Sample records for xps analysis revealed

  1. Transcription analysis of pilS and xpsEL genes from Xylella fastidiosa.

    PubMed

    Coltri, Patricia P; Rosato, Yoko B

    2005-04-01

    Xylella fastidiosa is a xylem-limited phytopathogen responsible for diseases in several plants such as citrus and coffee. Analysis of the bacterial genome revealed some putative pathogenicity-related genes that could help to elucidate the molecular mechanisms of plant-pathogen interactions. In the present work, the transcription of three genes of the bacterium, grown in defined and rich media and also in media containing host plant extracts (sweet orange, 'ponkan' and coffee) was analyzed by RT-PCR. The pilS gene, which encodes a sensor histidine kinase responsible for the biosynthesis of fimbriae, was transcribed when the bacterium was grown in more complex media such as PW and in medium containing plant extracts. The xps genes (xpsL and xpsE) which are related to the type II secretion system were also detected when the bacterium was grown in rich media and media with 'ponkan' and coffee extracts. It was thus observed that pilS and xpsEL genes of X. fastidiosa can be modulated by environmental factors and their expression is dependent on the nutritional status of the growth medium.

  2. Combined PIXE and XPS analysis on republican and imperial Roman coins

    NASA Astrophysics Data System (ADS)

    Daccà, A.; Prati, P.; Zucchiatti, A.; Lucarelli, F.; Mandò, P. A.; Gemme, G.; Parodi, R.; Pera, R.

    2000-03-01

    A combined PIXE and XPS analysis has been performed on a few Roman coins of the republican and imperial age. The purpose was to investigate via XPS the nature and extent of patina in order to be capable of extracting PIXE data relative to the coins bulk. The inclusion of elements from the surface layer, altered by oxidation and inclusion, is a known source of uncertainty in PIXE analyses of coins, performed to assess the composition and the provenance.

  3. AFM AND XPS Characterization of Zinc-Aluminum Alloy Coatings with Attention to Surface Dross and Flow Lines

    NASA Astrophysics Data System (ADS)

    Harding, Felipe A.; Alarcon, Nelson A.; Toledo, Pedro G.

    Surfaces of various zinc-aluminum alloy (Zn-Al) coated steel samples are studied with attention to foreign surface dross by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS/ESCA). AFM topographic maps of zinc-aluminum alloy surfaces free of dross reveal the perfect nanoscale details of two kinds of dendrites: branched and globular. In all magnifications the dendrites appear smooth and, in general, very clean. XPS analysis of the extreme surface of a Zn-Al sample reveals Al, Zn, Si and O as the main components. The XPS results show no segregation or separation of phases other than those indicated by the ternary Al-Zn-Si diagram. For surfaces of Zn-Al plagued with impurities, high resolution AFM topographic maps reveal three situations: (1) areas with well-defined dendrites, relatively free of dross; (2) areas with small, millimeter-sized black spots known as dross; and (3) areas with large black stains, known as flow lines. Dendrite deformation and dross accumulation increase notably in the neighborhood, apparently clean to the naked eye, of dross or flow lines. XPS results of areas with dross and flow lines indicate unacceptable high concentration of Si and important Si phase separation. These results, in the light of AFM work, reveal that dross and flow lines are a consequence of a high local concentration of Si from high melting point silica and silicate impurities in the Zn-Al alloy source.

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  5. [Quantitative surface analysis of Pt-Co, Cu-Au and Cu-Ag alloy films by XPS and AES].

    PubMed

    Li, Lian-Zhong; Zhuo, Shang-Jun; Shen, Ru-Xiang; Qian, Rong; Gao, Jie

    2013-11-01

    In order to improve the quantitative analysis accuracy of AES, We associated XPS with AES and studied the method to reduce the error of AES quantitative analysis, selected Pt-Co, Cu-Au and Cu-Ag binary alloy thin-films as the samples, used XPS to correct AES quantitative analysis results by changing the auger sensitivity factors to make their quantitative analysis results more similar. Then we verified the accuracy of the quantitative analysis of AES when using the revised sensitivity factors by other samples with different composition ratio, and the results showed that the corrected relative sensitivity factors can reduce the error in quantitative analysis of AES to less than 10%. Peak defining is difficult in the form of the integral spectrum of AES analysis since choosing the starting point and ending point when determining the characteristic auger peak intensity area with great uncertainty, and to make analysis easier, we also processed data in the form of the differential spectrum, made quantitative analysis on the basis of peak to peak height instead of peak area, corrected the relative sensitivity factors, and verified the accuracy of quantitative analysis by the other samples with different composition ratio. The result showed that the analytical error in quantitative analysis of AES reduced to less than 9%. It showed that the accuracy of AES quantitative analysis can be highly improved by the way of associating XPS with AES to correct the auger sensitivity factors since the matrix effects are taken into account. Good consistency was presented, proving the feasibility of this method.

  6. 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.

  7. Quantifying the Impact of Nanoparticle Coatings and Non-uniformities on XPS Analysis: Gold/silver Core-shell Nanoparticles

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

    Wang, Yung-Chen Andrew; Engelhard, Mark H.; Baer, Donald R.

    2016-03-07

    Abstract or short description: Spectral modeling of photoelectrons can serve as a valuable tool when combined with X-ray photoelectron spectroscopy (XPS) analysis. Herein, a new version of the NIST Simulation of Electron Spectra for Surface Analysis (SESSA 2.0) software, capable of directly simulating spherical multilayer NPs, was applied to model citrate stabilized Au/Ag-core/shell nanoparticles (NPs). The NPs were characterized using XPS and scanning transmission electron microscopy (STEM) to determine the composition and morphology of the NPs. The Au/Ag-core/shell NPs were observed to be polydispersed in size, non-circular, and contain off-centered Au-cores. Using the average NP dimensions determined from STEM analysis,more » SESSA spectral modeling indicated that washed Au/Ag-core shell NPs were stabilized with a 0.8 nm l« less

  8. Acetate- and thiol-capped monodisperse ruthenium nanoparticles: XPS, XAS, and HRTEM studies.

    PubMed

    Chakroune, Nassira; Viau, Guillaume; Ammar, Souad; Poul, Laurence; Veautier, Delphine; Chehimi, Mohamed M; Mangeney, Claire; Villain, Françoise; Fiévet, Fernand

    2005-07-19

    Monodisperse ruthenium nanoparticles were prepared by reduction of RuCl3 in 1,2-propanediol. The mean particle size was controlled by appropriate choice of the reduction temperature and the acetate ion concentration. Colloidal solutions in toluene were obtained by coating the metal particles with dodecanethiol. High-resolution transmission electron microscopy (HRTEM), X-ray photoelectron spectroscopy (XPS), and X-ray absorption spectroscopy (XANES and EXAFS for the Ru K-absorption edge) were performed on particles of two different diameters, 2 and 4 nm, and in different environments, polyol/acetate or thiol. For particles stored in polyol/acetate XPS studies revealed superficial oxidation limited to one monolayer and a surface coating containing mostly acetate ions. Analysis of the EXAFS spectra showed both oxygen and ruthenium atoms around the ruthenium atoms with a Ru-Ru coordination number N smaller than the bulk value, as expected for fine particles. In the case of 2 nm acetate-capped particles N is consistent with particles made up of a metallic core and an oxidized monolayer. For 2 nm thiol-coated particles, a Ru-S bond was evidenced by XPS and XAS. For the 4 nm particles XANES and XPS studies showed that most of the ruthenium atoms are in the zerovalent state. Nevertheless, in both cases, when capped with thiol, the Ru-Ru coordination number inferred from EXAFS is much smaller than for particles of the same size stored in polyol. This is attributed to a structural disorganization of the particles by thiol chemisorption. HRTEM studies confirm the marked dependence of the structural properties of the ruthenium particles on their chemical environment; they show the acetate-coated particles to be single crystals, whereas the thiol-coated particles appear to be polycrystalline.

  9. Versatile technique for assessing thickness of 2D layered materials by XPS

    NASA Astrophysics Data System (ADS)

    Zemlyanov, Dmitry Y.; Jespersen, Michael; Zakharov, Dmitry N.; Hu, Jianjun; Paul, Rajib; Kumar, Anurag; Pacley, Shanee; Glavin, Nicholas; Saenz, David; Smith, Kyle C.; Fisher, Timothy S.; Voevodin, Andrey A.

    2018-03-01

    X-ray photoelectron spectroscopy (XPS) has been utilized as a versatile method for thickness characterization of various two-dimensional (2D) films. Accurate thickness can be measured simultaneously while acquiring XPS data for chemical characterization of 2D films having thickness up to approximately 10 nm. For validating the developed technique, thicknesses of few-layer graphene (FLG), MoS2 and amorphous boron nitride (a-BN) layer, produced by microwave plasma chemical vapor deposition (MPCVD), plasma enhanced chemical vapor deposition (PECVD), and pulsed laser deposition (PLD) respectively, were accurately measured. The intensity ratio between photoemission peaks recorded for the films (C 1s, Mo 3d, B 1s) and the substrates (Cu 2p, Al 2p, Si 2p) is the primary input parameter for thickness calculation, in addition to the atomic densities of the substrate and the film, and the corresponding electron attenuation length (EAL). The XPS data was used with a proposed model for thickness calculations, which was verified by cross-sectional transmission electron microscope (TEM) measurement of thickness for all the films. The XPS method determines thickness values averaged over an analysis area which is orders of magnitude larger than the typical area in cross-sectional TEM imaging, hence provides an advanced approach for thickness measurement over large areas of 2D materials. The study confirms that the versatile XPS method allows rapid and reliable assessment of the 2D material thickness and this method can facilitate in tailoring growth conditions for producing very thin 2D materials effectively over a large area. Furthermore, the XPS measurement for a typical 2D material is non-destructive and does not require special sample preparation. Therefore, after XPS analysis, exactly the same sample can undergo further processing or utilization.

  10. Versatile technique for assessing thickness of 2D layered materials by XPS

    DOE PAGES

    Zemlyanov, Dmitry Y.; Jespersen, Michael; Zakharov, Dmitry N.; ...

    2018-02-07

    X-ray photoelectron spectroscopy (XPS) has been utilized as a versatile method for thickness characterization of various two-dimensional (2D) films. Accurate thickness can be measured simultaneously while acquiring XPS data for chemical characterization of 2D films having thickness up to approximately 10 nm. For validating the developed technique, thicknesses of few-layer graphene (FLG), MoS 2 and amorphous boron nitride (a-BN) layer, produced by microwave plasma chemical vapor deposition (MPCVD), plasma enhanced chemical vapor deposition (PECVD), and pulsed laser deposition (PLD) respectively, were accurately measured. The intensity ratio between photoemission peaks recorded for the films (C 1s, Mo 3d, B 1s) andmore » the substrates (Cu 2p, Al 2p, Si 2p) is the primary input parameter for thickness calculation, in addition to the atomic densities of the substrate and the film, and the corresponding electron attenuation length (EAL). The XPS data was used with a proposed model for thickness calculations, which was verified by cross-sectional transmission electron microscope (TEM) measurement of thickness for all the films. The XPS method determines thickness values averaged over an analysis area which is orders of magnitude larger than the typical area in cross-sectional TEM imaging, hence provides an advanced approach for thickness measurement over large areas of 2D materials. The study confirms that the versatile XPS method allows rapid and reliable assessment of the 2D material thickness and this method can facilitate in tailoring growth conditions for producing very thin 2D materials effectively over a large area. Furthermore, the XPS measurement for a typical 2D material is non-destructive and does not require special sample preparation. Furthermore, after XPS analysis, exactly the same sample can undergo further processing or utilization.« less

  11. Versatile technique for assessing thickness of 2D layered materials by XPS.

    PubMed

    Zemlyanov, Dmitry Y; Jespersen, Michael; Zakharov, Dmitry N; Hu, Jianjun; Paul, Rajib; Kumar, Anurag; Pacley, Shanee; Glavin, Nicholas; Saenz, David; Smith, Kyle C; Fisher, Timothy S; Voevodin, Andrey A

    2018-03-16

    X-ray photoelectron spectroscopy (XPS) has been utilized as a versatile method for thickness characterization of various two-dimensional (2D) films. Accurate thickness can be measured simultaneously while acquiring XPS data for chemical characterization of 2D films having thickness up to approximately 10 nm. For validating the developed technique, thicknesses of few-layer graphene (FLG), MoS 2 and amorphous boron nitride (a-BN) layer, produced by microwave plasma chemical vapor deposition (MPCVD), plasma enhanced chemical vapor deposition (PECVD), and pulsed laser deposition (PLD) respectively, were accurately measured. The intensity ratio between photoemission peaks recorded for the films (C 1s, Mo 3d, B 1s) and the substrates (Cu 2p, Al 2p, Si 2p) is the primary input parameter for thickness calculation, in addition to the atomic densities of the substrate and the film, and the corresponding electron attenuation length (EAL). The XPS data was used with a proposed model for thickness calculations, which was verified by cross-sectional transmission electron microscope (TEM) measurement of thickness for all the films. The XPS method determines thickness values averaged over an analysis area which is orders of magnitude larger than the typical area in cross-sectional TEM imaging, hence provides an advanced approach for thickness measurement over large areas of 2D materials. The study confirms that the versatile XPS method allows rapid and reliable assessment of the 2D material thickness and this method can facilitate in tailoring growth conditions for producing very thin 2D materials effectively over a large area. Furthermore, the XPS measurement for a typical 2D material is non-destructive and does not require special sample preparation. Therefore, after XPS analysis, exactly the same sample can undergo further processing or utilization.

  12. Versatile technique for assessing thickness of 2D layered materials by XPS

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

    Zemlyanov, Dmitry Y.; Jespersen, Michael; Zakharov, Dmitry N.

    X-ray photoelectron spectroscopy (XPS) has been utilized as a versatile method for thickness characterization of various two-dimensional (2D) films. Accurate thickness can be measured simultaneously while acquiring XPS data for chemical characterization of 2D films having thickness up to approximately 10 nm. For validating the developed technique, thicknesses of few-layer graphene (FLG), MoS 2 and amorphous boron nitride (a-BN) layer, produced by microwave plasma chemical vapor deposition (MPCVD), plasma enhanced chemical vapor deposition (PECVD), and pulsed laser deposition (PLD) respectively, were accurately measured. The intensity ratio between photoemission peaks recorded for the films (C 1s, Mo 3d, B 1s) andmore » the substrates (Cu 2p, Al 2p, Si 2p) is the primary input parameter for thickness calculation, in addition to the atomic densities of the substrate and the film, and the corresponding electron attenuation length (EAL). The XPS data was used with a proposed model for thickness calculations, which was verified by cross-sectional transmission electron microscope (TEM) measurement of thickness for all the films. The XPS method determines thickness values averaged over an analysis area which is orders of magnitude larger than the typical area in cross-sectional TEM imaging, hence provides an advanced approach for thickness measurement over large areas of 2D materials. The study confirms that the versatile XPS method allows rapid and reliable assessment of the 2D material thickness and this method can facilitate in tailoring growth conditions for producing very thin 2D materials effectively over a large area. Furthermore, the XPS measurement for a typical 2D material is non-destructive and does not require special sample preparation. Furthermore, after XPS analysis, exactly the same sample can undergo further processing or utilization.« less

  13. XPS Protocol for the Characterization of Pristine and Functionalized Single Wall Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Sosa, E. D.; Allada, R.; Huffman, C. B.; Arepalli, S.

    2009-01-01

    Recent interest in developing new applications for carbon nanotubes (CNT) has fueled the need to use accurate macroscopic and nanoscopic techniques to characterize and understand their chemistry. X-ray photoelectron spectroscopy (XPS) has proved to be a useful analytical tool for nanoscale surface characterization of materials including carbon nanotubes. Recent nanotechnology research at NASA Johnson Space Center (NASA-JSC) helped to establish a characterization protocol for quality assessment for single wall carbon nanotubes (SWCNTs). Here, a review of some of the major factors of the XPS technique that can influence the quality of analytical data, suggestions for methods to maximize the quality of data obtained by XPS, and the development of a protocol for XPS characterization as a complementary technique for analyzing the purity and surface characteristics of SWCNTs is presented. The XPS protocol is then applied to a number of experiments including impurity analysis and the study of chemical modifications for SWCNTs.

  14. Analysis of XPS spectra of Fe 2+ and Fe 3+ ions in oxide materials

    NASA Astrophysics Data System (ADS)

    Yamashita, Toru; Hayes, Peter

    2008-02-01

    Samples of the iron oxides Fe 0.94O, Fe 3O 4, Fe 2O 3, and Fe 2SiO 4 were prepared by high temperature equilibration in controlled gas atmospheres. The samples were fractured in vacuum and high resolution XPS spectra of the fractured surfaces were measured. The peak positions and peak shape parameters of Fe 3p for Fe 2+ and Fe 3+ were derived from the Fe 3p XPS spectra of the standard samples of 2FeO·SiO 2 and Fe 2O 3, respectively. Using these parameters, the Fe 3p peaks of Fe 3O 4 and Fe 1- yO are analysed. The results indicate that high resolution XPS techniques can be used to determine the Fe 2+/Fe 3+ ratios in metal oxides. The technique has the potential for application to other transition metal oxide systems.

  15. Applications of XPS in the characterization of Battery materials

    DOE PAGES

    Shutthanandan, Vaithiyalingam; Nandasiri, Manjula; Zheng, Jianming; ...

    2018-05-26

    In this study, technological development requires reliable power sources where energy storage devices are emerging as a critical component. Wide range of energy storage devices, Redox-flow batteries (RFB), Lithium ion based batteries (LIB), and Lithium-sulfur (LSB) batteries are being developed for various applications ranging from grid-scale level storage to mobile electronics. Material complexities associated with these energy storage devices with unique electrochemistry are formidable challenge which needs to be address for transformative progress in this field. X-ray photoelectron spectroscopy (XPS) - a powerful surface analysis tool - has been widely used to study these energy storage materials because of itsmore » ability to identify, quantify and image the chemical distribution of redox active species. However, accessing the deeply buried solid-electrolyte interfaces (which dictates the performance of energy storage devices) has been a challenge in XPS usage. Herein we report our recent efforts to utilize the XPS to gain deep insight about these interfaces under realistic conditions with varying electrochemistry involving RFB, LIB and LSB.« less

  16. Applications of XPS in the characterization of Battery materials

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

    Shutthanandan, Vaithiyalingam; Nandasiri, Manjula; Zheng, Jianming

    In this study, technological development requires reliable power sources where energy storage devices are emerging as a critical component. Wide range of energy storage devices, Redox-flow batteries (RFB), Lithium ion based batteries (LIB), and Lithium-sulfur (LSB) batteries are being developed for various applications ranging from grid-scale level storage to mobile electronics. Material complexities associated with these energy storage devices with unique electrochemistry are formidable challenge which needs to be address for transformative progress in this field. X-ray photoelectron spectroscopy (XPS) - a powerful surface analysis tool - has been widely used to study these energy storage materials because of itsmore » ability to identify, quantify and image the chemical distribution of redox active species. However, accessing the deeply buried solid-electrolyte interfaces (which dictates the performance of energy storage devices) has been a challenge in XPS usage. Herein we report our recent efforts to utilize the XPS to gain deep insight about these interfaces under realistic conditions with varying electrochemistry involving RFB, LIB and LSB.« less

  17. Versailles Project on Advanced Materials and Standards Interlaboratory Study on Measuring the Thickness and Chemistry of Nanoparticle Coatings Using XPS and LEIS.

    PubMed

    Belsey, Natalie A; Cant, David J H; Minelli, Caterina; Araujo, Joyce R; Bock, Bernd; Brüner, Philipp; Castner, David G; Ceccone, Giacomo; Counsell, Jonathan D P; Dietrich, Paul M; Engelhard, Mark H; Fearn, Sarah; Galhardo, Carlos E; Kalbe, Henryk; Won Kim, Jeong; Lartundo-Rojas, Luis; Luftman, Henry S; Nunney, Tim S; Pseiner, Johannes; Smith, Emily F; Spampinato, Valentina; Sturm, Jacobus M; Thomas, Andrew G; Treacy, Jon P W; Veith, Lothar; Wagstaffe, Michael; Wang, Hai; Wang, Meiling; Wang, Yung-Chen; Werner, Wolfgang; Yang, Li; Shard, Alexander G

    2016-10-27

    We report the results of a VAMAS (Versailles Project on Advanced Materials and Standards) inter-laboratory study on the measurement of the shell thickness and chemistry of nanoparticle coatings. Peptide-coated gold particles were supplied to laboratories in two forms: a colloidal suspension in pure water and; particles dried onto a silicon wafer. Participants prepared and analyzed these samples using either X-ray photoelectron spectroscopy (XPS) or low energy ion scattering (LEIS). Careful data analysis revealed some significant sources of discrepancy, particularly for XPS. Degradation during transportation, storage or sample preparation resulted in a variability in thickness of 53 %. The calculation method chosen by XPS participants contributed a variability of 67 %. However, variability of 12 % was achieved for the samples deposited using a single method and by choosing photoelectron peaks that were not adversely affected by instrumental transmission effects. The study identified a need for more consistency in instrumental transmission functions and relative sensitivity factors, since this contributed a variability of 33 %. The results from the LEIS participants were more consistent, with variability of less than 10 % in thickness and this is mostly due to a common method of data analysis. The calculation was performed using a model developed for uniform, flat films and some participants employed a correction factor to account for the sample geometry, which appears warranted based upon a simulation of LEIS data from one of the participants and comparison to the XPS results.

  18. Versailles Project on Advanced Materials and Standards Interlaboratory Study on Measuring the Thickness and Chemistry of Nanoparticle Coatings Using XPS and LEIS

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

    Belsey, Natalie A.; Cant, David J. H.; Minelli, Caterina

    We report the results of a VAMAS (Versailles Project on Advanced Materials and Standards) inter-laboratory study on the measurement of the shell thickness and chemistry of nanoparticle coatings. Peptide-coated gold particles were supplied to laboratories in two forms: a colloidal suspension in pure water and; particles dried onto a silicon wafer. Participants prepared and analyzed these samples using either X-ray photoelectron spectroscopy (XPS) or low energy ion scattering (LEIS). Careful data analysis revealed some significant sources of discrepancy, particularly for XPS. Degradation during transportation, storage or sample preparation resulted in a variability in thickness of 53 %. The calculation methodmore » chosen by XPS participants contributed a variability of 67 %. However, variability of 12 % was achieved for the samples deposited using a single method and by choosing photoelectron peaks that were not adversely affected by instrumental transmission effects. The study identified a need for more consistency in instrumental transmission functions and relative sensitivity factors, since this contributed a variability of 33 %. The results from the LEIS participants were more consistent, with variability of less than 10 % in thickness and this is mostly due to a common method of data analysis. The calculation was performed using a model developed for uniform, flat films and some participants employed a correction factor to account for the sample geometry, which appears warranted based upon a simulation of LEIS data from one of the participants and comparison to the XPS results.« less

  19. Morphology and Chemical Composition of soot particles emitted by Wood-burning Cook-Stoves: a HRTEM, XPS and Elastic backscattering Studies.

    NASA Astrophysics Data System (ADS)

    Carabali-Sandoval, G. A., Sr.; Castro, T.; Peralta, O.; De la Cruz, W.; Días, J.; Amelines, O.; Rivera-Hernández, M.; Varela, A.; Muñoz-Muñoz, F.; Policroniades, R.; Murillo, G.; Moreno, E.

    2014-12-01

    The morphology, microstructure and the chemical composition on surface of soot particles were studied by using high resolution transmission electron microscopy (HRTEM), X-ray photoelectron spectroscopy (XPS) and elastic backscattering spectrometry. In order to obtain freshly soot particles emitted by home-made wood-burning cook stoves, copper grids for Transmission Electron Microscope (TEM) were placed on the last two of an 8-stages MOUDI cascade impactor. The analysis of HRTEM micrographs revealed the nanostructure and the particle size of soot particles. The XPS survey spectra show a large carbon peak around 285 eV and the oxygen signal at 533 eV. Some differences observed in the carbon/oxygen (C/O) ratio of the particles probably depend on the combustion process efficiency of each cook-stove analyzed. The C-1s XPS spectra show an asymmetric broad peak and other with low intensity that corresponds to sp2 and sp3hybridization, which were fitted with a convolution using Gaussian functions. Elastic backscattering technique allows a chemical elemental analysis of samples and confirms the presence of C, O and Si observed by XPS. Additionally, the morphological properties of soot aggregates were analyzed calculating the border-based fractal dimension (Df). Particles exhibit complex shapes with high values of Df. Also, real-time absorption (σabs) and scattering (σsct) coefficients of fine (with aerodynamic diameter < 2.5 µm) soot particles were measured. The trend in σabs and σsct indicate that the cooking process has two important combustion stages which varied in its flaming strength, being vigorous in the first stage and soft in the second one.

  20. Structural, XPS and magnetic studies of pulsed laser deposited Fe doped Eu{sub 2}O{sub 3} thin film

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

    Kumar, Sandeep; Prakash, Ram, E-mail: rpgiuc@gmail.com; Choudhary, R.J.

    2015-10-15

    Highlights: • Growth of Fe doped Eu{sub 2}O{sub 3} thin films by PLD. • XRD and Raman’s spectroscopy used for structure confirmation. • The electronic states of Eu and Fe are confirmed by XPS. • Magnetic properties reveals room temperature magnetic ordering in deposited film. - Abstract: Fe (4 at.%) doped europium (III) oxide thin film was deposited on silicon (1 0 0) substrate by pulsed laser deposition technique. Structural, spectral and magnetic properties were studied by X-ray diffraction (XRD), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and magnetization measurements. XRD and Raman spectroscopy reveal that the grown film is singlemore » phased and belongs to the cubic structure of Eu{sub 2}O{sub 3}. XPS study of the Eu{sub 1.92}Fe{sub 0.08}O{sub 3} film shows that Fe exists in Fe{sup 3+} ionic state in the film. The film exhibits magnetic ordering at room temperature.« less

  1. Theoretical modeling of the uranium 4f XPS for U(VI) and U(IV) oxides

    NASA Astrophysics Data System (ADS)

    Bagus, Paul S.; Nelin, Connie J.; Ilton, Eugene S.

    2013-12-01

    A rigorous study is presented of the physical processes related to X-Ray photoelectron spectroscopy, XPS, in the 4f level of U oxides, which, as well as being of physical interest in themselves, are representative of XPS in heavy metal oxides. In particular, we present compelling evidence for a new view of the screening of core-holes that extends prior understandings. Our analysis of the screening focuses on the covalent mixing of high lying U and O orbitals as opposed to the, more common, use of orbitals that are nominally pure U or pure O. It is shown that this covalent mixing is quite different for the initial and final, core-hole, configurations and that this difference is directly related to the XPS satellite intensity. Furthermore, we show that the high-lying U d orbitals as well as the U(5f) orbital may both contribute to the core-hole screening, in contrast with previous work that has only considered screening through the U(5f) shell. The role of modifying the U-O interaction by changing the U-O distance has been investigated and an unexpected correlation between U-O distance and XPS satellite intensity has been discovered. The role of flourite and octahedral crystal structures for U(IV) oxides has been examined and relationships established between XPS features and the covalent interactions in the different structures. The physical views of XPS satellites as arising from shake processes or as arising from ligand to metal charge transfers are contrasted; our analysis provides strong support that shake processes give a more fundamental physical understanding than charge transfer. Our theoretical studies are based on rigorous, strictly ab initio determinations of the electronic structure of embedded cluster models of U oxides with formal U(VI) and U(IV) oxidation states. Our results provide a foundation that makes it possible to establish quantitative relationships between features of the XPS spectra and materials properties.

  2. Upgrade of the Surface Spectrometer at NEPOMUC for PAES, XPS and STM Investigations

    NASA Astrophysics Data System (ADS)

    Zimnik, S.; Lippert, F.; Hugenschmidt, C.

    2014-04-01

    The characterization of the elemental composition of surfaces is of great importance for the understanding of many surface processes, such as surface segregation or oxidation. Positron-annihilation-induced Auger Electron Spectroscopy (PAES) is a powerful technique for gathering information about the elemental composition of only the topmost atomic layer of a sample. The upgraded surface spectrometer at NEPOMUC (NEtron induced POsitron source MUniCh) enables a comprehensive surface analysis with the complementary techniques STM, XPS and PAES. A new X-ray source for X-ray induced photoelectron spectroscopy (XPS) was installed to gather additional information on oxidation states. A new scanning tunneling microscope (STM) is used as a complementary method to investigate with atomic resolution the surface electron density. The combination of PAES, XPS and STM allows the characterization of both the elemental composition, and the surface topology.

  3. XPS and bioactivity study of the bisphosphonate pamidronate adsorbed onto plasma sprayed hydroxyapatite coatings

    NASA Astrophysics Data System (ADS)

    McLeod, Kate; Kumar, Sunil; Smart, Roger St. C.; Dutta, Naba; Voelcker, Nicolas H.; Anderson, Gail I.; Sekel, Ron

    2006-12-01

    This paper reports the use of X-ray photoelectron spectroscopy (XPS) to investigate bisphosphonate (BP) adsorption onto plasma sprayed hydroxyapatite (HA) coatings commonly used for orthopaedic implants. BPs exhibit high binding affinity for the calcium present in HA and hence can be adsorbed onto HA-coated implants to exploit their beneficial properties for improved bone growth at the implant interface. A rigorous XPS analysis of pamidronate, a commonly used nitrogenous BP, adsorbed onto plasma sprayed HA-coated cobalt-chromium substrates has been carried out, aimed at: (a) confirming the adsorption of this BP onto HA; (b) studying the BP diffusion profile in the HA coating by employing the technique of XPS depth profiling; (c) confirming the bioactivity of the adsorbed BP. XPS spectra of plasma sprayed HA-coated discs exposed to a 10 mM aqueous BP solution (pamidronate) for periods of 1, 2 and 24 h showed nitrogen and phosphorous photoelectron signals corresponding to the BP, confirming its adsorption onto the HA substrate. XPS depth profiling of the 2 h BP-exposed HA discs showed penetration of the BP into the HA matrix to depths of at least 260 nm. The bioactivity of the adsorbed BP was confirmed by the observed inhibition of osteoclast (bone resorbing) cell activity. In comparison to the HA sample, the HA sample with adsorbed BP exhibited a 25-fold decrease in primary osteoclast cells.

  4. Morphological, chemical and structural characterisation of deciduous enamel: SEM, EDS, XRD, FTIR and XPS analysis.

    PubMed

    Zamudio-Ortega, C M; Contreras-Bulnes, R; Scougall-Vilchis, R J; Morales-Luckie, R A; Olea-Mejía, O F; Rodríguez-Vilchis, L E

    2014-09-01

    The purpose of this study was to characterise the enamel surface of sound deciduous teeth in terms of morphology, chemical composition, structure and crystalline phases. The enamel of 30 human deciduous teeth was examined by: Scanning Electron Microscopy (SEM), Energy Dispersive X-Ray Spectroscopy (EDS), X-ray Powder Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FTIR), and X-ray Photoelectron Spectroscopy (XPS). Chemical differences between incisors and canines were statistically evaluated using the Mann-Whitney U test (p ≤ 0.05). Three enamel patterns were observed by SEM: 'mostly smooth with some groves', 'abundant microporosities' and 'exposed prisms'. The average Ca/P molar ratios were 1.37 and 1.03 by EDS and XPS, respectively. The crystallite size determined by XRD was 210.82 ± 16.78 Å. The mean ratio between Ca bonded to phosphate and Ca bonded to hydroxyl was approximately 10:1. The enamel of sound deciduous teeth showed two main patterns: 'mostly smooth with some groves' and 'abundant microporosities'. 'Exposed prisms' was a secondary pattern. There were slight variations among the Ca/P molar ratios found by EDS and XPS, suggesting differences in the mineral content from the enamel surface to the interior. The crystalline phases found in enamel were hydroxyapatite and carbonate apatite, with major type B than type A carbonate incorporation.

  5. Cohort study comparing prostate photovaporisation with XPS 180W and HPS 120W laser.

    PubMed

    López, B; Capitán, C; Hernández, V; de la Peña, E; Jiménez-Valladolid, I; Guijarro, A; Pérez-Fernández, E; Llorente, C

    2016-01-01

    Prostate photovaporisation with Greenlight laser for the surgical treatment of benign prostate hyperplasia has rapidly evolve to the new XPS 180W. We have previously demonstrated the safety and efficacy of the HPS 120W. The aim of this study was to assess the functional and safety results, with a year of follow-up, of photovaporisation using the XPS 180W laser compared with its predecessor. A cohort study was conducted with a series of 191 consecutive patients who underwent photovaporisation between 1/2008 and 5/2013. The inclusion criteria were an international prostate symptom score (IPSS) >15 after medical failure, a prostate volume <80 cm(3) and a maximum flow <15 mL/s. We assessed preoperative and intraoperative variables (energy used, laser time and total surgical time), complications, catheter hours, length of stay and functional results (maximum flow, IPSS, prostate-specific antigen and prostate volume) at 3, 6 and 12 months. We analysed the homogeneity in preoperative characteristics of the 2 groups through univariate analysis techniques. The postoperative functional results were assessed through an analysis of variance of repeated measures with mixed models. A total of 109 (57.1%) procedures were performed using HPS 120W, and 82 (42.9%) were performed using XPS. There were no differences between the preoperative characteristics. We observed significant differences both in the surgical time and effective laser time in favour of the XPS system. This advantage was 11% (48 ± 15.7 vs. 53.8 ± 16.2, p<.05) and 9% (32.8 ± 11.7 vs. 36 ± 11.6, p<.05), respectively. There were no statistically significant differences in the rest of the analysed parameters. The technical improvements in the XPS 180W system help reduce surgical time, maintaining the safety and efficacy profile offered by the HPS 120W system, with completely superimposable results at 1 year of follow-up. Copyright © 2015 AEU. Publicado por Elsevier España, S.L.U. All rights reserved.

  6. XPS Study of Oxide/GaAs and SiO2/Si Interfaces

    NASA Technical Reports Server (NTRS)

    Grunthaner, F. J.; Grunthaner, P. J.; Vasquez, R. P.; Lewis, B. F.; Maserjian, J.; Madhukar, A.

    1982-01-01

    Concepts developed in study of SiO2/Si interface applied to analysis of native oxide/GaAs interface. High-resolution X-ray photoelectron spectroscopy (XPS) has been combined with precise chemical-profiling technique and resolution-enhancement methods to study stoichiometry of transitional layer. Results are presented in report now available.

  7. Compositional and surface characterization of HULIS by UV-Vis, FTIR, NMR and XPS: Wintertime study in Northern India

    NASA Astrophysics Data System (ADS)

    Kumar, Varun; Goel, Anubha; Rajput, Prashant

    2017-09-01

    This study (first attempt) characterizes HULIS (Humic Like Substances) in wintertime aerosols (n = 12 during day and nighttime each) from Indo-Gangetic Plain (IGP, at Kanpur) by using various state-of-the art techniques such as UV-VIS, FTIR, 1H NMR and XPS. Based on UV-Vis analysis the absorption coefficient at 365 nm (babs-365) of HULIS was found to average at 13.6 and 28.8 Mm-1 during day and nighttime, respectively. Relatively high babs-365 of HULIS during the nighttime is attributed to influence of fog-processing. However, the power fit of UV-Vis spectrum provided near similar AAE (absorption Angstrom exponent) value of HULIS centering at 4.9 ± 1.4 and 5.1 ± 1.3 during daytime and nighttime, respectively. FTIR spectra and its double derivative revealed the presence of various functional groups viz. alcohols, ketones aldehydes, carboxylic acids as well as unsaturated and saturated carbon bonds. 1H NMR spectroscopy was applied to quantify relative percentage of various types of hydrogen atoms contained in HULIS, whereas XPS technique provided information on surface composition and oxidation states of various elements present. A significantly high abundance of H‒C‒O group has been observed in HULIS (based on 1H NMR); 41.4± 2.7% and 30.9± 2.4% in day and nighttime, respectively. However, aromatic protons (Ar-H) were higher in nighttime samples (19.3± 1.8%) as compared to that in daytime samples (7.5 ± 1.9). XPS studies revealed presence of various species on the surface of HULIS samples. Carbon existed in 7 different chemical states while total nitrogen and sulfur exhibited 3 and 2 different oxidation states (respectively) on the surface of HULIS. This study reports structural information and absorption properties of HULIS which has implications to their role as cloud condensation nuclei and atmospheric direct radiative forcing.

  8. X ray photoelectron spectroscopy (XPS) analysis of Photosensitive ZrO2 array

    NASA Astrophysics Data System (ADS)

    Li, Y.; Zhao, G.; Zhu, R.; Kou, Z.

    2018-03-01

    Based on organic zirconium source as the starting material, by adding chemical modifiers which are made up with photosensitive ZrO2 sol. A uniformed ZrO2 array dot was fabricated with a mean diameter of around 800 nm. By using UV-vis spectra and X-ray photoelectron spectroscopy analysis method, studies the photosensitive ZrO2 gel film of photochemical reaction process and the photosensitive mechanism, to determine the zirconium atom centered chelate structure, reaction formed by metal chelate Zr atom for the center, and to establish the molecular model of the chelate. And studied the ultraviolet light in the process of the variation of the XPS spectra, Zr3d5/2 to 184.9 eV corresponding to the binding energy of the as the combination of state peak gradually reduce; By combining with the status of Zr-O peak gradually increase; The strength of the peak is gradually decline. This suggests that in the process of ultraviolet light photo chemical reaction happened. This study is of great significance to the micro fabrication of ZrO2 array not only to the memory devices but also to the optical devices.

  9. Silicon (100)/SiO2 by XPS

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

    Jensen, David S.; Kanyal, Supriya S.; Madaan, Nitesh

    2013-09-25

    Silicon (100) wafers are ubiquitous in microfabrication and, accordingly, their surface characteristics are important. Herein, we report the analysis of Si (100) via X-ray photoelectron spectroscopy (XPS) using monochromatic Al K radiation. Survey scans show that the material is primarily silicon and oxygen, and the Si 2p region shows two peaks that correspond to elemental silicon and silicon dioxide. Using these peaks the thickness of the native oxide (SiO2) was estimated using the equation of Strohmeier.1 The oxygen peak is symmetric. The material shows small amounts of carbon, fluorine, and nitrogen contamination. These silicon wafers are used as the basemore » material for subsequent growth of templated carbon nanotubes.« less

  10. Intensity analysis of XPS spectra to determine oxide uniformity - Application to SiO2/Si interfaces

    NASA Technical Reports Server (NTRS)

    Vasquez, R. P.; Grunthaner, F. J.

    1980-01-01

    A simple method of determining oxide uniformity is derived which requires no knowlege of film thickness, escape depth, or film composition. The method involves only the measurement of oxide and substrate intensities and is illustrated by analysis of XPS spectral data for thin SiO2 films grown both thermally and by low-temperature chemical vapor deposition on monocrystalline Si. A region 20-30 A thick is found near the SiO2/Si interface on thermally oxidized samples which has an inelastic mean free path 35% less than that found in the bulk oxide. This is interpreted as being due to lattice mismatch resulting in a strained region which is structurally, but not stoichiometrically, distinct from the bulk oxide.

  11. Parameter setting for peak fitting method in XPS analysis of nitrogen in sewage sludge

    NASA Astrophysics Data System (ADS)

    Tang, Z. J.; Fang, P.; Huang, J. H.; Zhong, P. Y.

    2017-12-01

    Thermal decomposition method is regarded as an important route to treat increasing sewage sludge, while the high content of N causes serious nitrogen related problems, then figuring out the existing form and content of nitrogen of sewage sludge become essential. In this study, XPSpeak 4.1 was used to investigate the functional forms of nitrogen in sewage sludge, peak fitting method was adopted and the best-optimized parameters were determined. According to the result, the N1s spectra curve can be resolved into 5 peaks: pyridine-N (398.7±0.4eV), pyrrole-N(400.5±0.3eV), protein-N(400.4eV), ammonium-N(401.1±0.3eV) and nitrogen oxide-N(403.5±0.5eV). Based on the the experimental data obtained from elemental analysis and spectrophotometry method, the optimum parameters of curve fitting method were decided: background type: Tougaard, FWHM 1.2, 50% Lorentzian-Gaussian. XPS methods can be used as a practical tool to analysis the nitrogen functional groups of sewage sludge, which can reflect the real content of nitrogen of different forms.

  12. XPS and 31P NMR inquiry of Eu3+-induced structural modification in SnO-containing phosphate glass

    NASA Astrophysics Data System (ADS)

    Jiménez, José A.; Fachini, Esteban Rosim; Zhao, Chunqing

    2018-07-01

    The influence of Eu3+ doping on the structural properties of SnO-containing phosphate glass has been investigated by X-ray photoelectron spectroscopy (XPS) and 31P nuclear magnetic resonance (NMR) spectroscopy. Oxygen 1s XPS data indicates that the Eu3+ doping results in a higher concentration of non-bridging oxygens in the glass matrix, whereas 31P NMR shows an increase in the terminal phosphate chain tetrahedral units, i.e. the amount of Q1 sites with only one bridging oxygen. Accordingly, both techniques agree with a depolymerization effect induced by the Eu3+ ions. Further, XPS reveals that together with the Eu3+ doping, the presence of Sn4+ is supported while the presence of Eu2+ is also indicated. The structural changes are then indicated to be a consequence of redox chemistry between Sn2+ and Eu3+ promoting a transition of tin from Sn2+ with a role as network former to Sn4+ acting as network modifier in the glass system.

  13. Study of fission-product segregation in used CANDU fuel by X-ray photoelectron spectroscopy (XPS) II

    NASA Astrophysics Data System (ADS)

    Hocking, William H.; Duclos, A. Michael; Johnson, Lawrence H.

    1994-03-01

    A thorough investigation of the grain-boundary chemistry of used CANDU fuel from one intact element has been conducted by X-ray photoelectron spectroscopy (XPS). Selected findings from more extensive XPS measurements on other used CANDU fuels exposed to storage conditions are included for comparison. Cesium, rubidium, tellurium and barium have been commonly observed, often reaching high degrees of surface enrichment, although their relative abundances can vary widely with a complex dependence on the fuel irradiation history. Lower concentrations of cadmium, molybdenum, strontium and iodine have also been occasionally detected. Except for iodine, chemical-shift data are indicative of oxidized species, possibly uranates. Segregation at monolayer-level coverages has been demonstrated by sequential XPS analysis and argon-ion sputtering. Calculations based on an idealized thin-film model are consistent with the depth profiles. The interpretation of these results is discussed in the context of previous studies, especially on LWR fuels.

  14. New insights into micro/nanoscale combined probes (nanoAuger, μXPS) to characterize Ag/Au@SiO2 core-shell assemblies

    NASA Astrophysics Data System (ADS)

    Ledeuil, J. B.; Uhart, A.; Soulé, S.; Allouche, J.; Dupin, J. C.; Martinez, H.

    2014-09-01

    This work has examined the elemental distribution and local morphology at the nanoscale of core@shell Ag/Au@SiO2 particles. The characterization of such complex metal/insulator materials becomes more efficient when using an initial cross-section method of preparation of the core@shell nanoparticles (ion milling cross polisher). The originality of this route of preparation allows one to obtain undamaged, well-defined and planar layers of cross-cut nano-objects. Once combined with high-resolution techniques of characterization (XPS, Auger and SEM), the process appears as a powerful way to minimize charging effects and enhance the outcoming electron signal (potentially affected by the topography of the material) during analysis. SEM experiments have unambiguously revealed the hollow-morphology of the metal core, while Auger spectroscopy observations showed chemical heterogeneity within the particles (as silver and gold are randomly found in the core ring). To our knowledge, this is the first time that Auger nano probe spectroscopy has been used and successfully optimized for the study of some complex metal/inorganic interfaces at such a high degree of resolution (~12 nm). Complementarily, XPS Au 4f and Ag 3d peaks were finally detected attesting the possibility of access to the whole chemistry of such nanostructured assemblies.This work has examined the elemental distribution and local morphology at the nanoscale of core@shell Ag/Au@SiO2 particles. The characterization of such complex metal/insulator materials becomes more efficient when using an initial cross-section method of preparation of the core@shell nanoparticles (ion milling cross polisher). The originality of this route of preparation allows one to obtain undamaged, well-defined and planar layers of cross-cut nano-objects. Once combined with high-resolution techniques of characterization (XPS, Auger and SEM), the process appears as a powerful way to minimize charging effects and enhance the outcoming

  15. Effects of Mn Ion Implantation on XPS Spectroscopy of GaN Thin Films

    NASA Astrophysics Data System (ADS)

    Majid, Abdul; Ahmad, Naeem; Rizwan, Muhammad; Khan, Salah Ud-Din; Ali, Fekri Abdulraqeb Ahmed; Zhu, Jianjun

    2018-02-01

    Gallium nitride (GaN) thin film was deposited onto a sapphire substrate and then implanted with 250 keV Mn ions at two different doses of 2 × 1016 ions/cm2 and 5 × 1016 ions/cm2. The as-grown and post-implantation-thermally-annealed samples were studied in detail using x-ray photoelectron spectroscopy (XPS). The XPS peaks of Ga 3 d, Ga 2 p, N 1 s, Mn 2 p and C 1 s were recorded in addition to a full survey of the samples. The doublet peaks of Ga 2 p for pure GaN were observed blue-shifted when compared with elemental Ga, and appeared further shifted to higher energies for the implanted samples. These observations point to changes in the bonds and the chemical environment of the host as a result of ion implantation. The results revealed broadening of the N 1 s peak after implantation, which is interpreted in terms of the presence of N-Mn bonds in addition to N-Ga bonds. The XPS spectra of Mn 2 p recorded for ion-implanted samples indicated splitting of Mn 2 p 1/2 and Mn 2 p 3/2 peaks higher than that for metallic Mn, which helps rule out the possibility of clustering and points to substitutional doping of Mn. These observations provide a framework that sheds light on the local environment of the material for understanding the mechanism of magnetic exchange interactions in Mn:GaN based diluted magnetic semiconductors.

  16. XPS characterization of silver exchanged ETS-10 and mordenite molecular sieves.

    PubMed

    Anson, A; Maham, Y; Lin, C C H; Kuznicki, T M; Kuznicki, S M

    2009-05-01

    Silver exchanged molecular sieves ETS-10 (Ag-ETS-10) and mordenite (Ag-mordenite) were dehydrated under vacuum at temperatures between 100 degrees C-350 degrees C. Changes in the state of the silver were studied using X-ray photoelectron spectroscopy (XPS). Silver cations in titanosilicate Ag-ETS-10 are fully reduced to Ag(0) at temperatures as low as 150 degrees C. The characteristic features of the XPS spectrum of silver in this Ag-ETS-10 species correspond to only metallic silver. The signal for metallic silver is not observed in the XPS spectrum of aluminosilicate Ag-mordenite, indicating that silver cations are not reduced, even after heating to 350 degrees C.

  17. Application of surface analysis to solve problems of wear

    NASA Technical Reports Server (NTRS)

    Buckley, D. H.

    1981-01-01

    Results are presented for the use of surface analytical tools including field ion microscopy, Auger emission spectroscopy analysis (AES), cylindrical mirror Auger analysis and X-ray photoelectron spectroscopy (XPS). Data from the field ion microscope reveal adhesive transfer (wear) at the atomic level with the formation of surface compounds not found in the bulk, and AES reveals that this transfer will occur even in the presence of surface oxides. Both AES and XPS reveal that in abrasive wear with silicon carbide and diamond contacting the transition metals, the surface and the abrasive undergo a chemical or structural change which effects wear. With silicon carbide, silicon volatilizes leaving behind a pseudo-graphitic surface and the surface of diamond is observed to graphitize.

  18. The Gaussian-Lorentzian Sum, Product, and Convolution (Voigt) functions in the context of peak fitting X-ray photoelectron spectroscopy (XPS) narrow scans

    NASA Astrophysics Data System (ADS)

    Jain, Varun; Biesinger, Mark C.; Linford, Matthew R.

    2018-07-01

    X-ray photoelectron spectroscopy (XPS) is arguably the most important vacuum technique for surface chemical analysis, and peak fitting is an indispensable part of XPS data analysis. Functions that have been widely explored and used in XPS peak fitting include the Gaussian, Lorentzian, Gaussian-Lorentzian sum (GLS), Gaussian-Lorentzian product (GLP), and Voigt functions, where the Voigt function is a convolution of a Gaussian and a Lorentzian function. In this article we discuss these functions from a graphical perspective. Arguments based on convolution and the Central Limit Theorem are made to justify the use of functions that are intermediate between pure Gaussians and pure Lorentzians in XPS peak fitting. Mathematical forms for the GLS and GLP functions are presented with a mixing parameter m. Plots are shown for GLS and GLP functions with mixing parameters ranging from 0 to 1. There are fundamental differences between the GLS and GLP functions. The GLS function better follows the 'wings' of the Lorentzian, while these 'wings' are suppressed in the GLP. That is, these two functions are not interchangeable. The GLS and GLP functions are compared to the Voigt function, where the GLS is shown to be a decent approximation of it. Practically, both the GLS and the GLP functions can be useful for XPS peak fitting. Examples of the uses of these functions are provided herein.

  19. An in situ XPS study of L-cysteine co-adsorbed with water on polycrystalline copper and gold

    NASA Astrophysics Data System (ADS)

    Jürgensen, Astrid; Raschke, Hannes; Esser, Norbert; Hergenröder, Roland

    2018-03-01

    The interactions of biomolecules with metal surfaces are important because an adsorbed layer of such molecules introduces complex reactive functionality to the substrate. However, studying these interactions is challenging: they usually take place in an aqueous environment, and the structure of the first few monolayers on the surface is of particular interest, as these layers determine most interfacial properties. Ideally, this requires surface sensitive analysis methods that are operated under ambient conditions, for example ambient pressure x-ray photoelectron spectroscopy (AP-XPS). This paper focuses on an AP-XPS study of the interaction of water vapour and l-Cysteine on polycrystalline copper and gold surfaces. Thin films of l-Cysteine were characterized with XPS in UHV and in a water vapour atmosphere (P ≤ 1 mbar): the structure of the adsorbed l-Cysteine layer depended on substrate material and deposition method, and exposure of the surface to water vapour led to the formation of hydrogen bonds between H2O molecules and the COO- and NH2 groups of adsorbed l-Cysteine zwitterions and neutral molecules, respectively. This study also proved that it is possible to investigate monolayers of biomolecules in a gas atmosphere with AP-XPS using a conventional laboratory Al-Kα x-ray source.

  20. Quantitative analysis of Ni2+/Ni3+ in Li[NixMnyCoz]O2 cathode materials: Non-linear least-squares fitting of XPS spectra

    NASA Astrophysics Data System (ADS)

    Fu, Zewei; Hu, Juntao; Hu, Wenlong; Yang, Shiyu; Luo, Yunfeng

    2018-05-01

    Quantitative analysis of Ni2+/Ni3+ using X-ray photoelectron spectroscopy (XPS) is important for evaluating the crystal structure and electrochemical performance of Lithium-nickel-cobalt-manganese oxide (Li[NixMnyCoz]O2, NMC). However, quantitative analysis based on Gaussian/Lorentzian (G/L) peak fitting suffers from the challenges of reproducibility and effectiveness. In this study, the Ni2+ and Ni3+ standard samples and a series of NMC samples with different Ni doping levels were synthesized. The Ni2+/Ni3+ ratios in NMC were quantitatively analyzed by non-linear least-squares fitting (NLLSF). Two Ni 2p overall spectra of synthesized Li [Ni0.33Mn0.33Co0.33]O2(NMC111) and bulk LiNiO2 were used as the Ni2+ and Ni3+ reference standards. Compared to G/L peak fitting, the fitting parameters required no adjustment, meaning that the spectral fitting process was free from operator dependence and the reproducibility was improved. Comparison of residual standard deviation (STD) showed that the fitting quality of NLLSF was superior to that of G/L peaks fitting. Overall, these findings confirmed the reproducibility and effectiveness of the NLLSF method in XPS quantitative analysis of Ni2+/Ni3+ ratio in Li[NixMnyCoz]O2 cathode materials.

  1. A ToF-SIMS and XPS study of protein adsorption and cell attachment across PEG-like plasma polymer films with lateral compositional gradients

    NASA Astrophysics Data System (ADS)

    Menzies, Donna J.; Jasieniak, Marek; Griesser, Hans J.; Forsythe, John S.; Johnson, Graham; McFarland, Gail A.; Muir, Benjamin W.

    2012-12-01

    In this work we report a detailed X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) study of poly(ethylene glycol) PEG-like chemical gradients deposited via plasma enhanced chemical vapour deposition (PECVD) at two different load powers using diethylene glycol dimethyl ether (DG) as a monomer. Principal component analysis (PCA) was applied to the ToF-SIMS data both before and after protein adsorption on the plasma polymer thin films. Results of the PCA loadings indicated a higher content of hydrocarbon fragments across the higher load power gradient, which adsorbed higher amounts of proteins. Gradients deposited at a lower load power retained a higher degree of monomer like functionality as did the central region directly underneath the knife edge electrode. Analysis of the adsorption of serum proteins (human serum albumin and fetal bovine serum) was monitored across the gradient films and increased with decreasing ether (PEG-like) film chemistries. The effect of protein incubation time on the levels adsorbed fetal bovine serum on the plasma polymer films was critical, with significantly more protein adsorbing after 24 hour incubation times on both gradient films. The attachment of HeLa cells on the gradients appeared to be dictated not only by the surface chemistry, but also by the adsorption of serum proteins. XPS analysis revealed that at surface ether concentrations of less than 70% in the gradient films, significant increases in protein and cell attachment were observed.

  2. XPS analysis of Al/EPDM bondlines from IUS SRM-1 polar bosses

    NASA Astrophysics Data System (ADS)

    Hemminger, Carol S.; Marquez, Nicholas

    1993-03-01

    A temperature-stress rupture method using partial immersion in liquid nitrogen was developed for the aluminum/EPDM rubber insulation bondline of the IUS SRM-1 polar bosses in order to investigate a corrosion problem. Subsequent XPS analysis of the ruptured bondline followed changes in the locus of failure as corrosion progressed. Samples from the forward polar bosses had a predominantly noncorroded appearance on the ruptured surfaces. The locus of failure was predominantly through the primer layer, which is distinguished by a high concentration of chlorinated hydrocarbon. The aft polar boss segments analyzed were characterized by the presence of corrosion over the entire mid-section of the ruptured aluminum to insulation bondline. The predominant corrosion product detected was aluminum oxide/hydroxide. The corroded bondline sections had significantly higher concentrations of aluminum oxide/hydroxide than the noncorroded areas, and lower concentrations of primer material. The temperature-stress rupture appeared to progress most readily through areas of thickened aluminum oxide/hydroxide infiltrated into the primer layer. In general there was a very good correlation between the calculated Cl:Al atomic % ratio, and the visual characterization of the extent of corrosion. The Cl:Al ratio, which represents the primer to corrosion product ratio at the locus of failure, varied from 0.4 to 47. With only a few exceptions, surfaces with a predominantly noncorroded appearance had Cl:Al ratios greater than 2, and surfaces with a heavily corroded appearance had Cl:Al ratios less than 1.

  3. New insights into micro/nanoscale combined probes (nanoAuger, μXPS) to characterize Ag/Au@SiO2 core-shell assemblies.

    PubMed

    Ledeuil, J B; Uhart, A; Soulé, S; Allouche, J; Dupin, J C; Martinez, H

    2014-10-07

    This work has examined the elemental distribution and local morphology at the nanoscale of core@shell Ag/Au@SiO2 particles. The characterization of such complex metal/insulator materials becomes more efficient when using an initial cross-section method of preparation of the core@shell nanoparticles (ion milling cross polisher). The originality of this route of preparation allows one to obtain undamaged, well-defined and planar layers of cross-cut nano-objects. Once combined with high-resolution techniques of characterization (XPS, Auger and SEM), the process appears as a powerful way to minimize charging effects and enhance the outcoming electron signal (potentially affected by the topography of the material) during analysis. SEM experiments have unambiguously revealed the hollow-morphology of the metal core, while Auger spectroscopy observations showed chemical heterogeneity within the particles (as silver and gold are randomly found in the core ring). To our knowledge, this is the first time that Auger nano probe spectroscopy has been used and successfully optimized for the study of some complex metal/inorganic interfaces at such a high degree of resolution (≈12 nm). Complementarily, XPS Au 4f and Ag 3d peaks were finally detected attesting the possibility of access to the whole chemistry of such nanostructured assemblies.

  4. Gold/silver core-shell 20 nm nanoparticles extracted from citrate solution examined by XPS

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

    Engelhard, Mark H.; Smith, Jordan N.; Baer, Donald R.

