatisation process offers excellent repeatability, and the time between sample preparation and analysis was short and constant, reducing artifact formation. Retention time locked (RTL) gas chromatography-mass spectrometry was used, resulting in reproducible retention times and GC-MS profiles. Two approaches were used for data analysis. XCMS followed by principal component analysis (approach 1) and AMDIS deconvolution combined with a commercially available program (Mass Profiler Professional) followed by principal component analysis (approach 2) were compared. Several features that were up- or down-regulated in the different types were detected. Copyright © 2011 Elsevier B.V. All rights reserved.

Metabolomic Insight into Lipid and Protein Profile in Diabetes Using Mass Spectrometry.

PubMed

Bukowiecka-Matusiak, Malgorzata; Chmielewska-Kassassir, Malgorzata; Szczesna, Dorota; Wozniak, Lucyna A

2016-01-01

In recent years, metabolomics has become a necessary tool for understanding the impact of external and pathological factors on the operation of biological systems. The first reports of metabolomics date back to the 1970s, however, the area only began to develop dynamically at the beginning of this century and has proved effective only during the present decade. The five primary tools used in this form of analysis are NMR spectrometry, HPLC, TLC-UV, GC-MS and LC-MS/MS, with MS as the most universal approach, particularly when used together with chromatographic separation and NMR. Diabetes mellitus type 2 (T2DM) is a rapidly growing problem with global consequences. The metabolomic approach has been extensively applied to examining T2DM, insulin resistance and obesity, not only to assess the development of the disease, but also to discover its potential biomarkers. The presented review summarizes current studies on lipidomic and proteomic profiles in the context of different types of diabetes mellitus disease (T1DM, T2DM and GDM), as determined by chromatography-coupled mass spectrometry.

Fast profiling of anthocyanins in wine by desorption nano-electrospray ionization mass spectrometry.

PubMed

Hartmanova, Lucie; Ranc, Vaclav; Papouskova, Barbora; Bednar, Petr; Havlicek, Vladimir; Lemr, Karel

2010-06-18

Desorption electrospray ionization (DESI) mass spectrometry appears to be a useful technique applicable in different areas (e.g. analysis of pharmaceuticals, identification of biologically active compounds in tissues, imaging mass spectrometry). Its modification termed desorption nano-electrospray (nano-DESI) was tested for analysis of anthocyanins. Acidifying of samples and acidic spray liquid (methanol:water=75:25 with 0.2% HCOOH) were essential for obtaining good quality spectra. Profiles of main anthocyanins in wine samples, two vintages (2005 and 2007) of three cultivars (Alibernet, Neronet and Rubinet), were successfully acquired. They were in agreement with results of LC/MS experiments (anthocyanins isolated by solid phase extraction were separated by mu-HPLC with gradient elution and detected by ESI-MS). Nano-DESI-MS data also allowed to determine ratio of two cultivars (Neronet and Rubinet) in their mixture and to detect coloring of wine by tenturier or elderberry extract. Detection of main anthocyanins in slices of wine grape, chokeberries and elderberries or in a wine stain on cotton fabric is also presented. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Study of multilayered SiGe semiconductor structures by X-ray diffractometry, grazing-incidence X-ray reflectometry, and secondary-ion mass spectrometry

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

Yunin, P. A., E-mail: yunin@ipmras.ru; Drozdov, Yu. N.; Drozdov, M. N.

2013-12-15

In this publication, we report the results of studying a multilayerd nonperiodic SiGe/Si structure by the methods of X-ray diffractometry, grazing-angle X-ray reflectometry, and secondary-ion mass spectrometry (SIMS). Special attention is paid to the processing of the component distribution profile using the SIMS method and to consideration of the most significant experimental distortions introduced by this method. A method for processing the measured composition distribution profile with subsequent consideration of the influence of matrix effects, variation in the etching rate, and remnants of ion sputtering is suggested. The results of such processing are compared with a structure model obtained uponmore » combined analysis of X-ray diffractometry and grazing-angle reflectometry data. Good agreement between the results is established. It is shown that the combined use of independent techniques makes it possible to improve the methods of secondary-ion mass spectrometry and grazing-incidence reflectometry as applied to an analysis of multilayered heteroepitaxial structures (to increase the accuracy and informativity of these methods)« less

Categorizing Cells on the Basis of their Chemical Profiles: Progress in Single-Cell Mass Spectrometry.