    Silver nanoparticles of many types are widely used in consumer and medical products. The surface chemistry of particles and the coatings that form during synthesis or use in many types of media can significantly impact the behaviors of particles including dissolution, transformation and biological or environmental impact. Consequently it is useful to be able to extract information about the thickness of surface coatings and other attributes of nanoparticles produced in a variety of ways. It has been demonstrated that X-ray Photoelectron Spectroscopy (XPS) can be reliably used to determine the thickness of organic and other nanoparticles coatings and shells. However,more » care is required to produce reliable and consistent information. Here we report the XPS spectra from gold/silver core-shell nanoparticles of nominal size 20 nm removed from a citrate saturated solution after one and two washing cycles. The Simulation of Electron Spectra for Surface Analysis (SESSA) program had been used to model peak amplitudes to obtain information on citrate coatings that remain after washing and demonstrate the presence of the gold core. This data is provided so that others can compare use of SESSA or other modeling approaches to quantify the nature of coatings to those already published and to explore the impacts particle non-uniformities on XPS signals from core-shell nanoparticles.« less

  5. Rondorfite-type structure — XPS and UV–vis study

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

    Dulski, M., E-mail: mateusz.dulski@smcebi.edu.pl; A.Chelkowski Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice; Bilewska, K., E-mail: kbilewska@us.edu.pl

    2015-10-15

    Highlights: • Structural and spectroscopic characterization of chlorosilicate mineral, rondorfite. • Characterization of main photoemission lines and valence band spectra. • The study of color origin’s using UV–vis spectroscopy. • Analysis of structural changes in context of origin of natural fluorescence. • Discussion of a new application possibilities of analyzed mineral - Abstract: This paper focuses on X-ray diffraction, X-ray photoelectron and UV–vis spectroscopy of two different (green, orange) rondorfite samples. The differences in the sample color originate from various O/Cl ratios. The orange color was found to be related either to the isomorphic substitution of Fe{sup 3+}/Al{sup 3+} formore » Mg{sup 2+}, the presence of atypical [MgO{sub 4}] tetrahedrons in crystal structure or electronegativity of the sample. The tetrahedron is known to be very prone to accumulation of impurities and substitute atoms. Moreover, the XPS data showed tetrahedrally coordinated Mg{sup 2+} and isomorphic substitution of Al{sup 3+}/Fe{sup 3+} for Mg{sup 2+}, which influences local disordering and the point defects density and distribution. Non-equilibrium chlorine positions inside the crystal cages as well as Ca-Cl bonds have also been found. The XPS measurements as a function of temperature indicate occurrence of a structural transformation at about 770 K which is accompanied by a rotation of silicate tetrahedra within magnesiosilicate pentamer and luminescence disappearance.« less

  6. Characterization of fossil remains using XRF, XPS and XAFS spectroscopies

    NASA Astrophysics Data System (ADS)

    Zougrou, I. M.; Katsikini, M.; Pinakidou, F.; Brzhezinskaya, M.; Papadopoulou, L.; Vlachos, E.; Tsoukala, E.; Paloura, E. C.

    2016-05-01

    Synchrotron radiation micro-X-Ray Fluorescence (μ-XRF), X-ray photoelectron (XPS) and X-ray Absorption Fine Structure (XAFS) spectroscopies are applied for the study of paleontological findings. More specifically the costal plate of a gigantic terrestrial turtle Titanochelon bacharidisi and a fossilized coprolite of the cave spotted hyena Crocuta crocuta spelaea are studied. Ca L 2,3-edge NEXAFS and Ca 2p XPS are applied for the identification and quantification of apatite and Ca containing minerals. XRF mapping and XAFS are employed for the study of the spatial distribution and speciation of the minerals related to the deposition environment.

  7. XUV Photometer System (XPS): New Dark-Count Corrections Model and Improved Data Products

    NASA Astrophysics Data System (ADS)

    Elliott, J. P.; Vanier, B.; Woods, T. N.

    2017-12-01

    We present newly updated dark-count calibrations for the SORCE XUV Photometer System (XPS) and the resultant improved data products released in March of 2017. The SORCE mission has provided a 14-year solar spectral irradiance record, and the XPS contributes to this record in the 0.1 nm to 40 nm range. The SORCE spacecraft has been operating in what is known as Day-Only Operations (DO-Op) mode since February of 2014. In this mode it is not possible to collect data, including dark-counts, when the spacecraft is in eclipse as we did prior to DO-Op. Instead, we take advantage of the position of the XPS filter-wheel, and collect these data when the wheel position is in a "dark" position. Further, in this mode dark data are not always available for all observations, requiring an extrapolation in order to calibrate data at these times. To extrapolate, we model this with a piece-wise 2D nonlinear least squares surface fit in the time and temperature dimensions. Our model allows us to calibrate XPS data into the DO-Op phase of the mission by extrapolating along this surface. The XPS version 11 data product release benefits from this new calibration. We present comparisons of the previous and current calibration methods in addition to planned future upgrades of our data products.

  8. Incorporation of low energy activated nitrogen onto HOPG surface: Chemical states and thermal stability studies by in-situ XPS and Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Chandran, Maneesh; Shasha, Michal; Michaelson, Shaul; Hoffman, Alon

    2016-09-01

    In this paper we report the chemical states analysis of activated nitrogen incorporated highly oriented pyrolytic graphite (HOPG) surface under well-controlled conditions. Nitrogen incorporation is carried out by two different processes: an indirect RF nitrogen plasma and low energy (1 keV) N2+ implantation. Bonding configuration, concentration and thermal stability of the incorporated nitrogen species by aforesaid processes are systematically compared by in-situ X-ray photoelectron spectroscopy (XPS). Relatively large concentration of nitrogen is incorporated onto RF nitride HOPG surface (16.2 at.%), compared to N2+ implanted HOPG surface (7.7 at.%). The evolution of N 1s components (N1, N2, N3) with annealing temperature is comprehensively discussed, which indicates that the formation and reorganization of local chemical bonding states are determined by the process of nitridation and not by the prior chemical conditioning (i.e., amorphization or hydrogenation) of the HOPG surface. A combined XPS and Raman spectroscopy studies revealed that N2+ implantation process resulted in a high level of defects to the HOPG surface, which cannot be annealed-out by heat treatment up to 1000 °C. On the other hand, the RF nitrogen plasma process did not produce a high level of surface defects, while incorporating nearly the same amount of stable nitrogen species.

  9. 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.

  10. Surface composition XPS analysis of a plasma treated polystyrene: Evolution over long storage periods.

    PubMed

    Ba, Ousmane M; Marmey, Pascal; Anselme, Karine; Duncan, Anthony C; Ponche, Arnaud

    2016-09-01

    A polystyrene surface (PS) was initially treated by cold nitrogen and oxygen plasma in order to incorporate in particular amine and hydroxyl functions, respectively. The evolution of the chemical nature of the surface was further monitored over a long time period (580 days) by chemical assay, XPS and contact angle measurements. Surface density quantification of primary amine groups was performed using three chemical amine assays: 4-nitrobenzaldehyde (4-NBZ), Sulfo succinimidyl 6-[3'(2 pyridyldithio)-pionamido] hexanoate (Sulfo-LC-SPDP) and iminothiolane (ITL). The results showed amine densities were in the range of 2 per square nanometer (comparable to the results described in the literature) after 5min of nitrogen plasma treatment. Over the time period investigated, chemical assays, XPS and contact angles suggest a drastic significant evolution of the chemical nature of the surface within the first two weeks. Beyond that time period and up to almost two years, nitrogen plasma modified substrates exhibits a slow and continuous oxidation whereas oxygen plasma modifed polystyrene surface is chemically stable after two weeks of storage. The latter appeared to "ease of" showing relatively mild changes within the one year period. Our results suggest that it may be preferable to wait for a chemical "stabilization" period of two weeks before subsequent covalent immobilization of proteins onto the surface. The originality of this work resides in the study of the plasma treated surface chemistry evolution over long periods of storage time (580 days) considerably exceeding those described in the literature. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Chemistry Characterization of Jet Aircraft Engine Particulate by XPS: Results from APEX III

    NASA Technical Reports Server (NTRS)

    Vander Wal, Randy L.; Bryg, Victoria M.

    2014-01-01

    This paper reports XPS analysis of jet exhaust particulate from a B737, Lear, ERJ, and A300 aircraft during the APEX III NASA led field campaign. Carbon hybridization and bonding chemistry are identified by high-resolution scans about the C1s core-shell region. Significant organic content as gauged by the sp3/sp2 ratio is found across engines and platforms. Polar oxygen functional groups include carboxylic, carbonyl and phenol with combined content of 20 percent or more. By lower resolution survey scans various elements including transition metals are identified along with lighter elements such as S, N, and O in the form of oxides. Burning additives within lubricants are probable sources of Na, Ba, Ca, Zn, P and possibly Sn. Elements present and their percentages varied significantly across all engines, not revealing any trend or identifiable cause for the differences, though the origin is likely the same for the same element when observed. This finding suggests that their presence can be used as a tracer for identifying soots from aircraft engines as well as diagnostic for monitoring engine performance and wear.

  12. 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.

  13. X-PEEM, XPS and ToF-SIMS characterisation of xanthate induced chalcopyrite flotation: Effect of pulp potential

    NASA Astrophysics Data System (ADS)

    Kalegowda, Yogesh; Chan, Yuet-Loy; Wei, Der-Hsin; Harmer, Sarah L.

    2015-05-01

    Synchrotron-based X-ray photoemission electron microscopy (X-PEEM), X-ray photo-electron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS) and ultraviolet visible spectroscopy were used to characterize the flotation behaviour of chalcopyrite with xanthate at different processing conditions. The flotation recovery of chalcopyrite decreased from 97% under oxidative conditions (Eh ~ 385 mV SHE, pH 4) to 41% at a reductive potential of - 100 mV SHE (at pH 9). X-PEEM images constructed from the metal L3 absorption edges were used to produce near-edge X-ray absorption fine structure (NEXAFS) spectra from regions of interest, allowing the variability in mineral surface chemistry of each mineral particle to be analysed, and the effect of pulp potential (Eh) on the flotation of chalcopyrite to be determined. XPS, ToF-SIMS and NEXAFS analyses of chalcopyrite particles at oxidative conditions show that the surface was mildly oxidised and covered with adsorbed molecular CuEX. The Cu 2p XPS and Cu L2,3 NEXAFS spectra were dominated by CuI species attributed to bulk chalcopyrite and adsorbed CuEX. At a reductive potential of - 100 mV SHE, an increase in concentration of CuI and FeIII oxides and hydroxides was observed. X-PEEM analysis was able to show the presence of a low percentage of CuII oxides (CuO or Cu(OH)2) with predominantly CuI oxide (Cu2O) which is not evident in Cu 2p XPS spectra.

  14. Surface Characterization of Polymer Blends by XPS and ToF-SIMS

    PubMed Central

    Chan, Chi Ming; Weng, Lu-Tao

    2016-01-01

    The surface properties of polymer blends are important for many industrial applications. The physical and chemical properties at the surface of polymer blends can be drastically different from those in the bulk due to the surface segregation of the low surface energy component. X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary mass spectrometry (ToF-SIMS) have been widely used to characterize surface and bulk properties. This review provides a brief introduction to the principles of XPS and ToF-SIMS and their application to the study of the surface physical and chemical properties of polymer blends. PMID:28773777

  15. Dynamic XPS measurements of ultrathin polyelectrolyte films containing antibacterial Ag–Cu nanoparticles

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

    Taner-Camcı, Merve; Suzer, Sefik, E-mail: suzer@fen.bilkent.edu.tr

    Ultrathin films consisting of polyelectrolyte layers prepared by layer-by-layer deposition technique and containing also Ag and Cu nanoparticles exhibit superior antibacterial activity toward Escherichia coli. These films have been investigated with XPS measurements under square wave excitation at two different frequencies, in order to further our understanding about the chemical/physical nature of the nanoparticles. Dubbed as dynamical XPS, such measurements bring out similarities and differences among the surface structures by correlating the binding energy shifts of the corresponding XPS peaks. Accordingly, it is observed that the Cu2p, Ag3d of the metal nanoparticles, and S2p of cysteine, the stabilizer and themore » capping agent, exhibit similar shifts. On the other hand, the C1s, N1s, and S2p peaks of the polyelectrolyte layers shift differently. This finding leads us the claim that the Ag and Cu atoms are in a nanoalloy structure, capped with cystein, as opposed to phase separated entities.« less

  16. Arsenopyrite and pyrite bioleaching: evidence from XPS, XRD and ICP techniques.

    PubMed

    Fantauzzi, Marzia; Licheri, Cristina; Atzei, Davide; Loi, Giovanni; Elsener, Bernhard; Rossi, Giovanni; Rossi, Antonella

    2011-10-01

    In this work, a multi-technical bulk and surface analytical approach was used to investigate the bioleaching of a pyrite and arsenopyrite flotation concentrate with a mixed microflora mainly consisting of Acidithiobacillus ferrooxidans. X-ray diffraction, X-ray photoelectron spectroscopy (XPS) and X-ray-induced Auger electron spectroscopy mineral surfaces investigations, along with inductively coupled plasma-atomic emission spectroscopy and carbon, hydrogen, nitrogen and sulphur determination (CHNS) analyses, were carried out prior and after bioleaching. The flotation concentrate was a mixture of pyrite (FeS(2)) and arsenopyrite (FeAsS); after bioleaching, 95% of the initial content of pyrite and 85% of arsenopyrite were dissolved. The chemical state of the main elements (Fe, As and S) at the surface of the bioreactor feed particles and of the residue after bioleaching was investigated by X-ray photoelectron and X-ray excited Auger electron spectroscopy. After bioleaching, no signals of iron, arsenic and sulphur originating from pyrite and arsenopyrite were detected, confirming a strong oxidation and the dissolution of the particles. On the surfaces of the mineral residue particles, elemental sulphur as reaction intermediate of the leaching process and precipitated secondary phases (Fe-OOH and jarosite), together with adsorbed arsenates, was detected. Evidence of microbial cells adhesion at mineral surfaces was also produced: carbon and nitrogen were revealed by CHNS, and nitrogen was also detected on the bioleached surfaces by XPS. This was attributed to the deposition, on the mineral surfaces, of the remnants of a bio-film consisting of an extra-cellular polymer layer that had favoured the bacterial action. © Springer-Verlag 2011

  17. Interfaces in heterogeneous catalytic reactions: Ambient pressure XPS as a tool to unravel surface chemistry

    DOE PAGES

    Palomino, Robert M.; Hamlyn, Rebecca; Liu, Zongyuan; ...

    2017-04-27

    In this paper we provide a summary of the recent development of ambient pressure X-ray photoelectron spectroscopy (AP-XPS) and its application to catalytic surface chemistry. The methodology as well as significant advantages and challenges associated with this novel technique are described. Details about specific examples of using AP-XPS to probe surface chemistry under working reaction conditions for a number of reactions are explained: CO oxidation, water-gas shift (WGS), CO 2 hydrogenation, dry reforming of methane (DRM) and ethanol steam reforming (ESR). In conclusion, we discuss insights into the future development of the AP-XPS technique and its applications.

  18. Interfaces in heterogeneous catalytic reactions: Ambient pressure XPS as a tool to unravel surface chemistry

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

    Palomino, Robert M.; Hamlyn, Rebecca; Liu, Zongyuan

    In this paper we provide a summary of the recent development of ambient pressure X-ray photoelectron spectroscopy (AP-XPS) and its application to catalytic surface chemistry. The methodology as well as significant advantages and challenges associated with this novel technique are described. Details about specific examples of using AP-XPS to probe surface chemistry under working reaction conditions for a number of reactions are explained: CO oxidation, water-gas shift (WGS), CO 2 hydrogenation, dry reforming of methane (DRM) and ethanol steam reforming (ESR). In conclusion, we discuss insights into the future development of the AP-XPS technique and its applications.

  19. XPS analysis of activated carbon supported ionic liquids: Enhanced purity and reduced charging

    NASA Astrophysics Data System (ADS)

    Foelske-Schmitz, A.; Weingarth, D.; Kötz, R.

    2011-12-01

    Herein we report on XPS measurements on five different [EMIM] based ionic liquids (IL) prepared on activated carbon and aluminium supports. The anions were [TFSI], [BF4], [FAP], [B(CN)4] and [EtOSO3]. The results show that impurities such as O, Si or hydrocarbons were significantly reduced or no longer detected when preparation was performed on the high surface area carbon support. All core level spectra were fitted and for [EMIM][FAP], [EMIM][B(CN)4] and [EMIM][EtOSO3] de-convolution procedures of the C 1s lines are suggested. Comparison of the determined binding energies with published data strongly suggests that sample charging is irrelevant when preparation is performed on the activated carbon support. This observation is supposed to refer to the high capacitance of the high surface area carbon.

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

    PubMed

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

    2015-02-21

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

  1. Initial stages of oxide formation on the Zr surface at low oxygen pressure: An in situ FIM and XPS study

    PubMed Central

    Bespalov, I.; Datler, M.; Buhr, S.; Drachsel, W.; Rupprechter, G.; Suchorski, Y.

    2015-01-01

    An improved methodology of the Zr specimen preparation was developed which allows fabrication of stable Zr nanotips suitable for FIM and AP applications. Initial oxidation of the Zr surface was studied on a Zr nanotip by FIM and on a polycrystalline Zr foil by XPS, both at low oxygen pressure (10−8–10−7 mbar). The XPS data reveal that in a first, fast stage of oxidation, a Zr suboxide interlayer is formed which contains three suboxide components (Zr+1, Zr+2 and Zr+3) and is located between the Zr surface and a stoichiometric ZrO2 overlayer that grows in a second, slow oxidation stage. The sole suboxide layer has been observed for the first time at very early states of the oxidation (oxygen exposure ≤4 L). The Ne+ FIM observations are in accord with a two stage process of Zr oxide formation. PMID:25766998

  2. XPS analysis of 440C steel surfaces lubricated with perfluoropolyethers under sliding conditions in high vacuum

    NASA Technical Reports Server (NTRS)

    Herrera-Fierro, Pilar; Masuko, Masabumi; Jones, William R., Jr.; Pepper, Stephen V.

    1994-01-01

    This work presents the results of the X-Ray Photoelectron Spectroscopy (XPS) analysis of AISI 440C ball surfaces lubricated with perfluoropolyether (PFPE) oils after friction experiments under sliding conditions at high load in air and vacuum environments. The PFPE lubricants tested were Demnum S100, Fomblin Z-25, and Krytox 143AB. It was found that all the PFPE lubricants were degraded by sliding contact causing the formation of inorganic fluorides on the metallic surfaces and a layer of organic decomposition products. KRYTOX 143AB was the least reactive of the three lubricants tested. It was also found that metal fluoride formed at off-scar areas. This suggests the formation of reactive species, such as COF2 or R(sub f)COF, during sliding experiments, which can diffuse through the lubricant film and react with the metallic surfaces away from the contact region. Comparison of reference specimens before sliding with those that had undergone the sliding tests showed that the amount of non-degraded PFPE remaining on the surface of the balls after the sliding experiments was greater than that of the balls without sliding.

  3. XPS study of the effect of hydrocarbon contamination on polytetrafluoroethylene (teflon) exposed to atomic oxygen

    NASA Technical Reports Server (NTRS)

    Golub, Morton A.; Wydeven, Theodore; Cormia, Robert D.

    1991-01-01

    The presence of hydrocarbon contamination on the surface of polytetrafluoroethylene (PTFE) markedly affects the oxygen uptake, and hence the wettability, of this polymer when exposed to an oxygen plasma. As revealed by X-ray photoelectron spectroscopy (XPS) analysis, the oxygen-to-carbon ratio (O/C) for such a polymer can increase sharply, and correspondingly the fluorine-to-carbon ratio (F/C) can decrease sharply, at very short exposure times; at longer times, however, such changes in the O/C and F/C ratios reverse direction, and these ratios then assume values similar to those of the unexposed PTFE. The greater the extent of hydrocarbon contamination in the PTFE, the larger are the amplitudes of the 'spikes' in the O/C- and F/C-exposure time plots. In contrast, a pristine PTFE experiences a very small, monotonic increase of surface oxidation or O/C ratio with time of exposure to oxygen atoms, while the F/C ratio is virtually unchanged from that of the unexposed polymer (2.0). Unless the presence of adventitious hydrocarbon is taken into account, anomalous surface properties relating to polymer adhesion may be improperly ascribed to PTFE exposed to an oxygen plasma.

  4. In-situ XPS analysis of oxidized and reduced plasma deposited ruthenium-based thin catalytic films

    NASA Astrophysics Data System (ADS)

    Balcerzak, Jacek; Redzynia, Wiktor; Tyczkowski, Jacek

    2017-12-01

    A novel in-situ study of the surface molecular structure of catalytically active ruthenium-based films subjected to the oxidation (in oxygen) and reduction (in hydrogen) was performed in a Cat-Cell reactor combined with a XPS spectrometer. The films were produced by the plasma deposition method (PEMOCVD). It was found that the films contained ruthenium at different oxidation states: metallic (Ru0), RuO2 (Ru+4), and other RuOx (Ru+x), of which content could be changed by the oxidation or reduction, depending on the process temperature. These results allow to predict the behavior of the Ru-based catalysts in different redox environments.

  5. A first-principles core-level XPS study on the boron impurities in germanium crystal

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

    Yamauchi, Jun; Yoshimoto, Yoshihide; Suwa, Yuji

    2013-12-04

    We systematically investigated the x-ray photoelectron spectroscopy (XPS) core-level shifts and formation energies of boron defects in germanium crystals and compared the results to those in silicon crystals. Both for XPS core-level shifts and formation energies, relationship between defects in Si and Ge is roughly linear. From the similarity in the formation energy, it is expected that the exotic clusters like icosahedral B12 exist in Ge as well as in Si.

  6. XPS studies of nitrogen doping niobium used for accelerator applications

    NASA Astrophysics Data System (ADS)

    Yang, Ziqin; Lu, Xiangyang; Tan, Weiwei; Zhao, Jifei; Yang, Deyu; Yang, Yujia; He, Yuan; Zhou, Kui

    2018-05-01

    Nitrogen doping study on niobium (Nb) samples used for the fabrication of superconducting radio frequency (SRF) cavities was carried out. The samples' surface treatment was attempted to replicate that of the Nb SRF cavities, which includes heavy electropolishing (EP), nitrogen doping and the subsequent EP with different amounts of material removal. The surface chemical composition of Nb samples with different post treatments has been studied by XPS. The chemical composition of Nb, O, C and N was presented before and after Gas Cluster Ion Beam (GCIB) etching. No signals of poorly superconducting nitrides NbNx was found on the surface of any doped Nb sample with the 2/6 recipe before GCIB etching. However, in the depth range greater than 30 nm, the content of N element is below the XPS detection precision scope even for the Nb sample directly after nitrogen doping treatment with the 2/6 recipe.

  7. XPS analysis of the effect of fillers on PTFE transfer film development in sliding contacts

    NASA Technical Reports Server (NTRS)

    Blanchet, T. A.; Kennedy, F. E.; Jayne, D. T.

    1993-01-01

    The development of transfer films atop steel counterfaces in contact with unfilled and bronze-filled PTFE has been studied using X-ray photoelectron spectroscopy. The sliding apparatus was contained within the vacuum of the analytical system, so the effects of the native oxide, hydrocarbon, and adsorbed gaseous surface layers of the steel upon the PTFE transfer behavior could be studied in situ. For both the filled and the unfilled PTFE, cleaner surfaces promoted greater amounts of transfer. Metal fluorides, which formed at the transfer film/counterface interface, were found solely in cases where the native oxide had been removed to expose the metallic surface prior to sliding. These fluorides also were found at clean metal/PTFE interfaces formed in the absence of frictional contact. A fraction of these fluorides resulted from irradiation damage inherent in XPS analysis. PTFE transfer films were found to build up with repeated sliding passes, by a process in which strands of transfer filled in the remaining counterface area. Under these reported test conditions, the transfer process is not expected to continue atop previously deposited transfer films. The bronze-filled composite generated greater amounts of transfer than the unfilled PTFE. The results are discussed relative to the observed increase in wear resistance imparted to PTFE by a broad range of inorganic fillers.

  8. Effect of nitrogen plasma afterglow on the surface charge effect resulted during XPS surface analysis of amorphous carbon nitride thin films

    NASA Astrophysics Data System (ADS)

    Kayed, Kamal

    2018-06-01

    The aim of this paper is to investigate the relationship between the micro structure and the surface charge effect resulted during XPS surface analysis of amorphous carbon nitride thin films prepared by laser ablation method. The study results show that the charge effect coefficient (E) is not just a correction factor. We found that the changes in this coefficient value due to incorporation of nitrogen atoms into the carbon network are related to the spatial configurations of the sp2 bonded carbon atoms, order degree and sp2 clusters size. In addition, results show that the curve E vs. C(sp3)-N is a characteristic curve of the micro structure. This means that using this curve makes it easy to sorting the samples according to the micro structure (hexagonal rings or chains).

  9. Applications Performance on NAS Intel Paragon XP/S - 15#

    NASA Technical Reports Server (NTRS)

    Saini, Subhash; Simon, Horst D.; Copper, D. M. (Technical Monitor)

    1994-01-01

    The Numerical Aerodynamic Simulation (NAS) Systems Division received an Intel Touchstone Sigma prototype model Paragon XP/S- 15 in February, 1993. The i860 XP microprocessor with an integrated floating point unit and operating in dual -instruction mode gives peak performance of 75 million floating point operations (NIFLOPS) per second for 64 bit floating point arithmetic. It is used in the Paragon XP/S-15 which has been installed at NAS, NASA Ames Research Center. The NAS Paragon has 208 nodes and its peak performance is 15.6 GFLOPS. Here, we will report on early experience using the Paragon XP/S- 15. We have tested its performance using both kernels and applications of interest to NAS. We have measured the performance of BLAS 1, 2 and 3 both assembly-coded and Fortran coded on NAS Paragon XP/S- 15. Furthermore, we have investigated the performance of a single node one-dimensional FFT, a distributed two-dimensional FFT and a distributed three-dimensional FFT Finally, we measured the performance of NAS Parallel Benchmarks (NPB) on the Paragon and compare it with the performance obtained on other highly parallel machines, such as CM-5, CRAY T3D, IBM SP I, etc. In particular, we investigated the following issues, which can strongly affect the performance of the Paragon: a. Impact of the operating system: Intel currently uses as a default an operating system OSF/1 AD from the Open Software Foundation. The paging of Open Software Foundation (OSF) server at 22 MB to make more memory available for the application degrades the performance. We found that when the limit of 26 NIB per node out of 32 MB available is reached, the application is paged out of main memory using virtual memory. When the application starts paging, the performance is considerably reduced. We found that dynamic memory allocation can help applications performance under certain circumstances. b. Impact of data cache on the i860/XP: We measured the performance of the BLAS both assembly coded and Fortran

  10. A comprehensive study of catalytic, morphological and electronic properties of ligand-protected gold nanoclusters using XPS, STM, XAFS, and TPD techniques

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

    Wu, Qiyuan; Cen, Jiajie; Zhao, Yue

    Ultra-small gold nanoclusters were synthesized via a ligand exchange method and deposited onto different TiO2 supports to study their properties. STM imaging revealed that the as-synthesized gold nanoclusters had 2-D morphology consisting of monolayers of gold atoms. In conclusion, subsequent XPS, XAFS, and CO oxidation TPD results indicated that heat treatments of gold clusters at different temperatures significantly altered their electronic and catalytic properties due to ligand deprotection and cluster agglomeration.

  11. A comprehensive study of catalytic, morphological and electronic properties of ligand-protected gold nanoclusters using XPS, STM, XAFS, and TPD techniques

    DOE PAGES

    Wu, Qiyuan; Cen, Jiajie; Zhao, Yue; ...

    2017-12-08

    Ultra-small gold nanoclusters were synthesized via a ligand exchange method and deposited onto different TiO2 supports to study their properties. STM imaging revealed that the as-synthesized gold nanoclusters had 2-D morphology consisting of monolayers of gold atoms. In conclusion, subsequent XPS, XAFS, and CO oxidation TPD results indicated that heat treatments of gold clusters at different temperatures significantly altered their electronic and catalytic properties due to ligand deprotection and cluster agglomeration.

  12. The (001) 3C SiC surface termination and band structure after common wet chemical etching procedures, stated by XPS, LEED, and HREELS

    NASA Astrophysics Data System (ADS)

    Tengeler, Sven; Kaiser, Bernhard; Ferro, Gabriel; Chaussende, Didier; Jaegermann, Wolfram

    2018-01-01

    The (001) surface of cubic silicon carbide (3C SiC) after cleaning, Ar sputtering and three different wet chemical etching procedures was thoroughly investigated via (angle resolved) XPS, HREELS, and LEED. While Ar sputtering was found to be unsuitable for surface preparation, all three employed wet chemical etching procedures (piranha/NH4F, piranha/HF, and RCA) provide a clean surface. HF as oxide removal agent tends to result in fluorine traces on the sample surface, despite thorough rinsing. All procedures yield a 1 × 1 Si-OH/C-H terminated surface. However, the XPS spectra reveal some differences in the resulting surface states. NH4F for oxide removal produces a flat band situation, whereas the other two procedures result in a slight downward (HF) or upward (RCA) band bending. Because the band bending is small, it can be concluded that the number of unsaturated surface defects is low.

  13. X-ray Photoelectron Spectroscopy (XPS), Rutherford Back Scattering (RBS) studies

    NASA Technical Reports Server (NTRS)

    Neely, W. C.; Bozak, M. J.; Williams, J. R.

    1993-01-01

    X-ray photoelectron spectroscopy (XPS), Rutherford Back Scattering (RBS) studies of each of sample received were completed. Since low angle X-ray could not be performed because of instrumentation problems, Auger spectrometry was employed instead. The results of these measurements for each of the samples is discussed in turn.

  14. XPS and ToF-SIMS analysis of natural rubies and sapphires heat-treated in a reducing (5 mol% H 2/Ar) atmosphere

    NASA Astrophysics Data System (ADS)

    Achiwawanich, S.; James, B. D.; Liesegang, J.

    2008-12-01

    Surface effects on Mong Hsu rubies and Kanchanaburi sapphires after heat treatment in a controlled reducing atmosphere (5 mol% H 2/Ar) have been investigated using advanced surface science techniques including X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Visual appearance of the gemstones is clearly affected by the heat treatment in a reducing atmosphere. Kanchanaburi sapphires, in particular, exhibit Fe-containing precipitates after the heat treatment which have not been observed in previous studies under an inert atmosphere. Significant correlation between changes in visual appearance of the gemstones and variations in surface concentration of trace elements, especially Ti and Fe are observed. The XPS and ToF-SIMS results suggest that; (1) a reducing atmosphere affects the oxidation state of Fe; (2) dissociation of Fe-Ti interaction may occur during heat treatment.

  15. XPS analysis of PE and EVA samples irradiated at different γ-doses

    NASA Astrophysics Data System (ADS)

    Dorey, Samuel; Gaston, Fanny; Marque, Sylvain R. A.; Bortolotti, Benjamin; Dupuy, Nathalie

    2018-01-01

    The principal plastic materials used for the fluid contact and storage in the biopharmaceutical industry are mainly made up of semi-crystalline polymers, polyolefins, PVC, Siloxane and PET. The polyethylene (PE) and the polypropylene (PP) are often used as fluid contact in multi-layer materials like films. As one sterilisation way of single-use plastic devices used in medical and pharmaceutical fields can take place via γ-irradiation, the effect of sterilization on plastics must be investigated. The irradiation process leads to the production of radicals, which can generate changes in the polymer structure and on the polymer surface. It is well known that the presence of oxygen with free radicals precede the generation of peroxide species so called ROS (reactive oxygen species) which are highly reactive. The purpose of this work is to investigate the γ-rays impact on the surface of PE (polyethylene) and EVA (polyethylene vinyl alcohol) based films when ionized at different doses. X-ray Photoelectron Spectroscopy (XPS) was applied to determine the surface compositions of the polymers to highlight the different chemical moieties generated during the γ-irradiation process and to monitor the potential presence of the ROS.

  16. New Pt/Alumina model catalysts for STM and in situ XPS studies

    NASA Astrophysics Data System (ADS)

    Nartova, Anna V.; Gharachorlou, Amir; Bukhtiyarov, Andrey V.; Kvon, Ren I.; Bukhtiyarov, Valerii I.

    2017-04-01

    The new Pt/alumina model catalysts for STM and in situ XPS studies based on thin alumina film formed over the conductive substrate are proposed. Procedure of platinum deposition developed for porous alumina was adapted for the model alumina support. The set of Pt/AlOx-film samples with the different mean platinum particle size was prepared. Capabilities of in situ XPS investigations of the proposed catalysts were demonstrated in study of NO decomposition on platinum nanoparticles. It is shown that proposed model catalysts behave similarly to Pt/γ-Al2O3 and provide the new opportunities for the instrumental studies of platinum catalysts due to resolving several issues (charging, heating, screening) that are typical for the investigation of the porous oxide supported catalysts.

  17. XPS and UPS studies on electronic structure of Li 2O

    NASA Astrophysics Data System (ADS)

    Tanaka, Satoru; Taniguchi, Masaki; Tanigawa, Hisashi

    2000-12-01

    The adsorption behavior of H 2O on Li 2O was studied by X-ray photo electron spectroscopy (XPS) and ultraviolet photo electron spectroscopy (UPS). XPS and UPS spectra of Li 2O single crystals which were exposed to different pressure of H 2O vapor were observed. In O(1s) region, two peaks were observed and they were assigned to O(1s) in precipitated LiOH on the surface and O(1s) in Li 2O. After H 2O exposure, a peak broadening and an appearance of a new peak were observed at the higher binding energy region than O(1s) in Li 2O. They were attributed to surface -OH and H 2O molecule adsorbed on the surface. The adsorption behavior of H 2O was discussed from the observation of electronic structure in Li 2O surface.

  18. XPS Spectra Analysis of Ti2+, Ti3+ Ions and Dye Photodegradation Evaluation of Titania-Silica Mixed Oxide Nanoparticles

    NASA Astrophysics Data System (ADS)

    Chinh, Vu Duc; Broggi, Alessandra; Di Palma, Luca; Scarsella, Marco; Speranza, Giorgio; Vilardi, Giorgio; Thang, Pham Nam

    2018-04-01

    TiO2-SiO2 mixed oxides have been prepared by the sol-gel technique from tetrabutyl orthotitanate and tetraethyl orthosilicate. The prepared materials were characterized by x-ray diffraction, scanning electron microscopy, energy dispersive x-ray spectroscopy, nitrogen physisorption, Fourier-transform infrared spectroscopy (FT-IR) and x-ray photoelectron spectroscopy (XPS). The results indicate that the TiO2-SiO2 mixed oxides have a large surface area and a nanoscale size. FT-IR spectra show that Ti atoms are bonded to silica by oxygen bridging atoms in Ti-O-Si bonds. The titanium valence states in TiO2-SiO2 mixed oxides were investigated by XPS, and their spectra report the presence of Ti2+ and Ti3+ cations for high silica concentration, suggesting the formation of oxygen vacancies. The photocatalytic activity of the prepared materials has been evaluated for the photodegradation of methylene blue (MB). The mixed oxides were activated by means of a UV light source, and the concentration of MB was monitored by UV-Vis spectroscopy. The synthesized TiO2-SiO2 shows significantly higher MB removal efficiency in comparison with that of the commercial TiO2 Degussa, P25.

  19. RECENT XPS STUDIES OF THE EFFECT OF PROCESSING ON NB SRF SURFACES

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

    Hui Tian; Binping Xiao; Michael Kelley

    XPS studies have consistently shown that Nb surfaces for SRF chiefly comprise of a few nm of Nb2O5 on top of Nb metal, with minor amounts of Nb sub-oxides. Nb samples after BCP/EP treatment with post-baking at the various conditions have been examined by using synchrotron based XPS. Despite the confounding influence of surface roughness, certain outcomes are clear. Lower-valence Nb species are always and only associated with the metal/oxide interface, but evidence for an explicit layer structure or discrete phases is lacking. Post-baking without air exposure shows decreased oxide layer thickness and increased contribution from lower valence species, butmore » spectra obtained after subsequent air exposure cannot be distinguished from those obtained prior to baking, though the SRF performance improvement remains.« less

  20. Surface analysis of glass fibres using XPS and AFM: case study of glass fibres recovered from the glass fibre reinforced polymer using chemical recycling

    NASA Astrophysics Data System (ADS)

    Nzioka, A. M.; Kim, Y. J.

    2018-01-01

    In this study, we present the results of an experimental study of the use of the X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) to characterise the coatings of the recovered E - glass fibres. The recovered E - glass fibres were obtained using chemical recycling process coupled with ultrasound cavitation. The objective of this study was to analyse the impact of chemical recycling and the ultrasound cavitation process on the sizing properties of the recovered fibres. We obtained the recovered fibres and sized using 1 wt% 3 - aminopropyltriethoxysilane (APS). Part of the sized fibres was washed with acetone and analysed all the sample fibres using AFM and XPS. Results showed the different composition of sizing after extraction using acetone. We compared the results of this study with that of virgin clean glass fibres.

  1. Samarium electrodeposited acetate and oxide thin films on stainless steel substrate characterized by XPS

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

    Myhre, Kristian; Burns, Jonathan; Meyer, Harry

    Characterization of a samarium thin film deposited on a stainless steel substrate using molecular electrodeposition was carried out using a Thermo Scientific K-Alpha X-ray photoelectron spectrometer. We studied two types of samarium electrodeposition samples, one as-deposited and one heated to 700 °C in an air flow. Survey scans include peaks coming from the stainless steel substrate, such as Fe and Cr. An X-ray photoelectron spectroscopy (XPS) survey spectrum, Sm 3d, C 1s, and O 1s narrow scans are shown. It was determined that the heating process decomposed the deposited Sm acetate to Sm 2O 3 using XPS.

  2. Samarium electrodeposited acetate and oxide thin films on stainless steel substrate characterized by XPS

    DOE PAGES

    Myhre, Kristian; Burns, Jonathan; Meyer, Harry; ...

    2016-06-01

    Characterization of a samarium thin film deposited on a stainless steel substrate using molecular electrodeposition was carried out using a Thermo Scientific K-Alpha X-ray photoelectron spectrometer. We studied two types of samarium electrodeposition samples, one as-deposited and one heated to 700 °C in an air flow. Survey scans include peaks coming from the stainless steel substrate, such as Fe and Cr. An X-ray photoelectron spectroscopy (XPS) survey spectrum, Sm 3d, C 1s, and O 1s narrow scans are shown. It was determined that the heating process decomposed the deposited Sm acetate to Sm 2O 3 using XPS.

  3. Determination of trace metals in TSP and PM2.5 materials collected in the Metropolitan Area of Monterrey, Mexico: A characterization study by XPS, ICP-AES and SEM-EDS

    NASA Astrophysics Data System (ADS)

    González, Lucy T.; Longoria Rodríguez, F. E.; Sánchez-Domínguez, M.; Cavazos, Aleyda; Leyva-Porras, C.; Silva-Vidaurri, L. G.; Askar, Karim Acuña; Kharissov, B. I.; Villarreal Chiu, J. F.; Alfaro Barbosa, J. M.

    2017-11-01

    The concentration levels of trace metals of toxicological importance were evaluated in the total suspended particles (TSP) and particulate matter smaller than 2.5 μm (PM2.5) collected in the Metropolitan Area of Monterrey (MAM) in Mexico. Samples were characterized by inductively coupled plasma atomic emission spectroscopy (ICP-AES), X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy with an energy-dispersive spectroscopy system (SEM-EDS). In addition, the data were statistically treated by the methodology of Pearson Correlation (PC) and Principal Components Analysis (PCA) to identify the possible emitting sources. Surface analysis of the particulate matter (PM) by XPS revealed that the most abundant elements were Ca, Al, Na, Zn, Cu and Mg. The deconvolution of the Ca2p, Zn2p and Cu2p signals showed that the main contributors were CaCO3, ZnO and Cu/Cu2O, respectively. The bulk analysis of the PM by ICP-AES showed Fe, Cu and Zn as the most abundant elements. Fe-rich particles presented two different morphologies: the prismatic particles were associated with a natural origin, while the spherical particles with anthropogenic sources. The Zn and Cu were predominantly observed in the sampling stations with high vehicular traffic, and the emitting sources were associated with the burning of fuels from automobiles and the wear of the tires and brakes. The highest concentration of Pb was detected in the sampling station located near the industrial zones, and its cause was associated with the ceramic and glass industries, the burning of fuel oil in power plants and the production of lead-based batteries for automobiles.

  4. Colloidal diatomite, radionickel, and humic substance interaction: a combined batch, XPS, and EXAFS investigation.

    PubMed

    Sheng, Guodong; Shen, Runpu; Dong, Huaping; Li, Yimin

    2013-06-01

    This work determined the influence of humic acid (HA) and fulvic acid (FA) on the interaction mechanism and microstructure of Ni(II) onto diatomite by using batch experiments, X-ray photoelectron spectroscopy (XPS), and extended X-ray absorption fine structure (EXAFS) methods. Macroscopic and spectroscopic experiments have been combined to see the evolution of the interaction mechanism and microstructure of Ni(II) in the presence of HA/FA as compared with that in the absence of HA/FA. The results indicated that the interaction of Ni(II) with diatomite presents the expected solution pH edge at 7.0, which is modified by addition of HA/FA. In the presence of HA/FA, the interaction of Ni(II) with diatomite increased below solution pH 7.0, while Ni(II) interaction decreased above solution pH 7.0. XPS analysis suggested that the enrichment of Ni(II) onto diatomite may be due to the formation of (≡SO)2Ni. EXAFS results showed that binary surface complexes and ternary surface complexes of Ni(II) can be simultaneously formed in the presence of HA/FA, whereas only binary surface complexes of Ni(II) are formed in the absence of HA/FA, which contribute to the enhanced Ni(II) uptake at low pH values. The results observed in this work are important for the evaluation of Ni(II) and related radionuclide physicochemical behavior in the natural soil and water environment.

  5. XPS and biocompatibility studies of titania film on anodized NiTi shape memory alloy.

    PubMed

    Chu, C L; Wang, R M; Hu, T; Yin, L H; Pu, Y P; Lin, P H; Dong, Y S; Guo, C; Chung, C Y; Yeung, K W K; Chu, Paul K

    2009-01-01

    A dense titania film is fabricated in situ on NiTi shape memory alloy (SMA) by anodic oxidation in a Na(2)SO(4) electrolyte. The microstructure of the titania film and its influence on the biocompatibility of NiTi SMA are investigated by scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), inductively coupled plasma mass spectrometry (ICPMS), hemolysis analysis, and platelet adhesion test. The results indicate that the titania film has a Ni-free zone near the surface and can effectively block the release of harmful Ni ions from the NiTi substrate in simulated body fluids. Moreover, the wettability, hemolysis resistance, and thromboresistance of the NiTi sample are improved by this anodic oxidation method.

  6. Investigating early stages of biocorrosion with XPS: AISI 304 stainless steel exposed to Burkholderia species

    NASA Astrophysics Data System (ADS)

    Johansson, Leena-Sisko; Saastamoinen, Tuomas

    1999-04-01

    We have investigated the interactions of an exopolymer-producing bacteria, Burkholderia sp. with polished AISI 304 stainless steel substrates using X-ray photoelectron spectroscopy (XPS). Steel coupons were exposed to the pure bacteria culture in a specially designed flowcell for 6 h during which the experiment was monitored in situ with an optical microscope. XPS results verified the formation of biofilm containing extracellular polymer on all the samples exposed to bacteria. Sputter results indicated that some ions needed for metabolic processes were trapped within the biofilm. Changes in the relative Fe concentration and Fe 2p peak shape indicated that also iron had accumulated into the biofilm.

  7. NEXAFS and XPS characterization of molecular oxygen adsorbed on Ni(100) at 80 K

    NASA Astrophysics Data System (ADS)

    Kim, C. M.; Jeong, H. S.; Kim, E. H.

    2000-07-01

    X-ray photoelectron spectroscopy (XPS), thermal desorption spectroscopy (TDS) and near edge extended X-ray absorption fine structure (NEXAFS) have been combined to investigate the adsorption of oxygen on Ni(100) at 80 K. Three O(1s) XPS features were observed at 530.0, 531.1 and 534.7 eV when the Ni(100) surface was exposed to 600 L of oxygen at 80 K. They are assigned as O 2-, O 1- and molecular oxygen species, respectively. The presence of molecular oxygen has been confirmed by TDS and NEXAFS. Molecular O 2 on Ni(100) is oriented perpendicular to the surface, and the OO bond length is estimated to be 1.24 Å, based on the NEXAFS σ ∗ resonance energy.

  8. Quantification of the toxic hexavalent chromium content in an organic matrix by X-ray photoelectron spectroscopy (XPS) and ultra-low-angle microtomy (ULAM)

    NASA Astrophysics Data System (ADS)

    Greunz, Theresia; Duchaczek, Hubert; Sagl, Raffaela; Duchoslav, Jiri; Steinberger, Roland; Strauß, Bernhard; Stifter, David

    2017-02-01

    Cr(VI) is known for its corrosion inhibitive properties and is, despite legal regulations, still a potential candidate to be added to thin (1-3 μm) protective coatings applied on, e.g., electrical steel as used for transformers, etc. However, Cr(VI) is harmful to the environment and to the human health. Hence, a reliable quantification of it is of decisive interest. Commonly, an alkaline extraction with a photometric endpoint detection of Cr(VI) is used for such material systems. However, this procedure requires an accurate knowledge on sample parameters such as dry film thickness and coating density that are occasionally associated with significant experimental errors. We present a comprehensive study of a coating system with a defined Cr(VI) pigment concentration applied on electrical steel. X-ray photoelectron spectroscopy (XPS) was employed to resolve the elemental chromium concentration and the chemical state. Turning to the fact that XPS is extremely surface sensitive (<10 nm) and that the lowest commonly achievable lateral resolution is a number of times higher than the coating thickness (∼2 μm), a bulk analysis was achieved with XPS line scans on extended wedge-shaped tapers through the coating. For that purpose a special sample preparation step performed on an ultra-microtome was required prior to analysis. Since a temperature increase leads to a reduction of Cr(VI) we extend our method on samples, which were subjected to different curing temperatures. We show that our proposed approach now allows to determine the elemental and Cr(VI) concentration and distribution inside the coating.

  9. Electron spectroscopy analysis

    NASA Technical Reports Server (NTRS)

    Gregory, John C.

    1992-01-01

    The Surface Science Laboratories at the University of Alabama in Huntsville (UAH) are equipped with x-ray photoelectron spectroscopy (XPS or ESCA) and Auger electron spectroscopy (AES) facilities. These techniques provide information from the uppermost atomic layers of a sample, and are thus truly surface sensitive. XPS provides both elemental and chemical state information without restriction on the type of material that can be analyzed. The sample is placed into an ultra high vacuum (UHV) chamber and irradiated with x-rays which cause the ejection of photoelectrons from the sample surface. Since x-rays do not normally cause charging problems or beam damage, XPS is applicable to a wide range of samples including metals, polymers, catalysts, and fibers. AES uses a beam of high energy electrons as a surface probe. Following electronic rearrangements within excited atoms by this probe, Auger electrons characteristic of each element present are emitted from the sample. The main advantage of electron induced AES is that the electron beam can be focused down to a small diameter and localized analysis can be carried out. On the rastering of this beam synchronously with a video display using established scanning electron microscopy techniques, physical images and chemical distribution maps of the surface can be produced. Thus very small features, such as electronic circuit elements or corrosion pits in metals, can be investigated. Facilities are available on both XPS and AES instruments for depth-profiling of materials, using a beam of argon ions to sputter away consecutive layers of material to reveal sub-surface (and even semi-bulk) analyses.

  10. XPS and EELS characterization of Mn2SiO4, MnSiO3 and MnAl2O4

    NASA Astrophysics Data System (ADS)

    Grosvenor, A. P.; Bellhouse, E. M.; Korinek, A.; Bugnet, M.; McDermid, J. R.

    2016-08-01

    X-ray Photoelectron Spectroscopy (XPS) and Electron Energy Loss Spectroscopy (EELS) are strong candidate techniques for characterizing steel surfaces and substrate-coating interfaces when investigating the selective oxidation and reactive wetting of advanced high strength steels (AHSS) during the continuous galvanizing process. However, unambiguous identification of ternary oxides such as Mn2SiO4, MnSiO3, and MnAl2O4 by XPS or EELS, which can play a significant role in substrate reactive wetting, is difficult due to the lack of fully characterized standards in the literature. To resolve this issue, samples of Mn2SiO4, MnSiO3 and MnAl2O4 were synthesized and characterized by XPS and EELS. The unique features of the XPS and EELS spectra for the Mn2SiO4, MnSiO3 and MnAl2O4 standards were successfully derived, thereby allowing investigators to fully differentiate and identify these oxides at the surface and subsurface of Mn, Si and Al alloyed AHSS using these techniques.

  11. Americium(III) capture using phosphonic acid-functionalized silicas with different mesoporous morphologies: adsorption behavior study and mechanism investigation by EXAFS/XPS.

    PubMed

    Zhang, Wen; He, Xihong; Ye, Gang; Yi, Rong; Chen, Jing

    2014-06-17

    Efficient capture of highly toxic radionuclides with long half-lives such as Americium-241 is crucial to prevent radionuclides from diffusing into the biosphere. To reach this purpose, three different types of mesoporous silicas functionalized with phosphonic acid ligands (SBA-POH, MCM-POH, and BPMO-POH) were synthesized via a facile procedure. The structure, surface chemistry, and micromorphology of the materials were fully characterized by (31)P/(13)C/(29)Si MAS NMR, XPS, and XRD analysis. Efficient adsorption of Am(III) was realized with a fast rate to reach equilibrium (within 10 min). Influences including structural parameters and functionalization degree on the adsorption behavior were investigated. Slope analysis of the equilibrium data suggested that the coordination with Am(III) involved the exchange of three protons. Moreover, extended X-ray absorption fine structure (EXAFS) analysis, in combination with XPS survey, was employed for an in-depth probe into the binding mechanism by using Eu(III) as a simulant due to its similar coordination behavior and benign property. The results showed three phosphonic acid ligands were coordinated to Eu(III) in bidentate fashion, and Eu(P(O)O)3(H2O) species were formed with the Eu-O coordination number of 7. These phosphonic acid-functionalized mesoporous silicas should be promising for the treatment of Am-containing radioactive liquid waste.

  12. Comparing XPS on bare and capped ZrN films grown by plasma enhanced ALD: Effect of ambient oxidation

    NASA Astrophysics Data System (ADS)

    Muneshwar, Triratna; Cadien, Ken

    2018-03-01

    In this article we compare x-ray photoelectron spectroscopy (XPS) measurements on bare- and capped- zirconium nitride (ZrN) films to investigate the effect of ambient sample oxidation on the detected bound O in the form of oxide ZrO2 and/or oxynitride ZrOxNy. ZrN films in both bare- and Al2O3/AlN capped- XPS samples were grown by plasma-enhanced atomic layer deposition (PEALD) technique using tetrakis dimethylamino zirconium (TDMAZr) precursor, forming gas (5% H2, rest N2) inductively coupled plasma (ICP), and as received research grade process gases under identical process conditions. Capped samples were prepared by depositing 1 nm thick PEALD AlN on ZrN, followed by additional deposition of 1 nm thick ALD Al2O3, without venting of ALD reactor. On bare ZrN sample at room temperature, spectroscopic ellipsometry (SE) measurements with increasing ambient exposure times (texp) showed a self-limiting surface oxidation with the oxide thickness (dox) approaching 3.7 ± 0.02 nm for texp > 120 min. In XPS data measured prior to sample sputtering (tsput = 0), ZrO2 and ZrOxNy were detected in bare- samples, whereas only ZrN and Al2O3/AlN from capping layer were detected in capped- samples. For bare-ZrN samples, appearance of ZrO2 and ZrOxNy up to sputter depth (dsput) of 15 nm in depth-profile XPS data is in contradiction with measured dox = 3.7 nm, but explained from sputtering induced atomic inter-diffusion within analyzed sample. Appearance of artifacts in the XPS spectra from moderately sputtered (dsput = 0.2 nm and 0.4 nm) capped-ZrN sample, provides an evidence to ion-bombardment induced modifications within analyzed sample.

  13. In vivo characterization of magnesium alloy biodegradation using electrochemical H2 monitoring, ICP-MS, and XPS.

    PubMed

    Zhao, Daoli; Wang, Tingting; Nahan, Keaton; Guo, Xuefei; Zhang, Zhanping; Dong, Zhongyun; Chen, Shuna; Chou, Da-Tren; Hong, Daeho; Kumta, Prashant N; Heineman, William R

    2017-03-01

    The effect of widely different corrosion rates of Mg alloys on four parameters of interest for in vivo characterization was evaluated: (1) the effectiveness of transdermal H 2 measurements with an electrochemical sensor for noninvasively monitoring biodegradation compared to the standard techniques of in vivo X-ray imaging and weight loss measurement of explanted samples, (2) the chemical compositions of the corrosion layers of the explanted samples by XPS, (3) the effect on animal organs by histology, and (4) the accumulation of corrosion by-products in multiple organs by ICP-MS. The in vivo biodegradation of three magnesium alloys chosen for their widely varying corrosion rates - ZJ41 (fast), WKX41 (intermediate) and AZ31 (slow) - were evaluated in a subcutaneous implant mouse model. Measuring H 2 with an electrochemical H 2 sensor is a simple and effective method to monitor the biodegradation process in vivo by sensing H 2 transdermally above magnesium alloys implanted subcutaneously in mice. The correlation of H 2 levels and biodegradation rate measured by weight loss shows that this non-invasive method is fast, reliable and accurate. Analysis of the insoluble biodegradation products on the explanted alloys by XPS showed all of them to consist primarily of Mg(OH) 2 , MgO, MgCO 3 and Mg 3 (PO 4 ) 2 with ZJ41 also having ZnO. The accumulation of magnesium and zinc were measured in 9 different organs by ICP-MS. Histological and ICP-MS studies reveal that there is no significant accumulation of magnesium in these organs for all three alloys; however, zinc accumulation in intestine, kidney and lung for the faster biodegrading alloy ZJ41 was observed. Although zinc accumulates in these three organs, no toxicity response was observed in the histological study. ICP-MS also shows higher levels of magnesium and zinc in the skull than in the other organs. Biodegradable devices based on magnesium and its alloys are promising because they gradually dissolve and thereby

  14. Toward a better determination of dairy powders surface composition through XPS matrices development.

    PubMed

    Nikolova, Y; Petit, J; Sanders, C; Gianfrancesco, A; Scher, J; Gaiani, C

    2015-01-01

    The surface composition of dairy powders prepared by mixing various amounts of micellar casein (MC), whey proteins isolate (WPI), lactose, and anhydrous milk fat (AMF) was investigated by XPS measurements. The use of matrices are generally accepted to transform surface atomic composition (i.e., C, O, N contents) into surface component composition (i.e., lactose, proteins, lipids). These atomic-based matrices were revisited and two new matrices based on the surface bond composition were developed. Surface compositions obtained from atomic and bond-based matrices were compared. A successful matrix allowing good correlations between XPS predicted and theoretical surface composition for powders free from fat was identified. Nevertheless, samples containing milk fat were found to present a possible segregation of components owing to the AMF overrepresentation on the surface. Supplementary analyses (FTIR, SEM) were carried out in order to investigate the homogeneity of the mixtures. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. In situ NAP-XPS spectroscopy during methane dry reforming on ZrO2/Pt(1 1 1) inverse model catalyst

    NASA Astrophysics Data System (ADS)

    Rameshan, C.; Li, H.; Anic, K.; Roiaz, M.; Pramhaas, V.; Rameshan, R.; Blume, R.; Hävecker, M.; Knudsen, J.; Knop-Gericke, A.; Rupprechter, G.

    2018-07-01

    Due to the need of sustainable energy sources, methane dry reforming is a useful reaction for conversion of the greenhouse gases CH4 and CO2 to synthesis gas (CO  +  H2). Syngas is the basis for a wide range of commodity chemicals and can be utilized for fuel production via Fischer–Tropsch synthesis. The current study focuses on spectroscopic investigations of the surface and reaction properties of a ZrO2/Pt inverse model catalyst, i.e. ZrO2 particles (islands) grown on a Pt(1 1 1) single crystal, with emphasis on in situ near ambient pressure x-ray photoelectron spectroscopy (NAP-XPS) during MDR reaction. In comparison to technological systems, model catalysts facilitate characterization of the surface (oxidation) state, surface adsorbates, and the role of the metal-support interface. Using XPS and infrared reflection absorption spectroscopy we demonstrated that under reducing conditions (UHV or CH4) the ZrO2 particles transformed to an ultrathin ZrO2 film that started to cover (wet) the Pt surface in an SMSI-like fashion, paralleled by a decrease in surface/interface oxygen. In contrast, (more oxidizing) dry reforming conditions with a 1:1 ratio of CH4 and CO2 were stabilizing the ZrO2 particles on the model catalyst surface (or were even reversing the strong metal support interaction (SMSI) effect), as revealed by in situ XPS. Carbon deposits resulting from CH4 dissociation were easily removed by CO2 or by switching to dry reforming conditions (673–873 K). Thus, at these temperatures the active Pt surface remained free of carbon deposits, also preserving the ZrO2/Pt interface.