PubMed

Comi, Troy J; Do, Thanh D; Rubakhin, Stanislav S; Sweedler, Jonathan V

2017-03-22

The chemical differences between individual cells within large cellular populations provide unique information on organisms' homeostasis and the development of diseased states. Even genetically identical cell lineages diverge due to local microenvironments and stochastic processes. The minute sample volumes and low abundance of some constituents in cells hinder our understanding of cellular heterogeneity. Although amplification methods facilitate single-cell genomics and transcriptomics, the characterization of metabolites and proteins remains challenging both because of the lack of effective amplification approaches and the wide diversity in cellular constituents. Mass spectrometry has become an enabling technology for the investigation of individual cellular metabolite profiles with its exquisite sensitivity, large dynamic range, and ability to characterize hundreds to thousands of compounds. While advances in instrumentation have improved figures of merit, acquiring measurements at high throughput and sampling from large populations of cells are still not routine. In this Perspective, we highlight the current trends and progress in mass-spectrometry-based analysis of single cells, with a focus on the technologies that will enable the next generation of single-cell measurements.

Distribution of Pb-210 in Spanish Soils: Study of the Atmospheric Contribution

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

Barrera, M.; Romero, M. L.; Valino, F.

The vertical distribution of activity and inventories of atmospheric Pb-210 is being studied in Spanish soils, aiming to establish the reference levels in the zone, based on the type of soil and the annual rainfall. A homogeneous distribution grid (approx. 150x150 km each cell) has been established covering the peninsular land, trying to combine the varying soil types (remaining undisturbed for the last 50 years) and the closeness to meteorological stations. Sampling has been performed by extracting undisturbed soil cylinders of 6 cm diameter and 120 cm length, with an impact penetrometer, and the soil cores have been sectioned inmore » slices of 3 cm thick. The analysis of Pb-210 has been performed using a gamma spectrometry system with coaxial HPGe detector sensitive at low energies (46.5 keV emission). The geometry of measured samples is thin enough (approx. 2 cm) to minimize self-absorption corrections. The work presents the results obtained so far. The Pb-210 activity profiles exhibit the characteristic decreasing shape with depth, showing maximum levels at the surface, and reaching the equilibrium activity with Ra-226 at a maximum depth depending on different environmental conditions. The unsupported Pb-210 inventory values are in the usual range (1000-5000 Bq/m{sup 2}), showing a positive correlation with the averaged annual rainfall. These reference levels could be used in posterior studies of anthropogenic alteration of soils, evaluation of erosion and desertification processes.« less

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.

Determination of natural organic matter and iron binding capacity in fen samples

NASA Astrophysics Data System (ADS)

Kügler, Stefan; Cooper, Rebecca E.; Frieder Mohr, Jan; Wichard, Thomas; Küsel, Kirsten

2017-04-01

Natural organic matter (NOM) plays an important role in ecosystem processes such as soil carbon stabilization, nutrient availability and metal complexation. Iron-NOM-complexes, for example, are known to increase the solubility and, as a result, the bioavailability of iron in natural environments leading to several effects on the microbial community. Due to the various functions of NOM in natural environments, there is a high level of interest in the characterization of the molecular composition. The complexity of NOM presents a significant challenge in the elucidation of its composition. However, the development and utilization of high resolution mass spectrometry (HR-MS) as a tool to detect single compounds in complex samples has spearheaded the effort to elucidate the composition of NOM. Over the past years, the accuracy of ion cyclotron- or Orbitrap mass spectrometers has increased dramatically resulting in the possibility to obtain a mass differentiation of the large number of compounds in NOM. Together these tools provide significant and powerful insight into the molecular composition of NOM. In the current study, we aim to understand abiotic and biotic interactions between NOM and metals, such as iron, found in the Schlöppnerbrunnen fen (Fichtelgebirge, Germany) and how these interactions impact the microbial consortia. We characterized the dissolved organic matter (DOM) as well as basic chemical parameters in the iron-rich (up to 20 mg (g wt peat)-1), slightly acidic (pH 4.8) fen to gain more information about DOM-metal interactions. This minerotrophic peatland connected to the groundwater has received Fe(II) released from the surrounding soils in the Lehstenbach catchment. Absorption spectroscopy (AAS), differential pulse polarography (DPP) and high resolution electrospray ionization mass spectrometry (HR-ESI-Orbitrap-MS) was applied to characterize the molecular composition of DOM in the peat water extract (PWE). We identified typical patterns for DOM illustrated by van Krevelen plots, which indicate the presence of different substance classes including condensed aromatics, lignins and tannins known to complex iron. Our results indicate a variety of potential Fe-DOM-complexes present in the PWE samples when iron is incorporated into the elemental composition search. Using DPP we determine the complexation capacity of iron in the natural matrix of the fen along with the identification of ligands in order to estimate the iron bioavailability for bacteria. As the microbial redox system of the fen is impacted by other metals in the environment, we perform comprehensive analysis of the entirety of metal ions and concentrations in the water samples. Dialysis chambers are currently installed in the iron-rich fen from which pore water samples will be collected at 1 cm increments between 0-20 cm depth to determine the depth profiles of Fe(II)- and Fe(III)-concentration and evaluate the influence of the depth profiles on the interplay between microorganism comprising the natural microbial redox system of the fen. We have shown that metal-DOM-pH interactions affect the bioavailable metal concentration in fen water systems. This information will pave the way for a better understanding of the bacterial recruitment of trace elements and microbial redox reactions.