  16. 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

  17. Ultrathin TiO(x) films on Pt(111): a LEED, XPS, and STM investigation.

    PubMed

    Sedona, Francesco; Rizzi, Gian Andrea; Agnoli, Stefano; Llabrés i Xamena, Francesc X; Papageorgiou, Anthoula; Ostermann, Dieter; Sambi, Mauro; Finetti, Paola; Schierbaum, Klaus; Granozzi, Gaetano

    2005-12-29

    Ultrathin ordered titanium oxide films on Pt(111) surface are prepared by reactive evaporation of Ti in oxygen. By varying the Ti dose and the annealing conditions (i.e., temperature and oxygen pressure), six different long-range ordered phases are obtained. They are characterized by means of low-energy electron diffraction (LEED), X-ray photoemission spectroscopy (XPS), and scanning tunneling microscopy (STM). By careful optimization of the preparative parameters, we find conditions where predominantly single phases of TiO(x), revealing distinct LEED pattern and STM images, are produced. XPS binding energy and photoelectron diffraction (XPD) data indicate that all the phases, except one (the stoichiometric rect-TiO2), are one monolayer thick and composed of a Ti-O bilayer with interfacial Ti. Atomically resolved STM images confirm that these TiO(x) phases wet the Pt surface, in contrast to rect-TiO2. This indicates their interface stabilization. At a low Ti dose (0.4 monolayer equivalents, MLE), an incommensurate kagomé-like low-density phase (k-TiO(x) phase) is observed where hexagons are sharing their vertexes. At a higher Ti dose (0.8 MLE), two denser phases are found, both characterized by a zigzag motif (z- and z'-TiO(x) phases), but with distinct rectangular unit cells. Among them, z'-TiO(x), which is obtained by annealing in ultrahigh vacuum (UHV), shows a larger unit cell. When the postannealing of the 0.8 MLE deposit is carried out at high temperatures and high oxygen partial pressures, the incommensurate nonwetting, fully oxidized rect-TiO2 is found The symmetry and lattice dimensions are almost identical with rect-VO2, observed in the system VO(x)/Pd(111). At a higher coverage (1.2 MLE), two commensurate hexagonal phases are formed, namely the w- [(square root(43) x square root(43)) R 7.6 degrees] and w'-TiO(x) phase [(7 x 7) R 21.8 degrees]. They show wagon-wheel-like structures and have slightly different lattice dimensions. Larger Ti deposits

  18. The Effect of Thermal and Mechanical Treatments on Kaolinite: Characterization by XPS and IEP Measurements.

    PubMed

    Torres Sánchez RM; Basaldella; Marco

    1999-07-15

    The surface transformations induced on kaolinite by different thermal and mechanical treatments have been investigated by means of X-ray photoelectron spectroscopy (XPS), Bremsstrahlung induced Auger spectroscopy, and isoelectric point (IEP) measurements. Heating the kaolinite at temperatures between 500 and 750 degrees C results in the change of a substantial fraction of surface Al from octahedral to tetrahedral coordination, which we associate with the dehydroxylation of kaolinite. Heating at 900 and 980 degrees C brings about the development of an octahedral Al fraction which is associated with the formation of gamma-Al(2)O(3). The development of an Al tetrahedral component in the Al KLL spectra of the mechanically treated (ground) samples has been also observed. The Si/Al atomic ratio obtained by XPS in the thermally treated samples is the same as that shown by the original kaolinite. However, the XPS data show a clear reduction of the Si/Al atomic ratio in the mechanically treated samples, which suggests that the mechanical treatment has induced an Al enrichment of the kaolinite surface. The IEP values indicated a thermal transformation to metakaolinite and mullite with the increase of temperature (750 to 980 degrees C). The IEP change for the milled samples can be only explained by assuming a 30% kaolinite coating by the Al oxide neoformed by grinding. Copyright 1999 Academic Press.

  19. [XPS analysis of beads formed by fuse breaking of electric copper wire].

    PubMed

    Wu, Ying; Meng, Qing-Shan; Wang, Xin-Ming; Gao, Wei; Di, Man

    2010-05-01

    The in-depth composition of beads formed by fuse breaking of the electric copper wire in different circumstances was studied by XPS with Ar+ ion sputtering. In addition, the measured Auger spectra and the calculated Auger parameters were compared for differentiation of the substances of Cu and Cu2O. Corresponding to the sputtering depth, the molten product on a bead induced directly by fuse breaking of the copper wire without cover may be distinguished as three portions: surface layer with a drastic decrease in carbon content; intermediate layer with a gentle change in oxygen content and gradually diminished carbon peak, and consisting of Cu2O; transition layer without Cu2O and with a rapid decrease in oxygen content. While the molten product on a bead formed by fuse breaking of the copper wire after its insulating cover had been burned out may be distinguished as two portions: surface layer with carbon content decreasing quickly; subsurface layer without Cu2O and with carbon and oxygen content decreasing gradually. Thus, it can be seen that there was an obvious interface between the layered surface product and the substrate for the first type of bead, while as to the second type of bead there was no interface. As a result, the presence of Cu2O and the quantitative results can be used to identify the molten product on a bead induced directly by fuse breaking of the copper wire without cover and the molten product on a bead formed by fuse breaking of the cupper wire after its insulating cover had been burned out, as a complementary technique for the judgments of fire cause.

  20. Highly efficient removal of heavy metals by polymer-supported nanosized hydrated Fe(III) oxides: behavior and XPS study.

    PubMed

    Pan, Bingjun; Qiu, Hui; Pan, Bingcai; Nie, Guangze; Xiao, Lili; Lv, Lu; Zhang, Weiming; Zhang, Quanxing; Zheng, Shourong

    2010-02-01

    The present study developed a polymer-based hybrid sorbent (HFO-001) for highly efficient removal of heavy metals [e.g., Pb(II), Cd(II), and Cu(II)] by irreversibly impregnating hydrated Fe(III) oxide (HFO) nanoparticles within a cation-exchange resin D-001 (R-SO(3)Na), and revealed the underlying mechanism based on X-ray photoelectron spectroscopy (XPS) study. HFO-001 combines the excellent handling, flow characteristics, and attrition resistance of conventional cation-exchange resins with the specific affinity of HFOs toward heavy metal cations. As compared to D-001, sorption selectivity of HFO-001 toward Pb(II), Cu(II), and Cd(II) was greatly improved from the Ca(II) competition at greater concentration. Column sorption results indicated that the working capacity of HFO-001 was about 4-6 times more than D-001 with respect to removal of three heavy metals from simulated electroplating water (pH approximately 4.0). Also, HFO-001 is particularly effective in removing trace Pb(II) and Cd(II) from simulated natural waters to meet the drinking water standard, with treatment volume orders of magnitude higher than D-001. The superior performance of HFO-001 was attributed to the Donnan membrane effect exerted by the host D-001 as well as to the impregnated HFO nanoparticles of specific interaction toward heavy metal cations, as further confirmed by XPS study on lead sorption. More attractively, the exhausted HFO-001 beads can be effectively regenerated by HCl-NaCl solution (pH 3) for repeated use without any significant capacity loss. (c) 2009 Elsevier Ltd. All rights reserved.

  1. XPS studies of MgO based magnetic tunnel junction structures

    NASA Astrophysics Data System (ADS)

    Read, John; Mather, Phil; Tan, Eileen; Buhrman, Robert

    2006-03-01

    The very high tunneling magnetoresistance (TMR) obtained in MgO magnetic tunnel junctions (MTJ)^(1,2) motivates the investigation of the electronic properties of the MgO barrier layer and the study of the ferromagnetic metal - MgO interface chemistry. Such large TMR values are predicted by theory due to the high degree of order apparent in the barrier and electrode materials. However, as grown ultra-thin MgO films generally contain defects that can influence electron transport properties through the creation of low energy states within the bulk MgO band-gap. We will report the results of x-ray photoelectron spectroscopy (XPS) studies of (001) textured ultra-thin MgO layers that are prepared by RF magnetron sputtering and electron beam evaporation on ordered ferromagnetic electrodes and in ordered MTJ structures with and without post growth vacuum annealing. XPS spectra for both MgO deposition techniques clearly indicate a surface oxygen species that is likely bound by defects in the oxide^(3) in half-formed junctions and improvements in MgO quality after counter electrode deposition. We will discuss our results regarding the chemical properties of the oxide and its interfaces directed towards possibly providing guidance to engineer improved MgO MTJ devices. [1] S.S.P. Parkin et. al., Nature Materials, 3, 862 (2004). [2] S. Yuasa et. al., Nature Materials, 3, 868 (2004). [3] E. Tan et. al. , Phys. Rev. B. , 71, 161401 (2005).

  2. Composite targets in HiPIMS plasmas: Correlation of in-vacuum XPS characterization and optical plasma diagnostics

    NASA Astrophysics Data System (ADS)

    Layes, Vincent; Monje, Sascha; Corbella, Carles; Schulz-von der Gathen, Volker; von Keudell, Achim; de los Arcos, Teresa

    2017-05-01

    In-vacuum characterization of magnetron targets after High Power Impulse Magnetron Sputtering (HiPIMS) has been performed by X-ray photoelectron spectroscopy (XPS). Al-Cr composite targets (circular, 50 mm diameter) mounted in two different geometries were investigated: an Al target with a small Cr disk embedded at the racetrack position and a Cr target with a small Al disk embedded at the racetrack position. The HiPIMS discharge and the target surface composition were characterized in parallel for low, intermediate, and high power conditions, thus covering both the Ar-dominated and the metal-dominated HiPIMS regimes. The HiPIMS plasma was investigated using optical emission spectroscopy and fast imaging using a CCD camera; the spatially resolved XPS surface characterization was performed after in-vacuum transfer of the magnetron target to the XPS chamber. This parallel evaluation showed that (i) target redeposition of sputtered species was markedly more effective for Cr atoms than for Al atoms; (ii) oxidation at the target racetrack was observed even though the discharge ran in pure Ar gas without O2 admixture, the oxidation depended on the discharge power and target composition; and (iii) a bright emission spot fixed on top of the inserted Cr disk appeared for high power conditions.

  3. Surface study of graphene ink for fine solid lines printed on BOPP Substrate in micro-flexographic printing using XPS analysis technique

    NASA Astrophysics Data System (ADS)

    Hassan, S.; Yusof, M. S.; Embong, Z.; Ding, S.; Maksud, M. I.

    2018-01-01

    Micro-flexographic printing is a combination of flexography and micro-contact printing technique. It is a new printing method for fine solid lines printing purpose. Graphene material has been used as depositing agent or printing ink in other printing technique like inkjet printing. This graphene ink is printed on biaxially oriented polypropylene (BOPP) by using Micro-flexographic printing technique. The choose of graphene as a printing ink is due to its wide application in producing electronic and micro-electronic devices such as Radio-frequency identification (RFID) and printed circuit board. The graphene printed on the surface of BOPP substrate was analyzed using X-Ray Photoelectron Spectroscopy (XPS). The positions for each synthetic component in the narrow scan are referred to the electron binding energy (eV). This research is focused on two narrow scan regions which are C 1s and O 1s. Further discussion of the narrow scan spectrum will be explained in detail. From the narrow scan analysis, it is proposed that from the surface adhesive properties of graphene, it is suitable as an alternative printing ink medium for Micro-flexographic printing technique in printing multiple fine solid lines at micro to nano scale feature.

  4. Multicenter study on costs associated with two surgical procedures: GreenLight XPS 180 W versus the gold standard transurethral resection of the prostate.

    PubMed

    Benejam-Gual, J M; Sanz-Granda, A; Budía, A; Extramiana, J; Capitán, C

    2014-01-01

    To analyze the costs associated with two surgical procedures for lower urinary tract symptoms secondary to benign prostatic hyperplasia: GreenLight XPS 180¦W versus the gold standard transurethral resection of the prostate. A multicenter, retrospective cost study was carried out from the National Health Service perspective, over a 3-month time period. Costs were broken down into pre-surgical, surgical and post-surgical phases. Data were extracted from records of patients operated sequentially, with IPSS=15, Qmax=15 mL/seg and a prostate volume of 40-80mL, adding only direct healthcare costs (€, 2013) associated with the procedure and management of complications. A total of 79 patients sequentially underwent GL XPS (n: 39) or TURP (n: 40) between July and October, 2013. Clinical outcomes were similar (94.9% and 92.5%, GL XPS and TURP, respectively) without significant differences (P=.67). The average direct cost per patient was reduced by €114 in GL XPS versus TURP patients; the cost was higher in the surgical phase with GL XPS (difference: €1,209; P<.001) but was lower in the post-surgical phase (difference: €-1,351; P<.001). The GreenLight XPS 180-W laser system is associated with a reduction in costs with respect to transurethral resection of prostate in the surgical treatment of LUTS secondary to PBH. This reduction is due to a shorter inpatient length of stay that offsets the cost of the new technology. Copyright © 2013 AEU. Published by Elsevier Espana. All rights reserved.

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

    PubMed

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

    2010-04-01

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

  6. A poly-epoxy surface explored by Hartree-Fock ΔSCF simulations of C1s XPS spectra

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

    Gavrielides, A.; Duguet, T., E-mail: thomas.duguet@ensiacet.fr, E-mail: Paul.Bagus@unt.edu; Esvan, J.

    Whereas poly-epoxy polymers represent a class of materials with a wide range of applications, the structural disorder makes them difficult to model. In the present work, we use good experimental model samples in the sense that they are pure, fully polymerized, flat and smooth, defect-free, and suitable for ultrahigh vacuum x-ray photoelectron spectroscopy, XPS, experiments. In parallel, we perform Hartree-Fock, HF, calculations of the binding energies, BEs, of the C1s electrons in a model molecule composed of the two constituents of the poly-epoxy sample. These C1s BEs were determined using the HF ΔSCF method, which is known to yield accuratemore » values, especially for the shifts of the BEs, ΔBEs. We demonstrate the benefits of combining rigorous theory with careful XPS measurements in order to obtain correct assignments of the C1s XPS spectra of the polymer sample. Both the relative binding energies—by the ΔSCF method—and relative intensities—in the sudden approximation, SA, are calculated. It results in an excellent match with the experimental spectra. We are able to identify 9 different chemical environments under the C1s peak, where an exclusively experimental work would have found only 3 contributions. In addition, we observe that some contributions are localized at discrete binding energies, whereas others allow a much wider range because of the variation of their second neighbor bound polarization. Therefore, HF-ΔSCF simulations significantly increase the spectral resolution of XPS and thus offer a new avenue for the exploration of the surface of polymers.« less

  7. Single-layer ZnS supported on Au(111): A combined XPS, LEED, STM and DFT study

    DOE PAGES

    Deng, Xingyi; Sorescu, Dan C.; Lee, Junseok

    2016-12-31

    Single-layer of ZnS, consisting of one atomic layer of ZnS(111) plane, has been grown on Au(111) and characterized using X-ray photoelectron spectroscopy (XPS), low energy electron diffraction (LEED) and scanning tunneling microscopy (STM). While the LEED measurement indicates a coincidence structure of ZnS-(3×3)/Au(111)-(4×4), high resolution STM images reveal hexagonal unit cells of 6.7×6.7 Å 2 and 11.6×11.6 Å 2, corresponding to √3 and 3 times the unit cell of the ideal zincblende ZnS-(1×1), respectively, depending on the tunneling conditions. Calculations based on density functional theory (DFT) indicate a significantly reconstructed non-planar structure of ZnS single-layer on Au(111) with 2/3 ofmore » the S anions being located nearly in the plane of the Zn cations and the rest 1/3 of the S anions protruding above the Zn plane. In conclusion, the calculated STM image shows similar characteristics to those of the experimental STM image. Additionally, the DFT calculations reveal the different bonding nature of the S anions in ZnS single-layer supported on Au(111).« less

  8. XPS studies of Mg doped GDC (Ce0.8Gd0.2O2-δ) for IT-SOFC

    NASA Astrophysics Data System (ADS)

    Tyagi, Deepak; Rao, P. Koteswara; Wani, B. N.

    2018-04-01

    Fuel Cells have gained much attention as efficient and environment friendly device for both stationary as well as mobile applications. For intermediate temperature SOFC (IT-SOFC), ceria based electrolytes are the most promising one, due to their higher ionic conductivity at relatively lower temperatures. Gd doped ceria is reported to be having the highest ionic conductivity. In the present work, Mg is codoped along with Gd and the electronic structure of the constituents is studied by XPS. XPS confirm that the Cerium is present in +4 oxidation state only which indicates that electronic conduction can be completely avoided.

  9. Elucidating the resistance to failure under tribological tests of various boron-based films by XPS and ToF-SIMS

    NASA Astrophysics Data System (ADS)

    Spadaro, F.; Rossi, A.; Lainé, E.; Woodward, P.; Spencer, N. D.

    2017-12-01

    Tribotests performed on boron-based thermal films have revealed higher mechanical durability and lower wear coefficients compared to results from tests performed on boron-free thermal films. In the current study, in order to follow and identify the tribochemical reactions taking place in the contact regions, post-characterization has been carried out on the steel ball and on the steel disc. The techniques adopted to achieve this goal were small-area X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary-ion mass spectroscopy (ToF-SIMS). The contact areas have been investigated before and after failure of the thermal films, revealing thermal-film removal inside the wear track on the disc and the presence of a transfer film in the contact area on the steel ball following tribotesting. Furthermore, borate contributions in the deeper layers within the tribo-stressed area on the disc were revealed at the end of the tribotest. These procedures shed light on the tribomechanical and tribochemical reactions taking place in the contact region, on the ability of boron species to sustain tribological stress and provide mechanical stability, and on the mechanical-mixing processes occurring within the sliding contacts. The mass spectra collected before tribotesting on all thermal films suggest the presence of phosphate- and borate-containing structures.

  10. Extended study on oxidation behaviors of UN0.68 and UN1.66 by XPS

    NASA Astrophysics Data System (ADS)

    Luo, Lizhu; Hu, Yin; Pan, Qifa; Long, Zhong; Lu, Lei; Liu, Kezhao; Wang, Xiaolin

    2018-04-01

    The surface oxidation behaviors of UN0.68 and UN1.66 thin films are investigated by X-ray photoelectron spectroscopy (XPS), and the traditional U4f/N1s, O1s, valence band spectra as well as the unconventional U4d and U5d spectra are collected for the understanding of their oxidation behavior in-depth. Similar asymmetrical peak shape of the U4f spectra to uranium is observed for both uranium nitrides, despite of a slight shift to higher energy side for UN1.66 clean surface. However, significant difference among the corresponding spectra of UN0.68 and UN1.66 during oxidation reveals the distinctive properties of each own. The coexistence of UO2-x, UO2 and UO2-x.Ny on UN0.68 surface results in the peculiar features of U4f spectra as well as the others within the XPS energy scale, where peaks of the oxidized species firstly shift to higher energy side compared to the clean surface, and then return closely towards those of stoichiometric UO2. For UN1.66, the generation of U-N-O ternary compounds on the surface is identified with the symmetrical U4f peaks at 379.9eV and 390.8 eV, which locate intermediate between UO2 and UN1.66, and gradually expanding to higher energy side during the progressive oxidation. Furthermore, the formation of N-O species on UN1.66 surface is also detected as an oxidation product. The metallic character of UN1.66 is identified by the intense signal at Fermi level, which is greatly suppressed by the increasing oxygen exposure and implies the weakening metallic properties of the as-generated U-N-O compounds. Higher uranium oxides, such as UO3 and U4O9, are deduced to be the final oxidation products, and a multistage mechanism for UN1.66 following the exposure to oxygen is discussed.

  11. XPS and Raman studies of Pt catalysts supported on activated carbon

    NASA Astrophysics Data System (ADS)

    Tyagi, Deepak; Varma, Salil; Bharadwaj, S. R.

    2018-04-01

    Activated carbon is a widely used support for dispersing noble metals in addition to its many applications. We have prepared platinum catalyst supported on activated carbon for HI decomposition reaction of I-S thermochemical process of hydrogen generation. These catalysts were characterized by XPS and Raman before and after using for the reaction. It was observed that platinum is present in zero oxidation state, while carbon is present is both sp2 and sp3 hybridized forms along with some amount of it bonded to oxygen.

  12. 13C NMR and XPS characterization of anion adsorbent with quaternary ammonium groups prepared from rice straw, corn stalk and sugarcane bagasse

    NASA Astrophysics Data System (ADS)

    Cao, Wei; Wang, Zhenqian; Zeng, Qingling; Shen, Chunhua

    2016-12-01

    Despite amino groups modified crop straw has been intensively studied as new and low-cost adsorbent for removal of anionic species from water, there is still a lack of clear characterization for amino groups, especially quaternary ammonium groups in the surface of crop straw. In this study, we used 13C NMR and XPS technologies to characterize adsorbents with quaternary ammonium groups prepared from rice straw, corn stalk and sugarcane bagasse. 13C NMR spectra clearly showed the presence of quaternary ammonium groups in lignocelluloses structure of modified crop straw. The increase of nitrogen observed in XPS survey spectra also indicated the existence of quaternary ammonium group in the surface of the adsorbents. The curve fitting of high-resolution XPS N1s and C1s spectra were conducted to probe the composition of nitrogen and carbon contained groups, respectively. The results showed the proportion of quaternary ammonium group significantly increased in the prepared adsorbent's surface that was dominated by methyl/methylene, hydroxyl, quaternary ammonium, ether and carbonyl groups. This study proved that 13C NMR and XPS could be successfully utilized for characterization of quaternary ammonium modified crop straw adsorbents.

  13. Effects of the low Earth orbit space environment on the surface chemistry of Kapton polyimide film: An XPS study

    NASA Technical Reports Server (NTRS)

    Lee, Myung; Rooney, William; Whiteside, James

    1992-01-01

    Kapton H (DuPont Trademark) polyimide specimens exposed to the low earth (LEO) space environment suffered significant weathering with surface erosions of approximately 8.0 microns. Despite these effects, no significant changes in bulk chemistry were observed. X-ray photoelectron spectroscopy (XPS) was used to determine local changes induced from approximately 25 percent in 1980 vintage ground control specimens to nearly 53 percent in space exposed specimens. The greatest increase was observed for the divalent oxygen moieties, although a slight increase in carbonyl oxygen was also measured. Furthermore, the chemical shifts of all XPS peaks of space-exposed Kapton are shifted to higher energy. This is consistent with a higher oxidation state of the space exposed surface. Finally, space exposed specimens had distinct silicon peaks (2p 100 eV and 2s 149 eV) in their XPS spectra in agreement with widespread reports of silicon contamination throughout the LDEF satellite. These results are discussed in terms of surface reactivity of the polyimide exposed to the LEO environment and the chemical nature of contaminants deposited on flight surfaces due to satellite outgassing.

  14. Structural model of homogeneous As–S glasses derived from Raman spectroscopy and high-resolution XPS

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

    Golovchak, R.; Shpotyuk, O.; Mccloy, J. S.

    2010-11-28

    The structure of homogeneous bulk As x S 100- x (25 ≤ x ≤ 42) glasses, prepared by the conventional rocking–melting–quenching method, was investigated using high-resolution X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy. It is shown that the main building blocks of their glass networks are regular AsS 3/2 pyramids and sulfur chains. In the S-rich domain, the existence of quasi-tetrahedral (QT) S = As(S 1/2) 3 units is deduced from XPS data, but with a concentration not exceeding ~3–5% of total atomic sites. Therefore, QT units do not appear as primary building blocks of the glass backbone in thesemore » materials, and an optimally-constrained network may not be an appropriate description for glasses when x < 40. Finally, it is shown that, in contrast to Se-based glasses, the ‘chain-crossing’ model is only partially applicable to sulfide glasses.« less

  15. A Chemical View on X-ray Photoelectron Spectroscopy: the ESCA Molecule and Surface-to-Bulk XPS Shifts.

    PubMed

    Delesma, Francisco A; Van den Bossche, Maxime; Grönbeck, Henrik; Calaminici, Patrizia; Köster, Andreas M; Pettersson, Lars G M

    2018-01-19

    In this paper we remind the reader of a simple, intuitive picture of chemical shifts in X-ray photoelectron spectroscopy (XPS) as the difference in chemical bonding between the probed atom and its neighbor to the right in the periodic table, the so called Z+1 approximation. We use the classical ESCA molecule, ethyl trifluoroacetate, and 4d-transition metals to explicitly demonstrate agreement between core-level shifts computed as differences between final core-hole states and the approach where each core-ionized atom is replaced by a Z+1 atom. In this final state, or total energy picture, the XPS shift arises due to the more or less unfavorable chemical bonding of the effective nitrogen in the carbon geometry for the ESCA molecule. Surface core level shifts in metals are determined by whether the Z+1 atom as an alloy segregates to the surface or is more soluble in the bulk. As further illustration of this more chemical picture, we compare the geometry of C 1s and O 1s core-ionized CO with that of, respectively, NO + and CF + . The scope is not to propose a new method to compute XPS shifts but rather to stress the validity of this simple interpretation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Spectroellipsometric, AFM and XPS probing of stainless steel surfaces subjected to biological influences

    NASA Astrophysics Data System (ADS)

    Vinnichenko, M.; Chevolleau, Th; Pham, M. T.; Poperenko, L.; Maitz, M. F.

    2002-11-01

    Surface modification of austenitic stainless steel (SS) 316L after incubation in growing cell cultures and cell-free media as control has been studied. The following treatments were applied: mouse fibrosarcoma cells L929 for 3 and 7 days, polymorphonuclear neutrophils for 3 and 7 days and human osteosarcoma cells SAOS-2 for 7 and 14 days. Cells were enzymatically removed in all cases. The modified surfaces were probed in comparison with untreated ones by means of spectroscopic ellipsometry (SE), X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). XPS shows the appearance of the peak of bonded nitrogen at 400.5 eV characteristic for adsorbed proteins on the surface for each type of cells and for the cell-free medium. Migration of Ni in the adsorbed layer is observed in all cases for samples after the cell cultures. The protein layer thickness is ellipsometrically determined to be within 2.5-6.0 nm for all treated samples with parameterization of its optical constants in Cauchy approach. The study showed that for such biological treatments of the SS the protein layer adsorption is the dominating process in the first 2 weeks, which could play a role in the process of corrosion by complex forming properties with metal ions.

  17. XPS study of the surface chemistry of UO2 (111) single crystal film

    NASA Astrophysics Data System (ADS)

    Maslakov, Konstantin I.; Teterin, Yury A.; Popel, Aleksej J.; Teterin, Anton Yu.; Ivanov, Kirill E.; Kalmykov, Stepan N.; Petrov, Vladimir G.; Springell, Ross; Scott, Thomas B.; Farnan, Ian

    2018-03-01

    A (111) air-exposed surface of UO2 thin film (150 nm) on (111) YSZ (yttria-stabilized zirconia) before and after the Ar+ etching and subsequent in situ annealing in the spectrometer analytic chamber was studied by XPS technique. The U 5f, U 4f and O 1s electron peak intensities were employed for determining the oxygen coefficient kO = 2 + x of a UO2+x oxide on the surface. It was found that initial surface (several nm) had kO = 2.20. A 20 s Ar+ etching led to formation of oxide UO2.12, whose composition does not depend significantly on the etching time (up to 180 s). Ar+ etching and subsequent annealing at temperatures 100-380 °C in vacuum was established to result in formation of stable well-organized structure UO2.12 reflected in the U 4f XPS spectra as high intensity (∼28% of the basic peak) shake-up satellites 6.9 eV away from the basic peaks, and virtually did not change the oxygen coefficient of the sample surface. This agrees with the suggestion that a stable (self-assembling) phase with the oxygen coefficient kO ≈ 2.12 forms on the UO2 surface.

  18. Chemical Visualization of a GaN p-n junction by XPS

    PubMed Central

    Caliskan, Deniz; Sezen, Hikmet; Ozbay, Ekmel; Suzer, Sefik

    2015-01-01

    We report on an operando XPS investigation of a GaN diode, by recording the Ga2p3/2 peak position under both forward and reverse bias. Areal maps of the peak positions under reverse bias are completely decoupled with respect to doped regions and allow a novel chemical visualization of the p-n junction in a 2-D fashion. Other electrical properties of the device, such as leakage current, resistivity of the domains are also tapped via recording line-scan spectra. Application of a triangular voltage excitation enables probing photoresponse of the device. PMID:26359762

  19. InP/ZnS nanocrystals: coupling NMR and XPS for fine surface and interface description.

    PubMed

    Virieux, Héloïse; Le Troedec, Marianne; Cros-Gagneux, Arnaud; Ojo, Wilfried-Solo; Delpech, Fabien; Nayral, Céline; Martinez, Hervé; Chaudret, Bruno

    2012-12-05

    Advanced (1)H, (13)C, and (31)P solution- and solid-state NMR studies combined with XPS were used to probe, at the molecular scale, the composition (of the core, the shell, and the interface) and the surface chemistry of InP/ZnS core/shell quantum dots prepared via a non-coordinating solvent strategy. The interface between the mismatched InP and ZnS phases is composed of an amorphous mixed oxide phase incorporating InPO(x) (with x = 3 and predominantly 4), In(2)O(3), and InO(y)(OH)(3-2y) (y = 0, 1). Thanks to the analysis of the underlying reaction mechanisms, we demonstrate that the oxidation of the upper part of the InP core is the consequence of oxidative conditions brought by decarboxylative coupling reactions (ketonization). These reactions occur during both the core preparation and the coating process, but according to different mechanisms.

  20. XPS study of ruthenium tris-bipyridine electrografted from diazonium salt derivative on microcrystalline boron doped diamond.

    PubMed

    Agnès, Charles; Arnault, Jean-Charles; Omnès, Franck; Jousselme, Bruno; Billon, Martial; Bidan, Gérard; Mailley, Pascal

    2009-12-28

    Boron doped diamond (BDD) functionalization has received an increasing interest during the last few years. Such an infatuation comes from the original properties of BDD, including chemical stability or an electrochemical window, that opens the way for the design of (bio)sensors or smart interfaces. In such a context, diazonium salts appear to be well suited for BDD functionalization as they enable covalent immobilization of functional entities such as enzymes or DNA. In this study we report microcrystalline BDD functionalization with a metallic complex, ruthenium tris(bipyridine), using the p-(tris(bipyridine)Ru(2+))phenyl diazonium salt. Electrografting using cyclic voltammetry (CV) allowed the formation of a ruthenium complex film that was finely characterized using electrochemistry and X-ray photoelectron spectroscopy (XPS). Moreover, we showed that chronopotentiometry (CP) is a convenient tool to monitor Ru complex film deposition through the control of the electrochemical pulse parameters (i.e. current density and pulse duration). Finally, such a control was demonstrated through the correlation between electrochemical and XPS characterizations.

  1. XPS and NRA investigations during the fabrication of gold nanostructured functionalized screen-printed sensors for the detection of metallic pollutants

    NASA Astrophysics Data System (ADS)

    Jasmin, Jean-Philippe; Miserque, Frédéric; Dumas, Eddy; Vickridge, Ian; Ganem, Jean-Jacques; Cannizzo, Caroline; Chaussé, Annie

    2017-03-01

    An all covalent nanostructured lead sensor was built by the successive grafting of gold nanoparticles and carboxylic ligands at the surface of self-adhesive carbon screen-printed electrodes (SPEs). Surface analysis techniques were used in each step in order to investigate the structuration of this sensor. The self-adhesive surfaces were made from the electrochemical grafting of p-phenylenediamine at the surface of the SPEs via diazonium salts chemistry. The quantity of grafted aniline functions, estimated by Nuclear Reaction Analysis (NRA) performed with p-phenylenediamine labelled with 15N isotope, is in agreement with an almost complete coverage of the electrode surface. The subsequent diazotization of the aniline functions at the surface of the SPEs was performed; X-ray Photoelectron Spectroscopy (XPS) allowed us to consider a quantitative conversion of the aniline functions into diazonium moieties. The spontaneous grafting of gold nanoparticles on the as-obtained reactive surfaces ensures the nanostructuration of the material, and XPS studies showed that the covalent bonding of the gold nanoparticles at the surface of the SPEs induces a change both in the Au-4f (gold nanoparticles) and Cl-2p (carbon ink) core level signals. These unusual observations are explained by an interaction between the carbon ink constituting the substrate and the gold nanoparticles. Heavy and toxic metals are considered of major environmental concern because of their non-biodegradability. In a final step, the grafting of the carboxylic ligands at the surface of the SPEs and an accumulation step in the presence of lead(II) cations allowed us to evidence the interest of nanostructured materials as metallic pollutants sensors.

  2. Sorption of Eu(III) on attapulgite studied by batch, XPS, and EXAFS techniques.

    PubMed

    Fan, Q H; Tan, X L; Li, J X; Wang, X K; Wu, W S; Montavon, G

    2009-08-01

    The effects of pH, ionic strength, and temperature on sorption of Eu(III) on attapulgite were investigated in the presence and absence of fulvic acid (FA) and humic acid (HA). The results indicated that the sorption of Eu(III) on attapulgite was strongly dependent on pH and ionic strength, and independent of temperature. In the presence of FA/HA, Eu(III) sorption was enhanced at pH < 4, decreased at pH range of 4-6, and then increased again at pH > 7. The X-ray photoelectron spectroscopy (XPS) analysis suggested that the sorption of Eu(III) might be expressed as is identical to X3Eu0, is identical to S(w)OHEu3+, and is identical to SOEu-OOC-/HA in the ternary Eu/HN/attapulgite system. The extended X-ray absorption fine structure (EXAFS) analysis of Eu-HA complexes indicated that the distances of d(Eu-O) decreased from 2.415 to 2.360 angstroms with increasing pH from 1.76 to 9.50, whereas the coordination number (N) decreased from approximately 9.94 to approximately 8.56. Different complexation species were also found for the different addition sequences of HA and Eu(III) to attapulgite suspension. The results are important to understand the influence of humic substances on Eu(III) behavior in the natural environment.

  3. The adsorption of methyl iodide on uranium and uranium dioxide: Surface characterization using X-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES)

    NASA Astrophysics Data System (ADS)

    Dillard, J. G.; Moers, H.; Klewe-Nebenius, H.; Kirch, G.; Pfennig, G.; Ache, H. J.

    1984-09-01

    The adsorption of methyl iodide on uranium and on uranium dioxide has been studied at 25 °C. Surfaces of the substrates were characterized before and after adsorption by X-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES). The XPS binding energy results indicate that CH 3I adsorption on uranium yields a carbide-type carbon, UC, and uranium iodide, UI 3. On uranium dioxide the carbon electron binding energy measurements are consistent with the formation of a hydrocarbon, —CH 3-type moiety. The interpretation of XPS and AES spectral features for CH 3I adsorption on uranium suggest that a complex dissociative adsorption reaction takes place. Adsorption of CH 3I on UO 2 occurs via a dissociative process. Saturation coverage occurs on uranium at approximately two langmuir (1 L = 10 -6 Torr s) exposure whereas saturation coverage on uranium dioxide is found at about five langmuir.

  4. Surface and electronic structure of Bi-Ca-Sr-Cu-O superconductors studied by LEED, UPS and XPS

    NASA Astrophysics Data System (ADS)

    Shen, Z.-X.; Lindberg, P. A. P.; Wells, B. O.; Lindau, I.; Spicer, W. E.; Mitzi, D. B.; Eom, C. B.; Kapitulnik, A.; Geballe, T. H.; Soukiassian, P.

    1989-02-01

    Single crystal and polycrystalline samples of Bi2CaSr2Cu2O8 have been studied by various surface sensitive techniques, including low energy electron diffraction (LEED), ultraviolet photoemission spectroscopy (UPS) and x-ray photoemission spectroscopy (XPS). The surface structure of the single crystals was characterized by LEED to be consistent with that of the bulk structure. Our data suggest that Bi2CaSr2Cu2O8 single crystals are very stable in the ultrahigh vacuu. No change of XPS spectra with temperature was observed. We have also studied the electronic structure of Bi2Sr2CuO6, which has a lower superconducting transition temperature Tc. Comparing the electronic structure of the two Bi-Ca-Sr-Cu-O superconductors, an important difference in the density of states near EF was observed which seems to be related to the difference in Tc.

  5. Chemical and morphological characterization of TSP and PM2.5 by SEM-EDS, XPS and XRD collected in the metropolitan area of Monterrey, Mexico

    NASA Astrophysics Data System (ADS)

    González, Lucy T.; Rodríguez, F. E. Longoria; Sánchez-Domínguez, M.; Leyva-Porras, C.; Silva-Vidaurri, L. G.; Acuna-Askar, Karim; Kharisov, B. I.; Villarreal Chiu, J. F.; Alfaro Barbosa, J. M.

    2016-10-01

    Total suspended particles (TSP) and particles smaller than 2.5 μm (PM2.5) were collected at four sites in the metropolitan area of Monterrey (MAM) in Mexico. The samples were characterized by X-ray Diffraction (XRD), X-ray Photoelectron Spectroscopy (XPS), and Scanning Electron Microscopy (SEM). In order to determine the possible sources of emissions of atmospheric particulate matter, a principal component analysis (PCA) was performed. The XRD results showed that the major crystalline compounds found in the TPS were CaCO3 and SiO2; while in the PM2.5 CaSO4 was found. The XPS analysis showed that the main elements found on the surface of the particles were C, O, Si, Ca, S, and N. The deconvolution carried out on the high-resolution spectra for C1s, S2p and N1s, showed that the aromatics, sulfates and pyrrolic-amides were the main groups contributing to the signal of these elements, respectively. The C-rich particles presented a spherical morphology, while the Ca- and Si-based particles mostly showed a prismatic shape. The PCA analysis together with the results obtained from the characterization techniques, suggested that the main contributors to the CaCO3 particles collected in the PM were most probably produced and emitted into the atmosphere by local construction industries and exploitation of rich-deposits of calcite. Meanwhile, the SiO2 found in the MAM originated from the suspension of geological material abundant in the region, and the carbon particles were mainly produced by the combustion of fossil fuels.

  6. Reaction of Si nanopowder with water investigated by FT-IR and XPS

    NASA Astrophysics Data System (ADS)

    Imamura, Kentaro; Kobayashi, Yuki; Matsuda, Shinsuke; Akai, Tomoki; Kobayashi, Hikaru

    2017-08-01

    The initial reaction of Si nanopowder with water to generate hydrogen is investigated using FT-IR and XPS measurements. Si nanopowder is fabricated using the simple beads milling method. For HF-etched Si nanopowder, strong peaks due to Si-H and Si-H2 stretching vibrational modes and a weak shoulder peak due to Si-H3 are observed. Although no peaks due to oxide is observed in the Si 2p XPS spectrum, weak vibrational peaks due to HSiO2 and HSiO3 species are observable. The hydrogen generation rate greatly increases with pH, indicating that the reacting species is hydroxide ions (OH- ions). After the reaction, the intensities of the peaks due to SiH and SiH2 species decrease while those for HSiO, HSiO2, and HSiO3 species increase. This result demonstrates that OH- ions attack Si back-bonds, with surface Si-H bonds remaining. After initial reaction of HF-etched Si nanopowder with heavy water, vibrational peaks for SiD, SiDH, and SiDH2 appear, and then, a peak due to DSiO3 species is observed, but no peaks due to DSiO2 and DSiO species are observable. This result indicates that SiD, SiDH, and SiDH2 species are formed by substitution reactions, followed by oxidation of back-bonds to form DSiO3 species. After immersion in D2O for a day, 37% H atoms on the surface are replaced to D atoms.

  7. Morphological and XPS study of ball milled Fe1-xAlx (0.3≤x≤0.6) alloys

    NASA Astrophysics Data System (ADS)

    Rajan, Sandeep; Kumar, Anil; Vyas, Anupam; Brajpuriya, Ranjeet

    2018-05-01

    The paper presents mechanical and XPS study of ball milled Fe1-xAlx (0.3≤x≤0.6) alloys. The author prepared the solid solution of Fe(Al) with different composition of Al by using mechanical alloying (MA) technique. The MA process induces a progressive dissolution of Al into Fe, resulted in the formation of an extended Fe(Al) solid solution with the bcc structure after 5 hr of milling. The SEM Images shows that the initial shape of particles disappeared completely, and their structure became a mixture of small and large angular-shaped crystallites with different sizes. The TEM micrograph also confirms the reduction in crystallite size and alloy formation. XPS study shows the shift in the binding energy position of both Fe and Al Peaks provide strong evidence of Fe(Al) phase formation after milling.

  8. Evaluation of the surface properties of PTFE foam coating filter media using XPS and contact angle measurements

    NASA Astrophysics Data System (ADS)

    Park, Byung Hyun; Lee, Myong-Hwa; Kim, Sang Bum; Jo, Young Min

    2011-02-01

    A newly developed PTFE foam coating filter was developed which can be used for hot gas cleaning at temperatures up to 250 °C. The emulsion-type PTFE was coated onto a woven glass fiber using a foam coating method. The filter surface was closely examined using X-ray photoelectron spectroscopy (XPS) and contact angle measurements. The XPS results were used to determine the binding force between the carbon and fluorine of PTFE, which imparts coating stability to the filter medium. More than 95% of the bonds of the PTFE foam coating filter were between carbon and fluorine, and this filter demonstrated excellent hydrophobic and good oleophobic properties at the same time. The contact angles of liquid droplets on the filter surface were used to predict the potential wetability of the filter against water or oil. In addition, the very low surface free energy of the filter medium, which was evaluated using the Owens-Wendt method, demonstrates a very stable surface and a high de-dusting quality.

  9. A quantitative model and the experimental evaluation of the liquid fuel layer for the downward flame spread of XPS foam.

    PubMed

    Luo, Shengfeng; Xie, Qiyuan; Tang, Xinyi; Qiu, Rong; Yang, Yun

    2017-05-05

    The objective of this work is to investigate the distinctive mechanisms of downward flame spread for XPS foam. It was physically considered as a moving down of narrow pool fire instead of downward surface flame spread for normal solids. A method was developed to quantitatively analyze the accumulated liquid fuel based on the experimental measurement of locations of flame tips and burning rates. The results surprisingly showed that about 80% of the generated hot liquid fuel remained in the pool fire during a certain period. Most of the consumed solid XPS foam didn't really burn away but transformed as the liquid fuel in the downward moving pool fire, which might be an important promotion for the fast fire development. The results also indicated that the dripping propensity of the hot liquid fuel depends on the total amount of the hot liquid accumulated in the pool fire. The leading point of the flame front curve might be the breach of the accumulated hot liquid fuel if it is enough for dripping. Finally, it is suggested that horizontal noncombustible barriers for preventing the accumulation and dripping of liquid fuel are helpful for vertical confining of XPS fire. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Surface characterization of LDEF carbon fiber/polymer matrix composites

    NASA Technical Reports Server (NTRS)

    Grammer, Holly L.; Wightman, James P.; Young, Philip R.; Slemp, Wayne S.

    1995-01-01

    XPS (x-ray photoelectron spectroscopy) and SEM (scanning electron microscopy) analysis of both carbon fiber/epoxy matrix and carbon fiber/polysulfone matrix composites revealed significant changes in the surface composition as a result of exposure to low-earth orbit. The carbon 1s curve fit XPS analysis in conjunction with the SEM photomicrographs revealed significant erosion of the polymer matrix resins by atomic oxygen to expose the carbon fibers of the composite samples. This erosion effect on the composites was seen after 10 months in orbit and was even more obvious after 69 months.

  11. A XPS Study of the Passivity of Stainless Steels Influenced by Sulfate-Reducing Bacteria.

    NASA Astrophysics Data System (ADS)

    Chen, Guocun

    The influence of sulfate-reducing bacteria (SRB) on the passivity of type 304 and 317L stainless steels (SS) was investigated by x-ray photoelectron spectroscopy (XPS), microbiological and electrochemical techniques. Samples were exposed to SRB, and then the resultant surfaces were analyzed by XPS, and the corrosion resistance by potentiodynamic polarization in deaerated 0.1 M HCl. To further understand their passivity, the SRB-exposed samples were analyzed by XPS after potentiostatic polarization at a passive potential in the hydrochloric solution. The characterization was performed under two surface conditions: unrinsed and rinsed by deaerated alcohol and deionized water. Comparisons were made with control samples immersed in uninoculated medium. SRB caused a severe loss of the passivity of 304 SS through sulfide formation and possible additional activation to form hexavalent chromium. The sulfides included FeS, FeS_2, Cr_2S _3, NiS and possibly Fe_ {rm 1-x}S. The interaction took place nonuniformly, resulting in undercutting of the passive film and preferential hydration of inner surface layers. The bacterial activation of the Cr^{6+ }^ecies was magnified by subsequent potentiostatic polarization. In contrast, 317L SS exhibited a limited passivity. The sulfides were formed mainly in the outer layers. Although Cr^{6+}^ecies were observed after the exposure, they were dissolved upon polarization. Since 317L SS has a higher Mo content, its higher passivity was ascribed to Mo existing as molybdate on the surface and Mo^{5+} species in the biofilm. Consequently, the interaction of SRB with Mo was studied. It was observed that molybdate could be retained on the surfaces of Mo coupons by corrosion products. In the presence of SRB, however, a considerable portion of the molybdate interacted with intermediate sulfur -containing proteins, forming Mo(V)-S complexes and reducing bacterial growth and sulfate reduction. The limited insolubility of the Mo(V)-S complexes in 0

  12. Conservation of artists' acrylic emulsion paints: XPS, NEXAFS and ATR-FTIR studies of wet cleaning methods

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

    Willneff, E. A.; Ormsby, B. A.; Stevens, J. S.

    Works of art prepared with acrylic emulsion paints became commercially available in the 1960s. It is increasingly necessary to undertake and optimise cleaning and preventative conservation treatments to ensure their longevity. Model artists' acrylic paint films covered with artificial soiling were thus prepared on a canvas support and exposed to a variety of wet cleaning treatments based on aqueous or hydrocarbon solvent systems. This included some with additives such as chelating agents and/or surfactants, and microemulsion systems made specifically for conservation practice. The impact of cleaning (soiling removal) on the paint film surface was examined visually and correlated with resultsmore » of attenuated total reflection Fourier transform infrared, XPS and near-edge X-ray absorption fine structure analyses – three spectroscopic techniques with increasing surface sensitivity ranging from approximately $-$ 1000, 10 and 5 nm, respectively. Visual analysis established the relative cleaning efficacy of the wet cleaning treatments in line with previous results. X-ray spectroscopy analysis provided significant additional findings, including evidence for (i) surfactant extraction following aqueous swabbing, (ii) modifications to pigment following cleaning and (iii) cleaning system residues.« less

  13. Conservation of artists' acrylic emulsion paints: XPS, NEXAFS and ATR-FTIR studies of wet cleaning methods

    DOE PAGES

    Willneff, E. A.; Ormsby, B. A.; Stevens, J. S.; ...

    2014-02-17

    Works of art prepared with acrylic emulsion paints became commercially available in the 1960s. It is increasingly necessary to undertake and optimise cleaning and preventative conservation treatments to ensure their longevity. Model artists' acrylic paint films covered with artificial soiling were thus prepared on a canvas support and exposed to a variety of wet cleaning treatments based on aqueous or hydrocarbon solvent systems. This included some with additives such as chelating agents and/or surfactants, and microemulsion systems made specifically for conservation practice. The impact of cleaning (soiling removal) on the paint film surface was examined visually and correlated with resultsmore » of attenuated total reflection Fourier transform infrared, XPS and near-edge X-ray absorption fine structure analyses – three spectroscopic techniques with increasing surface sensitivity ranging from approximately $-$ 1000, 10 and 5 nm, respectively. Visual analysis established the relative cleaning efficacy of the wet cleaning treatments in line with previous results. X-ray spectroscopy analysis provided significant additional findings, including evidence for (i) surfactant extraction following aqueous swabbing, (ii) modifications to pigment following cleaning and (iii) cleaning system residues.« less

  14. Ageing of plasma-mediated coatings with embedded silver nanoparticles on stainless steel: An XPS and ToF-SIMS investigation

    NASA Astrophysics Data System (ADS)

    Zanna, S.; Saulou, C.; Mercier-Bonin, M.; Despax, B.; Raynaud, P.; Seyeux, A.; Marcus, P.

    2010-09-01

    Nanocomposite thin films (˜170 nm), composed of silver nanoparticles enclosed in an organosilicon matrix, were deposited onto stainless steel, with the aim of preventing biofilm formation. The film deposition was carried out under cold plasma conditions, combining radiofrequency (RF) glow discharge fed with argon and hexamethyldisiloxane and simultaneous silver sputtering. XPS and ToF-SIMS were used to characterize Ag-organosilicon films in native form and after ageing in saline solution (NaCl 0.15 M), in order to further correlate their lifetime with their anti-fouling properties. Two coatings with significantly different silver contents (7.5% and 20.3%) were tested. Surface analysis confirmed the presence of metallic silver in the pristine coating and revealed significant modifications after immersion in the saline solution. Two different ageing mechanisms were observed, depending on the initial silver concentration in the film. For the sample exhibiting the low silver content (7.5%), the metal amount decreased at the surface in contact with the solution, due to the release of silver from the coating. As a result, after a 2-day exposure, silver nanoparticles located at the extreme surface were entirely released, whereas silver is still present in the inner part of the film. The coating thickness was not modified during ageing. In contrast, for the high silver content film (20.3%), the thickness decreased with immersion time, due to significant silver release and matrix erosion, assigned to a percolation-like effect. However, after 18 days of immersion, the delamination process stopped and a thin strongly bounded layer remained on the stainless steel surface.

  15. Reduction of mixed Mn-Zr oxides: in situ XPS and XRD studies.

    PubMed

    Bulavchenko, O A; Vinokurov, Z S; Afonasenko, T N; Tsyrul'nikov, P G; Tsybulya, S V; Saraev, A A; Kaichev, V V

    2015-09-21

    A series of mixed Mn-Zr oxides with different molar ratios Mn/Zr (0.1-9) have been prepared by coprecipitation of manganese and zirconium nitrates and characterized by X-ray diffraction (XRD) and BET methods. It has been found that at concentrations of Mn below 30 at%, the samples are single-phase solid solutions (MnxZr1-xO2-δ) based on a ZrO2 structure. X-ray photoelectron spectroscopy (XPS) measurements showed that manganese in these solutions exists mainly in the Mn(4+) state on the surface. An increase in Mn content mostly leads to an increase in the number of Mn cations in the structure of solid solutions; however, a part of the manganese cations form Mn2O3 and Mn3O4 in the crystalline and amorphous states. The reduction of these oxides with hydrogen was studied by a temperature-programmed reduction technique, in situ XRD, and near ambient pressure XPS in the temperature range from 100 to 650 °C. It was shown that the reduction of the solid solutions MnxZr1-xO2-δ proceeds via two stages. During the first stage, at temperatures between 100 and 500 °C, the Mn cations incorporated into the solid solutions MnxZr1-xO2-δ undergo partial reduction. During the second stage, at temperatures between 500 and 700 °C, Mn cations segregate on the surface of the solid solution. In the samples with more than 30 at% Mn, the reduction of manganese oxides was observed: Mn2O3 → Mn3O4 → MnO.

  16. A Multicenter Randomized Noninferiority Trial Comparing GreenLight-XPS Laser Vaporization of the Prostate and Transurethral Resection of the Prostate for the Treatment of Benign Prostatic Obstruction: Two-yr Outcomes of the GOLIATH Study.

    PubMed

    Thomas, James A; Tubaro, Andrea; Barber, Neil; d'Ancona, Frank; Muir, Gordon; Witzsch, Ulrich; Grimm, Marc-Oliver; Benejam, Joan; Stolzenburg, Jens-Uwe; Riddick, Antony; Pahernik, Sascha; Roelink, Herman; Ameye, Filip; Saussine, Christian; Bruyère, Franck; Loidl, Wolfgang; Larner, Tim; Gogoi, Nirjan-Kumar; Hindley, Richard; Muschter, Rolf; Thorpe, Andrew; Shrotri, Nitin; Graham, Stuart; Hamann, Moritz; Miller, Kurt; Schostak, Martin; Capitán, Carlos; Knispel, Helmut; Bachmann, Alexander

    2016-01-01

    The GOLIATH study is a 2-yr trial comparing transurethral resection of prostate (TURP) to photoselective vaporization with the GreenLight XPS Laser System (GL-XPS) for the treatment of benign prostatic obstruction (BPO). Noninferiority of GL-XPS to TURP was demonstrated based on a 6-mo follow-up from the study. To determine whether treatment effects observed at 6 mo between GL-XPS and TURP was maintained at the 2-yr follow-up. Prospective randomized controlled trial at 29 centers in nine European countries involving 281 patients with BPO. Photoselective vaporization using the 180-W GreenLight GL-XPS or conventional (monopolar or bipolar) TURP. The primary outcome was the International Prostate Symptom Score for which a margin of three was used to evaluate the noninferiority of GL-XPS. Secondary outcomes included Qmax, prostate volume, prostate specific antigen, Overactive Bladder Questionnaire Short Form, International Consultation on Incontinence Questionnaire Short Form, occurrence of surgical retreatment, and freedom from complications. One hundred and thirty-six patients were treated using GL-XPS and 133 using TURP. Noninferiority of GL-XPS on International Prostate Symptom Score, Qmax, and freedom from complications was demonstrated at 6-mo and was sustained at 2-yr. The proportion of patients complication-free through 24-mo was 83.6% GL-XPS versus 78.9% TURP. Reductions in prostate volume and prostate specific antigen were similar in both arms and sustained over the course of the trial. Compared with the 1(st) yr of the study, very few adverse events or retreatments were reported in either arm. Treatment differences in the Overactive Bladder Questionnaire Short Form observed at 12-mo were not statistically significant at 24-mo. A limitation was that patients and treating physicians were not blinded to the therapy. Twenty-four-mo follow-up data demonstrated that GL-XPS provides a durable surgical option for the treatment of BPO that exhibits efficacy and

  17. XPS Investigation on Changes in UO 2 Speciation following Exposure to Humidity

    DOE PAGES

    Donald, Scott B.; Davisson, M. Lee; Nelson, Art J.

    2016-04-27

    High purity UO 2powder samples were subjected to accelerated aging under controlled conditions with relative humidity ranging from 34% to 98%. Characterization of the chemical speciation of the products was accomplished using X-ray photoelectron spectroscopy (XPS). A shift to higher uranium oxidation states was found to be directly correlated to increased relative humidity exposure. In addition, the relative abundance of O 2-, OH -, and H 2O was found to vary with exposure time. Therefore, it is expected that uranium oxide materials exposed to high relative humidity conditions during processing and storage would display a similar increase in average uraniummore » valence.« less

  18. XPS-XRF hybrid metrology enabling FDSOI process

    NASA Astrophysics Data System (ADS)

    Hossain, Mainul; Subramanian, Ganesh; Triyoso, Dina; Wahl, Jeremy; Mcardle, Timothy; Vaid, Alok; Bello, A. F.; Lee, Wei Ti; Klare, Mark; Kwan, Michael; Pois, Heath; Wang, Ying; Larson, Tom

    2016-03-01

    Planar fully-depleted silicon-on-insulator (FDSOI) technology potentially offers comparable transistor performance as FinFETs. pFET FDOSI devices are based on a silicon germanium (cSiGe) layer on top of a buried oxide (BOX). Ndoped interfacial layer (IL), high-k (HfO2) layer and the metal gate stacks are then successively built on top of the SiGe layer. In-line metrology is critical in precisely monitoring the thickness and composition of the gate stack and associated underlying layers in order to achieve desired process control. However, any single in-line metrology technique is insufficient to obtain the thickness of IL, high-k, cSiGe layers in addition to Ge% and N-dose in one single measurement. A hybrid approach is therefore needed that combines the capabilities of more than one measurement technique to extract multiple parameters in a given film stack. This paper will discuss the approaches, challenges, and results associated with the first-in-industry implementation of XPS-XRF hybrid metrology for simultaneous detection of high-k thickness, IL thickness, N-dose, cSiGe thickness and %Ge, all in one signal measurement on a FDSOI substrate in a manufacturing fab. Strong correlation to electrical data for one or more of these measured parameters will also be presented, establishing the reliability of this technique.

  19. XPS/NEXAFS spectroscopic and conductance studies of glycine on AlGaN/GaN transistor devices

    NASA Astrophysics Data System (ADS)

    Myers, Matthew; Khir, Farah Liyana Muhammad; Home, Michael A.; Mennell, Christopher; Gillbanks, Jeremy; Tadich, Anton; Baker, Murray V.; Nener, Brett D.; Parish, Giacinta

    2018-03-01

    We report on a study using a combination of XPS/NEXAFS and conductivity measurements to develop a fundamental understanding of how dipolar molecules interact with the heterostructure device surface and affect the device conductivity of AlGaN/GaN heterostructure-based transistors. In such structures, which are increasingly being investigated for chemical and biological sensing, a 2-dimensional electron gas spontaneously forms at the layer interface that is sensitive to the charge characteristics of the exposed surface. Glycine, chosen for this study because it is the simplest of the amino acids and is known to form a zwitterionic configuration when stabilized through intermolecular interactions, was evaporated under ultra-high vacuum conditions onto the device surface and subsequently both XPS/NEXAFS and conductivity measurements were conducted. NEXAFS spectra show a preferential orientation for the Glycine molecules on the surface and evidence for both neutral and zwitterionic species on the surface. In situ conductivity measurements suggest that the negatively charged carboxylate group is closest to the surface. These results are a unique and pivotal contribution to the previous and at times conflicting literature on the zwitterionic nature of Glycine.

  20. Eu(III) sorption to TiO2 (anatase and rutile): batch, XPS, and EXAFS studies.

    PubMed

    Tan, Xiaoli; Fan, Qiaohui; Wang, Xiangke; Grambow, Bernd

    2009-05-01

    The sorption of Eu(III) on anatase and rutile was studied as a function of ionic strength, humic acid (HA, 7.5 mg/L), and electrolyte anions over a large range of pH (2-12). The presence of HA significantly affected Eu(III) sorption to anatase and rutile. The sorption of Eu(III) on anatase and rutile was independent of ionic strength. Results of an X-ray photoelectron spectroscopy (XPS) analysis showed that Eu(III) was chemically present within the near-surface of TiO2 due to the formation of triple bond SOEu and triple bond SOHAEu complexes. An extended X-ray absorption fine structure (EXAFS) technique was applied to characterize the local structural environment of the adsorbed Eu(III), and the results indicated that Eu(III) was bound to about seven or eight O atoms at a distance of about 2.40 A. The functional groups of surface-bound HA were expected to be involved in the sorption process. The measured Eu-Ti distance confirmed the formation of inner-sphere sorption complexes on a TiO2 surface.

  1. Measurement of Thicknesses of High-κ Gate-Dielectric Films on Silicon by Angle-Resolved XPS

    NASA Astrophysics Data System (ADS)

    Powell, Cedric; Smekal, Werner; Werner, Wolfgang

    2006-03-01

    We report on the use of a new NIST database for the Simulation of Electron Spectra for Surface Analysis (SESSA) in measuring thicknesses of candidate high-κ gate-dielectric materials (HfO2, HfSiO4, ZrO2, and ZrSiO4) on silicon by angle-resolved XPS. For conventional measurements of film thicknesses, effective attenuation lengths (EALs) have been computed for these materials from SESSA as a function of film thickness and photoelectron emission angle (i.e., to simulate the effects of tilting the sample). These EALs are believed to be more accurate than similar EALs obtained from the transport approximation because realistic cross sections are used for both elastic and inelastic scattering in the film and substrate materials. We also present ``calibration curves'' showing calculated ratios of selected photoelectron intensities from thin films of HfO2 on Si with an intermediate SiO2 layer. These ratios provide a simple and convenient means of determining the thicknesses of SiO2 and HfO2 films for particular measurement conditions.

  2. Cities-LEAP Analysis Reveals Findings on the Most Efficient and Least

    Science.gov Websites

    Polluting Cities in the U.S. | State, Local, and Tribal Governments | NREL Cities-LEAP Analysis Reveals Findings on the Most Efficient and Least Polluting Cities in the U.S. Cities-LEAP Analysis Reveals Findings on the Most Efficient and Least Polluting Cities in the U.S. September 12, 2016 by Megan Day

  3. Physical and Chemical Behaviors of HCl on Ice Surface: Insights from an XPS and NEXAFS Study

    NASA Astrophysics Data System (ADS)

    Kong, X.; Waldner, A.; Orlando, F.; Birrer, M.; Artiglia, L.; Ammann, M.; Bartels-Rausch, T.

    2016-12-01

    Ice and snow play active roles for the water cycle, the energy budget of the Earth, and environmental chemistry in the atmosphere and cryosphere. Trace gases can be taken up by ice, and physical and chemical fates of the impurities could modify surface properties significantly and consequently influence atmospheric chemistry and the climate system. However, the understanding of chemical behaviour of impurities on ice surface are very poor, which is largely limited by the difficulties to apply high sensitivity experimental approaches to ambient air conditions, e.g. studies of volatile surfaces, because of the strict requirements of vacuum experimental conditions. In this study, we employed synchrotron-based X-ray photoelectron spectroscopy (XPS) and partial electron yield Near Edge X-ray Absorption Fine Structure (NEXAFS) in a state-of-the-art near-ambient pressure photoelectron (NAPP) spectroscopy end station. The NAPP enables to utilize the surface sensitive experimental methods, XPS and NEXAFS, on volatile surfaces, i.e. ice at temperatures approaching 0°C. XPS and NEXAFS together provide unique information of hydrogen bonding network, dopants surface concentration, dopant depth profile, and acidic dissociation on the surfaces1. Taking the advantages of the highly sensitive techniques, the adsorption, dissociation and depth profile of Hydrogen Chloride (HCl) on ice were studied. In brief, two states of Chloride on ice surface are identified from the adsorbed HCl, and they are featured with different depth profiles along the ice layers. Combining our results and previously reported constants from literatures (e.g. HCl diffusion coefficients in ice)2, a layered kinetic model has been constructed to fit the depth profiles of two states of Chloride. On the other side, pure ice and doped ice are compared for their surface structure change caused by temperature and the presence of HCl, which shows how the strong acid affect the ice surface in turn. 1. Orlando, F., et

  4. Surface Propensity of Atmospherically Relevant Amino Acids Studied by XPS.

    PubMed

    Mocellin, Alexandra; Gomes, Anderson Herbert de Abreu; Araújo, Oscar Cardoso; de Brito, Arnaldo Naves; Björneholm, Olle

    2017-04-27

    Amino acids constitute an important fraction of the water-soluble organic nitrogen (WSON) compounds in aerosols and are involved in many processes in the atmosphere. In this work, we applied X-ray photoelectron spectroscopy (XPS) to study aqueous solutions of four amino acids, glycine, alanine, valine, and methionine, in their zwitterionic forms. We found that amino acids with hydrophilic side chains and smaller size, GLY and ALA, tend to stay in the bulk of the liquid, while the hydrophobic and bigger amino acids, VAL and MET, are found to concentrate more on the surface. We found experimental evidence that the amino acids have preferential orientation relative to the surface, with the hydrophobic side chain being closer to the surface than the hydrophilic carboxylate group. The observed amino acid surface propensity has implications in atmospheric science as the surface interactions play a central role in cloud droplet formation, and they should be considered in climate models.

  5. Applications of time-of-flight secondary ion mass spectrometry (TOF-SIMS) and X-ray photoelectron spectroscopy (XPS) to study interactions of genetically engineered proteins with noble metal films

    NASA Astrophysics Data System (ADS)

    Suzuki, Noriaki

    Genetically engineered proteins for inorganics (GEPIs) belong to a new class of polypeptides that are designed to have specific affinities to inorganic materials. A "gold binding protein (GBP)" was chosen as a model protein for GEPIs to study the molecular origins of binding specificity to gold using Time-of-flight secondary ion mass spectrometry (TOF-SIMS) and X-ray photoelectron spectroscopy (XPS). TOF-SIMS, a surface-sensitive analytical instrument with extremely high mass resolutions, provides information on specific amino acid-surface interactions. We used "principal component analysis (PCA)" to analyze the data. We also introduced a new multivariate technique, "hierarchical cluster analysis (HCA)" to organize the data into meaningful structures by measuring a degree of "similarity" and "dissimilarity" of the data. This report discusses a combined use of PCA and HCA to elucidate the binding specificity of GBP to Au. Based on the knowledge gained from TOF-SIMS measurements, we further investigated the nature of the interaction between selected amino acids and noble metal surfaces by using X-ray photoelectron spectroscopy (XPS). We developed a unique capability to introduce water vapor during the adsorption of a single amino acid and applied this method to study the intrinsic nature of sidechain/Au interactions. To further apply this unique research protocol, we characterized another type of GEPI, "quartz binding protein (QBP)," to identify the possible binding sites. This thesis research aims to provide experimental protocols for analyzing short peptide-substrate interface from complex spectroscopic data by using multivariate analysis techniques.

  6. Observation of GaSe-SnO2 Heterostructure by XPS and AES

    NASA Astrophysics Data System (ADS)

    Tatsuyama, Chiei; Ichimura, Shoji; Iwakuro, Hiroaki

    1982-01-01

    The depth profile of the elemental composition of the GaSe-SnO2 heterostructure has been studied by XPS and AES. The SnO2 layer was prepared by spraying a solution of SnCl4 and SbCl3 in ethyl alcohol on to the the cleaved surface of GaSe heated to ˜400°C in air. After the solution had been sprayed on for about 5 secs., an SnO2 layer of thickness ˜460 Å formed, and a Ga2O3 layer of thickness ˜120 Å formed under the SnO2 layer. The Ga2O3 layer is a likely origin of the high-resistivity layer observed in the GaSe-SnO2 heterostructure.

  7. Atomistic characterisation of Li+ mobility and conductivity in Li(7-x)PS(6-x)Ix argyrodites from molecular dynamics simulations, solid-state NMR, and impedance spectroscopy.

    PubMed

    Pecher, Oliver; Kong, Shiao-Tong; Goebel, Thorsten; Nickel, Vera; Weichert, Katja; Reiner, Christof; Deiseroth, Hans-Jörg; Maier, Joachim; Haarmann, Frank; Zahn, Dirk

    2010-07-26

    The atomistic mechanisms of Li(+) ion mobility/conductivity in Li(7-x)PS(6-x)I(x) argyrodites are explored from both experimental and theoretical viewpoints. Ionic conductivity in the title compound is associated with a solid-solid phase transition, which was characterised by low-temperature differential scanning calorimetry, (7)Li and (127)I NMR investigations, impedance measurements and molecular dynamics simulations. The NMR signals of both isotopes are dominated by anisotropic interactions at low temperatures. A significant narrowing of the NMR signal indicates a motional averaging of the anisotropic interactions above 177+/-2 K. The activation energy to ionic conductivity was assessed from both impedance spectroscopy and molecular dynamics simulations. The latter revealed that a series of interstitial sites become accessible to the Li(+) ions, whilst the remaining ions stay at their respective sites in the argyrodite lattice. The interstitial positions each correspond to the centres of tetrahedra of S/I atoms, and differ only in terms of their common corners, edges, or faces with adjacent PS(4) tetrahedra. From connectivity analyses and free-energy rankings, a specific tetrahedron is identified as the key restriction to ionic conductivity, and is clearly differentiated from local mobility, which follows a different mechanism with much lower activation energy. Interpolation of the lattice parameters as derived from X-ray diffraction experiments indicates a homogeneity range for Li(7-x)PS(6-x)I(x) with 0.97 < or = x < or = 1.00. Within this range, molecular dynamics simulations predict Li(+) conductivity at ambient conditions to vary considerably.

  8. Surface Analysis of 4-Aminothiophenol Adsorption at Polycrystalline Platinum Electrodes

    NASA Technical Reports Server (NTRS)

    Rosario-Castro, Belinda I.; Fachini, Estevao R.; Contes, Enid J.; Perez-Davis, Marla E.; Cabrera, Carlos R.

    2008-01-01

    Formation of self-assembled monolayer (SAM) of 4-aminothiophenol (4-ATP) on polycrystalline platinum electrodes has been studied by surface analysis and electrochemistry techniques. The 4-ATP monolayer was characterized by cyclic voltammetry (CV), Raman spectroscopy, reflection absorption infrared (RAIR) spectroscopy, and X-ray photoelectron spectroscopy (XPS). Cyclic voltammetry (CV) experiments give an idea about the packing quality of the monolayer. RAIR and Raman spectra for 4-ATP modified platinum electrodes showed the characteristic adsorption bands for neat 4-ATP indicating the adsorption of 4-ATP molecules on platinum surface. The adsorption on platinum was also evidenced by the presence of sulfur and nitrogen peaks by XPS survey spectra of the modified platinum electrodes. High resolution XPS studies and RAIR spectrum for platinum electrodes modified with 4-ATP indicate that molecules are sulfur-bonded to the platinum surface. The formation of S-Pt bond suggests that ATP adsorption gives up an amino terminated SAM. Thickness of the monolayer was evaluated via angle-resolved XPS (AR-XPS) analyses. Derivatization of 4-ATP SAM was performed using 16-Br hexadecanoic acid.

  9. Dissolution of uranophane: An AFM, XPS, SEM and ICP study

    NASA Astrophysics Data System (ADS)

    Schindler, Michael; Freund, Michael; Hawthorne, Frank C.; Burns, Peter C.; Maurice, Patricia A.

    2009-05-01

    Dissolution experiments on single crystals of uranophane and uranophane-β, Ca(H 2O) 5[(UO 2)(SiO 3(OH)] 2, from the Shinkolobwe mine of the Democratic Republic of Congo, were done in an aqueous HCl solution of pH 3.5 for 3 h, in HCl solutions of pH 2 for 5, 10 and 30 min, and in Pb 2+-, Ba-, Sr-, Ca- and Mg-HCl solutions of pH 2 for 30 min. The basal surfaces of the treated uranophane crystals were examined using atomic-force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). Solutions after dissolution experiments on single crystals and synthetic powders were analysed with inductively coupled plasma-optical emission spectroscopy (ICP-OES) and mass spectroscopy (ICP-MS). The morphology of the observed etch pits (measured by AFM) were compared to the morphology, predicted on the basis of the bond-valence deficiency of polyhedron chains along the edges of the basal surface. Etch pits form in HCl solutions of pH 2. Their decrease in depth with the duration of the dissolution experiment is explained with the stepwave dissolution model, which describes the lowering of the surrounding area of an etch pit with continuous waves of steps emanated from the etch pit into the rest of the crystal surface. Hillocks form in an HCl solution of pH 3.5, and the chemical composition of the surface (as indicated by XPS) shows that these hillocks are the result of the precipitation of a uranyl-hydroxy-hydrate phase. Well-orientated hillocks form on the surface of uranophane in a SrCl 2-HCl solution of pH 2. They are part of an aged silica coating of composition Si 2O 2(OH) 4(H 2O) n. An amorphous layer forms on the surface of uranophane in a MgCl 2-HCl solution of pH 2, which has a composition and structure similar to silicic acid. Small crystallites of uranyl-hydroxy-hydrate phases form on the surface of uranophane after treatment in Pb(NO 3) 2-HCl and BaCl 2-HCl solutions of pH 2. Dissolution experiments on synthetic uranophane powders

  10. Stability of boron-doped graphene/copper interface: DFT, XPS and OSEE studies

    NASA Astrophysics Data System (ADS)

    Boukhvalov, D. W.; Zhidkov, I. S.; Kukharenko, A. I.; Slesarev, A. I.; Zatsepin, A. F.; Cholakh, S. O.; Kurmaev, E. Z.

    2018-05-01

    Two different types of boron-doped graphene/copper interfaces synthesized using two different flow rates of Ar through the bubbler containing the boron source were studied. X-ray photoelectron spectra (XPS) and optically stimulated electron emission (OSEE) measurements have demonstrated that boron-doped graphene coating provides a high corrosion resistivity of Cu-substrate with the light traces of the oxidation of carbon cover. The density functional theory calculations suggest that for the case of substitutional (graphitic) boron-defect only the oxidation near boron impurity is energetically favorable and creation of the vacancies that can induce the oxidation of copper substrate is energetically unfavorable. In the case of non-graphitic boron defects oxidation of the area, a nearby impurity is metastable that not only prevent oxidation but makes boron-doped graphene. Modeling of oxygen reduction reaction demonstrates high catalytic performance of these materials.

  11. A Novel Approach for the Treatment of Radiation-Induced Hemorrhagic Cystitis with the GreenLight™ XPS Laser

    PubMed Central

    Martinez, Daniel Roberto; Ercole, Cesar E; Lopez, Juan Gabriel; Parker, Justin; Hall, Mary K

    2015-01-01

    ABSTRACT Introduction: The treatment of pelvic malignancies with radiotherapy can develop severe sequelae, especially radiation-induced hemorrhagic cystitis. It is a progressive disease that can lead to the need for blood transfusion, hospitalizations, and surgical interventions. This tends to affect the quality of life of these patients, and management can at times be difficult. We have evaluated the GreenLight Xcelerated Performance System (XPS) with TruCoag, although primarily used for management of benign prostatic hypertrophy (BPH), for the treatment of radiation-induced hemorrhagic cystitis. Materials and Methods: After International Review Board (IRB) approval, a retrospective chart review was performed in addition to a literature search. A series of four male patients, mean age of 81 years, with radiation-induced hemorrhagic cystitis secondary to radiotherapy for pelvic malignancies (3 prostate cancer, 1 rectal cancer) were successfully treated with the GreenLight laser after unsuccessful treatment with current therapies described in the literature. Results: All four patients treated with the GreenLight laser had resolution of their hematuria after one treatment and were discharge from the hospital with clear urine. Conclusion: The GreenLight XPS laser shows promising results for the treatment of patients with radiation-induced hemorrhagic cystitis, and deserves further evaluation and validation, especially since there is limited data available in the literature regarding the use of this technology for the treatment of this devastating condition. PMID:26200555

  12. Depth profile composition studies of thin film CdS:Cu2S solar cells using XPS and AES

    NASA Astrophysics Data System (ADS)

    Bhide, V. G.; Salkalachen, S.; Rastogi, A. C.; Rao, C. N. R.; Hegde, M. S.

    1981-09-01

    Studies of the surface composition and depth profiles of thin film CdS:Cu2S solar cells based on the techniques of X-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES) are reported. Specimens were fabricated by the thermal deposition of polycrystalline CdS films onto silver-backed electrodes predeposited on window glass substrates, followed by texturization in hot HCl and chemical plating in a hot CuCl(I) bath for a few seconds to achieve the topotaxial growth of CuS films. The XPS and AES studies indicate the junction to be fairly diffused in the as-prepared cell, with heat treatment in air at 210 C sharpening the junction, improving the stoichiometry of the Cu2S layer and thus improving cell performance. The top copper sulfide layer is found to contain impurities such as Cd, Cl, O and C, which may be removed by mild Ar(+) ion beam etching. The presence of copper deep in the junction is invariably detected, apparently in the grain boundary region in the form of CuS or Cu(2+) trapped in the lattice. It is also noted that the nominal valence state of copper changes abruptly from Cu(+) to Cu(2+) across the junction.

  13. Nanopatterning of metal-coated silicon surfaces via ion beam irradiation: Real time x-ray studies reveal the effect of silicide bonding

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

    El-Atwani, Osman; Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907; Gonderman, Sean

    We investigated the effect of silicide formation on ion-induced nanopatterning of silicon with various ultrathin metal coatings. Silicon substrates coated with 10 nm Ni, Fe, and Cu were irradiated with 200 eV argon ions at normal incidence. Real time grazing incidence small angle x-ray scattering (GISAXS) and x-ray fluorescence (XRF) were performed during the irradiation process and real time measurements revealed threshold conditions for nanopatterning of silicon at normal incidence irradiation. Three main stages of the nanopatterning process were identified. The real time GISAXS intensity of the correlated peaks in conjunction with XRF revealed that the nanostructures remain for amore » time period after the removal of the all the metal atoms from the sample depending on the binding energy of the metal silicides formed. Ex-situ XPS confirmed the removal of all metal impurities. In-situ XPS during the irradiation of Ni, Fe, and Cu coated silicon substrates at normal incidence demonstrated phase separation and the formation of different silicide phases that occur upon metal-silicon mixing. Silicide formation leads to nanostructure formation due the preferential erosion of the non-silicide regions and the weakening of the ion induced mass redistribution.« less

  14. Ion beam modification of zinc white pigment characterized by ex situ and in situ μ-Raman and XPS

    NASA Astrophysics Data System (ADS)

    Beck, L.; Gutiérrez, P. C.; Miro, S.; Miserque, F.

    2017-10-01

    Zinc oxide, known as zinc white, is one of the principal white pigments developed in the 18th century and was used by the Impressionist painters. ZnO as artists' pigment has occasionally been characterized by X-ray and ion beam techniques, but these studies are limited by the potential for visible radiation effect. Ion beam modifications of zinc oxide have extensively been investigated, but mainly for electronic and industrial applications. In this paper, we focus our investigation on ion beam modification of ZnO used as pigment. Two irradiation conditions have been used: an external 3 MeV proton micro-beam representative of PIXE analysis and 2 MeV H+ and 1.2 MeV Au + beams in vacuum to investigate irradiation modifications in electronic and nuclear energy loss regimes. Ion beam modification was characterized by ex situ and in situ micro-Raman spectrometry and XPS. The results shows that IBA of zinc white can be carried out safely in historical paintings with low current and dose.

  15. Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont.

    PubMed

    Cai, Lin; Zhou, Guowei; Tian, Ren-Mao; Tong, Haoya; Zhang, Weipeng; Sun, Jin; Ding, Wei; Wong, Yue Him; Xie, James Y; Qiu, Jian-Wen; Liu, Sheng; Huang, Hui; Qian, Pei-Yuan

    2017-08-24

    Coral reefs are ecologically significant habitats. Coral-algal symbiosis confers ecological success on coral reefs and coral-microbial symbiosis is also vital to coral reefs. However, current understanding of coral-microbial symbiosis on a genomic scale is largely unknown. Here we report a potential microbial symbiont in corals revealed by metagenomics-based genomic study. Microbial cells in coral were enriched for metagenomic analysis and a high-quality draft genome of "Candidatus Prosthecochloris korallensis" was recovered by metagenome assembly and genome binning. Phylogenetic analysis shows "Ca. P. korallensis" belongs to the Prosthecochloris clade and is clustered with two Prosthecochloris clones derived from Caribbean corals. Genomic analysis reveals "Ca. P. korallensis" has potentially important ecological functions including anoxygenic photosynthesis, carbon fixation via the reductive tricarboxylic acid (rTCA) cycle, nitrogen fixation, and sulfur oxidization. Core metabolic pathway analysis suggests "Ca. P. korallensis" is a green sulfur bacterium capable of photoautotrophy or mixotrophy. Potential host-microbial interaction reveals a symbiotic relationship: "Ca. P. korallensis" might provide organic and nitrogenous nutrients to its host and detoxify sulfide for the host; the host might provide "Ca. P. korallensis" with an anaerobic environment for survival, carbon dioxide and acetate for growth, and hydrogen sulfide as an electron donor for photosynthesis.

  16. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit.

    PubMed

    Ashoori, Maryam; Burns, Catherine M; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamwork and leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams.

  17. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

    PubMed Central

    Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. Practitioner Summary: This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams PMID:24837514

  18. Surface analysis of 316 stainless steel treated with cold atmospheric plasma

    NASA Astrophysics Data System (ADS)

    Williams, David F.; Kellar, Ewen J. C.; Jesson, David A.; Watts, John F.

    2017-05-01

    The surface of 316 stainless steel has been modified using cold atmospheric plasma (CAP) to increase the surface free energy (by cleaning the and chemically activating the surface)IN preparation for subsequent processes such as painting, coating or adhesive bonding. The analyses carried out, on CAP treated 316 stainless steel surfaces, includes X-ray photoelectron spectroscopy (XPS), imaging XPS (iXPS), and surface free energy (SFE) analysis using contact angle measurements. The CAP treatment is shown to increase the SFE of as-received 316 stainless steel from ∼39 mJ m-1 to >72 mJ m-1 after a short exposure to the plasma torch. This was found to correlate to a reduction in adventitious carbon, as determined by XPS analysis of the surface. The reduction from ∼90 at% to ∼30% and ∼39 at%, after being plasma treated for 5 min and 15 s respectively, shows that the process is relatively quick at changing the surface. It is suggested that the mechanism that causes the increase in surface free energy is chain scission of the hydrocarbon contamination triggered by free electrons in the plasma plume followed by chemical functionalisation of the metal oxide surface and some of the remaining carbon contamination layer.

  19. Fabrication and characterization of ultrathin dextran layers: Time dependent nanostructure in aqueous environments revealed by OWLS.

    PubMed

    Saftics, Andras; Kurunczi, Sándor; Szekrényes, Zsolt; Kamarás, Katalin; Khánh, Nguyen Quoc; Sulyok, Attila; Bősze, Szilvia; Horvath, Robert

    2016-10-01

    Surface coatings of the polysaccharide dextran and its derivatives are key ingredients especially in label-free biosensors for the suppression of non-specific binding and for receptor immobilization. Nevertheless, the nanostructure of these ultrathin coatings and its tailoring by the variation of the preparation conditions have not been profoundly characterized and understood. In this work carboxymethylated dextran (CMD) was prepared and used for fabricating ultrathin surface coatings. A grafting method based on covalent coupling to aminosilane- and epoxysilane-functionalized surfaces was applied to obtain thin CMD layers. The carboxyl moiety of the CMD was coupled to the aminated surface by EDC-NHS reagents, while CMD coupling through epoxysilane molecules was performed without any additional reagents. The surface analysis following the grafting procedures consisted of X-ray photoelectron spectroscopy (XPS), attenuated total reflection infrared spectroscopy (ATR-IR), spectroscopic ellipsometry, atomic force microscopy (AFM) and optical waveguide lightmode spectroscopy (OWLS). The XPS and AFM measurements showed that the grafting resulted in a very thin dextran layer of a few nanometers. The OWLS method allowed devising the structure of the interfacial dextran layers by the evaluation of the optogeometrical parameters. The alteration in the nanostructure of the CMD layer with the chemical composition of the silane coverage and the pH of the grafting solution was revealed by in situ OWLS, specifically, lain down chains were found to be prevalent on the surface under neutral and basic conditions on epoxysilylated surfaces. The developed methodologies allowed to design and fabricate nanometer scale CMD layers with well-controlled surface structure, which are very difficult to characterize in aqueous environments using present instrumentations and highly hydrated surface layers. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Combined use of FE-SEM+EDS, ToF-SIMS, XPS, XRD and OM for the study of ancient gilded artefacts

    NASA Astrophysics Data System (ADS)

    Ingo, G. M.; Riccucci, C.; Pascucci, M.; Messina, E.; Giuliani, C.; Biocca, P.; Tortora, L.; Fierro, G.; Di Carlo, G.

    2018-07-01

    Gilded brooches dating back to 16th-17th centuries CE were investigated by means of integrated and complementary analytical techniques such as high spatial resolution field emission scanning electron microscopy coupled with energy dispersive X-ray spectrometry (FE-SEM+EDS), time of flight secondary ion mass spectrometry (ToF-SIMS), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and optical microscopy (OM). The results reveal in detail the surface and subsurface morphology and the chemical features of the micrometric decorative Au layer that has been deposited by means of the so-called fire-gilding technique based on the use of an amalgam. Moreover, the results allow to recognise chlorine, sulphur and phosphorous species as the main degradation agents and to identify the corrosion products naturally formed during the long-term interaction with the burial soil constituents. The findings show also that the galvanic coupling between the two dissimilar metals, i.e. Cu and Au, lead to enhancement of corrosion phenomena causing the spalling of the gold thin film and the disfigurement of the object. From a conservation point of view, the results suggest a targeted use of low-toxic inhibitors to hinder the detrimental role of chlorine as possible responsible of future further severe degradation phenomena. In conclusions, the micro and nano-chemical, structural and morphological investigations in a depth range from a few nanometers to micrometers have revealed the complex nature of corroded surface of ancient gold coated artefacts, highlighting some specific aspects related to their peculiar degradation mechanisms thus extending the scientific relevance of the tailored use of complementary and integrated surface and subsurface analytical techniques for the investigation of ancient coated artefacts.

  1. A combined ToF-SIMS and XPS study for the elucidation of the role of water in the performances of a Post-Plasma Process using LaMnO3+δ as catalyst in the total oxidation of trichloroethylene

    NASA Astrophysics Data System (ADS)

    Nuns, N.; Beaurain, A.; Dinh, M. T. Nguyen; Vandenbroucke, A.; De Geyter, N.; Morent, R.; Leys, C.; Giraudon, J.-M.; Lamonier, J.-F.

    2014-11-01

    LaMnO3+δ which is an environment-friendly and inexpensive material has been previously used as catalyst in Post-Plasma Catalysis (PPC) in the total oxidation of trichloroethylene (TCE) which is a solvent widely used in dry cleaning and degreasing processes. It has been shown that the process efficiency increases in moist air (RH = 18%).The issue we want to address herein is the effect of water on the location of chlorine at the surface of the catalyst as chlorine is able to alter the catalyst structure, activity and stability. Therefore, a combined Time of Flight-Secondary Ion Mass Spectrometry (ToF-SIMS) and X-ray Photoelectron Spectroscopy (XPS) study has been carried out on the fresh LaMnO3+δ catalyst (LM) and used catalysts after performing PPC with TCE diluted in dry synthetic air (LM0) or with industrial air containing water (LM18; 18 stands for the Relative Humidity) and CO2 (about 560 ppmv) at a temperature of 150 °C. XPS and ToF-SIMS results both show the presence of chlorine on the tested catalysts whose amount increases by exposure of the catalyst to the reactive mixture in dry synthetic air. XPS results reveal that chlorine is present as both chloride ion and covalent chlorine on LM0 while organic chlorinated residues are absent on LM18 catalyst. ToF-SIMS study indicates that lanthanum excess as oxide(hydroxide) partially covering the perovskite mainly transforms into LaOCl and to a minor extent into LaCl3. Extent of Mn chlorination seems to be favored over LM0 having a higher MnClx±/MnOCl± ionic ratio compared to LM18. Furthermore ToF-SIMS clearly identifies C1 chlorinated organic ions, mainly CH2Cl+ and CHCl2-, on LM0 which may contribute to the XPS Cl organic component. From the combined ToF-SIMS and XPS results it is found that water delays the surface degradation extent of the perovskite into related (oxy)(hydroxy)chlorinated inorganic phases by less molecular chlorine and related chlorine species on the catalyst surface. A reaction scheme of

  2. In situ formation of the active sites in Pd-Au bimetallic nanocatalysts for CO oxidation: NAP (near ambient pressure) XPS and MS study.

    PubMed

    Bukhtiyarov, A V; Prosvirin, I P; Saraev, A A; Klyushin, A Yu; Knop-Gericke, A; Bukhtiyarov, V I

    2018-06-07

    Model bimetallic Pd-Au/HOPG catalysts have been investigated in the CO oxidation reaction using a combination of NAP XPS and MS techniques. The samples have shown catalytic activity at temperatures above 150 °C. The redistribution of Au and Pd on the surface depending on the reaction conditions has been demonstrated using NAP XPS. The Pd enrichment of the bimetallic particles' surface under reaction gas mixture has been shown. Apparently, CO adsorption induces Pd segregation on the surface. Heating the sample under reaction conditions above 150 °C decomposes the Pd-CO state due to CO desorption and reaction and simultaneous Pd-Au alloy formation on the surface takes place. Cooling back down to RT results in reversible Pd segregation due to Pd-CO formation and the sample becomes inactive. It has been shown that in situ studies are necessary for investigation of the active sites in Pd-Au bimetallic systems.

  3. In situ laser annealing system for real-time surface kinetic analysis

    NASA Astrophysics Data System (ADS)

    Wang, Q.; Sun, Y.-M.; Zhao, W.; Campagna, J.; White, J. M.

    2002-11-01

    For real-time analysis during thermal annealing, a continuous wave CO2 infrared laser was coupled to a surface analysis system equipped for x-ray photoelectron spectroscopy (XPS) and ion scattering spectroscopy (ISS). The laser beam was directed into the vacuum chamber through a ZnSe window to the back side of the sample. With 10 W laser output, the sample temperature reached 563 K. The chamber remained below 10-8 Torr during annealing and allowed XPS and ISS data to be gathered as a function of time at selected temperatures. As a test example, real time Cu2O reduction at 563 K was investigated.

  4. Monitoring N3 dye adsorption and desorption on TiO2 surfaces: a combined QCM-D and XPS study.

    PubMed

    Wayment-Steele, Hannah K; Johnson, Lewis E; Tian, Fangyuan; Dixon, Matthew C; Benz, Lauren; Johal, Malkiat S

    2014-06-25

    Understanding the kinetics of dye adsorption and desorption on semiconductors is crucial for optimizing the performance of dye-sensitized solar cells (DSSCs). Quartz crystal microbalance with dissipation monitoring (QCM-D) measures adsorbed mass in real time, allowing determination of binding kinetics. In this work, we characterize adsorption of the common RuBipy dye N3 to the native oxide layer of a planar, sputter-coated titanium surface, simulating the TiO2 substrate of a DSSC. We report adsorption equilibrium constants consistent with prior optical measurements of N3 adsorption. Dye binding and surface integrity were also verified by scanning electron microscopy, energy-dispersive X-ray spectroscopy, and X-ray photoelectron spectroscopy (XPS). We further study desorption of the dye from the native oxide layer on the QCM sensors using tetrabutylammonium hydroxide (TBAOH), a commonly used industrial desorbant. We find that using TBAOH as a desorbant does not fully regenerate the surface, though little ruthenium or nitrogen is observed by XPS after desorption, suggesting that carboxyl moieties of N3 remain bound. We demonstrate the native oxide layer of a titanium sensor as a valid and readily available planar TiO2 morphology to study dye adsorption and desorption and begin to investigate the mechanism of dye desorption in DSSCs, a system that requires further study.

  5. Evaluation Metrics for the Paragon XP/S-15

    NASA Technical Reports Server (NTRS)

    Traversat, Bernard; McNab, David; Nitzberg, Bill; Fineberg, Sam; Blaylock, Bruce T. (Technical Monitor)

    1993-01-01

    On February 17th 1993, the Numerical Aerodynamic Simulation (NAS) facility located at the NASA Ames Research Center installed a 224 node Intel Paragon XP/S-15 system. After its installation, the Paragon was found to be in a very immature state and was unable to support a NAS users' workload, composed of a wide range of development and production activities. As a first step towards addressing this problem, we implemented a set of metrics to objectively monitor the system as operating system and hardware upgrades were installed. The metrics were designed to measure four aspects of the system that we consider essential to support our workload: availability, utilization, functionality, and performance. This report presents the metrics collected from February 1993 to August 1993. Since its installation, the Paragon availability has improved from a low of 15% uptime to a high of 80%, while its utilization has remained low. Functionality and performance have improved from merely running one of the NAS Parallel Benchmarks to running all of them faster (between 1 and 2 times) than on the iPSC/860. In spite of the progress accomplished, fundamental limitations of the Paragon operating system are restricting the Paragon from supporting the NAS workload. The maximum operating system message passing (NORMA IPC) bandwidth was measured at 11 Mbytes/s, well below the peak hardware bandwidth (175 Mbytes/s), limiting overall virtual memory and Unix services (i.e. Disk and HiPPI I/O) performance. The high NX application message passing latency (184 microns), three times than on the iPSC/860, was found to significantly degrade performance of applications relying on small message sizes. The amount of memory available for an application was found to be approximately 10 Mbytes per node, indicating that the OS is taking more space than anticipated (6 Mbytes per node).

  6. Integrative Analysis Reveals Regulatory Programs in Endometriosis

    PubMed Central

    Yang, Huan; Kang, Kai; Cheng, Chao; Mamillapalli, Ramanaiah; Taylor, Hugh S.

    2015-01-01

    Endometriosis is a common gynecological disease found in approximately 10% of reproductive-age women. Gene expression analysis has been performed to explore alterations in gene expression associated with endometriosis; however, the underlying transcription factors (TFs) governing such expression changes have not been investigated in a systematic way. In this study, we propose a method to integrate gene expression with TF binding data and protein–protein interactions to construct an integrated regulatory network (IRN) for endometriosis. The IRN has shown that the most regulated gene in endometriosis is RUNX1, which is targeted by 14 of 26 TFs also involved in endometriosis. Using 2 published cohorts, GSE7305 (Hover, n = 20) and GSE7307 (Roth, n = 36) from the Gene Expression Omnibus database, we identified a network of TFs, which bind to target genes that are differentially expressed in endometriosis. Enrichment analysis based on the hypergeometric distribution allowed us to predict the TFs involved in endometriosis (n = 40). This included known TFs such as androgen receptor (AR) and critical factors in the pathology of endometriosis, estrogen receptor α, and estrogen receptor β. We also identified several new ones from which we selected FOXA2 and TFAP2C, and their regulation was confirmed by quantitative real-time polymerase chain reaction and immunohistochemistry (IHC). Further, our analysis revealed that the function of AR and p53 in endometriosis is regulated by posttranscriptional changes and not by differential gene expression. Our integrative analysis provides new insights into the regulatory programs involved in endometriosis. PMID:26134036

  7. Stages of Se adsorption on Au(111): A combined XPS, LEED, TOF-DRS, and DFT study

    NASA Astrophysics Data System (ADS)

    Ruano, G.; Tosi, E.; Sanchez, E.; Abufager, P.; Martiarena, M. L.; Grizzi, O.; Zampieri, G.

    2017-08-01

    We have studied the adsorption of Se on the surface Au(111) using XPS, TOF-DRS, LEED and DFT calculations. The use of a doser that operates in vacuum allowed us to investigate all the stages of the adsorption from the clean surface up to the formation of multilayers. In the monolayer regime we have found two ordered phases with distinctive LEED patterns. The LEED pattern of the first phase presents three fractional spots arranged symmetrically around the positions of the spots in a √3x√3 pattern. The analysis of this pattern suggests the formation of either a nxn superstructure of √3x√3 domains with n=19 or n=22, or that the adsorption occurs without removing the 22x√3 herringbone reconstruction of the gold surface. This last possibility is in accordance with DFT calculations which show that the charge transfer to a Se adsorbate might not be enough to destabilize the surface reconstruction. Increasing the coverage, beyond 0.3 ML a new LEED pattern appears with broad spots which upon annealing at 150 °C become well defined indicating a 1×8 periodicity. At the highest doses we have observed the formation of multilayers with no discernible LEED pattern. The comparison with adsorption experiments carried out in liquid solutions show similarities and also some important differences.

  8. Application of surface analytical methods in thin film analysis

    NASA Astrophysics Data System (ADS)

    Wen, Xingu

    Self-assembly and the sol-gel process are two promising methods for the preparation of novel materials and thin films. In this research, these two methods were utilized to prepare two types of thin films: self-assembled monolayers of peptides on gold and SiO2 sol-gel thin films modified with Ru(II) complexes. The properties of the resulting thin films were investigated by several analytical techniques in order to explore their potential applications in biomaterials, chemical sensors, nonlinear optics and catalysis. Among the analytical techniques employed in the study, surface analytical techniques, such as X-ray photoelectron spectroscopy (XPS) and grazing angle reflection absorption Fourier transform infrared spectroscopy (RA-FTIR), are particularly useful in providing information regarding the compositions and structures of the thin films. In the preparation of peptide thin films, monodisperse peptides were self-assembled on gold substrate via the N-terminus-coupled lipoic acid. The film compositions were investigated by XPS and agreed well with the theoretical values. XPS results also revealed that the surface coverage of the self-assembled films was significantly larger than that of the physisorbed films and that the chemisorption between the peptides and gold surface was stable in solvent. Studies by angle dependent XPS (ADXPS) and grazing angle RA-FTIR indicated that the peptides were on average oriented at a small angle from the surface normal. By using a model of orientation distribution function, both the peptide tilt angle and film thickness can be well calculated. Ru(II) complex doped SiO2 sol-gel thin films were prepared by low temperature sol-gel process. The ability of XPS coupled with Ar + ion sputtering to provide both chemical and compositional depth profile information of these sol-gel films was evaluated. This technique, together with UV-VIS and electrochemical measurements, was used to investigate the stability of Ru complexes in the composite

  9. Identification of the silver state in the framework of Ag-containing zeolite by XRD, FTIR, photoluminescence, 109Ag NMR, EPR, DR UV-vis, TEM and XPS investigations.

    PubMed

    Popovych, Nataliia; Kyriienko, Pavlo; Soloviev, Sergiy; Baran, Rafal; Millot, Yannick; Dzwigaj, Stanislaw

    2016-10-26

    Silver has been identified in the framework of Ag x SiBEA zeolites (where x = 3-6 Ag wt%) by the combined use of XRD, 109 Ag MAS NMR, FTIR, diffuse reflectance UV-visible, EPR and XPS spectroscopy. The incorporation of Ag ions into the framework of SiBEA zeolite has been evidenced by XRD. The consumption of OH groups as a result of their reaction with the silver precursor has been monitored by FTIR and photoluminescence spectroscopy. The changes in the silver state as a function of Ag content and thermal and hydrogen treatment at 573 K have been identified by 109 Ag MAS NMR, EPR, DR UV-visible, TEM and XPS investigations. The acidity of AgSiBEA has been investigated by FTIR spectroscopy of adsorbed CO and pyridine used as probe molecules.

  10. Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

    PubMed

    Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

    2012-01-01

    Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

  11. Interfacial chemistry of a perfluoropolyether lubricant studied by XPS and TDS

    NASA Technical Reports Server (NTRS)

    Herrera-Fierro, Pilar C.; Jones, William R., Jr.; Pepper, Stephen V.

    1992-01-01

    The interfacial chemistry of Fomblin Z25, a commercial perfluoropolyether used as lubricant for space applications, with different metallic surfaces: 440C steel, gold and aluminum was studied. Thin layers of Fomblin Z25 were evaporated onto the oxide-free substrates and the interfacial chemistry studied using XPS and TDS. The reactions were induced by heating the substrate and by rubbing the substrate with a steel ball. Gold was found to be completely unreactive towards Fomblin at any temperature. Reaction at room temperature was observed only in the case of the aluminum substrate, the most reactive towards Fomblin Z25 of the substrates studied. It was necessary to heat the 440C steel substrate to 190 degree C to induce decomposition of the fluid. The degradation of the fluid was indicated by the formation of a debris layer at the interface. This debris layer, composed of inorganic and organic reaction products, when completely formed, passivated the surface from further attack to the Fromblin on top. The tribologically induced reactions on 440C steel formed a debris layer of similar chemical characteristics to the thermally induced layer. In all cases, the degradation reaction resulted in preferential consumption of the difluoroformyl carbon (-OCF2O-).

  12. Surface chemical properties of eutectic and frozen NaCl solutions probed by XPS and NEXAFS.

    PubMed

    Křepelová, Adéla; Huthwelker, Thomas; Bluhm, Hendrik; Ammann, Markus

    2010-12-17

    We study the surface of sodium chloride-water mixtures above, at, and below the eutectic temperature using X-ray photoelectron spectroscopy (XPS) and electron-yield near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The NaCl frozen solutions are mimicking sea-salt deposits in ice or snow. Sea-salt particles emitted from the oceans are a major contributor to the global aerosol burden and can act as a catalyst for heterogeneous chemistry or as cloud condensation nuclei. The nature of halogen ions at ice surfaces and their influence on surface melting of ice are of significant current interest. We found that the surface of the frozen solution, depending on the temperature, consists of ice and different NaCl phases, that is, NaCl, NaCl·2H(2)O, and surface-adsorbed water.

  13. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

    PubMed

    Priest, Henry D; Fox, Samuel E; Rowley, Erik R; Murray, Jessica R; Michael, Todd P; Mockler, Todd C

    2014-01-01

    Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

  14. Macroscopic and microscopic investigation of Ni(II) sequestration on diatomite by batch, XPS, and EXAFS techniques.

    PubMed

    Sheng, Guodong; Yang, Shitong; Sheng, Jiang; Hu, Jun; Tan, Xiaoli; Wang, Xiangke

    2011-09-15

    Sequestration of Ni(II) on diatomite as a function of time, pH, and temperature was investigated by batch, XPS, and EXAFS techniques. The ionic strength-dependent sorption at pH < 7.0 was consistent with outer-sphere surface complexation, while the ionic strength-independent sorption at pH = 7.0-8.6 was indicative of inner-sphere surface complexation. EXAFS results indicated that the adsorbed Ni(II) consisted of ∼6 O at R(Ni-O) ≈ 2.05 Å. EXAFS analysis from the second shell suggested that three phenomena occurred at the diatomite/water interface: (1) outer-sphere and/or inner-sphere complexation; (2) dissolution of Si which is the rate limiting step during Ni uptake; and (3) extensive growth of surface (co)precipitates. Under acidic conditions, outer-sphere complexation is the main mechanism controlling Ni uptake, which is in good agreement with the macroscopic results. At contact time of 1 h or 1 day or pH = 7.0-8.0, surface coprecipitates occur concurrently with inner-sphere complexes on diatomite surface, whereas at contact time of 1 month or pH = 10.0, surface (co)precipitates dominate Ni uptake. Furthermore, surface loading increases with temperature increasing, and surface coprecipitates become the dominant mechanism at elevated temperature. The results are important to understand Ni interaction with minerals at the solid-water interface, which is helpful to evaluate the mobility of Ni(II) in the natural environment.

  15. XPS and XANES studies of biomimetic composites based on B-type nano-hydroxyapatite

    NASA Astrophysics Data System (ADS)

    Goloshchapov, D. L.; Gushchin, M. S.; Kashkarov, V. M.; Seredin, P. V.; Ippolitov, Y. A.; Khmelevsky, N. O.; Aksenenko, A. Yu.

    2018-06-01

    The paper presents an investigation of the local atomic structure of nanocrystalline carbonate-substituted hydroxyapatite (CHAP) contained in biomimetic composites - analogues of intact human tooth tissues. Using the XPS technique, the presence of impurity Mg and F atoms and structurally bound carbon in CHAP, at the concentrations typical of apatite enamel and dentine was determined. The XANES method was used to study the changes occurring in P L2,3 spectra of biocomposites with CHAP, depending on the percentage of the amino acid matrix. The appearance of maxima in the spectra of XANES P L2,3 near 135.7 eV for the samples with the composition of amino acid complex/hydroxyapatite - 5/95, 25/75 and the splitting of a broad peak of 146.9 eV in the spectrum of a biocomposite with a composition of 40/60 indicates at the interaction of molecular complex of amino acids with atomic environment of phosphorus. This fact can be used in the fundamental medicine for synthesizing of new biomaterials in dentistry.

  16. Local coexistence of VO 2 phases revealed by deep data analysis

    DOE PAGES

    Strelcov, Evgheni; Ievlev, Anton; Tselev, Alexander; ...

    2016-07-07

    We report a synergistic approach of micro-Raman spectroscopic mapping and deep data analysis to study the distribution of crystallographic phases and ferroelastic domains in a defected Al-doped VO 2 microcrystal. Bayesian linear unmixing revealed an uneven distribution of the T phase, which is stabilized by the surface defects and uneven local doping that went undetectable by other classical analysis techniques such as PCA and SIMPLISMA. This work demonstrates the impact of information recovery via statistical analysis and full mapping in spectroscopic studies of vanadium dioxide systems, which is commonly substituted by averaging or single point-probing approaches, both of which suffermore » from information misinterpretation due to low resolving power.« less

  17. Surface modification of EPDM rubber by plasma treatment.

    PubMed

    Grythe, Kai Frode; Hansen, Finn Knut

    2006-07-04

    The effect of argon, oxygen, and nitrogen plasma treatment of solvent cast EPDM rubber films has been investigated by means of atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and surface energy measurements. Plasma treatment leads to changes in the surface energy from 25 to 70 mN/m. Treatment conditions influenced both the changes in surface energy and the stability, and it became more difficult to obtain good contact angle measurements after longer (> ca. 4 min) treatment times, probably because of an increasingly uneven surface structure. XPS analyses revealed that up to 20 at. % oxygen can be easily incorporated and that variations of approximately 5% can be controlled by the plasma conditions. Oxygen was mainly found in hydroxyl groups, but also as carbonyl and carboxyl. XPS analyses showed more stable surfaces than expected from contact angles, probably because XPS analysis is less surface sensitive than contact angle measurements. AFM measurements revealed different surface structures with the three gases. The surface roughness increased generally with treatment time, and dramatic changes could be observed at longer times. At short times, surface energy changes were much faster than the changes in surface structure, showing that plasma treatment conditions can be utilized to tailor both surface energies and surface structure of EPDM rubber.

  18. Interactions of gaseous molecules with X-ray photons and photoelectrons in AP-XPS study of solid surface in gas phase.

    PubMed

    Tao, Franklin Feng; Nguyen, Luan

    2018-04-18

    Studies of the surface of a catalyst in the gas phase via photoelectron spectroscopy is an important approach to establish a correlation between the surface of a catalyst under reaction conditions or during catalysis and its corresponding catalytic performance. Unlike the well understood interactions between photoelectrons and the atomic layers of a surface in ultrahigh vacuum (UHV) and the well-developed method of quantitative analysis of a solid surface in UHV, a fundamental understanding of the interactions between X-ray photons and gaseous molecules and between photoelectrons and molecules of the gas phase in ambient pressure X-ray photoelectron spectroscopy (AP-XPS) is lacking. Through well designed experiments, here the impact of the interactions between photoelectrons and gaseous molecules and interactions between X-ray photons and gaseous molecules on the intensity of the collected photoelectrons have been explored. How the changes in photoelectron intensity resulting from these interactions influence measurement of the authentic atomic ratio of element M to A of a solid surface has been discussed herein, and methods to correct the measured nominal atomic ratio of two elements of a solid surface upon travelling through a gas phase to its authentic atomic ratio have been developed.

  19. Oxygen accumulation on metal surfaces investigated by XPS, AES and LEIS, an issue for sputter depth profiling under UHV conditions

    NASA Astrophysics Data System (ADS)

    Steinberger, R.; Celedón, C. E.; Bruckner, B.; Roth, D.; Duchoslav, J.; Arndt, M.; Kürnsteiner, P.; Steck, T.; Faderl, J.; Riener, C. K.; Angeli, G.; Bauer, P.; Stifter, D.

    2017-07-01

    Depth profiling using surface sensitive analysis methods in combination with sputter ion etching is a common procedure for thorough material investigations, where clean surfaces free of any contamination are essential. Hence, surface analytic studies are mostly performed under ultra-high vacuum (UHV) conditions, but the cleanness of such UHV environments is usually overrated. Consequently, the current study highlights the in principle known impact of the residual gas on metal surfaces (Fe, Mg, Al, Cr and Zn) for various surface analytics methods, like X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES) and low-energy ion scattering (LEIS). The investigations with modern, state-of-the-art equipment showed different behaviors for the metal surfaces in UHV during acquisition: (i) no impact for Zn, even after long time, (ii) solely adsorption of oxygen for Fe, slight and slow changes for Cr and (iii) adsorption accompanied by oxide formation for Al and Mg. The efficiency of different counter measures was tested and the acquired knowledge was finally used for ZnMgAl coated steel to obtain accurate depth profiles, which exhibited before serious artifacts when data acquisition was performed in an inconsiderate way.

  20. Depth resolved compositional analysis of aluminium oxide thin film using non-destructive soft x-ray reflectivity technique

    NASA Astrophysics Data System (ADS)

    Sinha, Mangalika; Modi, Mohammed H.

    2017-10-01

    In-depth compositional analysis of 240 Å thick aluminium oxide thin film has been carried out using soft x-ray reflectivity (SXR) and x-ray photoelectron spectroscopy technique (XPS). The compositional details of the film is estimated by modelling the optical index profile obtained from the SXR measurements over 60-200 Å wavelength region. The SXR measurements are carried out at Indus-1 reflectivity beamline. The method suggests that the principal film region is comprised of Al2O3 and AlOx (x = 1.6) phases whereas the interface region comprised of SiO2 and AlOx (x = 1.6) mixture. The soft x-ray reflectivity technique combined with XPS measurements explains the compositional details of principal layer. Since the interface region cannot be analyzed with the XPS technique in a non-destructive manner in such a case the SXR technique is a powerful tool for nondestructive compositional analysis of interface region.

  1. The influence of methanol on the chemical state of PtRu anodes in a high-temperature direct methanol fuel cell studied in situ by synchrotron-based near-ambient pressure x-ray photoelectron spectroscopy

    NASA Astrophysics Data System (ADS)

    Saveleva, Viktoriia A.; Daletou, Maria K.; Savinova, Elena R.

    2017-01-01

    Synchrotron radiation-based near-ambient pressure x-ray photoelectron spectroscopy (NAP-XPS) has recently become a powerful tool for the investigation of interfacial phenomena in electrochemical power sources such as batteries and fuel cells. Here we present an in situ NAP-XPS study of the anode of a high-temperature direct methanol fuel cell with a phosphoric acid-doped hydrocarbon membrane, which reveals an enhanced flooding of the Pt3Ru anode with phosphoric acid in the presence of methanol. An analysis of the electrode surface composition depending on the cell voltage and on the presence of methanol reveals the strong influence of the latter on the extent of Pt oxidation and on the transformation of Ru into Ru (IV) hydroxide.

  2. Comparative analysis reveals that polyploidy does not decelerate diversification in fish.

    PubMed

    Zhan, S H; Glick, L; Tsigenopoulos, C S; Otto, S P; Mayrose, I

    2014-02-01

    While the proliferation of the species-rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary methodologies, we co-estimate speciation and extinction rates associated with polyploid vs. diploid fish lineages. Family-level analysis of Acipenseridae and Botiidae revealed no significant difference in diversification rates between polyploid and diploid relatives, while analysis of the subfamily Cyprininae revealed higher polyploid diversification. Additionally, order-level analysis of the polyploid Salmoniformes and its diploid sister clade, the Esociformes, did not support a significantly different net diversification rate between the two groups. Taken together, our results suggest that polyploidy is generally not associated with decreased diversification in fish - a pattern that stands in contrast to that previously observed in plants. While there are notable differences in the time frame examined in the two studies, our results suggest that polyploidy is associated with different diversification patterns in these two major branches of the eukaryote tree of life. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  3. An XPS study on the impact of relative humidity on the aging of UO 2 powders

    DOE PAGES

    Donald, Scott B.; Dai, Zurong R.; Davisson, M. Lee; ...

    2017-02-10

    High resolution x-ray photoemission spectroscopy (XPS) was used to characterize the chemical speciation of high purity uranium dioxide (UO 2) powder samples following aging for periods of up to one year under controlled conditions with relative humidity ranging from 34% to 98%. A systematic shift to higher uranium oxidation states, and thus an increase in the mean uranium valence, was found to directly correlate with the dose of water received (i.e. the product of exposure time and relative humidity). Exposure duration was found to have a greater impact on sample aging than relative humidity. Lastly, the sample aged at 98%more » relative humidity was found to have unique structural differences for exposure time beyond 180 days when observed by scanning electron microscopy (SEM).« less

  4. An XPS study on the impact of relative humidity on the aging of UO 2 powders

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

    Donald, Scott B.; Dai, Zurong R.; Davisson, M. Lee

    High resolution x-ray photoemission spectroscopy (XPS) was used to characterize the chemical speciation of high purity uranium dioxide (UO 2) powder samples following aging for periods of up to one year under controlled conditions with relative humidity ranging from 34% to 98%. A systematic shift to higher uranium oxidation states, and thus an increase in the mean uranium valence, was found to directly correlate with the dose of water received (i.e. the product of exposure time and relative humidity). Exposure duration was found to have a greater impact on sample aging than relative humidity. Lastly, the sample aged at 98%more » relative humidity was found to have unique structural differences for exposure time beyond 180 days when observed by scanning electron microscopy (SEM).« less

  5. Electrochemical and XPS study of LiFePO4 cathode nanocomposite with PPy/PEG conductive network

    NASA Astrophysics Data System (ADS)

    Fedorková, A.; Oriňáková, R.; Oriňák, A.; Kupková, M.; Wiemhöfer, H.-D.; Audinot, J. N.; Guillot, J.

    2012-08-01

    High performance PPy/PEG-LiFePO4 nanocomposites as cathode materials were synthesized by solvothermal method and simple chemical oxidative polymerization of pyrrole (Py) monomer on the surface of LiFePO4 particles. The samples were characterized by scanning electron microscope (SEM), energy dispersive X-ray spectroscopy (EDX), X-ray photoelectron spectrometry (XPS) and charge-discharge tests. PPyPEG hybrid layers decrease particle to particle contact resistance while the impedance measurements confirmed that the coating of PPy-PEG significantly decreases the charge transfer resistance of the electrode material. The initial discharge capacities of this sample at C/5 and 1C are 150 and 128 mAh/g, respectively. The results show that PPy/PEGLiFePO4 composites are more effective than bare LiFePO4 as cathode material.

  6. Analysis of microstructure in electro-spark deposited IN718 superalloy

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

    Anisimov, E.; Khan, A.K.; Ojo, O.A., E-mail: olanr

    2016-09-15

    The microstructure of electro-spark deposited (ESD) superalloy IN718 was studied by the use of scanning electron microscopy (SEM), electron backscatter diffraction (EBSD), transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS) techniques. In converse to general assumption, the extremely high cooling rate involved in the ESD process did not produce partitionless solidification that is devoid of second phase microconstituents in the material, nano-sized Laves phase and MC carbide particles were observed within the deposited layer. Notwithstanding the several thermal cycles involved in the process, the extremely low heat input of the process produced a deposited region that is free ofmore » the main strengthening phase of the alloy, γ″ phase precipitates, which is in contrast to what have been reported on laser deposition. Nevertheless, application of the standard full heat treatment of the alloy resulted in extensive formation of the γ″ phase precipitates and δ phase precipitates, the most stable secondary phase of the alloy, with nearly, if not complete, dissolution of the Laves phase particles. Furthermore, the XPS analysis done in the study revealed the formation of nano-oxides within the deposited layer, which increased the microhardness of the superalloy in the as-deposited condition and inhibited its grain growth during post-process heat treatment. The microstructure analysis done in this work is crucial to the understanding of properties of the superalloy processed by the ESD technique. - Highlights: •Electron microscopy analyses of electro-spark deposited IN 718 superalloy were performed. •Nano-sized secondary phase particles were observed within the deposited layer. •The study shows that the ESD did not produce partitionless solidification of the alloy.« less

  7. Oxidation of MnO(100) and NaMnO2 formation: Characterization of Mn2+ and Mn3+ surfaces via XPS and water TPD

    NASA Astrophysics Data System (ADS)

    Feng, Xu; Cox, David F.

    2018-09-01

    The oxidation of clean and Na precovered MnO(100) has been investigated by X-ray photoelectron spectroscopy (XPS), low energy electron diffraction (LEED) and temperature programmed desorption (TPD) of adsorbed water. XPS results indicate that Mn3O4-like and Mn2O3-like surfaces can be formed by various oxidation treatments of clean and nearly-stoichiometric MnO(100), while a NaMnO2-like surface can be produced by the oxidation of MnO(100) pre-covered with multilayers of metallic Na. Water TPD results indicate that water adsorption/desorption is sensitive to the available oxidation states of surface Mn cations, and can be used to distinguish between surfaces exposing Mn2+and Mn3+ cations, or a combination of these oxidation states. Carbon dioxide and water TPD results from the NaMnO2-like surface indicate that pre-adsorbed water blocks the uptake of CO2, while water displaces pre-adsorbed CO2. No indication of a strong reactive interaction is observed between CO2, water and the NaMnO2-like surface under the conditions of our study.

  8. Surface science approach to Pt/carbon model catalysts: XPS, STM and microreactor studies

    NASA Astrophysics Data System (ADS)

    Motin, Abdul Md.; Haunold, Thomas; Bukhtiyarov, Andrey V.; Bera, Abhijit; Rameshan, Christoph; Rupprechter, Günther

    2018-05-01

    Pt nanoparticles supported on carbon are an important technological catalyst. A corresponding model catalyst was prepared by physical vapor deposition (PVD) of Pt on sputtered HOPG (highly oriented pyrolytic graphite). The carbon substrate before and after sputtering as well as the Pt/HOPG system before and after Pt deposition and annealing were examined by XPS and STM. This yielded information on the surface density of defects, which serve as nucleation centres for Pt, and on the size distribution (mean size/height) of the Pt nanoparticles. Two different model catalysts were prepared with mean sizes of 2.0 and 3.6 nm, both turned out to be stable upon UHV-annealing to 300 °C. After transfer into a UHV-compatible flow microreactor and subsequent cleaning in UHV and under mbar pressure, the catalytic activity of the Pt/HOPG model system for ethylene hydrogenation was examined under atmospheric pressure flow conditions. This enabled to determine temperature-dependent conversion rates, turnover frequencies (TOFs) and activation energies. The catalytic results obtained are in line with the characteristics of technological Pt/C, demonstrating the validity of the current surface science based model catalyst approach.