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.

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.

Mass spectrometry. [review of techniques

NASA Technical Reports Server (NTRS)

Burlingame, A. L.; Kimble, B. J.; Derrick, P. J.

1976-01-01

Advances in mass spectrometry (MS) and its applications over the past decade are reviewed in depth, with annotated literature references. New instrumentation and techniques surveyed include: modulated-beam MS, chromatographic MS on-line computer techniques, digital computer-compatible quadrupole MS, selected ion monitoring (mass fragmentography), and computer-aided management of MS data and interpretation. Areas of application surveyed include: organic MS and electron impact MS, field ionization kinetics, appearance potentials, translational energy release, studies of metastable species, photoionization, calculations of molecular orbitals, chemical kinetics, field desorption MS, high pressure MS, ion cyclotron resonance, biochemistry, medical/clinical chemistry, pharmacology, and environmental chemistry and pollution studies.

Xeropreservation of Functionalized Lipid Biomarkers in Hyperarid Soils in the Atacama Desert

NASA Technical Reports Server (NTRS)

Wilhelm, Mary Beth; Davila, Alfonso F.; Eigenbrode, Jennifer L.; Parenteau, Mary N.; Jahnke, Linda L.; Liu, Xiao-Lei; Summons, Roger E.; Wray, James J.; Stamos, Brian N.; O'Reilly, Shane S.;

Detecting molecular forms of antithrombin by LC-MRM-MS: defining the measurands.

PubMed

Ruhaak, L Renee; Romijn, Fred P H T M; Smit, Nico P M; van der Laarse, Arnoud; Pieterse, Mervin M; de Maat, Moniek P M; Haas, Fred J L M; Kluft, Cornelis; Amiral, Jean; Meijer, Piet; Cobbaert, Christa M

2018-05-01

Antithrombin (AT) is a critical regulator of coagulation, and its overall activity is typically measured using functional tests. A large number of molecular forms of AT have been identified and each individual carries multiple molecular proteoforms representing variable activities. Conventional functional tests are completely blind for these proteoforms. A method that ensures properly defined measurands for AT is therefore needed. We here assess whether mass spectrometry technology, in particular multiple reaction monitoring (MRM), is suitable for the quantification of AT and the qualitative detection of its molecular proteoforms. Plasma proteins were denatured, reduced and alkylated prior to enzymatic digestion. MRM transitions were developed towards tryptic peptides and glycopeptides using AT purified from human plasma. For each peptide, three transitions were measured, and stable isotope-labeled peptides were used for quantitation. Completeness of digestion was assessed using digestion time curves. MRM transitions were developed for 19 tryptic peptides and 4 glycopeptides. Two peptides, FDTISEK and FATTFYQHLADSK, were used for quantitation, and using a calibration curve of isolated AT in 40 g/L human serum albumin, CVs below 3.5% were obtained for FDTISEK, whereas CVs below 8% were obtained for FATTFYQHLADSK. Of the 26 important AT mutations, 20 can be identified using this method, while altered glycosylation profiles can also be detected. We here show the feasibility of the liquid chromatography multiple reaction monitoring mass spectrometry (LC-MRM-MS) technique for the quantitation of AT and the qualitative analysis of most of its molecular proteoforms. Knowing the measurands will enable standardization of AT tests by providing in-depth information on the molecular proteoforms of AT.

The development of soil organic matter in restored biodiverse Jarrah forests of South-Western Australia as determined by ASE and GCMS.