  9. Surface chemical composition of human maxillary first premolar as assessed by X-ray photoelectron spectroscopy (XPS)

    NASA Astrophysics Data System (ADS)

    Lou, Leo; Nelson, Alan E.; Heo, Giseon; Major, Paul W.

    2008-08-01

    The surface chemical composition of dental enamel has been postulated as a contributing factor in the variation of bond strength of brackets bonded to teeth, and hence, the probability of bracket failure during orthodontic treatment. This study systematically investigated the chemical composition of 98 bonding surfaces of human maxillary premolars using X-ray photoelectron spectroscopy (XPS) to ascertain compositional differences between right and left first premolars. The major elements detected in all samples were calcium, phosphorus, oxygen, nitrogen and carbon. Surface compositions were highly variable between samples and several elements were found to be highly correlated. No statistical significant difference in the chemical composition of the maxillary right and left first premolars was found ( p > 0.05). Knowledge of the chemical composition of enamel surfaces will facilitate future studies that relate this information to the variations in dental enamel bond strength.

  10. Tracking the conversion of nitrogen during pyrolysis of antibiotic mycelial fermentation residues using XPS and TG-FTIR-MS technology.

    PubMed

    Zhu, Xiangdong; Yang, Shijun; Wang, Liang; Liu, Yuchen; Qian, Feng; Yao, Wenqing; Zhang, Shicheng; Chen, Jianmin

    2016-04-01

    Antibiotic mycelial fermentation residues (AMFRs), which are emerging solid pollutants, have been recognized as hazardous waste in China since 2008. Nitrogen (N), which is an environmental sensitivity element, is largely retained in AMFR samples derived from fermentation substrates. Pyrolysis is a promising technology for the treatment of solid waste. However, the outcomes of N element during the pyrolysis of AMFRs are still unknown. In this study, the conversion of N element during the pyrolysis of AMFRs was tracked using XPS (X-ray photoelectron spectroscopy) and online TG-FTIR-MS (Thermogravimetry-Fourier transform infrared-Mass spectrometry) technology. In the AMFR sample, organic amine-N, pyrrolic-N, protein-N, pyridinic-N, was the main N-containing species. XPS results indicated that pyrrolic-N and pyridinic-N were retained in the AMFR-derived pyrolysis char. More stable species, such as N-oxide and quaternary-N, were also produced in the char. TG-FTIR-MS results indicated that NH3 and HCN were the main gaseous species, and their contents were closely related to the contents of amine-N and protein-N, and pyrrolic-N and pyridinic-N of AMFRs, respectively. Increases in heating rate enhanced the amounts of NH3 and HCN, but had less of an effect on the degradation degree of AMFRs. N-containing organic compounds, including amine-N, nitrile-N and heterocyclic-N, were discerned from the AMFR pyrolysis process. Their release range was extended with increasing of heating rate and carbon content of AMFR sample. This work will help to take appropriate measure to reduce secondary pollution from the treatment of AMFRs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. As-Received, Ozone Cleaned and Ar+ Sputtered Surfaces of Hafnium Oxide Grown by Atomic Layer Deposition and Studied by XPS

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

    Engelhard, Mark H.; Herman, Jacob A.; Wallace, Robert

    2012-06-27

    In this study, X-ray photoelectron spectroscopy (XPS) characterization was performed on 47 nm thick hafnium oxide (HfO{sub 2}) films grown by atomic layer deposition using TEMA-Hf/H{sub 2}O at 250 C substrate temperature. HfO{sub 2} is currently being studied as a possible replacement for Silicon Oxide (SiO{sub 2}) as a gate dielectric in electronics transistors. XPS spectra were collected on a Physical Electronics Quantum 2000 Scanning ESCA Microprobe using a monochromatic Al K{sub a} X-ray (1486.7 eV) excitation source. The sample was analyzed under the following conditions: as received, after UV irradiation for five minutes, and after sputter cleaning with 2more » kV Ar{sup +} ions for 180 seconds. Survey scans showed carbon, oxygen, and hafnium as the major species in the film, while the only minor species of argon and carbide was detected after sputtering. Adventitious carbon initially composed approximately 18.6 AT% of the surface, but after UV cleaning it was reduced to 2.4 AT%. This demonstrated that that the majority of carbon was due to adventitious carbon. However, after 2 kV Ar{sup +} sputtering there was still only trace amounts of carbon at {approx}1 AT%, Some of this trace carbon is now in the form of a carbide due to the interaction with Ar{sup +} used for sputter cleaning. Furthermore, the stoiciometric ratio of oxygen and hafnium is consistent with a high quality HfO{sub 2} film.« less

  12. Time-dependent investigation of sub-monolayers of Ni on Pd using Positron-annihilation induced Auger Electron Spectroscopy and XPS

    NASA Astrophysics Data System (ADS)

    Zimnik, Samantha; Piochacz, Christian; Vohburger, Sebastian; Hugenschmidt, Christoph

    2016-01-01

    The surface of a polycrystalline Pd-substrate covered with (sub-) monolayers of Ni was investigated with Positron-annihilation induced Auger Electron Spectroscopy (PAES). Comparative studies using conventional AES induced by electrons and X-rays showed the outstanding surface sensitivity of PAES. Time-dependent PAES was performed on a 0.5 ML Ni cover layer on Pd and compared with conventional X-ray induced Photoelectron Spectroscopy (XPS) in order to observe changes in the elemental composition of the surface. The PAES results appear to show a migration of Ni atoms into the Pd substrate, whereas the Ni signal shows a decrease of 12% within 13 h with respect to the initial value.

  13. Reference binding energies of transition metal carbides by core-level x-ray photoelectron spectroscopy free from Ar+ etching artefacts

    NASA Astrophysics Data System (ADS)

    Greczynski, G.; Primetzhofer, D.; Hultman, L.

    2018-04-01

    We report x-ray photoelectron spectroscopy (XPS) core level binding energies (BE's) for the widely-applicable groups IVb-VIb transition metal carbides (TMCs) TiC, VC, CrC, ZrC, NbC, MoC, HfC, TaC, and WC. Thin film samples are grown in the same deposition system, by dc magnetron co-sputtering from graphite and respective elemental metal targets in Ar atmosphere. To remove surface contaminations resulting from exposure to air during sample transfer from the growth chamber into the XPS system, layers are either (i) Ar+ ion-etched or (ii) UHV-annealed in situ prior to XPS analyses. High resolution XPS spectra reveal that even gentle etching affects the shape of core level signals, as well as BE values, which are systematically offset by 0.2-0.5 eV towards lower BE. These destructive effects of Ar+ ion etch become more pronounced with increasing the metal atom mass due to an increasing carbon-to-metal sputter yield ratio. Systematic analysis reveals that for each row in the periodic table (3d, 4d, and 5d) C 1s BE increases from left to right indicative of a decreased charge transfer from TM to C atoms, hence bond weakening. Moreover, C 1s BE decreases linearly with increasing carbide/metal melting point ratio. Spectra reported here, acquired from a consistent set of samples in the same instrument, should serve as a reference for true deconvolution of complex XPS cases, including multinary carbides, nitrides, and carbonitrides.

  14. Surface characterization of LDEF materials

    NASA Astrophysics Data System (ADS)

    Wightman, J. P.; Grammer, Holly Little

    1993-10-01

    The NASA Long Duration Exposure Facility (LDEF), a passive experimental satellite, was placed into low-Earth orbit by the Shuttle Challenger in Apr. 1984. The LDEF spent an unprecedented 69 months in space. The flight and recovery of the LDEF provided a wealth of information on the longterm space environmental effects of a variety of materials exposed to the low-Earth orbit environment. Surface characterization of LDEF materials included polymers, composites, thermal control paints, and aluminum. X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES), scanning electron microscopy (SEM), and contact angle analysis were used to document changes in both the surface composition and surface chemistry of these materials. Detailed XPS analysis of the polymer systems, such as Kapton, polyimide polysiloxane copolymers, and fluorinated ethylene propylene thermal blankets on the backside of the LDEF revealed significant changes in both the surface composition and surface chemistry as a result of exposure to the low-Earth orbit environment. Polymer systems such as Kapton, polyimide polysiloxane copolymers, and polysulfone showed a common trend of decreasing carbon content and increasing oxygen content with respect to the control sample. Carbon 1s curve fit XPS analysis of the composite samples, in conjunction with SEM photomicrographs, revealed significant ablation of the polymer matrix resin to expose the carbon fibers of the composite during exposure to the space environment. Surface characterization of anodized aluminum tray clamps, which were located at regular intervals over the entire LDEF frame, provided the first results to evaluate the extent of contamination with respect to position on the LDEF. The XPS results clearly showed that the amount and state of both silicon and fluorine contamination were directly dependent upon the position of the tray clamp on the LDEF.

  15. Surface characterization of LDEF materials

    NASA Technical Reports Server (NTRS)

    Wightman, J. P.; Grammer, Holly Little

    1993-01-01

    The NASA Long Duration Exposure Facility (LDEF), a passive experimental satellite, was placed into low-Earth orbit by the Shuttle Challenger in Apr. 1984. The LDEF spent an unprecedented 69 months in space. The flight and recovery of the LDEF provided a wealth of information on the longterm space environmental effects of a variety of materials exposed to the low-Earth orbit environment. Surface characterization of LDEF materials included polymers, composites, thermal control paints, and aluminum. X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES), scanning electron microscopy (SEM), and contact angle analysis were used to document changes in both the surface composition and surface chemistry of these materials. Detailed XPS analysis of the polymer systems, such as Kapton, polyimide polysiloxane copolymers, and fluorinated ethylene propylene thermal blankets on the backside of the LDEF revealed significant changes in both the surface composition and surface chemistry as a result of exposure to the low-Earth orbit environment. Polymer systems such as Kapton, polyimide polysiloxane copolymers, and polysulfone showed a common trend of decreasing carbon content and increasing oxygen content with respect to the control sample. Carbon 1s curve fit XPS analysis of the composite samples, in conjunction with SEM photomicrographs, revealed significant ablation of the polymer matrix resin to expose the carbon fibers of the composite during exposure to the space environment. Surface characterization of anodized aluminum tray clamps, which were located at regular intervals over the entire LDEF frame, provided the first results to evaluate the extent of contamination with respect to position on the LDEF. The XPS results clearly showed that the amount and state of both silicon and fluorine contamination were directly dependent upon the position of the tray clamp on the LDEF.

  16. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    PubMed Central

    2013-01-01

    Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also

  17. Surface study of stainless steel electrode deposition from soil electrokinetic (EK) treatment using X-ray photoelectron spectroscopy (XPS)

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

    Embong, Zaidi, E-mail: zaidi@uthm.edu.my; Research Centre for Soft Soils; Johar, Saffuwan

    2015-04-29

    Electrokinetic (EK) remediation relies upon application of a low-intensity direct current through the soil between stainless steel electrodes that are divided into a cathode array and an anode array. This mobilizes charged species, causing ions and water to move toward the electrodes. Metal ions and positively charged organic compounds move toward the cathode. Anions such as chloride, fluoride, nitrate, and negatively charged organic compounds move toward the anode. Here, this remediation techniques lead to a formation of a deposition at the both cathode and anode surface that mainly contributed byanion and cation from the remediated soil. In this research, Renggam-Jerangaumore » soil species (HaplicAcrisol + RhodicFerralsol) with a surveymeter reading of 38.0 ± 3.9 μR/hr has been investigation in order to study the mobility of the anion and cation under the influence electric field. Prior to the EK treatment, the elemental composition of the soil and the stainless steel electrode are measured using XRF analyses. Next, the soil sample is remediated at a constant electric potential of 30 V within an hour of treatment period. A surface study for the deposition layer of the cathode and anode using X-ray Photoelectron spectroscopy (XPS) revealed that a narrow photoelectron signal from oxygen O 1s, carbon, C 1s silica, Si 2p, aluminium, Al 2p and chromium, Cr 2p exhibited on the electrode surface and indicate that a different in photoelectron intensity for each element on both electrode surface. In this paper, the mechanism of Si{sup 2+} and Al{sup 2+} cation mobility under the influence of voltage potential between the cathode and anode will be discussed in detail.« less

  18. Co-occurrence correlations of heavy metals in sediments revealed using network analysis.

    PubMed

    Liu, Lili; Wang, Zhiping; Ju, Feng; Zhang, Tong

    2015-01-01

    In this study, the correlation-based study was used to identify the co-occurrence correlations among metals in marine sediment of Hong Kong, based on the long-term (from 1991 to 2011) temporal and spatial monitoring data. 14 stations out of the total 45 marine sediment monitoring stations were selected from three representative areas, including Deep Bay, Victoria Harbour and Mirs Bay. Firstly, Spearman's rank correlation-based network analysis was conducted as the first step to identify the co-occurrence correlations of metals from raw metadata, and then for further analysis using the normalized metadata. The correlations patterns obtained by network were consistent with those obtained by the other statistic normalization methods, including annual ratios, R-squared coefficient and Pearson correlation coefficient. Both Deep Bay and Victoria Harbour have been polluted by heavy metals, especially for Pb and Cu, which showed strong co-occurrence with other heavy metals (e.g. Cr, Ni, Zn and etc.) and little correlations with the reference parameters (Fe or Al). For Mirs Bay, which has better marine sediment quality compared with Deep Bay and Victoria Harbour, the co-occurrence patterns revealed by network analysis indicated that the metals in sediment dominantly followed the natural geography process. Besides the wide applications in biology, sociology and informatics, it is the first time to apply network analysis in the researches of environment pollutions. This study demonstrated its powerful application for revealing the co-occurrence correlations among heavy metals in marine sediments, which could be further applied for other pollutants in various environment systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Preparation of γ-LiV2O5 from polyoxovanadate cluster Li7[V15O36(CO3)] as a high-performance cathode material and its reaction mechanism revealed by operando XAFS

    NASA Astrophysics Data System (ADS)

    Wang, Heng; Isobe, Jin; Shimizu, Takeshi; Matsumura, Daiju; Ina, Toshiaki; Yoshikawa, Hirofumi

    2017-08-01

    γ-phase LiV2O5, which shows superior electrochemical performance as cathode material in Li-ion batteries, was prepared by annealing the polyoxovanadate cluster Li7 [V15O36(CO3)]. The reaction mechanism was studied using operando X-ray absorption fine structure (XAFS), powder X-ray diffraction (PXRD), and X-ray photoelectron spectroscopy (XPS) analyses. The X-ray absorption near edge structure (XANES) and XPS results reveal that γ-LiV2O5 undergoes two-electron redox reaction per V2O5 pyramid unit, resulting in a large reversible capacity of 260 Ah/kg. The extended X-ray absorption fine structure (EXAFS) and PXRD analyses also suggest that the V-V distance slightly increases, due to the reduction of V5+ to V4+ during Li ion intercalation as the material structure is maintained. As a result, γ-LixV2O5 shows highly reversible electrochemical reaction with x = 0.1-1.9.

  20. Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells

    PubMed Central

    Liu, Bing; Gao, Yankun; Ruan, Hai-Bin; Chen, Yue

    2016-01-01

    Proline hydroxylation is a critical cellular mechanism regulating oxygen-response pathways in tumor initiation and progression. Yet, its substrate diversity and functions remain largely unknown. Here, we report a system-wide analysis to characterize proline hydroxylation substrates in cancer cells using an immunoaffinity-purification assisted proteomics strategy. We identified 562 sites from 272 proteins in HeLa cells. Bioinformatic analysis revealed that proline hydroxylation substrates are significantly enriched with mRNA processing and stress-response cellular pathways with canonical and diverse flanking sequence motifs. Structural analysis indicates a significant enrichment of proline hydroxylation participating in the secondary structure of substrate proteins. Our study identified and validated Brd4, a key transcription factor, as a novel proline hydroxylation substrate. Functional analysis showed that the inhibition of proline hydroxylation pathway significantly reduced the proline hydroxylation abundance on Brd4 and affected Brd4-mediated transcriptional activity as well as cell proliferation in AML leukemia cells. Taken together, our study identified a broad regulatory role of proline hydroxylation in cellular oxygen-sensing pathways and revealed potentially new targets that dynamically respond to hypoxia microenvironment in tumor cells. PMID:27764789

  1. Data-Independent Acquisition-Based Quantitative Proteomic Analysis Reveals Potential Biomarkers of Kidney Cancer.

    PubMed

    Song, Yimeng; Zhong, Lijun; Zhou, Juntuo; Lu, Min; Xing, Tianying; Ma, Lulin; Shen, Jing

    2017-12-01

    Renal cell carcinoma (RCC) is a malignant and metastatic cancer with 95% mortality, and clear cell RCC (ccRCC) is the most observed among the five major subtypes of RCC. Specific biomarkers that can distinguish cancer tissues from adjacent normal tissues should be developed to diagnose this disease in early stages and conduct a reliable prognostic evaluation. Data-independent acquisition (DIA) strategy has been widely employed in proteomic analysis because of various advantages, including enhanced protein coverage and reliable data acquisition. In this study, a DIA workflow is constructed on a quadrupole-Orbitrap LC-MS platform to reveal dysregulated proteins between ccRCC and adjacent normal tissues. More than 4000 proteins are identified, 436 of these proteins are dysregulated in ccRCC tissues. Bioinformatic analysis reveals that multiple pathways and Gene Ontology items are strongly associated with ccRCC. The expression levels of L-lactate dehydrogenase A chain, annexin A4, nicotinamide N-methyltransferase, and perilipin-2 examined through RT-qPCR, Western blot, and immunohistochemistry confirm the validity of the proteomic analysis results. The proposed DIA workflow yields optimum time efficiency and data reliability and provides a good choice for proteomic analysis in biological and clinical studies, and these dysregulated proteins might be potential biomarkers for ccRCC diagnosis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. X-ray photoelectron spectroscopy on 1-peso and 2-pesos of the Argentine Republic

    NASA Astrophysics Data System (ADS)

    Gard, Faramarz S.; Duffo, Gustavo; Bergamasco, Pablo; Forlerer, Elena

    2018-04-01

    Relative concentrations of nickel and copper at the surface of the ring and centre parts of 1-peso and 2-pesos Argentine coins have been studied by means of X-ray photoemission spectroscopy (XPS). It has been observed Ni-enrichment at the surface of the ring (silvery) part of a 1-peso, minted in 1994, whereas the XPS data reveals lack of nickel at the surface of the centre (silvery) part of a 2-pesos, minted in 2016. This discrepancy is explained by analyzing the XPS peaks of oxygen and carbon, and is suggested to be related to the contamination layer on the surface of the coins. The XPS analysis of the golden parts of the coins, namely the centre part of the 1-peso and the ring part of the 2-pesos coins were inconclusive, due to the small amount of the Ni (nominally %2) used in those parts. The possible oxidations states of the metals at the surface of the untreated and treated coins with the artificial human sweat were also identified.

  3. Near-ambient pressure XPS of high-temperature surface chemistry in Sr2Co2O5 thin films

    DOE PAGES

    Hong, Wesley T.; Stoerzinger, Kelsey; Crumlin, Ethan J.; ...

    2016-02-11

    Transition metal perovskite oxides are promising electrocatalysts for the oxygen reduction reaction (ORR) in fuel cells, but a lack of fundamental understanding of oxide surfaces impedes the rational design of novel catalysts with improved device efficiencies. In particular, understanding the surface chemistry of oxides is essential for controlling both catalytic activity and long-term stability. Thus, elucidating the physical nature of species on perovskite surfaces and their catalytic enhancement would generate new insights in developing oxide electrocatalysts. In this article, we perform near-ambient pressure XPS of model brownmillerite Sr 2Co 2O 5 (SCO) epitaxial thin films with different crystallographic orientations. Detailedmore » analysis of the Co 2p spectra suggests that the films lose oxygen as a function of temperature. Moreover, deconvolution of the O 1s spectra shows distinct behavior for (114)-oriented SCO films compared to (001)-oriented SCO films, where an additional bulk oxygen species is observed. These findings indicate a change to a perovskite-like oxygen chemistry that occurs more easily in (114) SCO than (001) SCO, likely due to the orientation of oxygen vacancy channels out-of-plane with respect to the film surface. This difference in surface chemistry is responsible for the anisotropy of the oxygen surface exchange coefficient of SCO and may contribute to the enhanced ORR kinetics of La 0.8Sr 0.2CoO 3-δ thin films by SCO surface particles observed previously.« less

  4. Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

    PubMed Central

    Wen, Dingqiao; Yu, Yun; Hahn, Matthew W.; Nakhleh, Luay

    2016-01-01

    The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of ‘network thinking’ and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence. PMID:26808290

  5. Solar Ion Processing of Major Element Surface Compositions of Mature Mare Soils: Insights from Combined XPS and Analytical TEM Observations

    NASA Technical Reports Server (NTRS)

    Christoffersen, R.; Dukes, C.; Keller, L. P.; Baragiola, R.

    2012-01-01

    Solar wind ions are capable of altering the sur-face chemistry of the lunar regolith by a number of mechanisms including preferential sputtering, radiation-enhanced diffusion and sputter erosion of space weathered surfaces containing pre-existing compositional profiles. We have previously reported in-situ ion irradiation experiments supported by X-ray photoelectron spectroscopy (XPS) and analytical TEM that show how solar ions potentially drive Fe and Ti reduction at the monolayer scale as well as the 10-100 nm depth scale in lunar soils [1]. Here we report experimental data on the effect of ion irradiation on the major element surface composition in a mature mare soil.

  6. Genomewide DNA methylation analysis in combat veterans reveals a novel locus for PTSD.

    PubMed

    Mehta, D; Bruenig, D; Carrillo-Roa, T; Lawford, B; Harvey, W; Morris, C P; Smith, A K; Binder, E B; Young, R McD; Voisey, J

    2017-11-01

    Epigenetic modifications such as DNA methylation may play a key role in the aetiology and serve as biomarkers for post-traumatic stress disorder (PTSD). We performed a genomewide analysis to identify genes whose DNA methylation levels are associated with PTSD. A total of 211 individuals comprising Australian male Vietnam War veterans (n = 96) and males from a general population belonging to the Grady Trauma Project (n = 115) were included. Genomewide DNA methylation was performed from peripheral blood using the Illumina arrays. Data analysis was performed using generalized linear regression models. Differential DNA methylation of 17 previously reported PTSD candidate genes was associated with PTSD symptom severity. Genomewide analyses revealed CpG sites spanning BRSK1, LCN8, NFG and DOCK2 genes were associated with PTSD symptom severity. We replicated the findings of DOCK2 in an independent cohort. Pathway analysis revealed that among the associated genes, genes within actin cytoskeleton and focal adhesion molecular pathways were enriched. These data highlight the role of DNA methylation as biomarkers of PTSD. The results support the role of previous candidates and uncover novel genes associated with PTSD, such as DOCK2. This study contributes to our understanding of the biological underpinnings of PTSD. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  7. Structural and electrochemical analysis of chemically synthesized microcubic architectured lead selenide thin films

    NASA Astrophysics Data System (ADS)

    Bhat, T. S.; Shinde, A. V.; Devan, R. S.; Teli, A. M.; Ma, Y. R.; Kim, J. H.; Patil, P. S.

    2018-01-01

    The present work deals with the synthesis of lead selenide (PbSe) thin films by simple and cost-effective chemical bath deposition method with variation in deposition time. The structural, morphological, and electrochemical properties of as-deposited thin films were examined using characterization techniques such as X-ray diffraction spectroscopy (XRD), field-emission scanning electron microscopy (FE-SEM), X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV), galvanostatic charge-discharge and electrochemical impedance spectroscopy. XRD reveals formation of rock salt phase cubic structured PbSe. FE-SEM images show the formation of microcubic structured morphology. The existence of the PbSe is confirmed from the XPS analysis. On the other hand, CV curves show four reaction peaks corresponding to oxidation [PbSe and Pb(OH)2] and reduction (PbO2 and Pb(OH)2) at the surface of PbSe thin films. The PbSe:2 sample deposited for 80 min. shows maximum specific capacitance of 454 ± 5 F g- 1 obtained at 0.25 mA cm- 2 current density. The maximum energy density of 69 Wh kg- 1 was showed by PbSe:2 electrode with a power density of 1077 W kg- 1. Furthermore, electrochemical impedance studies of PbSe:2 thin film show 80 ± 3% cycling stability even after 500 CV cycles. Such results show the importance of microcubic structured PbSe thin film as an anode in supercapacitor devices.

  8. Genomic analysis reveals secondary glioblastoma after radiotherapy in a subset of recurrent medulloblastomas.

    PubMed

    Phi, Ji Hoon; Park, Ae Kyung; Lee, Semin; Choi, Seung Ah; Baek, In-Pyo; Kim, Pora; Kim, Eun-Hye; Park, Hee Chul; Kim, Byung Chul; Bhak, Jong; Park, Sung-Hye; Lee, Ji Yeoun; Wang, Kyu-Chang; Kim, Dong-Seok; Shim, Kyu Won; Kim, Se Hoon; Kim, Chae-Yong; Kim, Seung-Ki

    2018-06-01

    Despite great advances in understanding of molecular pathogenesis and achievement of a high cure rate in medulloblastoma, recurrent medulloblastomas are still dismal. Additionally, misidentification of secondary malignancies due to histological ambiguity leads to misdiagnosis and eventually to inappropriate treatment. Nevertheless, the genomic characteristics of recurrent medulloblastomas are poorly understood, largely due to a lack of matched primary and recurrent tumor tissues. We performed a genomic analysis of recurrent tumors from 17 pediatric medulloblastoma patients. Whole transcriptome sequencing revealed that a subset of recurrent tumors initially diagnosed as locally recurrent medulloblastomas are secondary glioblastomas after radiotherapy, showing high similarity to the non-G-CIMP proneural subtype of glioblastoma. Further analysis, including whole exome sequencing, revealed missense mutations or complex gene fusion events in PDGFRA with augmented expression in the secondary glioblastomas after radiotherapy, implicating PDGFRA as a putative driver in the development of secondary glioblastomas after treatment exposure. This result provides insight into the possible application of PDGFRA-targeted therapy in these second malignancies. Furthermore, genomic alterations of TP53 including 17p loss or germline/somatic mutations were also found in most of the secondary glioblastomas after radiotherapy, indicating a crucial role of TP53 alteration in the process. On the other hand, analysis of recurrent medulloblastomas revealed that the most prevalent alterations are the loss of 17p region including TP53 and gain of 7q region containing EZH2 which already exist in primary tumors. The 7q gain events are frequently accompanied by high expression levels of EZH2 in both primary and recurrent medulloblastomas, which provides a clue to a new therapeutic target to prevent recurrence. Considering the fact that it is often challenging to differentiate between recurrent

  9. Elemental content of enamel and dentin after bleaching of teeth (a comparative study between laser-induced breakdown spectroscopy and x-ray photoelectron spectroscopy)

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

    Imam, H.; Ahmed, Doaa; Eldakrouri, Ashraf

    2013-06-21

    The elemental content of the superficial and inner enamel as well as that of dentin was analyzed using laser-induced breakdown spectroscopy (LIBS) and x-ray photoelectron spectroscopy (XPS) of bleached and unbleached tooth specimens. It is thus clear from the spectral analysis using both the LIBS and XPS technique that elemental changes (though insignificant within the scopes of this study) of variable intensities do occur on the surface of the enamel and extend deeper to reach dentin. The results of the LIBS revealed a slight reduction in the calcium levels in the bleached compared to the control specimens in all themore » different bleaching groups and in both enamel and dentin. The good correlation found between the LIBS and XPS results demonstrates the possibility of LIBS technique for detection of minor loss in calcium and phosphorus in enamel and dentin.« less

  10. Genomic analysis of primordial dwarfism reveals novel disease genes.

    PubMed

    Shaheen, Ranad; Faqeih, Eissa; Ansari, Shinu; Abdel-Salam, Ghada; Al-Hassnan, Zuhair N; Al-Shidi, Tarfa; Alomar, Rana; Sogaty, Sameera; Alkuraya, Fowzan S

    2014-02-01

    Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis.

  11. Genomic analysis of primordial dwarfism reveals novel disease genes

    PubMed Central

    Shaheen, Ranad; Faqeih, Eissa; Ansari, Shinu; Abdel-Salam, Ghada; Al-Hassnan, Zuhair N.; Al-Shidi, Tarfa; Alomar, Rana; Sogaty, Sameera; Alkuraya, Fowzan S.

    2014-01-01

    Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis. PMID:24389050

  12. Systematic analysis of the gerontome reveals links between aging and age-related diseases

    PubMed Central

    Fernandes, Maria; Wan, Cen; Tacutu, Robi; Barardo, Diogo; Rajput, Ashish; Wang, Jingwei; Thoppil, Harikrishnan; Thornton, Daniel; Yang, Chenhao; Freitas, Alex

    2016-01-01

    Abstract In model organisms, over 2,000 genes have been shown to modulate aging, the collection of which we call the ‘gerontome’. Although some individual aging-related genes have been the subject of intense scrutiny, their analysis as a whole has been limited. In particular, the genetic interaction of aging and age-related pathologies remain a subject of debate. In this work, we perform a systematic analysis of the gerontome across species, including human aging-related genes. First, by classifying aging-related genes as pro- or anti-longevity, we define distinct pathways and genes that modulate aging in different ways. Our subsequent comparison of aging-related genes with age-related disease genes reveals species-specific effects with strong overlaps between aging and age-related diseases in mice, yet surprisingly few overlaps in lower model organisms. We discover that genetic links between aging and age-related diseases are due to a small fraction of aging-related genes which also tend to have a high network connectivity. Other insights from our systematic analysis include assessing how using datasets with genes more or less studied than average may result in biases, showing that age-related disease genes have faster molecular evolution rates and predicting new aging-related drugs based on drug-gene interaction data. Overall, this is the largest systems-level analysis of the genetics of aging to date and the first to discriminate anti- and pro-longevity genes, revealing new insights on aging-related genes as a whole and their interactions with age-related diseases. PMID:28175300

  13. Integrated systems analysis reveals a molecular network underlying autism spectrum disorders

    PubMed Central

    Li, Jingjing; Shi, Minyi; Ma, Zhihai; Zhao, Shuchun; Euskirchen, Ghia; Ziskin, Jennifer; Urban, Alexander; Hallmayer, Joachim; Snyder, Michael

    2014-01-01

    Autism is a complex disease whose etiology remains elusive. We integrated previously and newly generated data and developed a systems framework involving the interactome, gene expression and genome sequencing to identify a protein interaction module with members strongly enriched for autism candidate genes. Sequencing of 25 patients confirmed the involvement of this module in autism, which was subsequently validated using an independent cohort of over 500 patients. Expression of this module was dichotomized with a ubiquitously expressed subcomponent and another subcomponent preferentially expressed in the corpus callosum, which was significantly affected by our identified mutations in the network center. RNA-sequencing of the corpus callosum from patients with autism exhibited extensive gene mis-expression in this module, and our immunochemical analysis showed that the human corpus callosum is predominantly populated by oligodendrocyte cells. Analysis of functional genomic data further revealed a significant involvement of this module in the development of oligodendrocyte cells in mouse brain. Our analysis delineates a natural network involved in autism, helps uncover novel candidate genes for this disease and improves our understanding of its molecular pathology. PMID:25549968

  14. Conformal SiO2 coating of sub-100 nm diameter channels of polycarbonate etched ion-track channels by atomic layer deposition

    PubMed Central

    Sobel, Nicolas; Lukas, Manuela; Spende, Anne; Stühn, Bernd; Trautmann, Christina

    2015-01-01

    Summary Polycarbonate etched ion-track membranes with about 30 µm long and 50 nm wide cylindrical channels were conformally coated with SiO2 by atomic layer deposition (ALD). The process was performed at 50 °C to avoid thermal damage to the polymer membrane. Analysis of the coated membranes by small angle X-ray scattering (SAXS) reveals a homogeneous, conformal layer of SiO2 in the channels at a deposition rate of 1.7–1.8 Å per ALD cycle. Characterization by infrared and X-ray photoelectron spectroscopy (XPS) confirms the stoichiometric composition of the SiO2 films. Detailed XPS analysis reveals that the mechanism of SiO2 formation is based on subsurface crystal growth. By dissolving the polymer, the silica nanotubes are released from the ion-track membrane. The thickness of the tube wall is well controlled by the ALD process. Because the track-etched channels exhibited diameters in the range of nanometres and lengths in the range of micrometres, cylindrical tubes with an aspect ratio as large as 3000 have been produced. PMID:25821688

  15. Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia.

    PubMed

    Damaraju, E; Allen, E A; Belger, A; Ford, J M; McEwen, S; Mathalon, D H; Mueller, B A; Pearlson, G D; Potkin, S G; Preda, A; Turner, J A; Vaidya, J G; van Erp, T G; Calhoun, V D

    2014-01-01

    Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length), and a dynamic sense, computed using sliding windows (44 s in length) and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual), as well as reduced connectivity (hypoconnectivity) between sensory networks from all modalities. Dynamic analysis suggests that (1), on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2), that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical-subcortical antagonism (anti-correlations) and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity. Group

  16. Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia

    PubMed Central

    Damaraju, E.; Allen, E.A.; Belger, A.; Ford, J.M.; McEwen, S.; Mathalon, D.H.; Mueller, B.A.; Pearlson, G.D.; Potkin, S.G.; Preda, A.; Turner, J.A.; Vaidya, J.G.; van Erp, T.G.; Calhoun, V.D.

    2014-01-01

    Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length), and a dynamic sense, computed using sliding windows (44 s in length) and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual), as well as reduced connectivity (hypoconnectivity) between sensory networks from all modalities. Dynamic analysis suggests that (1), on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2), that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical–subcortical antagonism (anti-correlations) and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity. Group

  17. Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

    PubMed

    Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

    2018-05-01

    The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

  18. Surface Coverage and Structure of Mixed DNA/Alkylthiol Monolayers on Gold: Characterization by XPS, NEXAFS, and Fluorescence Intensity Measurements

    PubMed Central

    Lee, Chi-Ying; Gong, Ping; Harbers, Gregory M.; Grainger, David W.; Castner, David G.; Gamble, Lara J.

    2006-01-01

    Self-assembly of thiol-terminated single-stranded DNA (HS-ssDNA) on gold has served as an important model system for DNA immobilization at surfaces. Here, we report a detailed study of the surface composition and structure of mixed self-assembled DNA monolayers containing a short alkylthiol surface diluent [11-mercapto-1-undecanol (MCU)] on gold supports. These mixed DNA monolayers were studied with X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS), and fluorescence intensity measurements. XPS results on sequentially adsorbed DNA/MCU monolayers on gold indicated that adsorbed MCU molecules first incorporate into the HS-ssDNA monolayer and, upon longer MCU exposures, displace adsorbed HS-ssDNA molecules from the surface. Thus, HS-ssDNA surface coverage steadily decreased with MCU exposure time. Polarization-dependent NEXAFS and fluorescence results both show changes in signals consistent with changes in DNA orientation after only 30 min of MCU exposure. NEXAFS polarization dependence (followed by monitoring the N 1s → π* transition) of the mixed DNA monolayers indicated that the DNA nucleotide base ring structures are oriented more parallel to the gold surface compared to DNA bases in pure HS-ssDNA monolayers. This indicates that HS-ssDNA oligomers reorient toward a more-upright position upon MCU incorporation. Fluorescence intensity results using end-labeled DNA probes on gold show little observable fluorescence on pure HS-ssDNA monolayers, likely due to substrate quenching effects between the fluorophore and the gold. MCU diluent incorporation into HS-ssDNA monolayers initially increases DNA fluorescence signal by densifying the chemisorbed monolayer, prompting an upright orientation of the DNA, and moving the terminal fluorophore away from the substrate. Immobilized DNA probe density and DNA target hybridization in these mixed DNA monolayers, as well as effects of MCU diluent on DNA hybridization in complex

  19. An association network analysis among microeukaryotes and bacterioplankton reveals algal bloom dynamics.

    PubMed

    Tan, Shangjin; Zhou, Jin; Zhu, Xiaoshan; Yu, Shichen; Zhan, Wugen; Wang, Bo; Cai, Zhonghua

    2015-02-01

    Algal blooms are a worldwide phenomenon and the biological interactions that underlie their regulation are only just beginning to be understood. It is established that algal microorganisms associate with many other ubiquitous, oceanic organisms, but the interactions that lead to the dynamics of bloom formation are currently unknown. To address this gap, we used network approaches to investigate the association patterns among microeukaryotes and bacterioplankton in response to a natural Scrippsiella trochoidea bloom. This is the first study to apply network approaches to bloom dynamics. To this end, terminal restriction fragment (T-RF) length polymorphism analysis showed dramatic changes in community compositions of microeukaryotes and bacterioplankton over the blooming period. A variance ratio test revealed significant positive overall associations both within and between microeukaryotic and bacterioplankton communities. An association network generated from significant correlations between T-RFs revealed that S. trochoidea had few connections to other microeukaryotes and bacterioplankton and was placed on the edge. This lack of connectivity allowed for the S. trochoidea sub-network to break off from the overall network. These results allowed us to propose a conceptual model for explaining how changes in microbial associations regulate the dynamics of an algal bloom. In addition, key T-RFs were screened by principal components analysis, correlation coefficients, and network analysis. Dominant T-RFs were then identified through 18S and 16S rRNA gene clone libraries. Results showed that microeukaryotes clustered predominantly with Dinophyceae and Perkinsea while the majority of bacterioplankton identified were Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. The ecologi-cal roles of both were discussed in the context of these findings. © 2014 Phycological Society of America.

  20. Proton transfer and hydrogen bonding in the organic solid state: a combined XRD/XPS/ssNMR study of 17 organic acid-base complexes.

    PubMed

    Stevens, Joanna S; Byard, Stephen J; Seaton, Colin C; Sadiq, Ghazala; Davey, Roger J; Schroeder, Sven L M

    2014-01-21

    The properties of nitrogen centres acting either as hydrogen-bond or Brønsted acceptors in solid molecular acid-base complexes have been probed by N 1s X-ray photoelectron spectroscopy (XPS) as well as (15)N solid-state nuclear magnetic resonance (ssNMR) spectroscopy and are interpreted with reference to local crystallographic structure information provided by X-ray diffraction (XRD). We have previously shown that the strong chemical shift of the N 1s binding energy associated with the protonation of nitrogen centres unequivocally distinguishes protonated (salt) from hydrogen-bonded (co-crystal) nitrogen species. This result is further supported by significant ssNMR shifts to low frequency, which occur with proton transfer from the acid to the base component. Generally, only minor chemical shifts occur upon co-crystal formation, unless a strong hydrogen bond is formed. CASTEP density functional theory (DFT) calculations of (15)N ssNMR isotropic chemical shifts correlate well with the experimental data, confirming that computational predictions of H-bond strengths and associated ssNMR chemical shifts allow the identification of salt and co-crystal structures (NMR crystallography). The excellent agreement between the conclusions drawn by XPS and the combined CASTEP/ssNMR investigations opens up a reliable avenue for local structure characterization in molecular systems even in the absence of crystal structure information, for example for non-crystalline or amorphous matter. The range of 17 different systems investigated in this study demonstrates the generic nature of this approach, which will be applicable to many other molecular materials in organic, physical, and materials chemistry.

  1. Using risk analysis to reveal opportunities for the management of unplanned ignitions in wilderness

    Treesearch

    Kevin Barnett; Carol Miller; Tyron J. Venn

    2016-01-01

    A goal of fire management in wilderness is to allow fire to play its natural ecological role without intervention. Unfortunately, most unplanned ignitions in wilderness are suppressed, in part because of the risk they might pose to values outside of the wilderness. We capitalize on recent advances in fire risk analysis to demonstrate a risk-based approach for revealing...

  2. Analysis of Ti and TiO2 nanolayers by total reflection X-ray photoelectron spectroscopy

    NASA Astrophysics Data System (ADS)

    Kubala-Kukuś, A.; Banaś, D.; Stabrawa, I.; Szary, K.; Sobota, D.; Majewska, U.; Wudarczyk-Moćko, J.; Braziewicz, J.; Pajek, M.

    2018-07-01

    Total reflection X-ray photoelectron spectroscopy (TRXPS) is applied in the analysis of Ti and TiO2 nanolayers deposited on silicon and silicon dioxide substrates. The idea of application of total-reflection phenomenon for exciting X-ray used in the XPS technique is briefly discussed. The experimental setup and measurement conditions for the studied Ti and TiO2 layers are presented. The XPS spectra were registered both for the non-total and total reflection regimes. The survey spectra and C1s, N1s, Ti2p and O1s photoelectron peaks are shown. For energy calibration, the position of C1s photoelectron peak was applied (C-C component, binding energy 284.8 eV). The peak to background ratios are discussed as regards the dependence of the excitation angle. An increase of this ratio for the glancing angle 1°, being below critical angle of the X-ray beam and sample material, results in an improvement of XPS detection limit by factor up to 2. In the case of the Ti nanolayer, additionally, the thickness of the overlayer TiO2 is determined. As an example of applying the TRXPS technique, the analysis of Ti nanolayers implanted by highly charged Xe35+ ions of 280 keV energy is discussed. The Xe3d and O1s photoelectron peaks are presented and discussed.

  3. Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns

    PubMed Central

    Álvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M.

    2013-01-01

    The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas ‘sensu stricto’ isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria. PMID:24116076

  4. Decision Makers Use Norms, Not Cost-Benefit Analysis, When Choosing to Conceal or Reveal Unfair Rewards

    PubMed Central

    Heimann, Marco; Girotto, Vittorio; Legrenzi, Paolo; Bonnefon, Jean-François

    2013-01-01

    We introduce the Conceal or Reveal Dilemma, in which individuals receive unfair benefits, and must decide whether to conceal or to reveal this unfair advantage. This dilemma has two important characteristics: it does not lend itself easily to cost-benefit analysis, neither to the application of any strong universal norm. As a consequence, it is ideally suited to the study of interindividual and intercultural variations in moral-economic norms. In this paper we focus on interindividual variations, and we report four studies showing that individuals cannot be swayed by financial incentives to conceal or to reveal, and follow instead fixed, idiosyncratic strategies. We discuss how this result can be extended to individual and cultural variations in the tendency to display or to hide unfair rewards. PMID:24066040

  5. Decision makers use norms, not cost-benefit analysis, when choosing to conceal or reveal unfair rewards.

    PubMed

    Heimann, Marco; Girotto, Vittorio; Legrenzi, Paolo; Bonnefon, Jean-François

    2013-01-01

    We introduce the Conceal or Reveal Dilemma, in which individuals receive unfair benefits, and must decide whether to conceal or to reveal this unfair advantage. This dilemma has two important characteristics: it does not lend itself easily to cost-benefit analysis, neither to the application of any strong universal norm. As a consequence, it is ideally suited to the study of interindividual and intercultural variations in moral-economic norms. In this paper we focus on interindividual variations, and we report four studies showing that individuals cannot be swayed by financial incentives to conceal or to reveal, and follow instead fixed, idiosyncratic strategies. We discuss how this result can be extended to individual and cultural variations in the tendency to display or to hide unfair rewards.

  6. Investigation of the interfacial reaction between metal and fluorine-contained polyimides

    NASA Astrophysics Data System (ADS)

    Yang, Ching-Yu; Chen, J. S.; Hsu, S. L. C.

    2005-07-01

    In this work, thin metal films (Cr and Ta) were deposited on fluorine-contained polyimides, 6FDA-BisAAF, and 6FDA-PPD. The chemical states of the metal/polyimide samples were characterized by using x-ray photoelectron spectroscopy (XPS). XPS analysis reveals that metal-C, C-O, and metal-O bondings are present in metallized 6FDA-BisAAF and 6FDA-PPD. C-F bonds are observed in bare 6FDA-BisAAF and 6FDA-PPD however, they are not seen in the metallized samples. Disappearance of the C-F bonding is attributed to the disruption of CF3 side groups from the main chains of 6FDA-BisAAF and 6FDA-PPD when the chains are exposed to the plasma during the metal deposition. Nevertheless, the disruption of CF3 side groups also creates sites for the formation of metal-C or C-O bondings, which provide a positive adhesion strength at the metal/polyimide interface, as revealed by the tape test.

  7. Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N'Dama.

    PubMed

    Kim, Soo-Jin; Ka, Sojeong; Ha, Jung-Woo; Kim, Jaemin; Yoo, DongAhn; Kim, Kwondo; Lee, Hak-Kyo; Lim, Dajeong; Cho, Seoae; Hanotte, Olivier; Mwai, Okeyo Ally; Dessie, Tadelle; Kemp, Stephen; Oh, Sung Jong; Kim, Heebal

    2017-05-12

    Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. While many studies investigated the adaptation of overall African cattle, genetic characteristics of each breed have been poorly studied. We performed the comparative genome-wide analysis to assess evidence for subspeciation within species at the genetic level in trypanotolerant N'Dama cattle. We analysed genetic variation patterns in N'Dama from the genomes of 101 cattle breeds including 48 samples of five indigenous African cattle breeds and 53 samples of various commercial breeds. Analysis of SNP variances between cattle breeds using wMI, XP-CLR, and XP-EHH detected genes containing N'Dama-specific genetic variants and their potential associations. Functional annotation analysis revealed that these genes are associated with ossification, neurological and immune system. Particularly, the genes involved in bone formation indicate that local adaptation of N'Dama may engage in skeletal growth as well as immune systems. Our results imply that N'Dama might have acquired distinct genotypes associated with growth and regulation of regional diseases including trypanosomiasis. Moreover, this study offers significant insights into identifying genetic signatures for natural and artificial selection of diverse African cattle breeds.

  8. Surface analysis of graphite fiber reinforced polyimide composites

    NASA Technical Reports Server (NTRS)

    Messick, D. L.; Progar, D. J.; Wightman, J. P.

    1983-01-01

    Several techniques have been used to establish the effect of different surface pretreatments on graphite-polyimide composites. Composites were prepared from Celion 6000 graphite fibers and the polyimide LARC-160. Pretreatments included mechanical abrasion, chemical etching and light irradiation. Scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) were used in the analysis. Contact angle of five different liquids of varying surface tensions were measured on the composites. SEM results showed polymer-rich peaks and polymer-poor valleys conforming to the pattern of the release cloth used durng fabrication. Mechanically treated and light irradiated samples showed varying degrees of polymer peak removal, with some degradation down to the graphite fibers. Minimal changes in surface topography were observed on concentrations of surface fluorine even after pretreatment. The light irradiation pretreatment was most effective at reducing surface fluorine concentrations whereas chemical pretreatment was the least effective. Critical surface tensions correlated directly with the surface fluorine to carbon ratios as calculated from XPS.

  9. Analysis of self-overlap reveals trade-offs in plankton swimming trajectories

    PubMed Central

    Bianco, Giuseppe; Mariani, Patrizio; Visser, Andre W.; Mazzocchi, Maria Grazia; Pigolotti, Simone

    2014-01-01

    Movement is a fundamental behaviour of organisms that not only brings about beneficial encounters with resources and mates, but also at the same time exposes the organism to dangerous encounters with predators. The movement patterns adopted by organisms should reflect a balance between these contrasting processes. This trade-off can be hypothesized as being evident in the behaviour of plankton, which inhabit a dilute three-dimensional environment with few refuges or orienting landmarks. We present an analysis of the swimming path geometries based on a volumetric Monte Carlo sampling approach, which is particularly adept at revealing such trade-offs by measuring the self-overlap of the trajectories. Application of this method to experimentally measured trajectories reveals that swimming patterns in copepods are shaped to efficiently explore volumes at small scales, while achieving a large overlap at larger scales. Regularities in the observed trajectories make the transition between these two regimes always sharper than in randomized trajectories or as predicted by random walk theory. Thus, real trajectories present a stronger separation between exploration for food and exposure to predators. The specific scale and features of this transition depend on species, gender and local environmental conditions, pointing at adaptation to state and stage-dependent evolutionary trade-offs. PMID:24789560

  10. Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

    PubMed Central

    Dudley, Joel T.; Chen, Rong; Sanderford, Maxwell; Butte, Atul J.; Kumar, Sudhir

    2012-01-01

    Genome-wide disease association studies contrast genetic variation between disease cohorts and healthy populations to discover single nucleotide polymorphisms (SNPs) and other genetic markers revealing underlying genetic architectures of human diseases. Despite scores of efforts over the past decade, many reproducible genetic variants that explain substantial proportions of the heritable risk of common human diseases remain undiscovered. We have conducted a multispecies genomic analysis of 5,831 putative human risk variants for more than 230 disease phenotypes reported in 2,021 studies. We find that the current approaches show a propensity for discovering disease-associated SNPs (dSNPs) at conserved genomic positions because the effect size (odds ratio) and allelic P value of genetic association of an SNP relates strongly to the evolutionary conservation of their genomic position. We propose a new measure for ranking SNPs that integrates evolutionary conservation scores and the P value (E-rank). Using published data from a large case-control study, we demonstrate that E-rank method prioritizes SNPs with a greater likelihood of bona fide and reproducible genetic disease associations, many of which may explain greater proportions of genetic variance. Therefore, long-term evolutionary histories of genomic positions offer key practical utility in reassessing data from existing disease association studies, and in the design and analysis of future studies aimed at revealing the genetic basis of common human diseases. PMID:22389448

  11. Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia.

    PubMed

    Leavey, Katherine; Bainbridge, Shannon A; Cox, Brian J

    2015-01-01

    Preeclampsia (PE) is a life-threatening hypertensive pathology of pregnancy affecting 3-5% of all pregnancies. To date, PE has no cure, early detection markers, or effective treatments short of the removal of what is thought to be the causative organ, the placenta, which may necessitate a preterm delivery. Additionally, numerous small placental microarray studies attempting to identify "PE-specific" genes have yielded inconsistent results. We therefore hypothesize that preeclampsia is a multifactorial disease encompassing several pathology subclasses, and that large cohort placental gene expression analysis will reveal these groups. To address our hypothesis, we utilized known bioinformatic methods to aggregate 7 microarray data sets across multiple platforms in order to generate a large data set of 173 patient samples, including 77 with preeclampsia. Unsupervised clustering of these patient samples revealed three distinct molecular subclasses of PE. This included a "canonical" PE subclass demonstrating elevated expression of known PE markers and genes associated with poor oxygenation and increased secretion, as well as two other subclasses potentially representing a poor maternal response to pregnancy and an immunological presentation of preeclampsia. Our analysis sheds new light on the heterogeneity of PE patients, and offers up additional avenues for future investigation. Hopefully, our subclassification of preeclampsia based on molecular diversity will finally lead to the development of robust diagnostics and patient-based treatments for this disorder.

  12. Comparative analysis reveals the underlying mechanism of vertebrate seasonal reproduction.

    PubMed

    Ikegami, Keisuke; Yoshimura, Takashi

    2016-02-01

    Animals utilize photoperiodic changes as a calendar to regulate seasonal reproduction. Birds have highly sophisticated photoperiodic mechanisms and functional genomics analysis in quail uncovered the signal transduction pathway regulating avian seasonal reproduction. Birds detect light with deep brain photoreceptors. Long day (LD) stimulus induces secretion of thyroid-stimulating hormone (TSH) from the pars tuberalis (PT) of the pituitary gland. PT-derived TSH locally activates thyroid hormone (TH) in the hypothalamus, which induces gonadotropin-releasing hormone (GnRH) and hence gonadotropin secretion. However, during winter, low temperatures increase serum TH for adaptive thermogenesis, which accelerates germ cell apoptosis by activating the genes involved in metamorphosis. Therefore, TH has a dual role in the regulation of seasonal reproduction. Studies using TSH receptor knockout mice confirmed the involvement of PT-derived TSH in mammalian seasonal reproduction. In addition, studies in mice revealed that the tissue-specific glycosylation of TSH diversifies its function in the circulation to avoid crosstalk. In contrast to birds and mammals, one of the molecular machineries necessary for the seasonal reproduction of fish are localized in the saccus vasculosus from the photoreceptor to the neuroendocrine output. Thus, comparative analysis is a powerful tool to uncover the universality and diversity of fundamental properties in various organisms. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. XPS investigations of tribolayers formed on TiN and (Ti,Re)N coatings

    NASA Astrophysics Data System (ADS)

    Oktay, Serkan; Kahraman, Zafer; Urgen, Mustafa; Kazmanli, Kursat

    2015-02-01

    TiN and (Ti,Re)N coatings were deposited on high-speed-steel substrates by a hybrid coating system composed of cathodic arc PVD and magnetron sputtering techniques. In order to keep rhenium content low (8 ± 1.9 at.%) in the coating, magnetron sputtering technique was utilized to evaporate rhenium. The (Ti,Re)N coating consisted of TiN and ReNx (x > 1.33) phases. The hardness of TiN and (Ti,Re)N were 31 GPa and 29 GPa (± 2 GPa), respectively. Tribological behaviors of the samples were tested against Al2O3 balls at 21 °C (RT) and 150 °C (HT) by reciprocating wear technique. The tribolayers were analyzed by XPS technique. Friction coefficients of TiN were 0.56, 0.35 for 21 °C and 150 °C tests, respectively. Rhenium addition to TiN drastically dropped the friction coefficients to 0.22 and 0.17 for RT and HT samples. Rhenium addition also improved the wear resistance of the coating at both test temperatures. For TiN, main oxide component of the tribolayers was Ti2O3 for RT tests and TiO2 for HT tests. The oxide layer formed on (Ti,Re)N were the mixture of TiO2, Tisbnd Osbnd N, ReO2 and Re2O7 for both test temperatures. Re2O7 provided very low friction coefficient to (Ti,Re)N. The findings are consistent with the crystal chemistry approach.

  14. U-Zr alloy: XPS and TEM study of surface passivation

    NASA Astrophysics Data System (ADS)

    Paukov, M.; Tkach, I.; Huber, F.; Gouder, T.; Cieslar, M.; Drozdenko, D.; Minarik, P.; Havela, L.

    2018-05-01

    Surface reactivity of Uranium metal is an important factor limiting its practical applications. Bcc alloys of U with various transition metals are much less reactive than pure Uranium. So as to specify the mechanism of surface protection, we have been studying the U-20 at.% Zr alloy by photoelectron spectroscopy and transmission electron microscopy. The surface was studied in as-obtained state, in various stages of surface cleaning, and during an isochronal annealing cycle. The analysis based on U-4f, Zr-3p, and O-1 s spectra shows that a Zr-rich phase segregates at the surface at temperatures exceeding 550 K, which provides a self-assembled coating. The comparison of oxygen exposure of the stoichiometric and coated surfaces shows that the coating is efficiently preventing the oxidation of uranium even at elevated temperatures. The coating can be associated with the UZr2+x phase. TEM study indicated that the coating is about 20 nm thick. For the clean state, the U-4f core-level lines of the bcc alloy are practically identical to those of α-U, revealing similar delocalization of the 5f electronic states.

  15. Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov.

    PubMed

    Ehrmann, Matthias A; Müller, Martin R A; Vogel, Rudi F

    2003-01-01

    Genotypic fingerprinting to analyse the bacterial flora of an industrial sourdough revealed a coherent group of strains which could not be associated with a valid species. Comparative 16S rDNA sequence analysis showed that these strains formed a homogeneous cluster distinct from their closest relatives, Lactobacillus farciminis, Lactobacillus alimentarius and Lactobacillus kimchii. To characterize them further, physiological (sugar fermentation, formation of DL-lactate, hydrolysis of arginine, growth temperature, CO2 production) and chemotaxonomic properties have been determined. The DNA G +C content was 37.5 0.2 mol%. The peptidoglycan was of the lysine-D-iso-asparagine (L-Lys-D-Asp) type. The strains were homofermentative, Gram-positive, catalase-negative, non-spore-forming, non-motile rods. They were found as a major stable component of a rye flour sourdough fermentation. Physiological, biochemical as well as genotypic data suggested them to be a new species of the genus Lactobacillus. This was confirmed by DNA-DNA hybridization of genomic DNA, and the name Lactobacillus mindensis is proposed. The type strain of this species is DSM 14500T (=LMG 21508T).

  16. Dynamic transcriptional signature and cell fate analysis reveals plasticity of individual neural plate border cells

    PubMed Central

    Roellig, Daniela; Tan-Cabugao, Johanna; Esaian, Sevan; Bronner, Marianne E

    2017-01-01

    The ‘neural plate border’ of vertebrate embryos contains precursors of neural crest and placode cells, both defining vertebrate characteristics. How these lineages segregate from neural and epidermal fates has been a matter of debate. We address this by performing a fine-scale quantitative temporal analysis of transcription factor expression in the neural plate border of chick embryos. The results reveal significant overlap of transcription factors characteristic of multiple lineages in individual border cells from gastrula through neurula stages. Cell fate analysis using a Sox2 (neural) enhancer reveals that cells that are initially Sox2+ cells can contribute not only to neural tube but also to neural crest and epidermis. Moreover, modulating levels of Sox2 or Pax7 alters the apportionment of neural tube versus neural crest fates. Our results resolve a long-standing question and suggest that many individual border cells maintain ability to contribute to multiple ectodermal lineages until or beyond neural tube closure. DOI: http://dx.doi.org/10.7554/eLife.21620.001 PMID:28355135

  17. Simple quantification of surface carboxylic acids on chemically oxidized multi-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Gong, Hyejin; Kim, Seong-Taek; Lee, Jong Doo; Yim, Sanggyu

    2013-02-01

    The surface of multi-walled carbon nanotube (MWCNT) was chemically oxidized using nitric acid and sulfuric-nitric acid mixtures. Thermogravimetric analysis, transmission electron microscopy and infrared spectroscopy revealed that the use of acid mixtures led to higher degree of oxidation. More quantitative identification of surface carboxylic acids was carried out using X-ray photoelectron spectroscopy (XPS) and acid-base titration. However, these techniques are costly and require very long analysis times to promptly respond to the extent of the reaction. We propose a much simpler method using pH measurements and pre-determined pKa value in order to estimate the concentration of carboxylic acids on the oxidized MWCNT surfaces. The results from this technique were consistent with those obtained from XPS and titration, and it is expected that this simple quantification method can provide a cheap and fast way to monitor and control the oxidation reaction of MWCNT.