PubMed

Lin, Deborah S; Greenwood, Paul F; George, Suman; Somerfield, Paul J; Tibbett, Mark

2011-08-01

Soil organic matter (SOM) is known to increase with time as landscapes recover after a major disturbance; however, little is known about the evolution of the chemistry of SOM in reconstructed ecosystems. In this study, we assessed the development of SOM chemistry in a chronosequence (space for time substitution) of restored Jarrah forest sites in Western Australia. Replicated samples were taken at the surface of the mineral soil as well as deeper in the profile at sites of 1, 3, 6, 9, 12, and 17 years of age. A molecular approach was developed to distinguish and quantify numerous individual compounds in SOM. This used accelerated solvent extraction in conjunction with gas chromatography mass spectrometry. A novel multivariate statistical approach was used to assess changes in accelerated solvent extraction (ASE)-gas chromatography-mass spectrometry (GCMS) spectra. This enabled us to track SOM developmental trajectories with restoration time. Results showed total carbon concentrations approached that of native forests soils by 17 years of restoration. Using the relate protocol in PRIMER, we demonstrated an overall linear relationship with site age at both depths, indicating that changes in SOM chemistry were occurring. The surface soils were seen to approach native molecular compositions while the deeper soil retained a more stable chemical signature, suggesting litter from the developing diverse plant community has altered SOM near the surface. Our new approach for assessing SOM development, combining ASE-GCMS with illuminating multivariate statistical analysis, holds great promise to more fully develop ASE for the characterisation of SOM.

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.

Depth-dependent Concentrations of Cosmogenic 10Be, 26Al, 36Cl, HEc, NEc, and ARc in the Old Woman Iron Meteorite

NASA Astrophysics Data System (ADS)

Lavielle, B.; Nishiizumi, K.; Marti, K.; Jeannot, J.-P.; Caffee, M. W.; Finkel, R. C.

1995-09-01

We report measurements of 1OBe7 26AI, 36CI, and of light noble gases in 6 samples of the type IIB Old Woman iron meteorite. The aim of this work is to study the depth dependence of the production rates of cosmogenic nuclides in iron meteorites. Old Woman is a large single mass of 2753 kg. Five samples have been taken from a slice of about 100 cm x 50 cm. One other sample was located roughly 40 cm above the center of the slice in a perpendicular direction. The distances between any two samples vary from 36.5 cm to 57.5 cm. Studies of cosmogenic nuclides in samples of known locations are very useful for the validation of models describing the production of cosmogenic nuclides in meteorites. Cosmogenic radionuclides were measured by accelerator mass spectrometry at Lawrence Livermore National Laboratory. Partial results have been reported earlier [1]. Concentrations of 4He, 21Ne and 38Ar in aliquots of the samples were determined by conventional mass spectrometry using an isotopic dilution method. The ratio 3He/4He appears to be almost constant with a value of 0.12 - ().13. This is about half the value generally observed in iron meteorites. Similar low ratios have been previously observed in some irons and in chondritic metal and reflect diffusion losses of 3H 12,31. The ratios 4He/38Ar, 4He/21Ne and 36Ar/38Ar are similar to those observed in iron meteorites indicating no significant losses of 4He. The measured ratio S = 4He/21Ne which represents one of the best indicators of shielding depth in iron meteorites, varies from 310 to 375 in samples from the slice. By using this as a shielding parameter, profiles were obtained for the different nuclides investigated in this work. Systematic decreases from the surface to the center of the meteorite are observed and the center of the meteoroid can be determined. As expected from nuclear systematics, the ratio 36Cl/36Ar is almost constant. The ratio 36Cl/10Be is relatively constant with a mean value of 4.7 indicating that the terrestrial age of Old Woman is probably less than 50,000 years. References: [1] Nishiizumi K. et al (1991) Meteoritics, 26, 379-380. [2] Schultz L. (1967) EPSL, 2, 87-89. [3] Graf T. et al., this volume.

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.

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

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.

Processing MALDI mass spectra to improve mass spectral direct tissue analysis

NASA Astrophysics Data System (ADS)

Norris, Jeremy L.; Cornett, Dale S.; Mobley, James A.; Andersson, Malin; Seeley, Erin H.; Chaurand, Pierre; Caprioli, Richard M.

2007-02-01

Profiling and imaging biological specimens using MALDI mass spectrometry has significant potential to contribute to our understanding and diagnosis of disease. The technique is efficient and high-throughput providing a wealth of data about the biological state of the sample from a very simple and direct experiment. However, in order for these techniques to be put to use for clinical purposes, the approaches used to process and analyze the data must improve. This study examines some of the existing tools to baseline subtract, normalize, align, and remove spectral noise for MALDI data, comparing the advantages of each. A preferred workflow is presented that can be easily implemented for data in ASCII format. The advantages of using such an approach are discussed for both molecular profiling and imaging mass spectrometry.