  18. Metagenomic analysis of Sichuan takin fecal sample viromes reveals novel enterovirus and astrovirus.

    PubMed

    Guan, Tian-Pei; Teng, Jade L L; Yeong, Kai-Yan; You, Zhang-Qiang; Liu, Hao; Wong, Samson S Y; Lau, Susanna K P; Woo, Patrick C Y

    2018-06-07

    The Sichuan takin inhabits the bamboo forests in the Eastern Himalayas and is considered as a national treasure of China with the highest legal protection and conservation status considered as vulnerable according to The IUCN Red List of Threatened Species. In this study, fecal samples of 71 Sichuan takins were pooled and deep sequenced. Among the 103,553 viral sequences, 21,961 were assigned to mammalian viruses. De novo assembly revealed genomes of an enterovirus and an astrovirus and contigs of circoviruses and genogroup I picobirnaviruses. Complete genome sequencing and phylogenetic analysis showed that Sichuan takin enterovirus is a novel serotype/genotype of the species Enterovirus G, with evidence of recombination. Sichuan takin astrovirus is a new subtype of bovine astrovirus, probably belonging to a new genogroup in the genus Mamastrovirus. Further studies will reveal whether these viruses can also be found in Mishmi takin and Shaanxi takin and their pathogenic potentials. Copyright © 2018 Elsevier Inc. All rights reserved.

  19. Ambient Pressure XPS Study of Mixed Conducting Perovskite-Type SOFC Cathode and Anode Materials under Well-Defined Electrochemical Polarization

    PubMed Central

    2015-01-01

    The oxygen exchange activity of mixed conducting oxide surfaces has been widely investigated, but a detailed understanding of the corresponding reaction mechanisms and the rate-limiting steps is largely still missing. Combined in situ investigation of electrochemically polarized model electrode surfaces under realistic temperature and pressure conditions by near-ambient pressure (NAP) XPS and impedance spectroscopy enables very surface-sensitive chemical analysis and may detect species that are involved in the rate-limiting step. In the present study, acceptor-doped perovskite-type La0.6Sr0.4CoO3-δ (LSC), La0.6Sr0.4FeO3-δ (LSF), and SrTi0.7Fe0.3O3-δ (STF) thin film model electrodes were investigated under well-defined electrochemical polarization as cathodes in oxidizing (O2) and as anodes in reducing (H2/H2O) atmospheres. In oxidizing atmosphere all materials exhibit additional surface species of strontium and oxygen. The polaron-type electronic conduction mechanism of LSF and STF and the metal-like mechanism of LSC are reflected by distinct differences in the valence band spectra. Switching between oxidizing and reducing atmosphere as well as electrochemical polarization cause reversible shifts in the measured binding energy. This can be correlated to a Fermi level shift due to variations in the chemical potential of oxygen. Changes of oxidation states were detected on Fe, which appears as FeIII in oxidizing atmosphere and as mixed FeII/III in H2/H2O. Cathodic polarization in reducing atmosphere leads to the reversible formation of a catalytically active Fe0 phase. PMID:26877827

  20. Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus.

    PubMed

    Vecsey, Christopher G; Peixoto, Lucia; Choi, Jennifer H K; Wimmer, Mathieu; Jaganath, Devan; Hernandez, Pepe J; Blackwell, Jennifer; Meda, Karuna; Park, Alan J; Hannenhalli, Sridhar; Abel, Ted

    2012-10-17

    Sleep deprivation is a common problem of considerable health and economic impact in today's society. Sleep loss is associated with deleterious effects on cognitive functions such as memory and has a high comorbidity with many neurodegenerative and neuropsychiatric disorders. Therefore, it is crucial to understand the molecular basis of the effect of sleep deprivation in the brain. In this study, we combined genome-wide and traditional molecular biological approaches to determine the cellular and molecular impacts of sleep deprivation in the mouse hippocampus, a brain area crucial for many forms of memory. Microarray analysis examining the effects of 5 h of sleep deprivation on gene expression in the mouse hippocampus found 533 genes with altered expression. Bioinformatic analysis revealed that a prominent effect of sleep deprivation was to downregulate translation, potentially mediated through components of the insulin signaling pathway such as the mammalian target of rapamycin (mTOR), a key regulator of protein synthesis. Consistent with this analysis, sleep deprivation reduced levels of total and phosphorylated mTOR, and levels returned to baseline after 2.5 h of recovery sleep. Our findings represent the first genome-wide analysis of the effects of sleep deprivation on the mouse hippocampus, and they suggest that the detrimental effects of sleep deprivation may be mediated by reductions in protein synthesis via downregulation of mTOR. Because protein synthesis and mTOR activation are required for long-term memory formation, our study improves our understanding of the molecular mechanisms underlying the memory impairments induced by sleep deprivation.

  1. A novel analysis strategy for integrating methylation and expression data reveals core pathways for thyroid cancer aetiology

    PubMed Central

    2015-01-01

    Background Recently, a wide range of diseases have been associated with changes in DNA methylation levels, which play a vital role in gene expression regulation. With ongoing developments in technology, attempts to understand disease mechanism have benefited greatly from epigenetics and transcriptomics studies. In this work, we have used expression and methylation data of thyroid carcinoma as a case study and explored how to optimally incorporate expression and methylation information into the disease study when both data are available. Moreover, we have also investigated whether there are important post-translational modifiers which could drive critical insights on thyroid cancer genetics. Results In this study, we have conducted a threshold analysis for varying methylation levels to identify whether setting a methylation level threshold increases the performance of functional enrichment. Moreover, in order to decide on best-performing analysis strategy, we have performed data integration analysis including comparison of 10 different analysis strategies. As a result, combining methylation with expression and using genes with more than 15% methylation change led to optimal detection rate of thyroid-cancer associated pathways in top 20 functional enrichment results. Furthermore, pooling the data from different experiments increased analysis confidence by improving the data range. Consequently, we have identified 207 transcription factors and 245 post-translational modifiers with more than 15% methylation change which may be important in understanding underlying mechanisms of thyroid cancer. Conclusion While only expression or only methylation information would not reveal both primary and secondary mechanisms involved in disease state, combining expression and methylation led to a better detection of thyroid cancer-related genes and pathways that are found in the recent literature. Moreover, focusing on genes that have certain level of methylation change improved the

  2. Combined Analysis of the Fruit Metabolome and Transcriptome Reveals Candidate Genes Involved in Flavonoid Biosynthesis in Actinidia arguta.

    PubMed

    Li, Yukuo; Fang, Jinbao; Qi, Xiujuan; Lin, Miaomiao; Zhong, Yunpeng; Sun, Leiming; Cui, Wen

    2018-05-15

    To assess the interrelation between the change of metabolites and the change of fruit color, we performed a combined metabolome and transcriptome analysis of the flesh in two different Actinidia arguta cultivars: "HB" ("Hongbaoshixing") and "YF" ("Yongfengyihao") at two different fruit developmental stages: 70d (days after full bloom) and 100d (days after full bloom). Metabolite and transcript profiling was obtained by ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometer and high-throughput RNA sequencing, respectively. The identification and quantification results of metabolites showed that a total of 28,837 metabolites had been obtained, of which 13,715 were annotated. In comparison of HB100 vs. HB70, 41 metabolites were identified as being flavonoids, 7 of which, with significant difference, were identified as bracteatin, luteolin, dihydromyricetin, cyanidin, pelargonidin, delphinidin and (-)-epigallocatechin. Association analysis between metabolome and transcriptome revealed that there were two metabolic pathways presenting significant differences during fruit development, one of which was flavonoid biosynthesis, in which 14 structural genes were selected to conduct expression analysis, as well as 5 transcription factor genes obtained by transcriptome analysis. RT-qPCR results and cluster analysis revealed that AaF3H , AaLDOX , AaUFGT , AaMYB , AabHLH , and AaHB2 showed the best possibility of being candidate genes. A regulatory network of flavonoid biosynthesis was established to illustrate differentially expressed candidate genes involved in accumulation of metabolites with significant differences, inducing red coloring during fruit development. Such a regulatory network linking genes and flavonoids revealed a system involved in the pigmentation of all-red-fleshed and all-green-fleshed A. arguta , suggesting this conjunct analysis approach is not only useful in understanding the relationship between genotype and phenotype

  3. Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations

    PubMed Central

    Förster, Frank; Beisser, Daniela; Grohme, Markus A.; Liang, Chunguang; Mali, Brahim; Siegl, Alexander Matthias; Engelmann, Julia C.; Shkumatov, Alexander V.; Schokraie, Elham; Müller, Tobias; Schnölzer, Martina; Schill, Ralph O.; Frohme, Marcus; Dandekar, Thomas

    2012-01-01

    Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant. PMID:22563243

  4. Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations.

    PubMed

    Förster, Frank; Beisser, Daniela; Grohme, Markus A; Liang, Chunguang; Mali, Brahim; Siegl, Alexander Matthias; Engelmann, Julia C; Shkumatov, Alexander V; Schokraie, Elham; Müller, Tobias; Schnölzer, Martina; Schill, Ralph O; Frohme, Marcus; Dandekar, Thomas

    2012-01-01

    Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.

  5. Dependency Network Analysis (DEPNA) Reveals Context Related Influence of Brain Network Nodes

    PubMed Central

    Jacob, Yael; Winetraub, Yonatan; Raz, Gal; Ben-Simon, Eti; Okon-Singer, Hadas; Rosenberg-Katz, Keren; Hendler, Talma; Ben-Jacob, Eshel

    2016-01-01

    Communication between and within brain regions is essential for information processing within functional networks. The current methods to determine the influence of one region on another are either based on temporal resolution, or require a predefined model for the connectivity direction. However these requirements are not always achieved, especially in fMRI studies, which have poor temporal resolution. We thus propose a new graph theory approach that focuses on the correlation influence between selected brain regions, entitled Dependency Network Analysis (DEPNA). Partial correlations are used to quantify the level of influence of each node during task performance. As a proof of concept, we conducted the DEPNA on simulated datasets and on two empirical motor and working memory fMRI tasks. The simulations revealed that the DEPNA correctly captures the network’s hierarchy of influence. Applying DEPNA to the functional tasks reveals the dynamics between specific nodes as would be expected from prior knowledge. To conclude, we demonstrate that DEPNA can capture the most influencing nodes in the network, as they emerge during specific cognitive processes. This ability opens a new horizon for example in delineating critical nodes for specific clinical interventions. PMID:27271458

  6. Phenotypic analysis of prostate-infiltrating lymphocytes reveals TH17 and Treg skewing.

    PubMed

    Sfanos, Karen Sandell; Bruno, Tullia C; Maris, Charles H; Xu, Lauren; Thoburn, Christopher J; DeMarzo, Angelo M; Meeker, Alan K; Isaacs, William B; Drake, Charles G

    2008-06-01

    Pathologic examination of prostate glands removed from patients with prostate cancer commonly reveals infiltrating CD4+ and CD8+ T cells. Little is known about the phenotype of these cells, despite accumulating evidence suggesting a potential role for chronic inflammation in the etiology of prostate cancer. We developed a technique that samples the majority of the peripheral prostate through serial needle aspirates. CD4+ prostate-infiltrating lymphocytes (PIL) were isolated using magnetic beads and analyzed for subset skewing using both flow cytometry and quantitative reverse transcription-PCR. The transcriptional profile of fluorescence-activated cell sorted prostate-infiltrating regulatory T cells (CD4+, CD25+, GITR+) was compared with naïve, peripheral blood T cells using microarray analysis. CD4+ PIL showed a paucity of TH2 (interleukin-4-secreting) cells, a surprising finding given the generally accepted association of these cells with chronic, smoldering inflammation. Instead, CD4+ PIL seemed to be skewed towards a regulatory Treg phenotype (FoxP3+) as well as towards the TH17 phenotype (interleukin-17+). We also found that a preponderance of TH17-mediated inflammation was associated with a lower pathologic Gleason score. These protein level data were reflected at the message level, as analyzed by quantitative reverse transcription-PCR. Microarray analysis of pooled prostate-infiltrating T(reg) revealed expected Treg-associated transcripts (FoxP3, CTLA-4, GITR, LAG-3) as well as a number of unique cell surface markers that may serve as additional Treg markers. Taken together, these data suggest that TH17 and/or Treg CD4+ T cells (rather than TH2 T cells) may be involved in the development or progression of prostate cancer.

  7. Experimental design and analysis of activators regenerated by electron transfer-atom transfer radical polymerization experimental conditions for grafting sodium styrene sulfonate from titanium substrates.

    PubMed

    Foster, Rami N; Johansson, Patrik K; Tom, Nicole R; Koelsch, Patrick; Castner, David G

    2015-09-01

    A 2 4 factorial design was used to optimize the activators regenerated by electron transfer-atom transfer radical polymerization (ARGET-ATRP) grafting of sodium styrene sulfonate (NaSS) films from trichlorosilane/10-undecen-1-yl 2-bromo-2-methylpropionate (ester ClSi) functionalized titanium substrates. The process variables explored were: (1) ATRP initiator surface functionalization reaction time; (2) grafting reaction time; (3) CuBr 2 concentration; and (4) reducing agent (vitamin C) concentration. All samples were characterized using x-ray photoelectron spectroscopy (XPS). Two statistical methods were used to analyze the results: (1) analysis of variance with [Formula: see text], using average [Formula: see text] XPS atomic percent as the response; and (2) principal component analysis using a peak list compiled from all the XPS composition results. Through this analysis combined with follow-up studies, the following conclusions are reached: (1) ATRP-initiator surface functionalization reaction times have no discernable effect on NaSS film quality; (2) minimum (≤24 h for this system) grafting reaction times should be used on titanium substrates since NaSS film quality decreased and variability increased with increasing reaction times; (3) minimum (≤0.5 mg cm -2 for this system) CuBr 2 concentrations should be used to graft thicker NaSS films; and (4) no deleterious effects were detected with increasing vitamin C concentration.

  8. Polyethylene imine modified hydrochar adsorption for chromium (VI) and nickel (II) removal from aqueous solution.

    PubMed

    Shi, Yuanji; Zhang, Tao; Ren, Hongqiang; Kruse, Andrea; Cui, Ruofan

    2018-01-01

    An adsorbent hydrochar was synthesized from corn cobs and modified with polyethylene imine (PEI). The hydrochars before and after modification were characterized by scanning electron microscopy, Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and thermogravimetric analysis. FTIR and XPS revealed that the PEI was grafted onto the hydrochar via ether and imine bonds formed with glutaraldehyde. The maximum adsorption capacities for Cr(VI) (33.663mg/g) and Ni(II) (29.059mg/g) on the modified hydrochars were 365% and 43.7% higher, respectively, than those on the unmodified hydrochar. A pseudo-second-order model described the adsorption of Ni(II) and Cr(VI) on all the adsorbents. The adsorption of Cr(VI) was endothermic, spontaneous, increased disorder, and obeyed the Langmuir model. By contrast, the adsorption of Ni(II) was exothermic, spontaneous, decreased disorder, and obeyed the Freundlich model. XPS confirmed that the adsorption sites and mechanisms for Ni(II) and Cr(VI) on the modified hydrochars were different. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Evolution of Eu valence and superconductivity in layered Eu0.5La0.5FBiS2 -xSex system

    NASA Astrophysics Data System (ADS)

    Mizuguchi, Y.; Paris, E.; Wakita, T.; Jinno, G.; Puri, A.; Terashima, K.; Joseph, B.; Miura, O.; Yokoya, T.; Saini, N. L.

    2017-02-01

    We have studied the effect of Se substitution on Eu valence in a layered Eu0.5La0.5FBiS2 -xSex superconductor using a combined analysis of x-ray absorption near-edge structure (XANES) and x-ray photoelectron spectroscopy (XPS) measurements. Eu L3-edge XANES spectra reveal that Eu is in the mixed valence state with coexisting Eu2 + and Eu3 +. The average Eu valence decreases sharply from ˜2.3 for x =0.0 to ˜2.1 for x =0.4 . Consistently, Eu 3 d XPS shows a clear decrease in the average valence by Se substitution. Bi 4 f XPS indicates that effective charge carriers in the BiCh2 (Ch = S, Se) layers are slightly increased by Se substitution. On the basis of the present results it has been discussed that the metallic character induced by Se substitution in Eu0.5La0.5FBiS2 -xSex is likely to be due to increased in-plane orbital overlap driven by reduced in-plane disorder that affects the carrier mobility.

  10. Metagenomic Analysis of the Sponge Discodermia Reveals the Production of the Cyanobacterial Natural Product Kasumigamide by 'Entotheonella'.

    PubMed

    Nakashima, Yu; Egami, Yoko; Kimura, Miki; Wakimoto, Toshiyuki; Abe, Ikuro

    2016-01-01

    Sponge metagenomes are a useful platform to mine cryptic biosynthetic gene clusters responsible for production of natural products involved in the sponge-microbe association. Since numerous sponge-derived bioactive metabolites are biosynthesized by the symbiotic bacteria, this strategy may concurrently reveal sponge-symbiont produced compounds. Accordingly, a metagenomic analysis of the Japanese marine sponge Discodermia calyx has resulted in the identification of a hybrid type I polyketide synthase-nonribosomal peptide synthetase gene (kas). Bioinformatic analysis of the gene product suggested its involvement in the biosynthesis of kasumigamide, a tetrapeptide originally isolated from freshwater free-living cyanobacterium Microcystis aeruginosa NIES-87. Subsequent investigation of the sponge metabolic profile revealed the presence of kasumigamide in the sponge extract. The kasumigamide producing bacterium was identified as an 'Entotheonella' sp. Moreover, an in silico analysis of kas gene homologs uncovered the presence of kas family genes in two additional bacteria from different phyla. The production of kasumigamide by distantly related multiple bacterial strains implicates horizontal gene transfer and raises the potential for a wider distribution across other bacterial groups.

  11. Surface studies of low molecular weight photolysis products from UV-ozone oxidised polystyrene

    NASA Astrophysics Data System (ADS)

    Davidson, M. R.; Mitchell, S. A.; Bradley, R. H.

    2005-05-01

    The production of low molecular weight oxidised material during UV-ozone treatment of polystyrene has been studied by XPS, GC-MS, FTIR and UV/visible spectroscopy. XPS analysis of the oxidised polystyrene surfaces before and after washing with water or methanol indicates that the removal of oxidation products and the surface that remains after washing is strongly dependent on the choice of solvent. Methanol washing removes a greater proportion of the more highly oxidised carbonyl and carboxyl groups resulting in a surface with a lower oxygen content than that remaining after water washing. Extended exposure to UV-ozone treatment reveals a two-stage oxidation process with mono-substituted benzene rings such as benzaldehyde, acetophenone and benzoic acid being produced at exposure times less than 15 min. Compounds, more typical of those formed via dehydration reactions of existing oxidised species, are produced at longer exposure times. UV-visible spectroscopy and Fourier transform infrared spectroscopy also confirm the presence of carboxylic acid, aromatic ketones and esters. Measurements of water contact angle on a 10 min treated surface reveals that methanol washing produces a more hydrophilic surface than water washing, the resulting water contact angles being 47° and 62° respectively. Ageing of methanol washed surfaces for 24 h leads to a recovery of the water contact angle back to 62° which suggests some form of post-washing surface relaxation process. Since XPS analyses show no increase in the oxygen concentration of the methanol washed surfaces after a 24 h ageing period, the increase in contact angle found with ageing is attributed to the reorientation of very near-surface functional groups i.e. within the XPS sampling depth.

  12. Application of modern surface analytical tools in the investigation of surface deterioration processes

    NASA Technical Reports Server (NTRS)

    Buckley, D. H.

    1983-01-01

    Surface profilometry and scanning electron microscopy were utilized to study changes in the surface of polymers when eroded. The X-ray photoelectron spectroscopy (XPS) and depth profile analysis indicate the corrosion of metal and ceramic surfaces and reveal the diffusion of certain species into the surface to produce a change in mechanical properties. Ion implantation, nitriding and plating and their effects on the surface are characterized. Auger spectroscopy analysis identified morphological properties of coatings applied to surfaces by sputter deposition.

  13. Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease.

    PubMed

    Lygirou, Vasiliki; Latosinska, Agnieszka; Makridakis, Manousos; Mullen, William; Delles, Christian; Schanstra, Joost P; Zoidakis, Jerome; Pieske, Burkert; Mischak, Harald; Vlahou, Antonia

    2018-04-17

    Cardiovascular disease (CVD) describes the pathological conditions of the heart and blood vessels. Despite the large number of studies on CVD and its etiology, its key modulators remain largely unknown. To this end, we performed a comprehensive proteomic analysis of blood plasma, with the scope to identify disease-associated changes after placing them in the context of existing knowledge, and generate a well characterized dataset for further use in CVD multi-omics integrative analysis. LC-MS/MS was employed to analyze plasma from 32 subjects (19 cases of various CVD phenotypes and 13 controls) in two steps: discovery (13 cases and 8 controls) and test (6 cases and 5 controls) set analysis. Following label-free quantification, the detected proteins were correlated to existing plasma proteomics datasets (plasma proteome database; PPD) and functionally annotated (Cytoscape, Ingenuity Pathway Analysis). Differential expression was defined based on identification confidence (≥ 2 peptides per protein), statistical significance (Mann-Whitney p value ≤ 0.05) and a minimum of twofold change. Peptides detected in at least 50% of samples per group were considered, resulting in a total of 3796 identified proteins (838 proteins based on ≥ 2 peptides). Pathway annotation confirmed the functional relevance of the findings (representation of complement cascade, fibrin clot formation, platelet degranulation, etc.). Correlation of the relative abundance of the proteins identified in the discovery set with their reported concentrations in the PPD was significant, confirming the validity of the quantification method. The discovery set analysis revealed 100 differentially expressed proteins between cases and controls, 39 of which were verified (≥ twofold change) in the test set. These included proteins already studied in the context of CVD (such as apolipoprotein B, alpha-2-macroglobulin), as well as novel findings (such as low density lipoprotein receptor related

  14. Analysis of the Transcriptional Differences between Indigenous and Invasive Whiteflies Reveals Possible Mechanisms of Whitefly Invasion

    PubMed Central

    Wang, Yong-Liang; Wang, Yu-Jun; Luan, Jun-Bo; Yan, Gen-Hong; Liu, Shu-Sheng; Wang, Xiao-Wei

    2013-01-01

    Background The whitefly Bemisa tabaci is a species complex of more than 31 cryptic species which include some of the most destructive invasive pests of crops worldwide. Among them, Middle East-Asia Minor 1 (MEAM1) and Mediterranean have invaded many countries and displaced the native whitefly species. The successful invasion of the two species is largely due to their wide range of host plants, high resistance to insecticides and remarkable tolerance to environmental stresses. However, the molecular differences between invasive and indigenous whiteflies remain largely unknown. Methodology/Principal Findings Here the global transcriptional difference between the two invasive whitefly species (MEAM1, MED) and one indigenous whitefly species (Asia II 3) were analyzed using the Illumina sequencing. Our analysis indicated that 2,422 genes between MEAM1 and MED; 3,073 genes between MEAM1 and Asia II 3; and 3,644 genes between MED and Asia II 3 were differentially expressed. Gene Ontology enrichment analysis revealed that the differently expressed genes between the invasive and indigenous whiteflies were significantly enriched in the term of ‘oxidoreductase activity’. Pathway enrichment analysis showed that carbohydrate, amino acid and glycerolipid metabolisms were more active in MEAM1 and MED than in Asia II 3, which may contribute to their differences in biological characteristics. Our analysis also illustrated that the majority of genes involved in ‘drug metabolic pathway’ were expressed at a higher level in MEAM1 and MED than in Asia II 3. Taken together, these results revealed that the genes related to basic metabolism and detoxification were expressed at an elevated level in the invasive whiteflies, which might be responsible for their higher resistance to insecticides and environmental stresses. Conclusions/Significance The extensive comparison of MEAM1, MED and Asia II 3 gene expression may serve as an invaluable resource for revealing the molecular

  15. XPS Study on the Stability and Transformation of Hydrate and Carbonate Phases within MgO Systems

    PubMed Central

    Rheinheimer, Vanessa; Unluer, Cise; Liu, Jiawei; Ruan, Shaoqin; Pan, Jisheng; Monteiro, Paulo J. M.

    2017-01-01

    MgO cements have great potential for carbon sequestration as they have the ability to carbonate and gain strength over time. The hydration of reactive MgO occurs at a similar rate as ordinary Portland cement (PC) and forms brucite (Mg(OH)2, magnesium hydroxide), which reacts with CO2 to form a range of hydrated magnesium carbonates (HMCs). However, the formation of HMCs within the MgO–CO2–H2O system depends on many factors, such as the temperature and CO2 concentration, among others, which play an important role in determining the rate and degree of carbonation, the type and stability of the produced HMCs and the associated strength development. It is critical to understand the stability and transformation pathway of HMCs, which are assessed here through the use of X-ray photoelectron spectroscopy (XPS). The effects of the CO2 concentration (in air or 10% CO2), exposure to high temperatures (up to 300 °C) and curing period (one or seven days) are reported. Observed changes in the binding energy (BE) indicate the formation of different components and the transformation of the hydrated carbonates from one form to another, which will influence the final performance of the carbonated blends. PMID:28772437

  16. Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer.

    PubMed

    Shah, Anup D; Inder, Kerry L; Shah, Alok K; Cristino, Alexandre S; McKie, Arthur B; Gabra, Hani; Davis, Melissa J; Hill, Michelle M

    2016-10-07

    Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and renal cell carcinoma. This analysis revealed that cancer development is associated with increased membrane raft-cytoskeleton interactions, with ∼40% of elevated lipid raft proteins being cytoskeletal components. Previous studies suggest a potential functional role for the raft-cytoskeleton in the action of the putative tumor suppressors PTRF/Cavin-1 and Merlin. To extend the observation, we examined lipid raft proteome modulation by an unrelated tumor suppressor opioid binding protein cell-adhesion molecule (OPCML) in ovarian cancer SKOV3 cells. In agreement with the other model systems, quantitative proteomics revealed that 39% of OPCML-depleted lipid raft proteins are cytoskeletal components, with microfilaments and intermediate filaments specifically down-regulated. Furthermore, protein-protein interaction network and simulation analysis showed significantly higher interactions among cancer raft proteins compared with general human raft proteins. Collectively, these results suggest increased cytoskeleton-mediated stabilization of lipid raft domains with greater molecular interactions as a common, functional, and reversible feature of cancer cells.

  17. Reaction of propane with the ordered NiO/Rh(1 1 1) studied by XPS and LEISS

    NASA Astrophysics Data System (ADS)

    Zhang, Hong; Wang, Wenyi; Chen, Mingshu; Wan, Huilin

    2018-05-01

    Nickel oxide has been reported to be an efficient catalyst for oxidative dehydrogenation of propane (ODP) to propene at low temperature. In this paper, ultrathin NiO films with various thickness were prepared on a Rh(1 1 1) surface and characterized by X-ray photoemission spectroscopy (XPS) and Low-energy ion scattering spectroscopy (LEISS). Results show that NiO forms a two-dimensional (2D) network with a O-Ni-O structure at submonolayer coverages, and a bulk-like NiO at multilayer coverages. The submonolayer NiO films are less stable than the thick ones when annealed in ultra-high vacuum (UHV) due to the strong interaction with the Rh substrate. Propane was dosed onto the model surfaces at different temperatures to investigate the activation of propane and reactivity of NiO films with propane. The reactions of propane with the thin and thick NiO films are significantly different. Propane activates on the O defect sites for the thick NiO films, whereas activation occurs on the interface of nickel oxide and substrate for the thin films with a higher activity.

  18. A Rasch analysis of the Brief Pain Inventory Interference subscale reveals three dimensions and an age bias.

    PubMed

    Walton, David M; Beattie, Tyler; Putos, Joseph; MacDermid, Joy C

    2016-06-01

    The Brief Pain Inventory is composed of two quantifiable scales: pain severity and pain interference. The reported factor structure of the interference subscale is not consistent in the extant literature, with no clear choice between a single- or two-factor structure. Here, we report on the results of Rasch-based analysis of the interference subscale using a large population-based ambulatory patient database (the Quebec Pain Registry). Observational cohort. A total of 1,000 responses were randomly drawn from a total database of 5,654 for this analysis. Both the original 7-item and an expanded 10-item version (Tyler 2002) of the interference subscale were evaluated. Rasch analysis revealed significant misfit of both versions of the scale, with the original 7-item version outperforming the expanded 10-item version. Analysis of dimensionality revealed that both versions showed improved model fit when considered two subscales (affective and physical interference) with the item on sleep interference removed or considered separately. Additionally, significant uniform differential item functioning was identified for 6 of the 7 original items when the sample was stratified by age above or below 55 years. The interference subscale achieved adequate model fit when considered as two separate subscales with age as a mediator of response, while interpreting the sleep interference item separately. A transformation matrix revealed that in all cases, ordinal-level change at the extreme ends of the scale appears to be more meaningful than does a similar change at the midpoints. The Interference subscale of the BPI should be interpreted as two separate subscales (Affective Interference, Physical Interference) with the sleep item removed or interpreted separately for optimal fit to the Rasch model. Implications for research and clinical use are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Phenotypic Analysis of Prostate-Infiltrating Lymphocytes Reveals TH17 and Treg Skewing

    PubMed Central

    Sfanos, Karen Sandell; Bruno, Tullia C.; Maris, Charles H.; Xu, Lauren; Thoburn, Christopher J.; DeMarzo, Angelo M.; Meeker, Alan K.; Isaacs, William B.; Drake, Charles G.

    2011-01-01

    Purpose Pathologic examination of prostate glands removed from patients with prostate cancer commonly reveals infiltrating CD4+ and CD8+ T cells. Little is known about the phenotype of these cells, despite accumulating evidence suggesting a potential role for chronic inflammation in the etiology of prostate cancer. Experimental Design We developed a technique that samples the majority of the peripheral prostate through serial needle aspirates. CD4+ prostate-infiltrating lymphocytes (PIL) were isolated using magnetic beads and analyzed for subset skewing using both flow cytometry and quantitative reverse transcription-PCR. The transcriptional profile of fluorescence-activated cell sorted prostate-infiltrating regulatory T cells (CD4+, CD25+, GITR+) was compared with naïve, peripheral blood T cells using microarray analysis. Results CD4+ PIL showed a paucity of TH2 (interleukin-4– secreting) cells, a surprising finding given the generally accepted association of these cells with chronic, smoldering inflammation. Instead, CD4+ PIL seemed to be skewed towards a regulatory Treg phenotype (FoxP3+) as well as towards the TH17 phenotype (interleukin-17+). We also found that a preponderance of TH17-mediated inflammation was associated with a lower pathologic Gleason score. These protein level data were reflected at the message level, as analyzed by quantitative reverse transcription-PCR. Microarray analysis of pooled prostate-infiltrating Treg revealed expected Treg-associated transcripts (FoxP3, CTLA-4, GITR, LAG-3) as well as a number of unique cell surface markers that may serve as additional Treg markers. Conclusion Taken together, these data suggest that TH17 and/or Treg CD4+ T cells (rather than TH2 T cells) may be involved in the development or progression of prostate cancer. PMID:18519750

  20. Latent class analysis reveals clinically relevant atopy phenotypes in 2 birth cohorts.

    PubMed

    Hose, Alexander J; Depner, Martin; Illi, Sabina; Lau, Susanne; Keil, Thomas; Wahn, Ulrich; Fuchs, Oliver; Pfefferle, Petra Ina; Schmaußer-Hechfellner, Elisabeth; Genuneit, Jon; Lauener, Roger; Karvonen, Anne M; Roduit, Caroline; Dalphin, Jean-Charles; Riedler, Josef; Pekkanen, Juha; von Mutius, Erika; Ege, Markus J

    2017-06-01

    Phenotypes of childhood-onset asthma are characterized by distinct trajectories and functional features. For atopy, definition of phenotypes during childhood is less clear. We sought to define phenotypes of atopic sensitization over the first 6 years of life using a latent class analysis (LCA) integrating 3 dimensions of atopy: allergen specificity, time course, and levels of specific IgE (sIgE). Phenotypes were defined by means of LCA in 680 children of the Multizentrische Allergiestudie (MAS) and 766 children of the Protection against allergy: Study in Rural Environments (PASTURE) birth cohorts and compared with classical nondisjunctive definitions of seasonal, perennial, and food sensitization with respect to atopic diseases and lung function. Cytokine levels were measured in the PASTURE cohort. The LCA classified predominantly by type and multiplicity of sensitization (food vs inhalant), allergen combinations, and sIgE levels. Latent classes were related to atopic disease manifestations with higher sensitivity and specificity than the classical definitions. LCA detected consistently in both cohorts a distinct group of children with severe atopy characterized by high seasonal sIgE levels and a strong propensity for asthma; hay fever; eczema; and impaired lung function, also in children without an established asthma diagnosis. Severe atopy was associated with an increased IL-5/IFN-γ ratio. A path analysis among sensitized children revealed that among all features of severe atopy, only excessive sIgE production early in life affected asthma risk. LCA revealed a set of benign, symptomatic, and severe atopy phenotypes. The severe phenotype emerged as a latent condition with signs of a dysbalanced immune response. It determined high asthma risk through excessive sIgE production and directly affected impaired lung function. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  1. Complete genome sequence analysis of novel human bocavirus reveals genetic recombination between human bocavirus 2 and human bocavirus 4.

    PubMed

    Khamrin, Pattara; Okitsu, Shoko; Ushijima, Hiroshi; Maneekarn, Niwat

    2013-07-01

    Epidemiological surveillance of human bocavirus (HBoV) was conducted on fecal specimens collected from hospitalized children with diarrhea in Chiang Mai, Thailand in 2011. By partial sequence analysis of VP1 gene, an unusual strain of HBoV (CMH-S011-11), was initially identified as HBoV4. The complete genome sequence of CMH-S011-11 was performed and analyzed further to clarify whether it was a recombinant strain or a new HBoV variant. Analysis of complete genome sequence revealed that the coding sequence starting from NS1, NP1 to VP1/VP2 was 4795 nucleotides long. Interestingly, the nucleotide sequence of NS1 gene of CMH-S011-11 was most closely related to the HBoV2 reference strains detected in Pakistan, which contradicted to the initial genotyping result of the partial VP1 region in the previous study. In addition, comparison of NP1 nucleotide sequence of CMH-S011-11 with those of other HBoV1-4 reference strains also revealed a high level of sequence identity with HBoV2. On the other hand, nucleotide sequence of VP1/VP2 gene of CMH-S011-11 was most closely related to those of HBoV4 reference strains detected in Nigeria. The overall full-length sequence analysis revealed that this CMH-S011-11 was grouped within HBoV4 species, but located in a separate branch from other HBoV4 prototype strains. Recombination analysis revealed that CMH-S011-11 was the result of recombination between HBoV2 and HBoV4 strains with the break point located near the start codon of VP2. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Comparative transcriptome analysis of pepper (Capsicum annuum) revealed common regulons in multiple stress conditions and hormone treatments.

    PubMed

    Lee, Sanghyeob; Choi, Doil

    2013-09-01

    Global transcriptome analysis revealed common regulons for biotic/abiotic stresses, and some of these regulons encoding signaling components in both stresses were newly identified in this study. In this study, we aimed to identify plant responses to multiple stress conditions and discover the common regulons activated under a variety of stress conditions. Global transcriptome analysis revealed that salicylic acid (SA) may affect the activation of abiotic stress-responsive genes in pepper. Our data indicate that methyl jasmonate (MeJA) and ethylene (ET)-responsive genes were primarily activated by biotic stress, while abscisic acid (ABA)-responsive genes were activated under both types of stresses. We also identified differentially expressed gene (DEG) responses to specific stress conditions. Biotic stress induces more DEGs than those induced by abiotic and hormone applications. The clustering analysis using DEGs indicates that there are common regulons for biotic or abiotic stress conditions. Although SA and MeJA have an antagonistic effect on gene expression levels, SA and MeJA show a largely common regulation as compared to the regulation at the DEG expression level induced by other hormones. We also monitored the expression profiles of DEG encoding signaling components. Twenty-two percent of these were commonly expressed in both stress conditions. The importance of this study is that several genes commonly regulated by both stress conditions may have future applications for creating broadly stress-tolerant pepper plants. This study revealed that there are complex regulons in pepper plant to both biotic and abiotic stress conditions.

  3. Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

    PubMed Central

    2013-01-01

    Background Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data. The aim of this study is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas aeruginosa isolated from the airways of cystic fibrosis patients. Results Our analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates. This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. Conclusions Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering and matrix factorization made it possible to reveal minor similarities among different groups of data, which other analytical methods failed to identify. We suggest that this analysis could be used to supplement current methods used to analyze DNA microarray data. PMID:24059747

  4. Friction and Wear of Iron in Corrosive Media

    NASA Technical Reports Server (NTRS)

    Rengstorff, G. W. P.; Miyoshi, K.; Buckley, D. H.

    1982-01-01

    Friction and wear experiments were conducted with elemental iron exposed to various corrosive media including two acids, base, and a salt. Studies involved various concentrations of nitric and sulfuric acids, sodium hydroxide, and sodium chloride. Load and reciprocating sliding speed were kept constant. With the base NaOH an increase in normality beyond 0.01 N resulted in a decrease in both friction and wear. X-ray photoelectron spectroscopy (XPS) analysis of the surface showed a decreasing concentration of ferric oxide (Fe2O3) on the iron surface with increasing NaOH concentration. With nitric acid (HNO3) friction decreased in solutions to 0.05 N, beyond which no further change in friction was observed. The concentration of Fe2O3 on the surface continued to increase with increasing normality. XPS analysis revealed the presence of sulfates in addition of Fe2O3 on surfaces exposed to sulfuric acid and iron chlorides but no sodium on surfaces exposed to NaCl.

  5. A Study of Ziegler–Natta Propylene Polymerization Catalysts by Spectroscopic Methods

    PubMed Central

    Tkachenko, Olga P.; Kucherov, Alexey V.; Kustov, Leonid M.; Virkkunen, Ville; Leinonen, Timo; Denifl, Peter

    2017-01-01

    Ziegler–Natta polymerization catalysts were characterized by a complex of surface- and bulk-sensitive methods (DRIFTS, XPS, ESR, and XAS = XANES + EXAFS). A diffuse-reflectance Fourier-transform IR spectroscopy (DRIFTS) study showed the presence of strong Lewis acid sites in different concentrations and absence of strong basic sites in the polymerization catalysts. X-ray photoelectron spectroscopy (XPS), electron-spin resonance (ESR), and (X-ray absorption near-edge structure (XANES) analysis revealed the presence of Ti4+, Ti3+, Ti2+, and Ti1+ species in the surface layers and in the bulk of catalysts. The samples under study differ drastically in terms of the number of ESR-visible paramagnetic sites. The EXAFS study shows the presence of a Cl atom as a nearest neighbor of the absorbing Ti atom. PMID:28772850

  6. Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    PubMed Central

    2014-01-01

    Abstract The version of this article published in BMC Genomics 2013, 14: 274, contains 9 unpublished genomes (Botryobasidium botryosum, Gymnopus luxurians, Hypholoma sublateritium, Jaapia argillacea, Hebeloma cylindrosporum, Conidiobolus coronatus, Laccaria amethystina, Paxillus involutus, and P. rubicundulus) downloaded from JGI website. In this correction, we removed these genomes after discussion with editors and data producers whom we should have contacted before downloading these genomes. Removing these data did not alter the principle results and conclusions of our original work. The relevant Figures 1, 2, 3, 4 and 6; and Table 1 have been revised. Additional files 1, 3, 4, and 5 were also revised. We would like to apologize for any confusion or inconvenience this may have caused. Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 94 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed

  7. Multiple maternal origins of Indonesian crowing chickens revealed by mitochondrial DNA analysis.

    PubMed

    Ulfah, Maria; Perwitasari, Dyah; Jakaria, Jakaria; Muladno, Muhammad; Farajallah, Achmad

    2017-03-01

    The utilization of Indonesian crowing chickens is increasing; as such, assessing their genetic structures is important to support the conservation of their genetic resources. This study analyzes the matrilineal evolution of Indonesian crowing chickens based on the mtDNA displacement loop D-loop region to clarify their phylogenetic relationships, possible maternal origin, and possible routes of chicken dispersal. The neighbor-joining tree reveals that the majority of Indonesian crowing chickens belong to haplogroups B, D, and E, but haplogroup D harbored most of them. The Bayesian analysis also reveals that Indonesian crowing chickens derive from Bekisar chicken, a hybrid of the green junglefowl, suggesting the possible contribution of green junglefowl to chicken domestication. There appear at least three maternal lineages of Indonesian chicken origins indicated by the median network profile of mtDNA D-loop haplotypes, namely (1) Chinese; (2) Chinese, Indian, and other Southeast Asian chickens; and (3) Indian, Chinese, Southeast Asian, Japanese, and European chickens. Chicken domestication might be centered in China, India, Indonesia, and other Southeast Asian countries, supporting multiple maternal origins of Indonesian crowing chickens. A systematic breeding program of indigenous chickens will be very important to retain the genetic diversity for future use and conservation.

  8. Proteomics Analysis of Tissue Samples Reveals Changes in Mitochondrial Protein Levels in Parathyroid Hyperplasia over Adenoma

    PubMed Central

    AKPINAR, GURLER; KASAP, MURAT; CANTURK, NUH ZAFER; ZULFIGAROVA, MEHIN; ISLEK, EYLÜL ECE; GULER, SERTAC ATA; SIMSEK, TURGAY; CANTURK, ZEYNEP

    2017-01-01

    Background/Aim: To unveil the pathophysiology of primary hyperparathyroidism, molecular details of parathyroid hyperplasia and adenoma have to be revealed. Such details will provide the tools necessary for differentiation of these two look-alike diseases. Therefore, in the present study, a comparative proteomic study using postoperative tissue samples from the parathyroid adenoma and parathyroid hyperplasia patients was performed. Materials and Methods: Protein extracts were prepared from tissue samples (n=8 per group). Protein pools were created for each group and subjected to DIGE and conventional 2DE. Following image analysis, spots representing the differentially regulated proteins were excised from the and used for identification via MALDI-TOF/TOF analysis. Results: The identities of 40 differentially-expressed proteins were revealed. Fourteen of these proteins were over-expressed in the hyperplasia while 26 of them were over-expressed in the adenoma. Conclusion: Most proteins found to be over-expressed in the hyperplasia samples were mitochondrial, underlying the importance of the mitochondrial activity as a potential biomarker for differentiation of parathyroid hyperplasia from adenoma. PMID:28446534

  9. Genomic analysis of Meckel–Gruber syndrome in Arabs reveals marked genetic heterogeneity and novel candidate genes

    PubMed Central

    Shaheen, Ranad; Faqeih, Eissa; Alshammari, Muneera J; Swaid, Abdulrahman; Al-Gazali, Lihadh; Mardawi, Elham; Ansari, Shinu; Sogaty, Sameera; Seidahmed, Mohammed Z; AlMotairi, Muhammed I; Farra, Chantal; Kurdi, Wesam; Al-Rasheed, Shatha; Alkuraya, Fowzan S

    2013-01-01

    Meckel–Gruber syndrome (MKS, OMIM #249000) is a multiple congenital malformation syndrome that represents the severe end of the ciliopathy phenotypic spectrum. Despite the relatively common occurrence of this syndrome among Arabs, little is known about its genetic architecture in this population. This is a series of 18 Arab families with MKS, who were evaluated clinically and studied using autozygome-guided mutation analysis and exome sequencing. We show that autozygome-guided candidate gene analysis identified the underlying mutation in the majority (n=12, 71%). Exome sequencing revealed a likely pathogenic mutation in three novel candidate MKS disease genes. These include C5orf42, Ellis–van-Creveld disease gene EVC2 and SEC8 (also known as EXOC4), which encodes an exocyst protein with an established role in ciliogenesis. This is the largest and most comprehensive genomic study on MKS in Arabs and the results, in addition to revealing genetic and allelic heterogeneity, suggest that previously reported disease genes and the novel candidates uncovered by this study account for the overwhelming majority of MKS patients in our population. PMID:23169490

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

    Ding, Laura; Harvey, Stephen P.; Teeter, Glenn

    We demonstrate the potential of X-ray photoelectron spectroscopy (XPS) to characterize new carrier-selective contacts (CSC) for solar cell application. We show that XPS not only provides information about the surface chemical properties of the CSC material, but that operando XPS, i.e. under light bias condition, can also directly measure the photovoltage that develops at the CSC/absorber interface, revealing device relevant information without the need of assembling a full solar cell. We present the application of the technique to molybdenum oxide hole-selective contact films on a crystalline silicon absorber.

  11. Multilocus analysis reveals three candidate genes for Chinese migraine susceptibility.

    PubMed

    An, X-K; Fang, J; Yu, Z-Z; Lin, Q; Lu, C-X; Qu, H-L; Ma, Q-L

    2017-08-01

    Several genome-wide association studies (GWASs) in Caucasian populations have identified 12 loci that are significantly associated with migraine. More evidence suggests that serotonin receptors are also involved in migraine pathophysiology. In the present study, a case-control study was conducted in a cohort of 581 migraine cases and 533 ethnically matched controls among a Chinese population. Eighteen polymorphisms from serotonin receptors and GWASs were selected, and genotyping was performed using a Sequenom MALDI-TOF mass spectrometry iPLEX platform. The genotypic and allelic distributions of MEF2D rs2274316 and ASTN2 rs6478241 were significantly different between migraine patients and controls. Univariate and multivariate analysis revealed significant associations of polymorphisms in the MEF2D and ASTN2 genes with migraine susceptibility. MEF2D, PRDM16 and ASTN2 were also found to be associated with migraine without aura (MO) and migraine with family history. And, MEF2D and ASTN2 also served as genetic risk factors for the migraine without family history. The generalized multifactor dimensionality reduction analysis identified that MEF2D and HTR2E constituted the two-factor interaction model. Our study suggests that the MEF2D, PRDM16 and ASTN2 genes from GWAS are associated with migraine susceptibility, especially MO, among Chinese patients. It appears that there is no association with serotonin receptor related genes. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  12. A Multi-technique Characterization of Adsorbed Protein Films: Orientation and Structure by ToF-SIMS, NEXAFS, SFG, and XPS

    NASA Astrophysics Data System (ADS)

    Baio, Joseph E.

    There are many techniques that allow surface scientists to study interfaces. However, few are routinely applied to probe biological surfaces. The work presented here demonstrates how detailed information about the conformation, orientation, chemical state, and molecular structure of biological molecules immobilized onto a surface can be assessed by electron spectroscopy, mass spectrometry, and nonlinear vibrational spectroscopy techniques. This investigation began with the development of simple model systems (small proteins, and peptides) and evolved into a study of more complex --- real world systems. Initially, two model systems based on the chemical and electrostatic immobilization of a small rigid protein (Protein G B1 domain, 6kDa) were built to develop the capabilities of time-of-flight secondary ion mass spectrometry (ToFSIMS), near edge X-ray absorption fine structure spectroscopy (NEXAFS) and sum frequency generation (SFG) spectroscopy as tools to probe the structure of surface immobilized proteins. X-ray photoelectron spectroscopy (XPS) was used to measure the amount of immobilized protein and ToF-SIMS sampled the amino acid composition of the exposed surface of the protein film. Within the ToF-SIMS spectra, an enrichment of secondary ions from amino acids located at opposite ends of the proteins were used to describe protein orientation. SFG spectral peaks characteristic of ordered alpha-helix and beta-sheet elements were observed for both systems and the phase of the peaks indicated a predominantly upright orientation for both the covalent and electrostatic configurations. Polarization dependence of the NEXAFS signal from the N 1s to pi* transition of the peptide bonds that make up the beta-sheets also indicated protein ordering at the surface. Building upon the Protein G B1 studies, the orientation and structure of a surface immobilized antibody (HuLys Fv: variant of humanized anti-lysozyme variable fragment, 26kDa) was characterized across two

  13. Effects of M=Si, Ga and Al for Co substitution on the electronic properties of RCo4M as probed by XPS

    NASA Astrophysics Data System (ADS)

    Laslo, A.; Dudric, R.; Neumann, M.; Isnard, O.; Coldea, M.; Pop, V.

    2014-12-01

    The electronic properties of RCo5-xMx (R=Er, Sm, Tm; M=Si, Ga, Al; x=0 and 1) compounds were investigated by X-ray photoelectron spectroscopy (XPS). The study was focused on the Co 3s exchange splitting, the valence bands and chemical shifts of the elements from the analyzed compounds. The Co 2p3/2 core-level chemical shifts were described by means of the Auger parameters and Wagner plot. The hybridization between the R 5d6s and M 3sp and 4sp states and Co 3d states leads to a partial filling of the Co 3d band and to a decrease of the Co magnetic moments in comparison with the value in pure Co metal, in good agreement with the magnetic measurements.

  14. Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis.

    PubMed

    Kurth, Daniel; Amadio, Ariel; Ordoñez, Omar F; Albarracín, Virginia H; Gärtner, Wolfgang; Farías, María E

    2017-04-21

    Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa's stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences. A functional analysis indicated that carbon fixation might occur not only by the Calvin-Benson cycle, but also through alternative pathways such as the reverse TCA cycle, and the reductive acetyl-CoA pathway. Deltaproteobacteria were involved both in sulfate reduction and nitrogen fixation. Significant differences were found when comparing the Socompa stromatolite metagenome to the Shark Bay (Australia) smooth mat metagenome: namely, those involving stress related processes, particularly, arsenic resistance. An in-depth analysis revealed a surprisingly diverse metabolism comprising all known types of As resistance and energy generating pathways. While the ars operon was the main mechanism, an important abundance of arsM genes was observed in selected phyla. The data resulting from this work will prove a cornerstone for further studies on this rare microbial community.

  15. Revealed preferences towards the appraisal of orphan drugs in Poland - multi criteria decision analysis.

    PubMed

    Kolasa, Katarzyna; Zwolinski, Krzysztof Miroslaw; Zah, Vladimir; Kaló, Zoltán; Lewandowski, Tadeusz

    2018-04-27

    A Multi Criteria Decision Analysis (MCDA) technique was adopted to reveal the preferences of the Appraisal Body of the Polish HTA agency towards orphan drugs (OMPs). There were 34 positive and 23 negative HTA recommendations out of 54 distinctive drug-indication pairs. The MCDA matrix consisted of 13 criteria, seven of which made the most impact on the HTA process. Appraisal of clinical evidence, cost of therapy, and safety considerations were the main contributors to the HTA guidance, whilst advancement of technology and manufacturing costs made the least impact. MCDA can be regarded as a valuable tool for revealing decision makers' preferences in the healthcare sector. Given that only roughly half of all criteria included in the MCDA matrix were deemed to make an impact on the HTA process, there is certainly some room for improvement with respect to the adaptation of a new approach towards the value assessment of OMPs in Poland.

  16. Problems at the Leading Edge of Space Weathering as Revealed by TEM Combined with Surface Science Techniques

    NASA Astrophysics Data System (ADS)

    Christoffersen, R.; Dukes, C. A.; Keller, L. P.; Rahman, Z.; Baragiola, R. A.

    2015-11-01

    Analytical field-emission TEM techniques cross-correlated with surface analyses by X-ray photoelectron spectroscopy (XPS) provides a unique two-prong approach for characterizing how solar wind ion processing contributes to space weathering.

  17. Impression of plasma voltage on growth of α-V2O5 nanostructured thin films

    NASA Astrophysics Data System (ADS)

    Sharma, Rabindar Kumar; Kumar, Prabhat; Reddy, G. B.

    2015-06-01

    In this communication, we synthesized vanadium pentoxide (α-V2O5) nanostructured thin films (NSTs) accompanied with nanoflakes/ nanoplates on the Ni-coated glass substrates employing plasma assisted sublimation process (PASP) as a function of plasma voltage (Vp). The effect of plasma voltage on structural, morphological, compositional, and vibrational properties have been studied systematically. The structural analysis divulged that all films deposited at different Vp have pure orthorhombic phase, no impurity phase is detected under resolution limit of XRD and XPS. The morphological studies of samples is carried out by SEM, revealed that features as well as alignment of V2O5 NSTs is greatly monitored by Vp and the film possessing the best features is obtained at 2500volt. In addition, XPS results reveal that V5+ oxidation state is the most prominent state in sample V2, which represents better stoichiometric nature of film. The vibrational study of all samples is performed by FTIR and strongly support the XRD observations. All the results are in consonance with each other.

  18. Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish.

    PubMed

    Winata, Cecilia L; Kondrychyn, Igor; Kumar, Vibhor; Srinivasan, Kandhadayar G; Orlov, Yuriy; Ravishankar, Ashwini; Prabhakar, Shyam; Stanton, Lawrence W; Korzh, Vladimir; Mathavan, Sinnakaruppan

    2013-10-01

    Zic3 regulates early embryonic patterning in vertebrates. Loss of Zic3 function is known to disrupt gastrulation, left-right patterning, and neurogenesis. However, molecular events downstream of this transcription factor are poorly characterized. Here we use the zebrafish as a model to study the developmental role of Zic3 in vivo, by applying a combination of two powerful genomics approaches--ChIP-seq and microarray. Besides confirming direct regulation of previously implicated Zic3 targets of the Nodal and canonical Wnt pathways, analysis of gastrula stage embryos uncovered a number of novel candidate target genes, among which were members of the non-canonical Wnt pathway and the neural pre-pattern genes. A similar analysis in zic3-expressing cells obtained by FACS at segmentation stage revealed a dramatic shift in Zic3 binding site locations and identified an entirely distinct set of target genes associated with later developmental functions such as neural development. We demonstrate cis-regulation of several of these target genes by Zic3 using in vivo enhancer assay. Analysis of Zic3 binding sites revealed a distribution biased towards distal intergenic regions, indicative of a long distance regulatory mechanism; some of these binding sites are highly conserved during evolution and act as functional enhancers. This demonstrated that Zic3 regulation of developmental genes is achieved predominantly through long distance regulatory mechanism and revealed that developmental transitions could be accompanied by dramatic changes in regulatory landscape.

  19. Surface analysis characterisation of gum binders used in modern watercolour paints

    NASA Astrophysics Data System (ADS)

    Sano, Naoko; Cumpson, Peter J.

    2016-02-01

    Conducting this study has demonstrated that not only SEM-EDX but also XPS can be an efficient tool for characterising watercolour paint surfaces. We find that surface effects are mediated by water. Once the powdered components in the watercolour come into contact with water they dramatically transform their chemical structures at the surface and show the presence of pigment components with a random dispersion within the gum layer. Hence the topmost surface of the paint is confirmed as being composed of the gum binder components. This result is difficult to confirm using just one analytical technique (either XPS or SEM-EDX). In addition, peak fitting of C1s XPS spectra suggests that the gum binder in the commercial watercolour paints is probably gum arabic (by comparison with the reference materials). This identification is not conclusive, but the combination techniques of XPS and SEM shows the surface structure with material distribution of the gum binder and the other ingredients of the watercolour paints. Therefore as a unique technique, XPS combined with SEM-EDX may prove a useful method in the study of surface structure for not only watercolour objects but also other art objects; which may in future help in the conservation for art.

  20. Characterization of nanostructured CuO-porous silicon matrix formed on copper-coated silicon substrate via electrochemical etching

    NASA Astrophysics Data System (ADS)

    Naddaf, M.; Mrad, O.; Al-zier, A.

    2014-06-01

    A pulsed anodic etching method has been utilized for nanostructuring of a copper-coated p-type (100) silicon substrate, using HF-based solution as electrolyte. Scanning electron microscopy reveals the formation of a nanostructured matrix that consists of island-like textures with nanosize grains grown onto fiber-like columnar structures separated with etch pits of grooved porous structures. Spatial micro-Raman scattering analysis indicates that the island-like texture is composed of single-phase cupric oxide (CuO) nanocrystals, while the grooved porous structure is barely related to formation of porous silicon (PS). X-ray diffraction shows that both the grown CuO nanostructures and the etched silicon layer have the same preferred (220) orientation. Chemical composition obtained by means of X-ray photoelectron spectroscopic (XPS) analysis confirms the presence of the single-phase CuO on the surface of the patterned CuO-PS matrix. As compared to PS formed on the bare silicon substrate, the room-temperature photoluminescence (PL) from the CuO-PS matrix exhibits an additional weak `blue' PL band as well as a blue shift in the PL band of PS (S-band). This has been revealed from XPS analysis to be associated with the enhancement in the SiO2 content as well as formation of the carbonyl group on the surface in the case of the CuO-PS matrix.

  1. 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

  2. Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis

    NASA Astrophysics Data System (ADS)

    Li, Yue; Zhang, Zhaolei

    2014-11-01

    Carcinogenesis consists of oncogenesis and metastasis, and intriguingly microRNAs (miRNAs) are involved in both processes. Although aberrant miRNA activities are prevalent in diverse tumor types, the exact mechanisms for how they regulate cancerous processes are not always clear. To this end, we performed a large-scale pan-cancer analysis via a novel probabilistic approach to infer recurrent miRNA-target interactions implicated in 12 cancer types using data from The Cancer Genome Atlas. We discovered ~20,000 recurrent miRNA regulations, which are enriched for cancer-related miRNAs/genes. Notably, miRNA 200 family (miR-200/141/429) is among the most prominent miRNA regulators, which is known to be involved in metastasis. Importantly, the recurrent miRNA regulatory network is not only enriched for cancer pathways but also for extracellular matrix (ECM) organization and ECM-receptor interactions. The results suggest an intriguing cancer mechanism involving miRNA-mediated cell-to-cell communication, which possibly involves delivery of tumorigenic miRNA messengers to adjacent cells via exosomes. Finally, survival analysis revealed 414 recurrent-prognostic associations, where both gene and miRNA involved in each interaction conferred significant prognostic power in one or more cancer types. Together, our comprehensive pan-cancer analysis provided not only biological insights into metastasis but also brought to bear the clinical relevance of the proposed recurrent miRNA-gene associations.

  3. Association genetics and transcriptome analysis reveal a gibberellin-responsive pathway involved in regulating photosynthesis.

    PubMed

    Xie, Jianbo; Tian, Jiaxing; Du, Qingzhang; Chen, Jinhui; Li, Ying; Yang, Xiaohui; Li, Bailian; Zhang, Deqiang

    2016-05-01

    Gibberellins (GAs) regulate a wide range of important processes in plant growth and development, including photosynthesis. However, the mechanism by which GAs regulate photosynthesis remains to be understood. Here, we used multi-gene association to investigate the effect of genes in the GA-responsive pathway, as constructed by RNA sequencing, on photosynthesis, growth, and wood property traits, in a population of 435 Populus tomentosa By analyzing changes in the transcriptome following GA treatment, we identified many key photosynthetic genes, in agreement with the observed increase in measurements of photosynthesis. Regulatory motif enrichment analysis revealed that 37 differentially expressed genes related to photosynthesis shared two essential GA-related cis-regulatory elements, the GA response element and the pyrimidine box. Thus, we constructed a GA-responsive pathway consisting of 47 genes involved in regulating photosynthesis, including GID1, RGA, GID2, MYBGa, and 37 photosynthetic differentially expressed genes. Single nucleotide polymorphism (SNP)-based association analysis showed that 142 SNPs, representing 40 candidate genes in this pathway, were significantly associated with photosynthesis, growth, and wood property traits. Epistasis analysis uncovered interactions between 310 SNP-SNP pairs from 37 genes in this pathway, revealing possible genetic interactions. Moreover, a structural gene-gene matrix based on a time-course of transcript abundances provided a better understanding of the multi-gene pathway affecting photosynthesis. The results imply a functional role for these genes in mediating photosynthesis, growth, and wood properties, demonstrating the potential of combining transcriptome-based regulatory pathway construction and genetic association approaches to detect the complex genetic networks underlying quantitative traits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights

  4. Paired Exome Analysis Reveals Clonal Evolution and Potential Therapeutic Targets in Urothelial Carcinoma.

    PubMed

    Lamy, Philippe; Nordentoft, Iver; Birkenkamp-Demtröder, Karin; Thomsen, Mathilde Borg Houlberg; Villesen, Palle; Vang, Søren; Hedegaard, Jakob; Borre, Michael; Jensen, Jørgen Bjerggaard; Høyer, Søren; Pedersen, Jakob Skou; Ørntoft, Torben F; Dyrskjøt, Lars

    2016-10-01

    Greater knowledge concerning tumor heterogeneity and clonality is needed to determine the impact of targeted treatment in the setting of bladder cancer. In this study, we performed whole-exome, transcriptome, and deep-focused sequencing of metachronous tumors from 29 patients initially diagnosed with early-stage bladder tumors (14 with nonprogressive disease and 15 with progressive disease). Tumors from patients with progressive disease showed a higher variance of the intrapatient mutational spectrum and a higher frequency of APOBEC-related mutations. Allele-specific expression was also higher in these patients, particularly in tumor suppressor genes. Phylogenetic analysis revealed a common origin of the metachronous tumors, with a higher proportion of clonal mutations in the ancestral branch; however, 19 potential therapeutic targets were identified as both ancestral and tumor-specific alterations. Few subclones were present based on PyClone analysis. Our results illuminate tumor evolution and identify candidate therapeutic targets in bladder cancer. Cancer Res; 76(19); 5894-906. ©2016 AACR. ©2016 American Association for Cancer Research.

  5. Genome-Wide SNP Analysis Reveals Distinct Origins of Trypanosoma evansi and Trypanosoma equiperdum

    PubMed Central

    Cuypers, Bart; Van den Broeck, Frederik; Van Reet, Nick; Meehan, Conor J.; Cauchard, Julien; Wilkes, Jonathan M.; Claes, Filip; Goddeeris, Bruno; Birhanu, Hadush; Dujardin, Jean-Claude; Laukens, Kris; Büscher, Philippe

    2017-01-01

    Abstract Trypanosomes cause a variety of diseases in man and domestic animals in Africa, Latin America, and Asia. In the Trypanozoon subgenus, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense cause human African trypanosomiasis, whereas Trypanosoma brucei brucei, Trypanosoma evansi, and Trypanosoma equiperdum are responsible for nagana, surra, and dourine in domestic animals, respectively. The genetic relationships between T. evansi and T. equiperdum and other Trypanozoon species remain unclear because the majority of phylogenetic analyses has been based on only a few genes. In this study, we have conducted a phylogenetic analysis based on genome-wide SNP analysis comprising 56 genomes from the Trypanozoon subgenus. Our data reveal that T. equiperdum has emerged at least once in Eastern Africa and T. evansi at two independent occasions in Western Africa. The genomes within the T. equiperdum and T. evansi monophyletic clusters show extremely little variation, probably due to the clonal spread linked to the independence from tsetse flies for their transmission. PMID:28541535

  6. Problems at the Leading Edge of Space Weathering as Revealed by TEM Combined with Surface Science Techniques

    NASA Technical Reports Server (NTRS)

    Christoffersen, R.; Dukes, C. A.; Keller, L. P.; Rahman, Z.; Baragiola, R. A.

    2015-01-01

    Both transmission electron micros-copy (TEM) and surface analysis techniques such as X-ray photoelectron spectroscopy (XPS) were instrumen-tal in making the first characterizations of material generated by space weathering in lunar samples [1,2]. Without them, the nature of nanophase metallic Fe (npFe0) correlated with the surface of lunar regolith grains would have taken much longer to become rec-ognized and understood. Our groups at JSC and UVa have been using both techniques in a cross-correlated way to investigate how the solar wind contributes to space weathering [e.g., 3]. These efforts have identified a number of ongoing problems and knowledge gaps. Key insights made by UVa group leader Raul Barag-iola during this work are gratefully remembered.

  7. Gene array analysis reveals a common Runx transcriptional program controlling cell adhesion and survival

    PubMed Central

    Wotton, Sandy; Terry, Anne; Kilbey, Anna; Jenkins, Alma; Herzyk, Pawel; Cameron, Ewan; Neil, James C.

    2008-01-01

    The Runx genes play divergent roles in development and cancer, where they can act either as oncogenes or tumour suppressors. We compared the effects of ectopic Runx expression in established fibroblasts, where all three genes produce an indistinguishable phenotype entailing epithelioid morphology and increased cell survival under stress conditions. Gene array analysis revealed a strongly overlapping transcriptional signature, with no examples of opposing regulation of the same target gene. A common set of 50 highly regulated genes was identified after further filtering on regulation by inducible RUNX1-ER. This set revealed a strong bias towards genes with annotated roles in cancer and development, and a preponderance of targets encoding extracellular or surface proteins, reflecting the marked effects of Runx on cell adhesion. Furthermore, in silico prediction of resistance to glucocorticoid growth inhibition was confirmed in fibroblasts and lymphoid cells expressing ectopic Runx. The effects of fibroblast expression of common RUNX1 fusion oncoproteins (RUNX1-ETO, TEL-RUNX1, CBFB-MYH11) were also tested. While two direct Runx activation target genes were repressed (Ncam1, Rgc32), the fusion proteins appeared to disrupt regulation of down-regulated targets (Cebpd, Id2, Rgs2) rather than impose constitutive repression. These results elucidate the oncogenic potential of the Runx family and reveal novel targets for therapeutic inhibition. PMID:18560354

  8. Fibrotic-like changes in degenerate human intervertebral discs revealed by quantitative proteomic analysis.

    PubMed

    Yee, A; Lam, M P Y; Tam, V; Chan, W C W; Chu, I K; Cheah, K S E; Cheung, K M C; Chan, D

    2016-03-01

    Intervertebral disc degeneration (IDD) can lead to symptomatic conditions including sciatica and back pain. The purpose of this study is to understand the extracellular matrix (ECM) changes in disc biology through comparative proteomic analysis of degenerated and non-degenerated human intervertebral disc (IVD) tissues of different ages. Seven non-degenerated (11-46 years of age) and seven degenerated (16-53 years of age) annulus fibrosus (AF) and nucleus pulposus (NP) samples were used. Proteins were extracted using guanidine hydrochloride, separated from large proteoglycans (PGs) by caesium chloride (CsCl) density gradient ultracentrifugation, and identified using liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS). For quantitative comparison, proteins were labeled with iTRAQ reagents. Collagen fibrils in the NP were assessed using scanning electron microscopy (SEM). In the AF, quantitative analysis revealed increased levels of HTRA1, COMP and CILP in degeneration when compared with samples from older individuals. Fibronectin showed increment with age and degeneration. In the NP, more CILP and CILP2 were present in degenerated samples of younger individuals. Reduced protein solubility was observed in degenerated and older non-degenerated samples correlated with an accumulation of type I collagen in the insoluble fibers. Characterization of collagen fibrils in the NP revealed smaller mean fibril diameters and decreased porosity in the degenerated samples. Our study identified distinct matrix changes associated with aging and degeneration in the intervertebral discs (IVDs). The nature of the ECM changes, together with observed decreased in solubility and changes in fibril diameter is consistent with a fibrotic-like environment. Copyright © 2015 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

  9. Network analysis reveals disrupted functional brain circuitry in drug-naive social anxiety disorder.

    PubMed

    Yang, Xun; Liu, Jin; Meng, Yajing; Xia, Mingrui; Cui, Zaixu; Wu, Xi; Hu, Xinyu; Zhang, Wei; Gong, Gaolang; Gong, Qiyong; Sweeney, John A; He, Yong

    2017-12-07

    Social anxiety disorder (SAD) is a common and disabling condition characterized by excessive fear and avoidance of public scrutiny. Psychoradiology studies have suggested that the emotional and behavior deficits in SAD are associated with abnormalities in regional brain function and functional connectivity. However, little is known about whether intrinsic functional brain networks in patients with SAD are topologically disrupted. Here, we collected resting-state fMRI data from 33 drug-naive patients with SAD and 32 healthy controls (HC), constructed functional networks with 34 predefined regions based on previous meta-analytic research with task-based fMRI in SAD, and performed network-based statistic and graph-theory analyses. The network-based statistic analysis revealed a single connected abnormal circuitry including the frontolimbic circuit (termed the "fear circuit", including the dorsolateral prefrontal cortex, ventral medial prefrontal cortex and insula) and posterior cingulate/occipital areas supporting perceptual processing. In this single altered network, patients with SAD had higher functional connectivity than HC. At the global level, graph-theory analysis revealed that the patients exhibited a lower normalized characteristic path length than HC, which suggests a disorder-related shift of network topology toward randomized configurations. SAD-related deficits in nodal degree, efficiency and participation coefficient were detected in the parahippocampal gyrus, posterior cingulate cortex, dorsolateral prefrontal cortex, insula and the calcarine sulcus. Aspects of abnormal connectivity were associated with anxiety symptoms. These findings highlight the aberrant topological organization of functional brain network organization in SAD, which provides insights into the neural mechanisms underlying excessive fear and avoidance of social interactions in patients with debilitating social anxiety. Copyright © 2017. Published by Elsevier Inc.

  10. Local Fine Structural Insight into Mechanism of Electrochemical Passivation of Titanium.

    PubMed

    Wang, Lu; Yu, Hongying; Wang, Ke; Xu, Haisong; Wang, Shaoyang; Sun, Dongbai

    2016-07-20

    Electrochemically formed passive film on titanium in 1.0 M H2SO4 solution and its thickness, composition, chemical state, and local fine structure are examined by Auger electron spectroscopy (AES), X-ray photoelectron spectroscopy (XPS), and X-ray absorption fine structure. AES analysis reveals that the thickness and composition of oxide film are proportional to the reciprocal of current density in potentiodynamic polarization. XPS depth profiles of the chemical states of titanium exhibit the coexistence of various valences cations in the surface. Quantitative X-ray absorption near edge structure analysis of the local electronic structure of the topmost surface (∼5.0 nm) shows that the ratio of [TiO2]/[Ti2O3] is consistent with that of passivation/dissolution of electrochemical activity. Theoretical calculation and analysis of extended X-ray absorption fine structure spectra at Ti K-edge indicate that both the structures of passivation and dissolution are distorted caused by the appearance of two different sites of Ti-O and Ti-Ti. And the bound water in the topmost surface plays a vital role in structural disorder confirmed by XPS. Overall, the increase of average Ti-O coordination causes the electrochemical passivation, and the dissolution is due to the decrease of average Ti-Ti coordination. The structural variations of passivation in coordination number and interatomic distance are in good agreement with the prediction of point defect model.

  11. Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas.

    PubMed

    Beltrami, Caroline Moraes; Dos Reis, Mariana Bisarro; Barros-Filho, Mateus Camargo; Marchi, Fabio Albuquerque; Kuasne, Hellen; Pinto, Clóvis Antônio Lopes; Ambatipudi, Srikant; Herceg, Zdenko; Kowalski, Luiz Paulo; Rogatto, Silvia Regina

    2017-01-01

    Papillary thyroid carcinoma (PTC) is a common endocrine neoplasm with a recent increase in incidence in many countries. Although PTC has been explored by gene expression and DNA methylation studies, the regulatory mechanisms of the methylation on the gene expression was poorly clarified. In this study, DNA methylation profile (Illumina HumanMethylation 450K) of 41 PTC paired with non-neoplastic adjacent tissues (NT) was carried out to identify and contribute to the elucidation of the role of novel genic and intergenic regions beyond those described in the promoter and CpG islands (CGI). An integrative and cross-validation analysis were performed aiming to identify molecular drivers and pathways that are PTC-related. The comparisons between PTC and NT revealed 4995 methylated probes (88% hypomethylated in PTC) and 1446 differentially expressed transcripts cross-validated by the The Cancer Genome Atlas data. The majority of these probes was found in non-promoters regions, distant from CGI and enriched by enhancers. The integrative analysis between gene expression and DNA methylation revealed 185 and 38 genes (mainly in the promoter and body regions, respectively) with negative and positive correlation, respectively. Genes showing negative correlation underlined FGF and retinoic acid signaling as critical canonical pathways disrupted by DNA methylation in PTC. BRAF mutation was detected in 68% (28 of 41) of the tumors, which presented a higher level of demethylation (95% hypomethylated probes) compared with BRAF wild-type tumors. A similar integrative analysis uncovered 40 of 254 differentially expressed genes, which are potentially regulated by DNA methylation in BRAF V600E-positive tumors. The methylation and expression pattern of six selected genes ( ERBB3 , FGF1 , FGFR2 , GABRB2 , HMGA2 , and RDH5 ) were confirmed as altered by pyrosequencing and RT-qPCR. DNA methylation loss in non-promoter, poor CGI and enhancer-enriched regions was a significant event in PTC

  12. Sexual dimorphic floral development in dioecious plants revealed by transcriptome, phytohormone, and DNA methylation analysis in Populus tomentosa.

    PubMed

    Song, Yuepeng; Ma, Kaifeng; Ci, Dong; Chen, Qingqing; Tian, Jiaxing; Zhang, Deqiang

    2013-12-01

    Dioecious plants have evolved sex-specific floral development mechanisms. However, the precise gene expression patterns in dioecious plant flower development remain unclear. Here, we used andromonoecious poplar, an exceptional model system, to eliminate the confounding effects of genetic background of dioecious plants. Comparative transcriptome and physiological analysis allowed us to characterize sex-specific development of female and male flowers. Transcriptome analysis identified genes significantly differentially expressed between the sexes, including genes related to floral development, phytohormone synthesis and metabolism, and DNA methylation. Correlation analysis revealed a significant correlation between phytohormone signaling and gene expression, identifying specific phytohormone-responsive genes and their cis-regulatory elements. Two genes related to DNA methylation, METHYLTRANSFERASE1 (MET1) and DECREASED DNA METHYLATION 1 (DDM1), which are located in the sex determination region of Chromosome XIX, have differential expression between female and male flowers. A time-course analysis revealed that MET1 and DDM1 expression may produce different DNA methylation levels in female and male flowers. Understanding the interactions of phytohormone signaling, DNA methylation and target gene expression should lead to a better understanding of sexual differences in floral development. Thus, this study identifies a set of candidate genes for further studies of poplar sexual dimorphism and relates sex-specific floral development to physiological and epigenetic changes.

  13. Whole-Genome Analysis Reveals that Mutations in Inositol Polyphosphate Phosphatase-like 1 Cause Opsismodysplasia

    PubMed Central

    Below, Jennifer E.; Earl, Dawn L.; Shively, Kathryn M.; McMillin, Margaret J.; Smith, Joshua D.; Turner, Emily H.; Stephan, Mark J.; Al-Gazali, Lihadh I.; Hertecant, Jozef L.; Chitayat, David; Unger, Sheila; Cohn, Daniel H.; Krakow, Deborah; Swanson, James M.; Faustman, Elaine M.; Shendure, Jay; Nickerson, Deborah A.; Bamshad, Michael J.

    2013-01-01

    Opsismodysplasia is a rare, autosomal-recessive skeletal dysplasia characterized by short stature, characteristic facial features, and in some cases severe renal phosphate wasting. We used linkage analysis and whole-genome sequencing of a consanguineous trio to discover that mutations in inositol polyphosphate phosphatase-like 1 (INPPL1) cause opsismodysplasia with or without renal phosphate wasting. Evaluation of 12 families with opsismodysplasia revealed that INPPL1 mutations explain ∼60% of cases overall, including both of the families in our cohort with more than one affected child and 50% of the simplex cases. PMID:23273567

  14. Genome-wide DNA methylation analysis reveals estrogen-mediated epigenetic repression of metallothionein-1 gene cluster in breast cancer.

    PubMed

    Jadhav, Rohit R; Ye, Zhenqing; Huang, Rui-Lan; Liu, Joseph; Hsu, Pei-Yin; Huang, Yi-Wen; Rangel, Leticia B; Lai, Hung-Cheng; Roa, Juan Carlos; Kirma, Nameer B; Huang, Tim Hui-Ming; Jin, Victor X

    2015-01-01

    Recent genome-wide analysis has shown that DNA methylation spans long stretches of chromosome regions consisting of clusters of contiguous CpG islands or gene families. Hypermethylation of various gene clusters has been reported in many types of cancer. In this study, we conducted methyl-binding domain capture (MBDCap) sequencing (MBD-seq) analysis on a breast cancer cohort consisting of 77 patients and 10 normal controls, as well as a panel of 38 breast cancer cell lines. Bioinformatics analysis determined seven gene clusters with a significant difference in overall survival (OS) and further revealed a distinct feature that the conservation of a large gene cluster (approximately 70 kb) metallothionein-1 (MT1) among 45 species is much lower than the average of all RefSeq genes. Furthermore, we found that DNA methylation is an important epigenetic regulator contributing to gene repression of MT1 gene cluster in both ERα positive (ERα+) and ERα negative (ERα-) breast tumors. In silico analysis revealed much lower gene expression of this cluster in The Cancer Genome Atlas (TCGA) cohort for ERα + tumors. To further investigate the role of estrogen, we conducted 17β-estradiol (E2) and demethylating agent 5-aza-2'-deoxycytidine (DAC) treatment in various breast cancer cell types. Cell proliferation and invasion assays suggested MT1F and MT1M may play an anti-oncogenic role in breast cancer. Our data suggests that DNA methylation in large contiguous gene clusters can be potential prognostic markers of breast cancer. Further investigation of these clusters revealed that estrogen mediates epigenetic repression of MT1 cluster in ERα + breast cancer cell lines. In all, our studies identify thousands of breast tumor hypermethylated regions for the first time, in particular, discovering seven large contiguous hypermethylated gene clusters.

  15. Towards the preparation of realistic model Ziegler-Natta catalysts: XPS study of the MgCl 2/TiCl 4 interaction with flat SiO 2/Si(1 0 0)

    NASA Astrophysics Data System (ADS)

    Siokou, Angeliki; Ntais, Spyridon

    2003-08-01

    Despite of the wide use of supported Ti based Ziegler-Natta catalysts in the olefin polymerization industry, questions concerning the role of each one of the catalyst components in the polymerization process, have not found a satisfactory answer yet. This is mainly because of the high sensitivity of these systems to oxygen and atmospheric moisture that makes their study in an atomic level rather complicated. Realistic surface science models of the pre-activated SiO 2 supported MgCl 2/TiCl 4 and TiCl 4 Ziegler-Natta catalysts were prepared by spin coating on flat conductive SiO 2/Si(1 0 0) supports under inert atmosphere. This preparation technique resembles the wet chemical impregnation which is the industrial method of the catalyst preparation. XPS analysis showed that the catalyst precursor anchors on the silica surface through bonding of the Ti atoms with surface silanes or siloxanes, while Mg is attached to the Ti through chlorine bridges. Thermal treatment of the catalysts at 723 K leads to total Cl desorption when MgCl 2 is not present while a significant amount of the Ti atoms is reduced to the Ti 3+ state.

  16. Intestinal transcriptome analysis revealed differential salinity adaptation between two tilapiine species.

    PubMed

    Ronkin, Dana; Seroussi, Eyal; Nitzan, Tali; Doron-Faigenboim, Adi; Cnaani, Avner

    2015-03-01

    Tilapias are a group of freshwater species, which vary in their ability to adapt to high salinity water. Osmotic regulation in fish is conducted mainly in the gills, kidney, and gastrointestinal tract (GIT). The mechanisms involved in ion and water transport through the GIT is not well-characterized, with only a few described complexes. Comparing the transcriptome of the anterior and posterior intestinal sections of a freshwater and saltwater adapted fish by deep-sequencing, we examined the salinity adaptation of two tilapia species: the high salinity-tolerant Oreochromis mossambicus (Mozambique tilapia), and the less salinity-tolerant Oreochromis niloticus (Nile tilapia). This comparative analysis revealed high similarity in gene expression response to salinity change between species in the posterior intestine and large differences in the anterior intestine. Furthermore, in the anterior intestine 68 genes were saltwater up-regulated in one species and down-regulated in the other species (47 genes up-regulated in O. niloticus and down-regulated in O. mossambicus, with 21 genes showing the reverse pattern). Gene ontology (GO) analysis showed a high proportion of transporter and ion channel function among these genes. The results of this study point to a group of genes that differed in their salinity-dependent regulation pattern in the anterior intestine as potentially having a role in the differential salinity tolerance of these two closely related species. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Global Analysis Reveals the Complexity of the Human Glomerular Extracellular Matrix

    PubMed Central

    Byron, Adam; Humphries, Jonathan D.; Randles, Michael J.; Carisey, Alex; Murphy, Stephanie; Knight, David; Brenchley, Paul E.; Zent, Roy; Humphries, Martin J.

    2014-01-01

    The glomerulus contains unique cellular and extracellular matrix (ECM) components, which are required for intact barrier function. Studies of the cellular components have helped to build understanding of glomerular disease; however, the full composition and regulation of glomerular ECM remains poorly understood. We used mass spectrometry-based proteomics of enriched ECM extracts for a global analysis of human glomerular ECM in vivo and identified a tissue-specific proteome of 144 structural and regulatory ECM proteins. This catalog includes all previously identified glomerular components plus many new and abundant components. Relative protein quantification showed a dominance of collagen IV, collagen I, and laminin isoforms in the glomerular ECM together with abundant collagen VI and TINAGL1. Protein network analysis enabled the creation of a glomerular ECM interactome, which revealed a core of highly connected structural components. More than one half of the glomerular ECM proteome was validated using colocalization studies and data from the Human Protein Atlas. This study yields the greatest number of ECM proteins relative to previous investigations of whole glomerular extracts, highlighting the importance of sample enrichment. It also shows that the composition of glomerular ECM is far more complex than previously appreciated and suggests that many more ECM components may contribute to glomerular development and disease processes. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000456. PMID:24436468

  18. Flame retardancy and thermal behavior of intumescent flame-retardant EVA composites with an efficient triazine-based charring agent

    NASA Astrophysics Data System (ADS)

    Xu, Bo; Ma, Wen; Wu, Xiao; Qian, Lijun; Jiang, Shan

    2018-04-01

    Intumescent flame retardant (IFR) EVA composites were prepared based on a hyperbranched triazine charring-foaming agent (HTCFA) and ammonium polyphosphate (APP). The synergistic effect of HTCFA and APP on the flame retardancy and thermal behavior of the composites were investigated through flammability tests, cone calorimeter measurements, thermogravimetric analysis (TGA) including evolved gas analysis (TG-IR) and residue analysis (Fourier transform infrared (FTIR), laser Raman spectroscopy (LRS), x-ray Photoelectron Spectroscopy (XPS) and scanning electron microscopy (SEM)). The flammability test results showed HTCFA/APP (1/3) system presented the best synergistic effect in flame-retardant EVA composites with the highest LOI value and UL-94 V-0 rating. As for cone calorimeter results, IFR changed the combustion behavior of EVA and resulted in remarkable decrease of flammability and smoke product. TGA results showed the synergistic effect between APP and HTCFA could strengthen the char-forming ability of composites. TG-IR results indicated the melt viscosities and gas release with increasing temperature were well-correlated for EVA/IFR composite. The residue analysis results from SEM, LRS, FT-IR and XPS revealed IFR promoted forming more compact graphitic char layer, connected by rich P–O–C and P–N structures.

  19. XPS-nanocharacterization of organic layers electrochemically grafted on the surface of SnO2 thin films to produce a new hybrid material coating

    NASA Astrophysics Data System (ADS)

    Drevet, R.; Dragoé, D.; Barthés-Labrousse, M. G.; Chaussé, A.; Andrieux, M.

    2016-10-01

    This work presents the synthesis and the characterization of hybrid material thin films obtained by the combination of two processes. The electrochemical grafting of organic layers made of carboxyphenyl moieties is carried out from the reduction of a diazonium salt on tin dioxide (SnO2) thin films previously deposited on Si substrates by metal organic chemical vapor deposition (MOCVD). Since the MOCVD experimental parameters impact the crystal growth of the SnO2 layer (i.e. its morphology and its texturation), various electrochemical grafting models can occur, producing different hybrid materials. In order to evidence the efficiency of the electrochemical grafting of the carboxyphenyl moieties, X-ray Photoelectron Spectroscopy (XPS) is used to characterize the first nanometers in depth of the synthesized hybrid material layer. Then three electrochemical grafting models are proposed.

  20. Band line-up determination at p- and n-type Al/4H-SiC Schottky interfaces using photoemission spectroscopy

    NASA Astrophysics Data System (ADS)

    Kohlscheen, J.; Emirov, Y. N.; Beerbom, M. M.; Wolan, J. T.; Saddow, S. E.; Chung, G.; MacMillan, M. F.; Schlaf, R.

    2003-09-01

    The band lineup of p- and n-type 4H-SiC/Al interfaces was determined using x-ray photoemission spectroscopy (XPS). Al was deposited in situ on ex situ cleaned SiC substrates in several steps starting at 1.2 Å up to 238 Å nominal film thickness. Before growth and after each growth step, the sample surface was characterized in situ by XPS. The analysis of the spectral shifts indicated that during the initial deposition stages the Al films react with the ambient surface contamination layer present on the samples after insertion into vacuum. At higher coverage metallic Al clusters are formed. The band lineups were determined from the analysis of the core level peak shifts and the positions of the valence bands maxima (VBM) depending on the Al overlayer thickness. Shifts of the Si 2p and C 1s XPS core levels occurred to higher (lower) binding energy for the p-(n-)type substrates, which was attributed to the occurrence of band bending due to Fermi-level equilibration at the interface. The hole injection barrier at the p-type interface was determined to be 1.83±0.1 eV, while the n-type interface revealed an electron injection barrier of 0.98±0.1 eV. Due to the weak features in the SiC valence bands measured by XPS, the VBM positions were determined using the Si 2p peak positions. This procedure required the determination of the Si 2p-to-VBM binding energy difference (99.34 eV), which was obtained from additional measurements.

  1. Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication

    PubMed Central

    Speller, Camilla F.; Kemp, Brian M.; Wyatt, Scott D.; Monroe, Cara; Lipe, William D.; Arndt, Ursula M.; Yang, Dongya Y.

    2010-01-01

    Although the cultural and nutritive importance of the turkey (Meleagris gallopavo) to precontact Native Americans and contemporary people worldwide is clear, little is known about the domestication of this bird compared to other domesticates. Mitochondrial DNA analysis of 149 turkey bones and 29 coprolites from 38 archaeological sites (200 BC–AD 1800) reveals a unique domesticated breed in the precontact Southwestern United States. Phylogeographic analyses indicate that this domestic breed originated from outside the region, but rules out the South Mexican domestic turkey (Meleagris gallopavo gallopavo) as a progenitor. A strong genetic bottleneck within the Southwest turkeys also reflects intensive human selection and breeding. This study points to at least two occurrences of turkey domestication in precontact North America and illuminates the intensity and sophistication of New World animal breeding practices. PMID:20133614

  2. Molecular evolution and diversification of snake toxin genes, revealed by analysis of intron sequences.

    PubMed

    Fujimi, T J; Nakajyo, T; Nishimura, E; Ogura, E; Tsuchiya, T; Tamiya, T

    2003-08-14

    The genes encoding erabutoxin (short chain neurotoxin) isoforms (Ea, Eb, and Ec), LsIII (long chain neurotoxin) and a novel long chain neurotoxin pseudogene were cloned from a Laticauda semifasciata genomic library. Short and long chain neurotoxin genes were also cloned from the genome of Laticauda laticaudata, a closely related species of L. semifasciata, by PCR. A putative matrix attached region (MAR) sequence was found in the intron I of the LsIII gene. Comparative analysis of 11 structurally relevant snake toxin genes (three-finger-structure toxins) revealed the molecular evolution of these toxins. Three-finger-structure toxin genes diverged from a common ancestor through two types of evolutionary pathways (long and short types), early in the course of evolution. At a later stage of evolution in each gene, the accumulation of mutations in the exons, especially exon II, by accelerated evolution may have caused the increased diversification in their functions. It was also revealed that the putative MAR sequence found in the LsIII gene was integrated into the gene after the species-level divergence.

  3. Network analysis of oyster transcriptome revealed a cascade of cellular responses during recovery after heat shock.

    PubMed

    Zhang, Lingling; Hou, Rui; Su, Hailin; Hu, Xiaoli; Wang, Shi; Bao, Zhenmin

    2012-01-01

    Oysters, as a major group of marine bivalves, can tolerate a wide range of natural and anthropogenic stressors including heat stress. Recent studies have shown that oysters pretreated with heat shock can result in induced heat tolerance. A systematic study of cellular recovery from heat shock may provide insights into the mechanism of acquired thermal tolerance. In this study, we performed the first network analysis of oyster transcriptome by reanalyzing microarray data from a previous study. Network analysis revealed a cascade of cellular responses during oyster recovery after heat shock and identified responsive gene modules and key genes. Our study demonstrates the power of network analysis in a non-model organism with poor gene annotations, which can lead to new discoveries that go beyond the focus on individual genes.

  4. Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues.

    PubMed

    Kadoki, Motohiko; Patil, Ashwini; Thaiss, Cornelius C; Brooks, Donald J; Pandey, Surya; Deep, Deeksha; Alvarez, David; von Andrian, Ulrich H; Wagers, Amy J; Nakai, Kenta; Mikkelsen, Tarjei S; Soumillon, Magali; Chevrier, Nicolas

    2017-10-05

    A fundamental challenge in immunology is to decipher the principles governing immune responses at the whole-organism scale. Here, using a comparative infection model, we observe immune signal propagation within and between organs to obtain a dynamic map of immune processes at the organism level. We uncover two inter-organ mechanisms of protective immunity mediated by soluble and cellular factors. First, analyzing ligand-receptor connectivity across tissues reveals that type I IFNs trigger a whole-body antiviral state, protecting the host within hours after skin vaccination. Second, combining parabiosis, single-cell analyses, and gene knockouts, we uncover a multi-organ web of tissue-resident memory T cells that functionally adapt to their environment to stop viral spread across the organism. These results have implications for manipulating tissue-resident memory T cells through vaccination and open up new lines of inquiry for the analysis of immune responses at the organism level. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Pretreatment and integrated analysis of spectral data reveal seaweed similarities based on chemical diversity.

    PubMed

    Wei, Feifei; Ito, Kengo; Sakata, Kenji; Date, Yasuhiro; Kikuchi, Jun

    2015-03-03

    Extracting useful information from high dimensionality and large data sets is a major challenge for data-driven approaches. The present study was aimed at developing novel integrated analytical strategies for comprehensively characterizing seaweed similarities based on chemical diversity. The chemical compositions of 107 seaweed and 2 seagrass samples were analyzed using multiple techniques, including Fourier transform infrared (FT-IR) and solid- and solution-state nuclear magnetic resonance (NMR) spectroscopy, thermogravimetry-differential thermal analysis (TG-DTA), inductively coupled plasma-optical emission spectrometry (ICP-OES), CHNS/O total elemental analysis, and isotope ratio mass spectrometry (IR-MS). The spectral data were preprocessed using non-negative matrix factorization (NMF) and NMF combined with multivariate curve resolution-alternating least-squares (MCR-ALS) methods in order to separate individual component information from the overlapping and/or broad spectral peaks. Integrated analysis of the preprocessed chemical data demonstrated distinct discrimination of differential seaweed species. Further network analysis revealed a close correlation between the heavy metal elements and characteristic components of brown algae, such as cellulose, alginic acid, and sulfated mucopolysaccharides, providing a componential basis for its metal-sorbing potential. These results suggest that this integrated analytical strategy is useful for extracting and identifying the chemical characteristics of diverse seaweeds based on large chemical data sets, particularly complicated overlapping spectral data.

  6. RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize

    PubMed Central

    Ren, Wen; Yang, Fengling; He, Hang; Zhao, Jiuran

    2015-01-01

    The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signal transduction pathway that is involved in plant development and stress responses. As the first component of this phosphorelay cascade, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascade to promote the appropriate cellular responses; however, the functions of MAPKKKs in maize are unclear. Here, we identified 71 MAPKKK genes, of which 14 were novel, based on a computational analysis of the maize (Zea mays L.) genome. Using an RNA-seq analysis in the leaf, stem and root of maize under well-watered and drought-stress conditions, we identified 5,866 differentially expressed genes (DEGs), including 8 MAPKKK genes responsive to drought stress. Many of the DEGs were enriched in processes such as drought stress, abiotic stimulus, oxidation-reduction, and metabolic processes. The other way round, DEGs involved in processes such as oxidation, photosynthesis, and starch, proline, ethylene, and salicylic acid metabolism were clearly co-expressed with the MAPKKK genes. Furthermore, a quantitative real-time PCR (qRT-PCR) analysis was performed to assess the relative expression levels of MAPKKKs. Correlation analysis revealed that there was a significant correlation between expression levels of two MAPKKKs and relative biomass responsive to drought in 8 inbred lines. Our results indicate that MAPKKKs may have important regulatory functions in drought tolerance in maize. PMID:26599013

  7. Network-based diffusion analysis reveals cultural transmission of lobtail feeding in humpback whales.

    PubMed

    Allen, Jenny; Weinrich, Mason; Hoppitt, Will; Rendell, Luke

    2013-04-26

    We used network-based diffusion analysis to reveal the cultural spread of a naturally occurring foraging innovation, lobtail feeding, through a population of humpback whales (Megaptera novaeangliae) over a period of 27 years. Support for models with a social transmission component was 6 to 23 orders of magnitude greater than for models without. The spatial and temporal distribution of sand lance, a prey species, was also important in predicting the rate of acquisition. Our results, coupled with existing knowledge about song traditions, show that this species can maintain multiple independently evolving traditions in its populations. These insights strengthen the case that cetaceans represent a peak in the evolution of nonhuman culture, independent of the primate lineage.

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

    Unuigbe, David M.; Harting, Margit; Jonah, Emmanuel O.

    The presence of native oxide on the surface of silicon nanoparticles is known to inhibit charge transport on the surfaces. Scanning electron microscopy (SEM) studies reveal that the particles in the printed silicon network have a wide range of sizes and shapes. High-resolution transmission electron microscopy reveals that the particle surfaces have mainly the (111)- and (100)-oriented planes which stabilizes against further oxidation of the particles. X-ray absorption spectroscopy (XANES) and X-ray photoelectron spectroscopy (XPS) measurements at the O 1s-edge have been utilized to study the oxidation and local atomic structure of printed layers of silicon nanoparticles which were milledmore » for different times. XANES results reveal the presence of the +4 (SiO 2) oxidation state which tends towards the +2 (SiO) state for higher milling times. Si 2pXPS results indicate that the surfaces of the silicon nanoparticles in the printed layers are only partially oxidized and that all three sub-oxide, +1 (Si 2O), +2 (SiO) and +3 (Si 2O 3), states are present. The analysis of the change in the sub-oxide peaks of the silicon nanoparticles shows the dominance of the +4 state only for lower milling times.« less

  9. Investigation of nanoparticulate silicon as printed layers using scanning electron microscopy, transmission electron microscopy, X-ray absorption spectroscopy and X-ray photoelectron spectroscopy

    DOE PAGES

    Unuigbe, David M.; Harting, Margit; Jonah, Emmanuel O.; ...

    2017-08-21

    The presence of native oxide on the surface of silicon nanoparticles is known to inhibit charge transport on the surfaces. Scanning electron microscopy (SEM) studies reveal that the particles in the printed silicon network have a wide range of sizes and shapes. High-resolution transmission electron microscopy reveals that the particle surfaces have mainly the (111)- and (100)-oriented planes which stabilizes against further oxidation of the particles. X-ray absorption spectroscopy (XANES) and X-ray photoelectron spectroscopy (XPS) measurements at the O 1s-edge have been utilized to study the oxidation and local atomic structure of printed layers of silicon nanoparticles which were milledmore » for different times. XANES results reveal the presence of the +4 (SiO 2) oxidation state which tends towards the +2 (SiO) state for higher milling times. Si 2pXPS results indicate that the surfaces of the silicon nanoparticles in the printed layers are only partially oxidized and that all three sub-oxide, +1 (Si 2O), +2 (SiO) and +3 (Si 2O 3), states are present. The analysis of the change in the sub-oxide peaks of the silicon nanoparticles shows the dominance of the +4 state only for lower milling times.« less

  10. Quantitative flux analysis reveals folate-dependent NADPH production

    NASA Astrophysics Data System (ADS)

    Fan, Jing; Ye, Jiangbin; Kamphorst, Jurre J.; Shlomi, Tomer; Thompson, Craig B.; Rabinowitz, Joshua D.

    2014-06-01

    ATP is the dominant energy source in animals for mechanical and electrical work (for example, muscle contraction or neuronal firing). For chemical work, there is an equally important role for NADPH, which powers redox defence and reductive biosynthesis. The most direct route to produce NADPH from glucose is the oxidative pentose phosphate pathway, with malic enzyme sometimes also important. Although the relative contribution of glycolysis and oxidative phosphorylation to ATP production has been extensively analysed, similar analysis of NADPH metabolism has been lacking. Here we demonstrate the ability to directly track, by liquid chromatography-mass spectrometry, the passage of deuterium from labelled substrates into NADPH, and combine this approach with carbon labelling and mathematical modelling to measure NADPH fluxes. In proliferating cells, the largest contributor to cytosolic NADPH is the oxidative pentose phosphate pathway. Surprisingly, a nearly comparable contribution comes from serine-driven one-carbon metabolism, in which oxidation of methylene tetrahydrofolate to 10-formyl-tetrahydrofolate is coupled to reduction of NADP+ to NADPH. Moreover, tracing of mitochondrial one-carbon metabolism revealed complete oxidation of 10-formyl-tetrahydrofolate to make NADPH. As folate metabolism has not previously been considered an NADPH producer, confirmation of its functional significance was undertaken through knockdown of methylenetetrahydrofolate dehydrogenase (MTHFD) genes. Depletion of either the cytosolic or mitochondrial MTHFD isozyme resulted in decreased cellular NADPH/NADP+ and reduced/oxidized glutathione ratios (GSH/GSSG) and increased cell sensitivity to oxidative stress. Thus, although the importance of folate metabolism for proliferating cells has been long recognized and attributed to its function of producing one-carbon units for nucleic acid synthesis, another crucial function of this pathway is generating reducing power.

  11. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

    PubMed Central

    Cenik, Can; Cenik, Elif Sarinay; Byeon, Gun W.; Grubert, Fabian; Candille, Sophie I.; Spacek, Damek; Alsallakh, Bilal; Tilgner, Hagen; Araya, Carlos L.; Tang, Hua; Ricci, Emiliano; Snyder, Michael P.

    2015-01-01

    Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy—many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation. PMID:26297486

  12. Analysis of microdissected neurons by 18O mass spectrometry reveals altered protein expression in Alzheimer's disease

    PubMed Central

    Hashimoto, Masakazu; Bogdanovic, Nenad; Nakagawa, Hiroyuki; Volkmann, Inga; Aoki, Mikio; Winblad, Bengt; Sakai, Jun; Tjernberg, Lars O

    2012-01-01

    Abstract It is evident that the symptoms of Alzheimer's disease (AD) are derived from severe neuronal damage, and especially pyramidal neurons in the hippocampus are affected pathologically. Here, we analysed the proteome of hippocampal neurons, isolated from post-mortem brains by laser capture microdissection. By using 18O labelling and mass spectrometry, the relative expression levels of 150 proteins in AD and controls were estimated. Many of the identified proteins are involved in transcription and nucleotide binding, glycolysis, heat-shock response, microtubule stabilization, axonal transport or inflammation. The proteins showing the most altered expression in AD were selected for immunohistochemical analysis. These analyses confirmed the altered expression levels, and showed in many AD cases a pathological pattern. For comparison, we also analysed hippocampal sections by Western blot. The expression levels found by this method showed poor correlation with the neuron-specific analysis. Hence, we conclude that cell-specific proteome analysis reveals differences in the proteome that cannot be detected by bulk analysis. PMID:21883897

  13. XPS Studies of Doped Polypyrrole Films

    DTIC Science & Technology

    1990-01-25

    XP11 and polymeric, poly(vinylsulfonate) and poly(4- styrensulfonate) anions. Electrostatic interaction between the polymer and the incorporated anions...verbaily, submitted for publication,o3 3S mm ( 2 x2 knjlliep oetor 4w published? "Overhead prolecter Elyes 0 Ne end~~~~~~~ elc oavlblt f te answer Is yes...at characterization with various surface analysis techniques 2 . In the present paper, the authors will describe thL micro- scopic structure of

  14. Comprehensive Gene expression meta-analysis and integrated bioinformatic approaches reveal shared signatures between thrombosis and myeloproliferative disorders

    PubMed Central

    Jha, Prabhash Kumar; Vijay, Aatira; Sahu, Anita; Ashraf, Mohammad Zahid

    2016-01-01

    Thrombosis is a leading cause of morbidity and mortality in patients with myeloproliferative disorders (MPDs), particularly polycythemia vera (PV) and essential thrombocythemia (ET). Despite the attempts to establish a link between them, the shared biological mechanisms are yet to be characterized. An integrated gene expression meta-analysis of five independent publicly available microarray data of the three diseases was conducted to identify shared gene expression signatures and overlapping biological processes. Using INMEX bioinformatic tool, based on combined Effect Size (ES) approaches, we identified a total of 1,157 differentially expressed genes (DEGs) (697 overexpressed and 460 underexpressed genes) shared between the three diseases. EnrichR tool’s rich library was used for comprehensive functional enrichment and pathway analysis which revealed “mRNA Splicing” and “SUMO E3 ligases SUMOylate target proteins” among the most enriched terms. Network based meta-analysis identified MYC and FN1 to be the most highly ranked hub genes. Our results reveal that the alterations in biomarkers of the coagulation cascade like F2R, PROS1, SELPLG and ITGB2 were common between the three diseases. Interestingly, the study has generated a novel database of candidate genetic markers, pathways and transcription factors shared between thrombosis and MPDs, which might aid in the development of prognostic therapeutic biomarkers. PMID:27892526

  15. Predicting vertical phase segregation in polymer-fullerene bulk heterojunction solar cells by free energy analysis.

    PubMed

    Clark, Michael D; Jespersen, Michael L; Patel, Romesh J; Leever, Benjamin J

    2013-06-12

    Blends of poly(3-hexylthiophene) (P3HT) and C61-butyric acid methyl ester (PCBM) are widely used as a model system for bulk heterojunction active layers developed for solution-processable, flexible solar cells. In this work, vertical concentration profiles within the P3HT:PCBM active layer are predicted based on a thermodynamic analysis of the constituent materials and typical solvents. Surface energies of the active layer components and a common transport interlayer blend, poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS), are first extracted using contact angle measurements coupled with the acid-base model. From this data, intra- and interspecies interaction free energies are calculated, which reveal that the thermodynamically favored arrangement consists of a uniformly blended "bulk" structure capped with a P3HT-rich air interface and a slightly PCBM-rich buried interface. Although the "bulk" composition is solely determined by P3HT:PCBM ratio, composition near the buried interface is dependent on both the blend ratio and interaction free energy difference between solvated P3HT and PCBM deposition onto PEDOT:PSS. In contrast, the P3HT-rich overlayer is independent of processing conditions, allowing kinetic formation of a PCBM-rich sublayer during film casting due to limitations in long-range species diffusion. These thermodynamic calculations are experimentally validated by angle-resolved X-ray photoelectron spectroscopy (XPS) and low energy XPS depth profiling, which show that the actual composition profiles of the cast and annealed films closely match the predicted behavior. These experimentally derived profiles provide clear evidence that typical bulk heterojunction active layers are predominantly characterized by thermodynamically stable composition profiles. Furthermore, the predictive capabilities of the comprehensive free energy approach are demonstrated, which will enable investigation of structurally integrated devices and novel active

  16. Determination of equilibrium structures of bromothymol blue revealed by using quantum chemistry with an aid of multivariate analysis of electronic absorption spectra

    NASA Astrophysics Data System (ADS)

    Shimada, Toru; Hasegawa, Takeshi

    2017-10-01

    The pH dependent chemical structures of bromothymol blue (BTB), which have long been under controversy, are determined by employing a combined technique of multivariate analysis of electronic absorption spectra and quantum chemistry. Principle component analysis (PCA) of the pH dependent spectra apparently reveals that only two chemical species are adequate to fully account for the color changes, with which the spectral decomposition is readily performed by using augmented alternative least-squares (ALS) regression analysis. The quantity variation by the ALS analysis also reveals the practical acid dissociation constant, pKa‧. The determination of pKa‧ is performed for various ionic strengths, which reveals the thermodynamic acid constant (pKa = 7.5) and the number of charge on each chemical species; the yellow form is negatively charged species of - 1 and the blue form that of - 2. On this chemical information, the quantum chemical calculation is carried out to find that BTB molecules take the pure quinoid form in an acid solution and the quinoid-phenolate form in an alkaline solution. The time-dependent density functional theory (TD-DFT) calculations for the theoretically determined chemical structures account for the peak shift of the electronic spectra. In this manner, the structures of all the chemical species appeared in equilibrium have finally been confirmed.

  17. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

    PubMed

    Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

    2016-01-12

    Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of

  18. Structural and Biophysical Analysis of BST-2/Tetherin Ectodomains Reveals an Evolutionary Conserved Design to Inhibit Virus Release

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

    Swiecki, M.; Allaire, M.; Scheaffer, S.

    2011-01-28

    BST-2/tetherin is a host antiviral molecule that functions to potently inhibit the release of enveloped viruses from infected cells. In return, viruses have evolved antagonists to this activity. BST-2 traps budding virions by using two separate membrane-anchoring regions that simultaneously incorporate into the host and viral membranes. Here, we detailed the structural and biophysical properties of the full-length BST-2 ectodomain, which spans the two membrane anchors. The 1.6-{angstrom} crystal structure of the complete mouse BST-2 ectodomain reveals an {approx}145-{angstrom} parallel dimer in an extended {alpha}-helix conformation that predominantly forms a coiled coil bridged by three intermolecular disulfides that are requiredmore » for stability. Sequence analysis in the context of the structure revealed an evolutionarily conserved design that destabilizes the coiled coil, resulting in a labile superstructure, as evidenced by solution x-ray scattering displaying bent conformations spanning 150 and 180 {angstrom} for the mouse and human BST-2 ectodomains, respectively. Additionally, crystal packing analysis revealed possible curvature-sensing tetrameric structures that may aid in proper placement of BST-2 during the genesis of viral progeny. Overall, this extended coiled-coil structure with inherent plasticity is undoubtedly necessary to accommodate the dynamics of viral budding while ensuring separation of the anchors.« less

  19. An XPS study of the stability of Fomblin Z25 on the native oxide of aluminum. [x ray photoelectron spectroscopy

    NASA Technical Reports Server (NTRS)

    Herrera-Fierro, Pilar; Pepper, Stephen V.; Jones, William R.

    1991-01-01

    Thin films of Fomblin Z25, a perfluoropolyalkylether lubricant, were vapor deposited onto clean, oxidized aluminum and sapphire surfaces, and their behavior at different temperatures was studied using x ray photoelectron spectroscopy (XPS) and thermal desorption spectroscopy (TDS). It was found that the interfacial fluid molecules decompose on the native oxide at room temperature, and continue to decompose at elevated temperatures, as previous studies had shown to occur on clean metal. TDS indicated that different degradation mechanisms were operative for clean and oxidized aluminum. On sapphire substrates, no reaction was observed at room temperature. Our conclusion is that the native oxide of aluminum is neither passive nor protective towards Fomblin Z25. At high temperatures (150 C) degradation of the polymer on sapphire produced a debris layer at the interface with a chemical composition similar to the one formed on aluminum oxide. Rubbing a Fomblin film on a single crystal sapphire also induced the decomposition of the lubricant in contact with the interface and the formulation of a debris layer.

  20. Distribution of triclosan-resistant genes in major pathogenic microorganisms revealed by metagenome and genome-wide analysis

    PubMed Central

    Khan, Raees; Roy, Nazish; Choi, Kihyuck

    2018-01-01

    The substantial use of triclosan (TCS) has been aimed to kill pathogenic bacteria, but TCS resistance seems to be prevalent in microbial species and limited knowledge exists about TCS resistance determinants in a majority of pathogenic bacteria. We aimed to evaluate the distribution of TCS resistance determinants in major pathogenic bacteria (N = 231) and to assess the enrichment of potentially pathogenic genera in TCS contaminated environments. A TCS-resistant gene (TRG) database was constructed and experimentally validated to predict TCS resistance in major pathogenic bacteria. Genome-wide in silico analysis was performed to define the distribution of TCS-resistant determinants in major pathogens. Microbiome analysis of TCS contaminated soil samples was also performed to investigate the abundance of TCS-resistant pathogens. We experimentally confirmed that TCS resistance could be accurately predicted using genome-wide in silico analysis against TRG database. Predicted TCS resistant phenotypes were observed in all of the tested bacterial strains (N = 17), and heterologous expression of selected TCS resistant genes from those strains conferred expected levels of TCS resistance in an alternative host Escherichia coli. Moreover, genome-wide analysis revealed that potential TCS resistance determinants were abundant among the majority of human-associated pathogens (79%) and soil-borne plant pathogenic bacteria (98%). These included a variety of enoyl-acyl carrier protein reductase (ENRs) homologues, AcrB efflux pumps, and ENR substitutions. FabI ENR, which is the only known effective target for TCS, was either co-localized with other TCS resistance determinants or had TCS resistance-associated substitutions. Furthermore, microbiome analysis revealed that pathogenic genera with intrinsic TCS-resistant determinants exist in TCS contaminated environments. We conclude that TCS may not be as effective against the majority of bacterial pathogens as previously presumed

  1. Enhancing Electrochemical Water-Splitting Kinetics by Polarization-Driven Formation of Near-Surface Iron(0): An In Situ XPS Study on Perovskite-Type Electrodes**

    PubMed Central

    Opitz, Alexander K; Nenning, Andreas; Rameshan, Christoph; Rameshan, Raffael; Blume, Raoul; Hävecker, Michael; Knop-Gericke, Axel; Rupprechter, Günther; Fleig, Jürgen; Klötzer, Bernhard

    2015-01-01

    In the search for optimized cathode materials for high-temperature electrolysis, mixed conducting oxides are highly promising candidates. This study deals with fundamentally novel insights into the relation between surface chemistry and electrocatalytic activity of lanthanum ferrite based electrolysis cathodes. For this means, near-ambient-pressure X-ray photoelectron spectroscopy (NAP-XPS) and impedance spectroscopy experiments were performed simultaneously on electrochemically polarized La0.6Sr0.4FeO3−δ (LSF) thin film electrodes. Under cathodic polarization the formation of Fe0 on the LSF surface could be observed, which was accompanied by a strong improvement of the electrochemical water splitting activity of the electrodes. This correlation suggests a fundamentally different water splitting mechanism in presence of the metallic iron species and may open novel paths in the search for electrodes with increased water splitting activity. PMID:25557533

  2. Large‐scale analysis reveals populational contributions of cortical spike rate and synchrony to behavioural functions

    PubMed Central

    Saiki, Akiko; Fujiwara‐Tsukamoto, Yoko; Sakai, Yutaka; Isomura, Yoshikazu

    2016-01-01

    a population of neuron pairs with spike synchrony does exist, and that some neuron pairs exhibit a dependence on movement phase during task performance. However, the population‐wide analysis revealed that spike synchrony was statistically independent of the movement phase and the spike rate‐based preferences of the pair for behavioural functions, whereas spike rates were clearly dependent on the movement phase. In fact, mutual information analyses revealed that the contribution of spike synchrony to the behavioural functions was small relative to the contribution of spike rate. Our large‐scale analysis revealed that cortical spike rate, rather than spike synchrony, contributes to population coding for movement. PMID:27488936

  3. Large-scale analysis reveals populational contributions of cortical spike rate and synchrony to behavioural functions.

    PubMed

    Kimura, Rie; Saiki, Akiko; Fujiwara-Tsukamoto, Yoko; Sakai, Yutaka; Isomura, Yoshikazu

    2017-01-01

    spike synchrony does exist, and that some neuron pairs exhibit a dependence on movement phase during task performance. However, the population-wide analysis revealed that spike synchrony was statistically independent of the movement phase and the spike rate-based preferences of the pair for behavioural functions, whereas spike rates were clearly dependent on the movement phase. In fact, mutual information analyses revealed that the contribution of spike synchrony to the behavioural functions was small relative to the contribution of spike rate. Our large-scale analysis revealed that cortical spike rate, rather than spike synchrony, contributes to population coding for movement. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

  4. Phenotypic Analysis Reveals that the 2010 Haiti Cholera Epidemic Is Linked to a Hypervirulent Strain

    PubMed Central

    Jones, Christopher J.; Wong, Jennifer; Queen, Jessica; Agarwal, Shivani; Yildiz, Fitnat H.

    2016-01-01

    Vibrio cholerae O1 El Tor strains have been responsible for pandemic cholera since 1961. These strains have evolved over time, spreading globally in three separate waves. Wave 3 is caused by altered El Tor (AET) variant strains, which include the strain with the signature ctxB7 allele that was introduced in 2010 into Haiti, where it caused a devastating epidemic. In this study, we used phenotypic analysis to compare an early isolate from the Haiti epidemic to wave 1 El Tor isolates commonly used for research. It is demonstrated that the Haiti isolate has increased production of cholera toxin (CT) and hemolysin, increased motility, and a reduced ability to form biofilms. This strain also outcompetes common wave 1 El Tor isolates for colonization of infant mice, indicating that it has increased virulence. Monitoring of CT production and motility in additional wave 3 isolates revealed that this phenotypic variation likely evolved over time rather than in a single genetic event. Analysis of available whole-genome sequences and phylogenetic analyses suggested that increased virulence arose from positive selection for mutations found in known and putative regulatory genes, including hns and vieA, diguanylate cyclase genes, and genes belonging to the lysR and gntR regulatory families. Overall, the studies presented here revealed that V. cholerae virulence potential can evolve and that the currently prevalent wave 3 AET strains are both phenotypically distinct from and more virulent than many El Tor isolates. PMID:27297393

  5. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans.

    PubMed

    Cenik, Can; Cenik, Elif Sarinay; Byeon, Gun W; Grubert, Fabian; Candille, Sophie I; Spacek, Damek; Alsallakh, Bilal; Tilgner, Hagen; Araya, Carlos L; Tang, Hua; Ricci, Emiliano; Snyder, Michael P

    2015-11-01

    Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy--many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation. © 2015 Cenik et al.; Published by Cold Spring Harbor Laboratory Press.

  6. Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids.

    PubMed

    Schmitz, Alexander; Fischer, Sabine C; Mattheyer, Christian; Pampaloni, Francesco; Stelzer, Ernst H K

    2017-03-03

    Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid's size and varies between 50% and 75% of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 10 5 to 1 × 10 6  cells/mm 3 . Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture.