Identification of Tyrosine Phosphorylated Proteins by SH2 Domain Affinity Purification and Mass Spectrometry.

PubMed

Buhs, Sophia; Gerull, Helwe; Nollau, Peter

2017-01-01

Phosphotyrosine signaling plays a major role in the control of many important biological functions such as cell proliferation and apoptosis. Deciphering of phosphotyrosine-dependent signaling is therefore of great interest paving the way for the understanding of physiological and pathological processes of signal transduction. On the basis of the specific binding of SH2 domains to phosphotyrosine residues, we here present an experimental workflow for affinity purification and subsequent identification of tyrosine phosphorylated proteins by mass spectrometry. In combination with SH2 profiling, a broadly applicable platform for the characterization of phosphotyrosine profiles in cell extracts, our pull down strategy enables researchers by now to identify proteins in signaling cascades which are differentially phosphorylated and selectively recognized by distinct SH2 domains.

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.

Co-registered Topographical, Band Excitation Nanomechanical, and Mass Spectral Imaging Using a Combined Atomic Force Microscopy/Mass Spectrometry Platform

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

Ovchinnikova, Olga S.; Tai, Tamin; Bocharova, Vera

The advancement of a hybrid atomic force microscopy/mass spectrometry imaging platform demonstrating for the first time co-registered topographical, band excitation nanomechanical, and mass spectral imaging of a surface using a single instrument is reported. The mass spectrometry-based chemical imaging component of the system utilized nanothermal analysis probes for pyrolytic surface sampling followed by atmospheric pressure chemical ionization of the gas phase species produced with subsequent mass analysis. We discuss the basic instrumental setup and operation and the multimodal imaging capability and utility are demonstrated using a phase separated polystyrene/poly(2-vinylpyridine) polymer blend thin film. The topography and band excitation images showedmore » that the valley and plateau regions of the thin film surface were comprised primarily of one of the two polymers in the blend with the mass spectral chemical image used to definitively identify the polymers at the different locations. Data point pixel size for the topography (390 nm x 390 nm), band excitation (781 nm x 781 nm), mass spectrometry (690 nm x 500 nm) images was comparable and submicrometer in all three cases, but the data voxel size for each of the three images was dramatically different. The topography image was uniquely a surface measurement, whereas the band excitation image included information from an estimated 10 nm deep into the sample and the mass spectral image from 110-140 nm in depth. Moreover, because of this dramatic sampling depth variance, some differences in the band excitation and mass spectrometry chemical images were observed and were interpreted to indicate the presence of a buried interface in the sample. The spatial resolution of the mass spectral image was estimated to be between 1.5 m 2.6 m, based on the ability to distinguish surface features in that image that were also observed in the other images.« less

Co-registered Topographical, Band Excitation Nanomechanical, and Mass Spectral Imaging Using a Combined Atomic Force Microscopy/Mass Spectrometry Platform

DOE PAGES

Ovchinnikova, Olga S.; Tai, Tamin; Bocharova, Vera; ...

2015-03-18

The advancement of a hybrid atomic force microscopy/mass spectrometry imaging platform demonstrating for the first time co-registered topographical, band excitation nanomechanical, and mass spectral imaging of a surface using a single instrument is reported. The mass spectrometry-based chemical imaging component of the system utilized nanothermal analysis probes for pyrolytic surface sampling followed by atmospheric pressure chemical ionization of the gas phase species produced with subsequent mass analysis. We discuss the basic instrumental setup and operation and the multimodal imaging capability and utility are demonstrated using a phase separated polystyrene/poly(2-vinylpyridine) polymer blend thin film. The topography and band excitation images showedmore » that the valley and plateau regions of the thin film surface were comprised primarily of one of the two polymers in the blend with the mass spectral chemical image used to definitively identify the polymers at the different locations. Data point pixel size for the topography (390 nm x 390 nm), band excitation (781 nm x 781 nm), mass spectrometry (690 nm x 500 nm) images was comparable and submicrometer in all three cases, but the data voxel size for each of the three images was dramatically different. The topography image was uniquely a surface measurement, whereas the band excitation image included information from an estimated 10 nm deep into the sample and the mass spectral image from 110-140 nm in depth. Moreover, because of this dramatic sampling depth variance, some differences in the band excitation and mass spectrometry chemical images were observed and were interpreted to indicate the presence of a buried interface in the sample. The spatial resolution of the mass spectral image was estimated to be between 1.5 m 2.6 m, based on the ability to distinguish surface features in that image that were also observed in the other images.« less

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.;

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.

Impurity profiling of trinitrotoluene using vacuum-outlet gas chromatography-mass spectrometry.

PubMed

Brust, Hanneke; Willemse, Sander; Zeng, Tuoyu; van Asten, Arian; Koeberg, Mattijs; van der Heijden, Antoine; Bolck, Annabel; Schoenmakers, Peter

2014-12-29

In this work, a reliable and robust vacuum-outlet gas chromatography-mass spectrometry (GC-MS) method is introduced for the identification and quantification of impurities in trinitrotoluene (TNT). Vacuum-outlet GC-MS allows for short analysis times; the analysis of impurities in TNT was performed in 4min. This study shows that impurity profiling of TNT can be used to investigate relations between TNT samples encountered in forensic casework. A wide variety of TNT samples were analyzed with the developed method. Dinitrobenzene, dinitrotoluene, trinitrotoluene and amino-dinitrotoluene isomers were detected at very low levels (<1wt.%) by applying the MS in selected-ion monitoring (SIM) mode. Limits of detection ranged from 6ng/mL for 2,6-dinitrotoluene to 43ng/mL for 4-amino-2,6-dinitrotoluene. Major impurities in TNT were 2,4-dinitrotoluene and 2,3,4-trinitrotoluene. Impurity profiles based on seven compounds showed to be useful to TNT samples from different sources. Statistical analysis of these impurity profiles using likelihood ratios demonstrated the potential to investigate whether two questioned TNT samples encountered in forensic casework are from the same source. Copyright © 2014 Elsevier B.V. All rights reserved.

Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus.

PubMed

Sanchez, Diego H; Lippold, Felix; Redestig, Henning; Hannah, Matthew A; Erban, Alexander; Krämer, Ute; Kopka, Joachim; Udvardi, Michael K

2008-03-01

The model legume Lotus japonicus was subjected to non-lethal long-term salinity and profiled at the ionomic, transcriptomic and metabolomic levels. Two experimental designs with various stress doses were tested: a gradual step acclimatization and an initial acclimatization approach. Ionomic profiling by inductively coupled plasma/atomic emission spectrometry (ICP-AES) revealed salt stress-induced reductions in potassium, phosphorus, sulphur, zinc and molybdenum. Microarray profiling using the Lotus Genechip allowed the identification of 912 probesets that were differentially expressed under the acclimatization regimes. Gas chromatography/mass spectrometry-based metabolite profiling identified 147 differentially accumulated soluble metabolites, indicating a change in metabolic phenotype upon salt acclimatization. Metabolic changes were characterized by a general increase in the steady-state levels of many amino acids, sugars and polyols, with a concurrent decrease in most organic acids. Transcript and metabolite changes exhibited a stress dose-dependent response within the range of NaCl concentrations used, although threshold and plateau behaviours were also observed. The combined observations suggest a successive and increasingly global requirement for the reprogramming of gene expression and metabolic pathways to maintain ionic and osmotic homeostasis. A simple qualitative model is proposed to explain the systems behaviour of plants during salt acclimatization.

Liquid chromatography/quadrupole-time-of-flight mass spectrometry with metabolic profiling of human urine as a tool for environmental analysis of dextromethorphan.

PubMed

Thurman, E Michael; Ferrer, Imma

2012-10-12

We use the combination of liquid chromatography/quadrupole-time-of-flight mass spectrometry (LC/Q-TOF-MS) and urine metabolic profiling to find and identify the metabolites of dextromethorphan, a common over-the-counter (OTC) cough suppressant. Next, we use the combination of ion masses, their MS/MS fragmentation, and retention times to determine dextromethorphan and its metabolites in surface water impacted by wastewater. Prior to this study, neither dextromethorphan nor its metabolites have been reported in surface water; in spite of its common use in over 100 various OTC medications. We found that the concentration of the dextrorphan metabolite in surface water greatly exceeded the parent compound by factors of 5-10 times, which reflects the urine profile, where parent compound is approximately <2% of the total excreted drug based on ion intensities. Urine profiling also indicated that glucuronide metabolites are major phase 2 products (92% of the total) in urine and then are completely hydrolyzed in wastewater to dextrorphan and N-demethyldextrorphan, which are phase 1 metabolites-a "kind of reversal" of human metabolism. Copyright © 2012 Elsevier B.V. All rights reserved.

Ripening and storage conditions of Chétoui and Arbequina olives: Part II. Effect on olive endogenous enzymes and virgin olive oil secoiridoid profile determined by high resolution mass spectrometry.

PubMed

Hachicha Hbaieb, Rim; Kotti, Faten; Cortes-Francisco, Nuria; Caixach, Josep; Gargouri, Mohamed; Vichi, Stefania

2016-11-01

Several factors affect virgin olive oil (VOO) phenolic profile. The aim of this study was to monitor olive hydrolytic (β-glucosidase) and oxidative (peroxydase, POX, and polyphenoloxydase, PPO) enzymes during olive ripening and storage and to determine their capacity to shape VOO phenolic profile. To this end, olives from the cultivars Chétoui and Arbequina were stored at 4°C or 25°C for 4weeks and their enzymatic activities and oil phenolic profiles were compared to those of ripening olives. We observed different trends in enzymes activities according to cultivar and storage temperature. Secoiridoid compounds, determined by high resolution mass spectrometry (HRMS), and their deacetoxylated, oxygenated, and deacetoxy-oxygenated derivatives were identified and their contents differed between the cultivars according to olive ripening degree and storage conditions. These differences could be due to β-glucosidase, POX and PPO activities changes during olive ripening and storage. Results also show that oxidised phenolic compounds could be a marker of VOO ''freshness". Copyright © 2016 Elsevier Ltd. All rights reserved.

Serum protein profiling and proteomics in autistic spectrum disorder using magnetic bead-assisted mass spectrometry.

PubMed

Taurines, Regina; Dudley, Edward; Conner, Alexander C; Grassl, Julia; Jans, Thomas; Guderian, Frank; Mehler-Wex, Claudia; Warnke, Andreas; Gerlach, Manfred; Thome, Johannes

2010-04-01

The pathophysiology of autistic spectrum disorder (ASD) is not fully understood and there are no diagnostic or predictive biomarkers. Proteomic profiling has been used in the past for biomarker research in several non-psychiatric and psychiatric disorders and could provide new insights, potentially presenting a useful tool for generating such biomarkers in autism. Serum protein pre-fractionation with C8-magnetic beads and protein profiling by matrix-assisted laser desorption/ionisation-time of flight-mass spectrometry (MALDI-ToF-MS) were used to identify possible differences in protein profiles in patients and controls. Serum was obtained from 16 patients (aged 8-18) and age-matched controls. Three peaks in the MALDI-ToF-MS significantly differentiated the ASD sample from the control group. Sub-grouping the ASD patients into children with and without comorbid Attention Deficit and Hyperactivity Disorder, ADHD (ASD/ADHD+ patients, n = 9; ASD/ADHD- patients, n = 7), one peak distinguished the ASD/ADHD+ patients from controls and ASD/ADHD- patients. Our results suggest that altered protein levels in peripheral blood of patients with ASD might represent useful biomarkers for this devastating psychiatric disorder.

Authentication of animal fats using direct analysis in real time (DART) ionization-mass spectrometry and chemometric tools.

PubMed

Vaclavik, Lukas; Hrbek, Vojtech; Cajka, Tomas; Rohlik, Bo-Anne; Pipek, Petr; Hajslova, Jana

2011-06-08

A combination of direct analysis in real time (DART) ionization coupled to time-of-flight mass spectrometry (TOFMS) and chemometrics was used for animal fat (lard and beef tallow) authentication. This novel instrumentation was employed for rapid profiling of triacylglycerols (TAGs) and polar compounds present in fat samples and their mixtures. Additionally, fat isolated from pork, beef, and pork/beef admixtures was analyzed. Mass spectral records were processed by principal component analysis (PCA) and stepwise linear discriminant analysis (LDA). DART-TOFMS profiles of TAGs were found to be more suitable for the purpose of discrimination among the examined fat types as compared to profiles of polar compounds. The LDA model developed using TAG data enabled not only reliable classification of samples representing neat fats but also detection of admixed lard and tallow at adulteration levels of 5 and 10% (w/w), respectively. The presented approach was also successfully applied to minced meat prepared from pork and beef with comparable fat content. Using the DART-TOFMS TAG profiles of fat isolated from meat mixtures, detection of 10% pork added to beef and vice versa was possible.

Regio- and stereospecific analysis of glycerolipids.

PubMed

Kuksis, Arnis; Itabashi, Yutaka

2005-06-01

In recent years researchers have recognized the potential value of comprehensive lipid profiling (lipidomics), which was invented and promoted by lipidologists who recognized the many valuable applications that grew out of the fields of DNA profiling (genomics) and protein profiling (proteonomics). Through lipid class-selective intrasource ionization and subsequent analysis of two-dimensional cross-peak intensities, the chemical identity and mass composition of individual molecular species of most lipid classes can now be determined in a chloroform extract. There remains, however, the necessity to distinguish the enantiomers and isobaric regioisomers resulting from enzymatic and chemical reactions, which conventional high performance liquid chromatography/mass spectrometry (HPLC/MS) has been slow to accommodate, and tandem MS unable to provide. While reversed-phase HPLC can separate regioisomers, normal-phase HPLC can resolve diastereomers, and chiral-phase HPLC can effect dramatic resolution of enantiomers, the full potential of the combined systems has seldom been exploited. The present chapter calls attention to both recent and earlier combinations of these methodologies with mass spectrometry, which allows the HPLC/ESI (electrospray ionization)-MS/MS separation and identification of enantiomeric diacylglycerols, triacylglycerols, and glycerophospholipids as well as their isobaric regioisomers. These developments permit further expansion of lipid profiling (lipidomics) and better understanding of lipid metabolism.

High-resolution proteomic profiling of spider venom: expanding the toxin diversity of Phoneutria nigriventer venom.

PubMed

Liberato, Tarcísio; Troncone, Lanfranco Ranieri Paolo; Yamashiro, Edson T; Serrano, Solange M T; Zelanis, André

2016-03-01

Here we present a proteomic characterization of Phoneutria nigriventer venom. A shotgun proteomic approach allowed the identification, for the first time, of O-glycosyl hydrolases (chitinases) in P. nigriventer venom. The electrophoretic profiles under nonreducing and reducing conditions, and protein identification by mass spectrometry, indicated the presence of oligomeric toxin structures in the venom. Complementary proteomic approaches allowed for a qualitative and semi-quantitative profiling of P. nigriventer venom complexity, expanding its known venom proteome diversity.

Diagnosis of gastroenterological diseases by metabolome analysis using gas chromatography-mass spectrometry.

PubMed

Yoshida, Masaru; Hatano, Naoya; Nishiumi, Shin; Irino, Yasuhiro; Izumi, Yoshihiro; Takenawa, Tadaomi; Azuma, Takeshi

2012-01-01

Recently, metabolome analysis has been increasingly applied to biomarker detection and disease diagnosis in medical studies. Metabolome analysis is a strategy for studying the characteristics and interactions of low molecular weight metabolites under a specific set of conditions and is performed using mass spectrometry and nuclear magnetic resonance spectroscopy. There is a strong possibility that changes in metabolite levels reflect the functional status of a cell because alterations in their levels occur downstream of DNA, RNA, and protein. Therefore, the metabolite profile of a cell is more likely to represent the current status of a cell than DNA, RNA, or protein. Thus, owing to the rapid development of mass spectrometry analytical techniques metabolome analysis is becoming an important experimental method in life sciences including the medical field. Here, we describe metabolome analysis using liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry (GC-MS), capillary electrophoresis-mass spectrometry, and matrix assisted laser desorption ionization-mass spectrometry. Then, the findings of studies about GC-MS-based metabolome analysis of gastroenterological diseases are summarized, and our research results are also introduced. Finally, we discuss the realization of disease diagnosis by metabolome analysis. The development of metabolome analysis using mass spectrometry will aid the discovery of novel biomarkers, hopefully leading to the early detection of various diseases.

Imaging mass spectrometry in drug development and toxicology.

PubMed

Karlsson, Oskar; Hanrieder, Jörg

2017-06-01

During the last decades, imaging mass spectrometry has gained significant relevance in biomedical research. Recent advances in imaging mass spectrometry have paved the way for in situ studies on drug development, metabolism and toxicology. In contrast to whole-body autoradiography that images the localization of radiolabeled compounds, imaging mass spectrometry provides the possibility to simultaneously determine the discrete tissue distribution of the parent compound and its metabolites. In addition, imaging mass spectrometry features high molecular specificity and allows comprehensive, multiplexed detection and localization of hundreds of proteins, peptides and lipids directly in tissues. Toxicologists traditionally screen for adverse findings by histopathological examination. However, studies of the molecular and cellular processes underpinning toxicological and pathologic findings induced by candidate drugs or toxins are important to reach a mechanistic understanding and an effective risk assessment strategy. One of IMS strengths is the ability to directly overlay the molecular information from the mass spectrometric analysis with the tissue section and allow correlative comparisons of molecular and histologic information. Imaging mass spectrometry could therefore be a powerful tool for omics profiling of pharmacological/toxicological effects of drug candidates and toxicants in discrete tissue regions. The aim of the present review is to provide an overview of imaging mass spectrometry, with particular focus on MALDI imaging mass spectrometry, and its use in drug development and toxicology in general.