  7. Portable total reflection x-ray fluorescence analysis in the identification of unknown laboratory hazards

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

    Liu, Ying, E-mail: liu.ying.48r@st.kyoto-u.ac.jp; Imashuku, Susumu; Sasaki, Nobuharu

    In this study, a portable total reflection x-ray fluorescence (TXRF) spectrometer was used to analyze unknown laboratory hazards that precipitated on exterior surfaces of cooling pipes and fume hood pipes in chemical laboratories. With the aim to examine the accuracy of TXRF analysis for the determination of elemental composition, analytical results were compared with those of wavelength-dispersive x-ray fluorescence spectrometry, scanning electron microscope and energy-dispersive x-ray spectrometry, energy-dispersive x-ray fluorescence spectrometry, inductively coupled plasma atomic emission spectrometry, x-ray diffraction spectrometry (XRD), and x-ray photoelectron spectroscopy (XPS). Detailed comparison of data confirmed that the TXRF method itself was not sufficient tomore » determine all the elements (Z > 11) contained in the samples. In addition, results suggest that XRD should be combined with XPS in order to accurately determine compound composition. This study demonstrates that at least two analytical methods should be used in order to analyze the composition of unknown real samples.« less

  8. Tribological properties and surface chemistry of silicon carbide at temperatures to 1500 C

    NASA Technical Reports Server (NTRS)

    Miyoshi, K.; Buckley, D. H.

    1981-01-01

    Silicon carbide surfaces were heated to 1500 C in a vacuum and analyzed at room temperature with X-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES). The basic unit of the surfaces was considered as a plane of a tetrahedron of either SiC4 and CSi4 composition. AES spectra were obtained from 250-1500 C, with an analysis depth of 1 nm revealed the presence of little Si and mostly graphite. XPS analysis depth was 2 nm or less, and Si was found in the second 1 nm. Sliding friction tests with single-crystal silicon carbide in contact with iron in a vacuum were characterized by a stock-slip value. The coefficient of friction increased with increasing temperature up to 400 C, then decreased with increasing temperature from 400-600 C. Reheating surfaces to 800 C after preheating them to that temperature produced no changes in AES readings. It is concluded that the maximum density of silicon and silicon-carbide is at 800 C, and the higher the sliding temperature, the more metal that is transferred.

  9. Effect of dielectric barrier discharge treatment on surface nanostructure and wettability of polylactic acid (PLA) nonwoven fabrics

    NASA Astrophysics Data System (ADS)

    Ren, Yu; Xu, Lin; Wang, Chunxia; Wang, Xiaona; Ding, Zhirong; Chen, Yuyue

    2017-12-01

    Polylactic acid (PLA) nonwoven fabrics are treated with atmospheric dielectric barrier discharge (DBD) plasma to improve surface wettability. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) show that micro- to nano-scale textures appear on the treated PLA surfaces dependent on the treatment time. X-ray photoelectron spectroscopy (XPS) analysis reveals that the DBD plasma treatments result in decreased carbon contents and increased oxygen contents as well as slightly increased nitrogen contents. The water contact angle decreases sharply with the increase of the DBD plasma treatment time. The super hydrophilic PLA surfaces (the water contact angle reached 0°) are obtained when the treatment time is longer than 90 s. Ninety days after the DBD plasma treatment, the XPS analysis shows that Csbnd O/Csbnd N and Cdbnd O/Osbnd Cdbnd O percentages decline for all treatment groups. However, the water contact angle is kept constant at 0° for the groups treated above 90 s, which could be due to the oxidized nano-structured layer on the DBD plasma treated PLA surfaces.

  10. Chemisorbed monolayers of corannulene penta-thioethers on gold.

    PubMed

    Angelova, Polina; Solel, Ephrath; Parvari, Galit; Turchanin, Andrey; Botoshansky, Mark; Gölzhäuser, Armin; Keinan, Ehud

    2013-02-19

    Penta(tert-butylthio)corannulene and penta(4-dimethylaminophenylthio)corannulene form highly stable monolayers on gold surfaces, as indicated by X-ray photoelectron spectroscopy (XPS). Formation of these homogeneous monolayers involves multivalent coordination of the five sulfur atoms to gold with the peripheral alkyl or aryl substituents pointing away from the surface. No dissociation of C-S bonds upon binding could be observed at room temperature. Yet, the XPS experiments reveal strong chemical bonding between the thioether groups and gold. Temperature-dependent XPS study shows that the thermal stability of the monolayers is higher than the typical stability of self-assembled monolayers (SAMs) of thiolates on gold.

  11. Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs.

    PubMed

    Chao, Tianle; Ji, Zhibin; Hou, Lei; Wang, Jin; Zhang, Chunlan; Wang, Guizhi; Wang, Jianmin

    2018-01-01

    As widely distributed domestic animals, sheep are an important species and the source of mutton. In this study, we aimed to evaluate the regulatory lncRNAs associated with muscle growth and development between high production mutton sheep (Dorper sheep and Qianhua Mutton Merino sheep) and low production mutton sheep (Small-tailed Han sheep). In total, 39 lncRNAs were found to be differentially expressed. Using co-expression analysis and functional annotation, 1,206 co-expression interactions were found between 32 lncRNAs and 369 genes, and 29 of these lncRNAs were found to be associated with muscle development, metabolism, cell proliferation and apoptosis. lncRNA-mRNA interactions revealed 6 lncRNAs as hub lncRNAs. Moreover, three lncRNAs and their associated co-expressed genes were demonstrated by cis-regulatory gene analyses, and we also found a potential regulatory relationship between the pseudogene lncRNA LOC101121401 and its parent gene FTH1. This study provides a genome-wide resolution of lncRNA and mRNA regulation in muscles from mutton sheep.

  12. Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs

    PubMed Central

    Chao, Tianle; Ji, Zhibin; Hou, Lei; Wang, Jin; Zhang, Chunlan

    2018-01-01

    As widely distributed domestic animals, sheep are an important species and the source of mutton. In this study, we aimed to evaluate the regulatory lncRNAs associated with muscle growth and development between high production mutton sheep (Dorper sheep and Qianhua Mutton Merino sheep) and low production mutton sheep (Small-tailed Han sheep). In total, 39 lncRNAs were found to be differentially expressed. Using co-expression analysis and functional annotation, 1,206 co-expression interactions were found between 32 lncRNAs and 369 genes, and 29 of these lncRNAs were found to be associated with muscle development, metabolism, cell proliferation and apoptosis. lncRNA–mRNA interactions revealed 6 lncRNAs as hub lncRNAs. Moreover, three lncRNAs and their associated co-expressed genes were demonstrated by cis-regulatory gene analyses, and we also found a potential regulatory relationship between the pseudogene lncRNA LOC101121401 and its parent gene FTH1. This study provides a genome-wide resolution of lncRNA and mRNA regulation in muscles from mutton sheep. PMID:29666768

  13. Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins

    PubMed Central

    Dallas, David C.; Citerne, Florine; Tian, Tian; Silva, Vitor L. M.; Kalanetra, Karen M.; Frese, Steven A.; Robinson, Randall C.; Mills, David A.; Barile, Daniela

    2015-01-01

    Scope The microorganisms that make up kefir grains are well known for lactose fermentation, but the extent to which they hydrolyze and consume milk proteins remains poorly understood. Peptidomics technologies were used to examine the proteolytic activity of kefir grains on bovine milk proteins. Methods and results Gel electrophoresis revealed substantial digestion of milk proteins by kefir grains, with mass spectrometric analysis showing the release of 609 protein fragments and alteration of the abundance of >1,500 peptides that derived from 27 milk proteins. Kefir contained 25 peptides identified from the literature as having biological activity, including those with antihypertensive, antimicrobial, immunomodulatory, opioid and anti-oxidative functions. 16S rRNA and shotgun metagenomic sequencing identified the principle taxa in the culture as Lactobacillus species. Conclusion The model kefir sample contained thousands of protein fragments released in part by kefir microorganisms and in part by native milk proteases. PMID:26616950

  14. Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins.

    PubMed

    Dallas, David C; Citerne, Florine; Tian, Tian; Silva, Vitor L M; Kalanetra, Karen M; Frese, Steven A; Robinson, Randall C; Mills, David A; Barile, Daniela

    2016-04-15

    The microorganisms that make up kefir grains are well known for lactose fermentation, but the extent to which they hydrolyze and consume milk proteins remains poorly understood. Peptidomics technologies were used to examine the proteolytic activity of kefir grains on bovine milk proteins. Gel electrophoresis revealed substantial digestion of milk proteins by kefir grains, with mass spectrometric analysis showing the release of 609 protein fragments and alteration of the abundance of >1500 peptides that derived from 27 milk proteins. Kefir contained 25 peptides identified from the literature as having biological activity, including those with antihypertensive, antimicrobial, immunomodulatory, opioid and anti-oxidative functions. 16S rRNA and shotgun metagenomic sequencing identified the principle taxa in the culture as Lactobacillus species. The model kefir sample contained thousands of protein fragments released in part by kefir microorganisms and in part by native milk proteases. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Ambient pressure XPS and IRRAS investigation of ethanol steam reforming on Ni–CeO 2(111) catalysts: An in situ study of C–C and O–H bond scission

    DOE PAGES

    Liu, Zongyuan; Duchon, Tomas; Wang, Huanru; ...

    2016-03-31

    Ambient-Pressure X-ray Photoelectron Spectroscopy (AP-XPS) and Infrared Reflection Absorption Spectroscopy (AP-IRRAS) have been used to elucidate the active sites and mechanistic steps associated with the ethanol steam reforming reaction (ESR) over Ni–CeO 2(111) model catalysts. Our results reveal that surface layers of the ceria substrate are both highly reduced and hydroxylated under reaction conditions while the small supported Ni nanoparticles are present as Ni 0/NixC. A multifunctional, synergistic role is highlighted in which Ni, CeO x and the interface provide an ensemble effect in the active chemistry that leads to H 2. Ni 0 is the active phase leading tomore » both C–C and C–H bond cleavage in ethanol and it is also responsible for carbon accumulation. On the other hand, CeO x is important for the deprotonation of ethanol/water to ethoxy and OH intermediates. The active state of CeO x is a Ce 3+(OH) x compound that results from extensive reduction by ethanol and the efficient dissociation of water. Additionally, we gain an important insight into the stability and selectivity of the catalyst by its effective water dissociation, where the accumulation of surface carbon can be mitigated by the increased presence of surface OH groups. As a result, the co-existence and cooperative interplay of Ni 0 and Ce 3+(OH) x through a metal–support interaction facilitate oxygen transfer, activation of ethanol/water as well as the removal of coke.« less

  16. Determination of equilibrium structures of bromothymol blue revealed by using quantum chemistry with an aid of multivariate analysis of electronic absorption spectra.

    PubMed

    Shimada, Toru; Hasegawa, Takeshi

    2017-10-05

    The pH dependent chemical structures of bromothymol blue (BTB), which have long been under controversy, are determined by employing a combined technique of multivariate analysis of electronic absorption spectra and quantum chemistry. Principle component analysis (PCA) of the pH dependent spectra apparently reveals that only two chemical species are adequate to fully account for the color changes, with which the spectral decomposition is readily performed by using augmented alternative least-squares (ALS) regression analysis. The quantity variation by the ALS analysis also reveals the practical acid dissociation constant, pK a '. The determination of pK a ' is performed for various ionic strengths, which reveals the thermodynamic acid constant (pK a =7.5) and the number of charge on each chemical species; the yellow form is negatively charged species of -1 and the blue form that of -2. On this chemical information, the quantum chemical calculation is carried out to find that BTB molecules take the pure quinoid form in an acid solution and the quinoid-phenolate form in an alkaline solution. The time-dependent density functional theory (TD-DFT) calculations for the theoretically determined chemical structures account for the peak shift of the electronic spectra. In this manner, the structures of all the chemical species appeared in equilibrium have finally been confirmed. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Unraveling the Molecular Weight Dependence of Interfacial Interactions in Poly(2-vinylpyridine)/Silica Nanocomposites

    DOE PAGES

    Voylov, Dmitry N.; Holt, Adam P.; Doughty, Benjamin; ...

    2017-01-10

    In this paper, the structure and polymer–nanoparticle interactions among physically adsorbed poly(2-vinylpyridine) chains on the surface of silica nanoparticles (NPs) were systematically studied as a function of molecular weight (MW) by sum frequency generation (SFG) and X-ray photoelectron (XPS) spectroscopies. Analysis of XPS data identified hydrogen bonds between the polymer and NPs, while SFG evaluated the change in the number of free OH sites on the NP’s surface. Our data revealed that the hydrogen bonds and amount of the free ¯OH sites have a significant dependence on the polymer’s MW. Finally, these results provide clear experimental evidence that the interactionmore » of physically adsorbed chains with nanoparticles is strongly MW dependent and aids in unraveling the microscopic mechanism responsible for the strong MW dependence of dynamics of the interfacial layer in polymer nanocomposites.« less

  18. Unraveling the Molecular Weight Dependence of Interfacial Interactions in Poly(2-vinylpyridine)/Silica Nanocomposites

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

    Voylov, Dmitry N.; Holt, Adam P.; Doughty, Benjamin

    In this paper, the structure and polymer–nanoparticle interactions among physically adsorbed poly(2-vinylpyridine) chains on the surface of silica nanoparticles (NPs) were systematically studied as a function of molecular weight (MW) by sum frequency generation (SFG) and X-ray photoelectron (XPS) spectroscopies. Analysis of XPS data identified hydrogen bonds between the polymer and NPs, while SFG evaluated the change in the number of free OH sites on the NP’s surface. Our data revealed that the hydrogen bonds and amount of the free ¯OH sites have a significant dependence on the polymer’s MW. Finally, these results provide clear experimental evidence that the interactionmore » of physically adsorbed chains with nanoparticles is strongly MW dependent and aids in unraveling the microscopic mechanism responsible for the strong MW dependence of dynamics of the interfacial layer in polymer nanocomposites.« less

  19. Automated image analysis reveals the dynamic 3-dimensional organization of multi-ciliary arrays

    PubMed Central

    Galati, Domenico F.; Abuin, David S.; Tauber, Gabriel A.; Pham, Andrew T.; Pearson, Chad G.

    2016-01-01

    ABSTRACT Multi-ciliated cells (MCCs) use polarized fields of undulating cilia (ciliary array) to produce fluid flow that is essential for many biological processes. Cilia are positioned by microtubule scaffolds called basal bodies (BBs) that are arranged within a spatially complex 3-dimensional geometry (3D). Here, we develop a robust and automated computational image analysis routine to quantify 3D BB organization in the ciliate, Tetrahymena thermophila. Using this routine, we generate the first morphologically constrained 3D reconstructions of Tetrahymena cells and elucidate rules that govern the kinetics of MCC organization. We demonstrate the interplay between BB duplication and cell size expansion through the cell cycle. In mutant cells, we identify a potential BB surveillance mechanism that balances large gaps in BB spacing by increasing the frequency of closely spaced BBs in other regions of the cell. Finally, by taking advantage of a mutant predisposed to BB disorganization, we locate the spatial domains that are most prone to disorganization by environmental stimuli. Collectively, our analyses reveal the importance of quantitative image analysis to understand the principles that guide the 3D organization of MCCs. PMID:26700722

  20. Synthesis and characterization of an effective organic/inorganic hybrid green corrosion inhibitive complex based on zinc acetate/Urtica Dioica

    NASA Astrophysics Data System (ADS)

    Salehi, E.; Naderi, Reza; Ramezanzadeh, B.

    2017-02-01

    This study aims at synthesis and characterization of an effective corrosion inhibitive complex based on zinc acetate/Urtica Dioica (ZnA-U.D) for corrosion protection of mild steel in chloride solution. The chemical structure and morphology of the complex were characterized by Fourier transform infrared spectroscopy (FT-IR), UV-vis, thermal gravimetric analysis (TGA), X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). The corrosion protection performance of the mild steel samples dipped in 3.5 wt.% NaCl solutions with and without ZnA-U.D extract was investigated by visual observations, open circuit potential (OCP) measurements, electrochemical impedance spectroscopy (EIS) and polarization test. Results revealed that the ZnA successfully chelated with organic inhibitive compounds (i.e Quercetin, Quinic acid, Caffeic acid, Hystamine and Serotonin) present in the U.D extract. The electrochemical measurements revealed the effective inhibition action of ZnA-U.D complex in the sodium chloride solution on the mild steel. The synergistic effect between Zn2+ and organic compounds present in the U.D extract resulted in protective film deposition on the steel surface, which was proved by SEM and XPS analyses.

  1. Impression of plasma voltage on growth of α-V{sub 2}O{sub 5} nanostructured thin films

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

    Sharma, Rabindar Kumar, E-mail: rkrksharma6@gmail.com; Kumar, Prabhat; Reddy, G. B.

    2015-06-24

    In this communication, we synthesized vanadium pentoxide (α-V{sub 2}O{sub 5}) nanostructured thin films (NST{sub s}) accompanied with nanoflakes/ nanoplates on the Ni-coated glass substrates employing plasma assisted sublimation process (PASP) as a function of plasma voltage (V{sub p}). The effect of plasma voltage on structural, morphological, compositional, and vibrational properties have been studied systematically. The structural analysis divulged that all films deposited at different V{sub p} have pure orthorhombic phase, no impurity phase is detected under resolution limit of XRD and XPS. The morphological studies of samples is carried out by SEM, revealed that features as well as alignment ofmore » V{sub 2}O{sub 5} NST{sub s} is greatly monitored by V{sub p} and the film possessing the best features is obtained at 2500volt. In addition, XPS results reveal that V{sup 5+} oxidation state is the most prominent state in sample V{sub 2}, which represents better stoichiometric nature of film. The vibrational study of all samples is performed by FTIR and strongly support the XRD observations. All the results are in consonance with each other.« less

  2. Half of 23 Belgian dog breeds has a compromised genetic diversity, as revealed by genealogical and molecular data analysis.

    PubMed

    Wijnrocx, K; François, L; Stinckens, A; Janssens, S; Buys, N

    2016-10-01

    The genetic diversity in 23 dog breeds raised in Belgium was investigated using both genealogical analysis and microsatellite markers. Some of these breeds are native breeds, with only small populations maintained. Pedigree and molecular data, obtained from the Belgian kennel club, were used to calculate the inbreeding coefficients, realised effective population size as well as probabilities of gene origin and average observed heterozygosity. Inbreeding coefficients ranged from 0.8 to 44.7% and realised effective population size varied between 3.2 and 829.1, according to the used method and breed. Mean observed heterozygosity ranged from 0.47 to 0.73. Both pedigree and molecular methods reveal low genetic diversity and presence of bottlenecks, especially in native Belgian breeds with small population sizes. Furthermore, principal component analysis on the set of investigated diversity parameters revealed no groups of breeds that could be identified in which similar breeding strategies could be applied to maintain genetic diversity. © 2016 Blackwell Verlag GmbH.

  3. Multivariate pattern analysis reveals subtle brain anomalies relevant to the cognitive phenotype in neurofibromatosis type 1.

    PubMed

    Duarte, João V; Ribeiro, Maria J; Violante, Inês R; Cunha, Gil; Silva, Eduardo; Castelo-Branco, Miguel

    2014-01-01

    Neurofibromatosis Type 1 (NF1) is a common genetic condition associated with cognitive dysfunction. However, the pathophysiology of the NF1 cognitive deficits is not well understood. Abnormal brain structure, including increased total brain volume, white matter (WM) and grey matter (GM) abnormalities have been reported in the NF1 brain. These previous studies employed univariate model-driven methods preventing detection of subtle and spatially distributed differences in brain anatomy. Multivariate pattern analysis allows the combination of information from multiple spatial locations yielding a discriminative power beyond that of single voxels. Here we investigated for the first time subtle anomalies in the NF1 brain, using a multivariate data-driven classification approach. We used support vector machines (SVM) to classify whole-brain GM and WM segments of structural T1 -weighted MRI scans from 39 participants with NF1 and 60 non-affected individuals, divided in children/adolescents and adults groups. We also employed voxel-based morphometry (VBM) as a univariate gold standard to study brain structural differences. SVM classifiers correctly classified 94% of cases (sensitivity 92%; specificity 96%) revealing the existence of brain structural anomalies that discriminate NF1 individuals from controls. Accordingly, VBM analysis revealed structural differences in agreement with the SVM weight maps representing the most relevant brain regions for group discrimination. These included the hippocampus, basal ganglia, thalamus, and visual cortex. This multivariate data-driven analysis thus identified subtle anomalies in brain structure in the absence of visible pathology. Our results provide further insight into the neuroanatomical correlates of known features of the cognitive phenotype of NF1. Copyright © 2012 Wiley Periodicals, Inc.

  4. Glycomics meets artificial intelligence - Potential of glycan analysis for identification of seropositive and seronegative rheumatoid arthritis patients revealed.

    PubMed

    Chocholova, Erika; Bertok, Tomas; Jane, Eduard; Lorencova, Lenka; Holazova, Alena; Belicka, Ludmila; Belicky, Stefan; Mislovicova, Danica; Vikartovska, Alica; Imrich, Richard; Kasak, Peter; Tkac, Jan

    2018-06-01

    In this study, one hundred serum samples from healthy people and patients with rheumatoid arthritis (RA) were analyzed. Standard immunoassays for detection of 10 different RA markers and analysis of glycan markers on antibodies in 10 different assay formats with several lectins were applied for each serum sample. A dataset containing 2000 data points was data mined using artificial neural networks (ANN). We identified key RA markers, which can discriminate between healthy people and seropositive RA patients (serum containing autoantibodies) with accuracy of 83.3%. Combination of RA markers with glycan analysis provided much better discrimination accuracy of 92.5%. Immunoassays completely failed to identify seronegative RA patients (serum not containing autoantibodies), while glycan analysis correctly identified 43.8% of these patients. Further, we revealed other critical parameters for successful glycan analysis such as type of a sample, format of analysis and orientation of captured antibodies for glycan analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Cluster analysis reveals seasonal variation of sperm subpopulations in extended boar semen

    PubMed Central

    IBĂNESCU, Iulian; LEIDING, Claus; BOLLWEIN, Heinrich

    2017-01-01

    This study aimed to identify motile sperm subpopulations in extended boar semen and to observe the presumptive seasonal variation in their distribution. Data from 4837 boar ejaculates collected over a two-year period were analyzed in terms of kinematic parameters by Computer Assisted Sperm Analysis (CASA). Individual sperm data were used to determine subgroups of motile sperm within the ejaculates using cluster analysis. Four motile sperm subpopulations (SP) were identified, with distinct movement patterns: SP1 sperm with high velocity and high linearity; SP2 sperm with high velocity but low linearity; SP3 sperm with low velocity but high linearity; and SP4 sperm with low velocity and low linearity. SP1 constituted the least overall proportion within the ejaculates (P < 0.05). Season of semen collection significantly influenced the different proportions of sperm subpopulations. Spring was characterized by similar proportions of SP1 and SP4 (NS) and higher proportions of SP3. Summer brought a decrease in both subgroups containing fast sperm (SP1 and SP2) (P < 0.05). During autumn, increases in SP2 and SP4 were recorded. Winter substantially affected the proportions of all sperm subpopulations (P < 0.05) and SP2 became the most represented subgroup, while SP1 (fast and linear) reached its highest proportion compared to other seasons. In conclusion, extended boar semen is structured in distinct motile sperm subpopulations whose proportions vary according to the season of collection. Summer and autumn seem to have a negative impact on the fast and linear subpopulation. Cluster analysis can be useful in revealing differences in semen quality that are not normally detected by classical evaluation based on mean values. PMID:29081440

  6. Surface analysis of anodized aluminum clamps from NASA-LDEF satellite

    NASA Technical Reports Server (NTRS)

    Grammer, H. L.; Wightman, J. P.; Young, Philip R.

    1992-01-01

    Surface analysis results of selected anodized aluminum clamps containing black (Z306) and white (A276) paints which received nearly six years of Low Earth Orbit (LEO) exposure on the Long Duration Exposure Facility are reported. Surface analytical techniques, including x-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES), and scanning electron microscopy/energy dispersive analysis by x-ray (SEM/EDAX), showed significant differences in the surface composition of these materials depending upon the position on the LDEF. Differences in the surface composition are attributed to varying amounts of atomic oxygen and vacuum ultraviolet radiation (VUV). Silicon containing compounds were the primary contaminant detected on the materials.

  7. Geometric morphometric analysis reveals age-related differences in the distal femur of Europeans.

    PubMed

    Cavaignac, Etienne; Savall, Frederic; Chantalat, Elodie; Faruch, Marie; Reina, Nicolas; Chiron, Philippe; Telmon, Norbert

    2017-12-01

    Few studies have looked into age-related variations in femur shape. We hypothesized that three-dimensional (3D) geometric morphometric analysis of the distal femur would reveal age-related differences. The purpose of this study was to show that differences in distal femur shape related to age could be identified, visualized, and quantified using three-dimensional (3D) geometric morphometric analysis. Geometric morphometric analysis was carried out on CT scans of the distal femur of 256 subjects living in the south of France. Ten landmarks were defined on 3D reconstructions of the distal femur. Both traditional metric and geometric morphometric analyses were carried out on these bone reconstructions. These analyses were used to identify trends in bone shape in various age-based subgroups (<40, 40-60, >60). Only the average bone shape of the < 40-year subgroup was statistically different from that of the other two groups. When the population was divided into two subgroups using 40 years of age as a threshold, the subject's age was correctly assigned 80% of the time. Age-related differences are present in this bone segment. This reliable, accurate method could be used for virtual autopsy and to perform diachronic and interethnic comparisons. Moreover, this study provides updated morphometric data for a modern population in the south of France. Manufacturers of knee replacement implants will have to adapt their prosthesis models as the population evolves over time.

  8. Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

    PubMed Central

    Malmstrom, Rex R; Rodrigue, Sébastien; Huang, Katherine H; Kelly, Libusha; Kern, Suzanne E; Thompson, Anne; Roggensack, Sara; Berube, Paul M; Henn, Matthew R; Chisholm, Sallie W

    2013-01-01

    Prochlorococcus is the numerically dominant photosynthetic organism throughout much of the world's oceans, yet little is known about the ecology and genetic diversity of populations inhabiting tropical waters. To help close this gap, we examined natural Prochlorococcus communities in the tropical Pacific Ocean using a single-cell whole-genome amplification and sequencing. Analysis of the gene content of just 10 single cells from these waters added 394 new genes to the Prochlorococcus pan-genome—that is, genes never before seen in a Prochlorococcus cell. Analysis of marker genes, including the ribosomal internal transcribed sequence, from dozens of individual cells revealed several representatives from two uncultivated clades of Prochlorococcus previously identified as HNLC1 and HNLC2. While the HNLC clades can dominate Prochlorococcus communities under certain conditions, their overall geographic distribution was highly restricted compared with other clades of Prochlorococcus. In the Atlantic and Pacific oceans, these clades were only found in warm waters with low Fe and high inorganic P levels. Genomic analysis suggests that at least one of these clades thrives in low Fe environments by scavenging organic-bound Fe, a process previously unknown in Prochlorococcus. Furthermore, the capacity to utilize organic-bound Fe appears to have been acquired horizontally and may be exchanged among other clades of Prochlorococcus. Finally, one of the single Prochlorococcus cells sequenced contained a partial genome of what appears to be a prophage integrated into the genome. PMID:22895163

  9. CO dissociation and CO hydrogenation on smooth and ion-bombarded Pd(1 1 1): SFG and XPS spectroscopy at mbar pressures

    NASA Astrophysics Data System (ADS)

    Rupprechter, G.; Kaichev, V. V.; Unterhalt, H.; Morkel, M.; Bukhtiyarov, V. I.

    2004-07-01

    The CO dissociation probability on transition metals is often invoked to explain the product distribution (selectivity) of catalytic CO hydrogenation. Along these lines, we have investigated CO adsorption and dissociation on smooth and ion-bombarded Pd(1 1 1) at pressures up to 1 mbar using vibrational sum frequency generation (SFG) and X-ray photoelectron spectroscopy (XPS). Under high pressure, CO adsorbate structures were observed that were identical to high-coverage structures in UHV. On ion-bombarded surfaces an additional species was detected which was attributed to CO bridge bonded to defect (low-coordinated) sites. On both surfaces, no indications of CO dissociation were found even after hours of 0.1 mbar CO exposure. However, exposing CO/H 2 mixtures to ion-bombarded Pd(1 1 1) produced carbonaceous deposits suggesting CH xO species as precursors for CO bond cleavage and that the formation of CH xO is facilitated by surface defects. The relevance of the observations for CO hydrogenation on Pd catalysts is discussed.

  10. Limitations of using Raman microscopy for the analysis of high-content-carbon-filled ethylene propylene diene monomer rubber.

    PubMed

    Ghanbari-Siahkali, Afshin; Almdal, Kristoffer; Kingshott, Peter

    2003-12-01

    The effects of laser irradiation on changes to the surface chemistry and structure of a commercially available ethylene propylene diene monomer (EPDM) rubber sample after Raman microscopy analysis was investigated. The Raman measurements were carried out with different levels of laser power on the sample, ranging from 4.55 mW to 0.09 mW. The surface of the EPDM was analyzed before and after laser exposure using X-ray photoelectron spectroscopy (XPS) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. The techniques have surface probe depths of approximately < or = 10 nm and 1 microm, respectively. Both sets of analysis show that ingredients of the blended EPDM rubber "bloom" to the surface as a result of local heating that takes place due to the absorption of laser by carbon black during the Raman analysis. Scanning electron microscopy (SEM) analysis was also performed on the Raman analyzed areas to visually illustrate the effects created due to laser light exposure (i.e., burning marks). The change in surface chemistry also occurs in regions a few millimeters from the exposed sites, indicating that the effect is quite long range. However, this phenomenon has no major influence, as far as XPS or ATR-FTIR results disclose, on the backbone structure of the rubber sample. The results indicate that precautions should be taken when analyzing complex blended polymer samples using Raman spectroscopy.

  11. Electronic structure and phase separation of superconducting and nonsuperconducting KxFe2-ySe2 revealed by x-ray photoemission spectroscopy

    NASA Astrophysics Data System (ADS)

    Oiwake, M.; Ootsuki, D.; Noji, T.; Hatakeda, T.; Koike, Y.; Horio, M.; Fujimori, A.; Saini, N. L.; Mizokawa, T.

    2013-12-01

    We have investigated the electronic structure of superconducting (SC) and nonsuperconducting (non-SC) KxFe2-ySe2 using x-ray photoemission spectroscopy (XPS). The spectral shape of the Fe 2p XPS is found to depend on the amount of Fe vacancies. The Fe 2p3/2 peak of the SC and non-SC Fe-rich samples is accompanied by a shoulder structure on the lower binding energy side, which can be attributed to the metallic phase embedded in the Fe2+ insulating phase. The absence of the shoulder structure in the non-SC Fe-poor sample allows us to analyze the Fe 2p spectra using a FeSe4 cluster model. The Fe 3d-Se 4p charge-transfer energy of the Fe2+ insulating phase is found to be ˜2.3 eV which is smaller than the Fe 3d-Fe 3d Coulomb interaction of ˜3.5 eV. This indicates that the Fe2+ insulating state is the charge-transfer type in the Zaanen-Sawatzky-Allen scheme. We also find a substantial change in the valence-band XPS as a function of Fe content and temperature. The metallic state at the Fermi level is seen in the SC and non-SC Fe-rich samples and tends to be enhanced with cooling in the SC sample.

  12. Transcriptome analysis reveals key roles of AtLBR-2 in LPS-induced defense responses in plants.

    PubMed

    Iizasa, Sayaka; Iizasa, Ei'ichi; Watanabe, Keiichi; Nagano, Yukio

    2017-12-29

    Lipopolysaccharide (LPS) from Gram-negative bacteria cause innate immune responses in animals and plants. The molecules involved in LPS signaling in animals are well studied, whereas those in plants are not yet as well documented. Recently, we identified Arabidopsis AtLBR-2, which binds to LPS from Pseudomonas aeruginosa (pLPS) directly and regulates pLPS-induced defense responses, such as pathogenesis-related 1 (PR1) expression and reactive oxygen species (ROS) production. In this study, we investigated the pLPS-induced transcriptomic changes in wild-type (WT) and the atlbr-2 mutant Arabidopsis plants using RNA-Seq technology. RNA-Seq data analysis revealed that pLPS treatment significantly altered the expression of 2139 genes, with 605 up-regulated and 1534 down-regulated genes in WT. Gene ontology (GO) analysis on these genes showed that GO terms, "response to bacterium", "response to salicylic acid (SA) stimulus", and "response to abscisic acid (ABA) stimulus" were enriched amongst only in up-regulated genes, as compared to the genes that were down-regulated. Comparative analysis of differentially expressed genes between WT and the atlbr-2 mutant revealed that 65 genes were up-regulated in WT but not in the atlbr-2 after pLPS treatment. Furthermore, GO analysis on these 65 genes demonstrated their importance for the enrichment of several defense-related GO terms, including "response to bacterium", "response to SA stimulus", and "response to ABA stimulus". We also found reduced levels of pLPS-induced conjugated SA glucoside (SAG) accumulation in atlbr-2 mutants, and no differences were observed in the gene expression levels in SA-treated WT and the atlbr-2 mutants. These 65 AtLBR-2-dependent up-regulated genes appear to be important for the enrichment of some defense-related GO terms. Moreover, AtLBR-2 might be a key molecule that is indispensable for the up-regulation of defense-related genes and for SA signaling pathway, which is involved in defense against

  13. Organometallic chemical vapor deposition of silicon nitride films enhanced by atomic nitrogen generated from surface-wave plasma

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

    Okada, H.; Kato, M.; Ishimaru, T.

    2014-02-20

    Organometallic chemical vapor deposition of silicon nitride films enhanced by atomic nitrogen generated from surface-wave plasma is investigated. Feasibility of precursors of triethylsilane (TES) and bis(dimethylamino)dimethylsilane (BDMADMS) is discussed based on a calculation of bond energies by computer simulation. Refractive indices of 1.81 and 1.71 are obtained for deposited films with TES and BDMADMS, respectively. X-ray photoelectron spectroscopy (XPS) analysis of the deposited film revealed that TES-based film coincides with the stoichiometric thermal silicon nitride.

  14. Systems-level analysis of risk genes reveals the modular nature of schizophrenia.

    PubMed

    Liu, Jiewei; Li, Ming; Luo, Xiong-Jian; Su, Bing

    2018-05-19

    Schizophrenia (SCZ) is a complex mental disorder with high heritability. Genetic studies (especially recent genome-wide association studies) have identified many risk genes for schizophrenia. However, the physical interactions among the proteins encoded by schizophrenia risk genes remain elusive and it is not known whether the identified risk genes converge on common molecular networks or pathways. Here we systematically investigated the network characteristics of schizophrenia risk genes using the high-confidence protein-protein interactions (PPI) from the human interactome. We found that schizophrenia risk genes encode a densely interconnected PPI network (P = 4.15 × 10 -31 ). Compared with the background genes, the schizophrenia risk genes in the interactome have significantly higher degree (P = 5.39 × 10 -11 ), closeness centrality (P = 7.56 × 10 -11 ), betweeness centrality (P = 1.29 × 10 -11 ), clustering coefficient (P = 2.22 × 10 -2 ), and shorter average shortest path length (P = 7.56 × 10 -11 ). Based on the densely interconnected PPI network, we identified 48 hub genes and 4 modules formed by highly interconnected schizophrenia genes. We showed that the proteins encoded by schizophrenia hub genes have significantly more direct physical interactions. Gene ontology (GO) analysis revealed that cell adhesion, cell cycle, immune system response, and GABR-receptor complex categories were enriched in the modules formed by highly interconnected schizophrenia risk genes. Our study reveals that schizophrenia risk genes encode a densely interconnected molecular network and demonstrates the modular nature of schizophrenia. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Acetylproteomic Analysis Reveals Functional Implications of Lysine Acetylation in Human Spermatozoa (sperm)*

    PubMed Central

    Yu, Heguo; Diao, Hua; Wang, Chunmei; Lin, Yan; Yu, Fudong; Lu, Hui; Xu, Wei; Li, Zheng; Shi, Huijuan; Zhao, Shimin; Zhou, Yuchuan; Zhang, Yonglian

    2015-01-01

    Male infertility is a medical condition that has been on the rise globally. Lysine acetylation of human sperm, an essential posttranslational modification involved in the etiology of sperm abnormality, is not fully understood. Therefore, we first generated a qualified pan-anti-acetyllysine monoclonal antibody to characterize the global lysine acetylation of uncapacitated normal human sperm with a proteomics approach. With high enrichment ratios that were up to 31%, 973 lysine-acetylated sites that matched to 456 human sperm proteins, including 671 novel lysine acetylation sites and 205 novel lysine-acetylated proteins, were identified. These proteins exhibited conserved motifs XXXKYXXX, XXXKFXXX, and XXXKHXXX, were annotated to function in multiple metabolic processes, and were localized predominantly in the mitochondrion and cytoplasmic fractions. Between the uncapacitated and capacitated sperm, different acetylation profiles in regard to functional proteins involved in sperm capacitation, sperm-egg recognition, sperm-egg plasma fusion, and fertilization were observed, indicating that acetylation of functional proteins may be required during sperm capacitation. Bioinformatics analysis revealed association of acetylated proteins with diseases and drugs. Novel acetylation of voltage-dependent anion channel proteins was also found. With clinical sperm samples, we observed differed lysine acetyltransferases and lysine deacetylases expression between normal sperm and abnormal sperm of asthenospermia or necrospermia. Furthermore, with sperm samples impaired by epigallocatechin gallate to mimic asthenospermia, we observed that inhibition of sperm motility was partly through the blockade of voltage-dependent anion channel 2 Lys-74 acetylation combined with reduced ATP levels and mitochondrial membrane potential. Taken together, we obtained a qualified pan-anti-acetyllysine monoclonal antibody, analyzed the acetylproteome of uncapacitated human sperm, and revealed

  16. Global Gene Expression Analysis in PKCα-/- Mouse Skin Reveals Structural Changes in the Dermis and Defective Wound Granulation Tissue.

    PubMed

    Cooper, Nichola H; Balachandra, Jeya P; Hardman, Matthew J

    2015-12-01

    The skin's mechanical integrity is maintained by an organized and robust dermal extracellular matrix (ECM). Resistance to mechanical disruption hinges primarily on homeostasis of the dermal collagen fibril architecture, which is regulated, at least in part, by members of the small leucine-rich proteoglycan (SLRP) family. Here we present data linking protein kinase C alpha (PKCα) to the regulated expression of multiple ECM components including SLRPs. Global microarray profiling reveals deficiencies in ECM gene expression in PKCα-/- skin correlating with abnormal collagen fibril morphology, disorganized dermal architecture, and reduced skin strength. Detailed analysis of the skin and wounds from wild-type and PKCα-/- mice reveals a failure to upregulate collagen and other ECM components in response to injury, resulting in delayed granulation tissue deposition in PKCα-/- wounds. Thus, our data reveal a previously unappreciated role for PKCα in the regulation of ECM structure and deposition during skin wound healing.

  17. REVEAL: Software Documentation and Platform Migration

    NASA Technical Reports Server (NTRS)

    Wilson, Michael A.; Veibell, Victoir T.; Freudinger, Lawrence C.

    2008-01-01

    The Research Environment for Vehicle Embedded Analysis on Linux (REVEAL) is reconfigurable data acquisition software designed for network-distributed test and measurement applications. In development since 2001, it has been successfully demonstrated in support of a number of actual missions within NASA s Suborbital Science Program. Improvements to software configuration control were needed to properly support both an ongoing transition to operational status and continued evolution of REVEAL capabilities. For this reason the project described in this report targets REVEAL software source documentation and deployment of the software on a small set of hardware platforms different from what is currently used in the baseline system implementation. This report specifically describes the actions taken over a ten week period by two undergraduate student interns and serves as a final report for that internship. The topics discussed include: the documentation of REVEAL source code; the migration of REVEAL to other platforms; and an end-to-end field test that successfully validates the efforts.

  18. Proteomic Analysis Reveals Differentially Regulated Protein Acetylation in Human Amyotrophic Lateral Sclerosis Spinal Cord

    PubMed Central

    Azadzoi, Kazem; Yang, Yun; Fei, Zhou; Dou, Kefeng; Kowall, Neil W.; Choi, Han-Pil; Vieira, Fernando; Yang, Jing-Hua

    2013-01-01

    Amyotrophic lateral sclerosis (ALS) is a progressive fatal neurodegenerative disease that primarily affects motor neurons in the brain and spinal cord. Histone deacetylase (HDAC) inhibitors have neuroprotective effects potentially useful for the treatment of neurodegenerative diseases including ALS; however, the molecular mechanisms underlying their potential efficacy is not well understood. Here we report that protein acetylation in urea-soluble proteins is differently regulated in post-mortem ALS spinal cord. Two-dimensional electrophoresis (2-DE) analysis reveals several protein clusters with similar molecular weight but different charge status. Liquid chromatography and tandem mass spectrometry (LC-MS/MS) identifies glial fibrillary acidic protein (GFAP) as the dominant component in the protein clusters. Further analysis indicates six heavily acetylated lysine residues at positions 89, 153, 189, 218, 259 and 331 of GFAP. Immunoprecipitation followed by Western blotting confirms that the larger form of GFAP fragments are acetylated and upregulated in ALS spinal cord. Further studies demonstrate that acetylation of the proteins additional to GFAP is differently regulated, suggesting that acetylation and/or deacetylation play an important role in pathogenesis of ALS. PMID:24312501

  19. Dependence of LTX plasma performance on surface conditions as determined by in situ analysis of plasma facing components

    NASA Astrophysics Data System (ADS)

    Lucia, M.; Kaita, R.; Majeski, R.; Bedoya, F.; Allain, J. P.; Abrams, T.; Bell, R. E.; Boyle, D. P.; Jaworski, M. A.; Schmitt, J. C.

    2015-08-01

    The Materials Analysis and Particle Probe (MAPP) diagnostic has been implemented on the Lithium Tokamak Experiment (LTX) at PPPL, providing the first in situ X-ray photoelectron spectroscopy (XPS) surface characterization of tokamak plasma facing components (PFCs). MAPP samples were exposed to argon glow discharge conditioning (GDC), lithium evaporations, and hydrogen tokamak discharges inside LTX. Samples were analyzed with XPS, and alterations to surface conditions were correlated against observed LTX plasma performance changes. Argon GDC caused the accumulation of nm-scale metal oxide layers on the PFC surface, which appeared to bury surface carbon and oxygen contamination and thus improve plasma performance. Lithium evaporation led to the rapid formation of a lithium oxide (Li2O) surface; plasma performance was strongly improved for sufficiently thick evaporative coatings. Results indicate that a 5 h argon GDC or a 50 nm evaporative lithium coating will both significantly improve LTX plasma performance.

  20. Proteomic analysis of three gonad types of swamp eel reveals genes differentially expressed during sex reversal.

    PubMed

    Sheng, Yue; Zhao, Wei; Song, Ying; Li, Zhigang; Luo, Majing; Lei, Quan; Cheng, Hanhua; Zhou, Rongjia

    2015-05-18

    A variety of mechanisms are engaged in sex determination in vertebrates. The teleost fish swamp eel undergoes sex reversal naturally and is an ideal model for vertebrate sexual development. However, the importance of proteome-wide scanning for gonad reversal was not previously determined. We report a 2-D electrophoresis analysis of three gonad types of proteomes during sex reversal. MS/MS analysis revealed a group of differentially expressed proteins during ovary to ovotestis to testis transformation. Cbx3 is up-regulated during gonad reversal and is likely to have a role in spermatogenesis. Rab37 is down-regulated during the reversal and is mainly associated with oogenesis. Both Cbx3 and Rab37 are linked up in a protein network. These datasets in gonadal proteomes provide a new resource for further studies in gonadal development.

  1. Combined far infrared RAIRS and XPS studies of TiCl 4 adsorption and reaction on Mg films

    NASA Astrophysics Data System (ADS)

    Pilling, M. J.; Fonseca, A. Amieiro; Cousins, M. J.; Waugh, K. C.; Surman, M.; Gardner, P.

    2005-08-01

    In recent years there has been an increase in interest in the study of model Ziegler-Natta catalysts used for the polymerisation of ethene and propene. Particular attention has focused on catalysts consisting of TiCl 4 on activated MgCl 2 accompanied by a co-catalyst, usually triethylaluminium (AlEt 3). As part of a wider project on the characterisation of model Ziegler-Natta catalysts we have investigated the interaction of TiCl 4 with metallic Mg films grown on a Au surface using X-ray photoelectron spectroscopy (XPS) and far infrared reflection absorption infrared spectroscopy. Somewhat surprisingly, the infrared spectra show little variation as a function of exposure to TiCl 4. A very broad asymmetric vibrational band grows in with maximum intensity at 382 cm -1. Three prominent low frequency shoulders are observed at approximately 360, 320, and 260 cm -1. For monolayer coverages of Mg the main band at 382 cm -1 is narrower, less asymmetric and accompanied by a prominent shoulder at 398 cm -1, which increases with increasing exposure to TiCl 4. TiCl 4 exposure in the presence of 5 × 10 -8 Torr of ethyl benzoate results in a change in line shape with low frequency broadening and a small shift in the frequency of the band. These spectra are discussed in the light of the possible constituent species making up the surface layer.

  2. Reactivity assay of surface carboxyl chain-ends of poly(ethylene terephthalate) (PET) film and track-etched microporous membranes using fluorine labelled- and/or 3H-labelled derivatization reagents: tandem analysis by X-ray photoelectron spectroscopy (XPS) and liquid scintillation counting (LSC)

    NASA Astrophysics Data System (ADS)

    Deldime, Michèle; Dewez, Jean-Luc; Schneider, Yves-Jacques; Marchand-Brynaert, Jacqueline

    1995-09-01

    Poly(ethylene terephthalate) (PET) films and track-etched microporous membranes of two different porosities were pretreated by hydrolysis and/or oxidation in order to enhance the amount of carboxyl chain-ends displayed on their surface. The reactivity of these carboxyl functions was determined by derivatization assays in which the reactions were carried out under conditions likely to be encountered in the coupling of water-soluble biochemical signals on the surface of biomaterials. Original reagents, fluorine-labelled and/or 3H-labelled aminoacid compounds, were used. The derivatized PET samples were examined by X-ray photoelectron spectroscopy (XPS) to characterize their apparent surfaces, and by liquid scintillation counting (LSC) to quantify the amount of tags fixed on their open surfaces. Using this dual assay technique, we analyzed the surface of microporous membranes which are currently used as substrates for cell culture systems.

  3. Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides

    DOE PAGES

    Wu, Chao; Xiong, Wei; Dai, Junbiao; ...

    2014-12-15

    We report that integrated and genome-based flux balance analysis, metabolomics, and 13C-label profiling of phototrophic and heterotrophic metabolism in Chlorella protothecoides, an oleaginous green alga for biofuel. The green alga Chlorella protothecoides, capable of autotrophic and heterotrophic growth with rapid lipid synthesis, is a promising candidate for biofuel production. Based on the newly available genome knowledge of the alga, we reconstructed the compartmentalized metabolic network consisting of 272 metabolic reactions, 270 enzymes, and 461 encoding genes and simulated the growth in different cultivation conditions with flux balance analysis. Phenotype-phase plane analysis shows conditions achieving theoretical maximum of the biomass andmore » corresponding fatty acid-producing rate for phototrophic cells (the ratio of photon uptake rate to CO 2 uptake rate equals 8.4) and heterotrophic ones (the glucose uptake rate to O 2 consumption rate reaches 2.4), respectively. Isotope-assisted liquid chromatography-mass spectrometry/mass spectrometry reveals higher metabolite concentrations in the glycolytic pathway and the tricarboxylic acid cycle in heterotrophic cells compared with autotrophic cells. We also observed enhanced levels of ATP, nicotinamide adenine dinucleotide (phosphate), reduced, acetyl-Coenzyme A, and malonyl-Coenzyme A in heterotrophic cells consistently, consistent with a strong activity of lipid synthesis. To profile the flux map in experimental conditions, we applied nonstationary 13C metabolic flux analysis as a complementing strategy to flux balance analysis. We found that the result reveals negligible photorespiratory fluxes and a metabolically low active tricarboxylic acid cycle in phototrophic C. protothecoides. In comparison, high throughput of amphibolic reactions and the tricarboxylic acid cycle with no glyoxylate shunt activities were measured for heterotrophic cells. Lastly, taken together, the metabolic network modeling

  4. IL-10 Dysregulation in Acute Mountain Sickness Revealed by Transcriptome Analysis

    PubMed Central

    Liu, Bao; Chen, Jian; Zhang, Long; Gao, Yixing; Cui, Jianhua; Zhang, Erlong; Xu, Gang; Liang, Yan; Liang, Yu; Wang, Jian; Gao, Yuqi

    2017-01-01

    Acute mountain sickness (AMS), which may progress to life-threatening high-altitude cerebral edema, is a major threat to millions of people who live in or travel to high altitude. Although studies have revealed the risk factors and pathophysiology theories of AMS, the molecular mechanisms of it do not comprehensively illustrate. Here, we used a system-level methodology, RNA sequencing, to explore the molecular mechanisms of AMS at genome-wide level in 10 individuals. After exposure to high altitude, a total of 1,164 and 1,322 differentially expressed transcripts were identified in AMS and non-AMS groups, respectively. Among them, only 328 common transcripts presented between the two groups. Immune and inflammatory responses were overrepresented in participants with AMS, but not in non-AMS individuals. Anti-inflammatory cytokine IL10 and inflammation cytokines IF17F and CCL8 exhibited significantly different genetic connectivity in AMS compared to that of non-AMS individuals based on network analysis. IL10 was downregulated and both IF17F and CCL8 were upregulated in AMS individuals. Moreover, the serum concentration of IL10 significantly decreased in AMS patients after exposure to high altitude (p = 0.001) in another population (n = 22). There was a large negative correlation between the changes in IL10 concentration, r(22) = −0.52, p = 0.013, and Lake Louise Score. Taken together, our analysis provides unprecedented characterization of AMS transcriptome and identifies that genes involved in immune and inflammatory responses were disturbed in AMS individuals by high-altitude exposure. The reduction of IL10 after exposure to high altitude was associated with AMS. PMID:28611780

  5. Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis.

    PubMed

    Liu, Wenjun; Zhang, Jiachao; Wu, Chunyan; Cai, Shunfeng; Huang, Weiqiang; Chen, Jing; Xi, Xiaoxia; Liang, Zebin; Hou, Qiangchuan; Zhou, Bing; Qin, Nan; Zhang, Heping

    2016-10-06

    The human gut microbiota varies considerably among world populations due to a variety of factors including genetic background, diet, cultural habits and socioeconomic status. Here we characterized 110 healthy Mongolian adults gut microbiota by shotgun metagenomic sequencing and compared the intestinal microbiome among Mongolians, the Hans and European cohorts. The results showed that the taxonomic profile of intestinal microbiome among cohorts revealed the Actinobaceria and Bifidobacterium were the key microbes contributing to the differences among Mongolians, the Hans and Europeans at the phylum level and genus level, respectively. Metagenomic species analysis indicated that Faecalibacterium prausnitzii and Coprococcus comeswere enrich in Mongolian people which might contribute to gut health through anti-inflammatory properties and butyrate production, respectively. On the other hand, the enriched genus Collinsella, biomarker in symptomatic atherosclerosis patients, might be associated with the high morbidity of cardiovascular and cerebrovascular diseases in Mongolian adults. At the functional level, a unique microbial metabolic pathway profile was present in Mongolian's gut which mainly distributed in amino acid metabolism, carbohydrate metabolism, energy metabolism, lipid metabolism, glycan biosynthesis and metabolism. We can attribute the specific signatures of Mongolian gut microbiome to their unique genotype, dietary habits and living environment.

  6. Gene expression analysis reveals schizophrenia-associated dysregulation of immune pathways in peripheral blood mononuclear cells.

    PubMed

    Gardiner, Erin J; Cairns, Murray J; Liu, Bing; Beveridge, Natalie J; Carr, Vaughan; Kelly, Brian; Scott, Rodney J; Tooney, Paul A

    2013-04-01

    Peripheral blood mononuclear cells (PBMCs) represent an accessible tissue source for gene expression profiling in schizophrenia that could provide insight into the molecular basis of the disorder. This study used the Illumina HT_12 microarray platform and quantitative real time PCR (QPCR) to perform mRNA expression profiling on 114 patients with schizophrenia or schizoaffective disorder and 80 non-psychiatric controls from the Australian Schizophrenia Research Bank (ASRB). Differential expression analysis revealed altered expression of 164 genes (59 up-regulated and 105 down-regulated) in the PBMCs from patients with schizophrenia compared to controls. Bioinformatic analysis indicated significant enrichment of differentially expressed genes known to be involved or associated with immune function and regulating the immune response. The differential expression of 6 genes, EIF2C2 (Ago 2), MEF2D, EVL, PI3, S100A12 and DEFA4 was confirmed by QPCR. Genome-wide expression analysis of PBMCs from individuals with schizophrenia was characterized by the alteration of genes with immune system function, supporting the hypothesis that the disorder has a significant immunological component in its etiology. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Meta-analysis of human gene expression in response to Mycobacterium tuberculosis infection reveals potential therapeutic targets.

    PubMed

    Wang, Zhang; Arat, Seda; Magid-Slav, Michal; Brown, James R

    2018-01-10

    With the global emergence of multi-drug resistant strains of Mycobacterium tuberculosis, new strategies to treat tuberculosis are urgently needed such as therapeutics targeting potential human host factors. Here we performed a statistical meta-analysis of human gene expression in response to both latent and active pulmonary tuberculosis infections from nine published datasets. We found 1655 genes that were significantly differentially expressed during active tuberculosis infection. In contrast, no gene was significant for latent tuberculosis. Pathway enrichment analysis identified 90 significant canonical human pathways, including several pathways more commonly related to non-infectious diseases such as the LRRK2 pathway in Parkinson's disease, and PD-1/PD-L1 signaling pathway important for new immuno-oncology therapies. The analysis of human genome-wide association studies datasets revealed tuberculosis-associated genetic variants proximal to several genes in major histocompatibility complex for antigen presentation. We propose several new targets and drug-repurposing opportunities including intravenous immunoglobulin, ion-channel blockers and cancer immuno-therapeutics for development as combination therapeutics with anti-mycobacterial agents. Our meta-analysis provides novel insights into host genes and pathways important for tuberculosis and brings forth potential drug repurposing opportunities for host-directed therapies.

  8. Metabolomics analysis reveals 6-benzylaminopurine as a stimulator for improving lipid and DHA accumulation of Aurantiochytriumsp.

    PubMed

    Yu, Xin-Jun; Sun, Jie; Zheng, Jian-Yong; Sun, Ya-Qi; Wang, Zhao

    2016-04-01

    Phytohormones are chemical messengers that have a positive effect on biodiesel production of microalgae at low concentrations. However, the effect of phytohormone 6-benzylaminopurine on lipid and docosahexaenoic acid (DHA) production in marine DHA-producer Aurantiochytrium has never been reported. In this study, a GC-MS-based metabolomics method combined with a multivariate analysis is applied to reveal the metabolic mechanism of 6-benzylaminopurine enhancing production of lipid and DHA in Aurantiochytrium sp.YLH70. In total, 71 metabolites were identified by GC-MS. The PCA model revealed that 76.9% of metabolite variation was related to 6-benzylaminopurine treatment, and overall metabolomics profiles between the 6-benzylaminopurine and control groups were clearly discriminated. Forty-six metabolites identified by the PLS-DA model were responsible for responding to 6-benzylaminopurine. Metabolic analysis showed that 6-benzylaminopurine could accelerate the rate of utilization of glucose in Aurantiochytrium sp. YLH70, and the metabolic flux from glycolysis, TCA cycle and mevalonate pathway to fatty acids biosynthesis was promoted. Moreover, the anti-stress mechanism in Aurantiochytrium sp.YLH70 might be induced by 6-benzylaminopurine. Metabolomics is a suitable tool to discover the metabolic mechanism for improving lipid and DHA accumulation in a microorganism. 6-benzylaminopurine has the potential to stimulate lipid and DHA production of Aurantiochytrium sp.YLH70 for industrial purposes. © 2015 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

  9. Independent component analysis of DTI data reveals white matter covariances in Alzheimer's disease

    NASA Astrophysics Data System (ADS)

    Ouyang, Xin; Sun, Xiaoyu; Guo, Ting; Sun, Qiaoyue; Chen, Kewei; Yao, Li; Wu, Xia; Guo, Xiaojuan

    2014-03-01

    Alzheimer's disease (AD) is a progressive neurodegenerative disease with the clinical symptom of the continuous deterioration of cognitive and memory functions. Multiple diffusion tensor imaging (DTI) indices such as fractional anisotropy (FA) and mean diffusivity (MD) can successfully explain the white matter damages in AD patients. However, most studies focused on the univariate measures (voxel-based analysis) to examine the differences between AD patients and normal controls (NCs). In this investigation, we applied a multivariate independent component analysis (ICA) to investigate the white matter covariances based on FA measurement from DTI data in 35 AD patients and 45 NCs from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. We found that six independent components (ICs) showed significant FA reductions in white matter covariances in AD compared with NC, including the genu and splenium of corpus callosum (IC-1 and IC-2), middle temporal gyral of temporal lobe (IC-3), sub-gyral of frontal lobe (IC-4 and IC-5) and sub-gyral of parietal lobe (IC-6). Our findings revealed covariant white matter loss in AD patients and suggest that the unsupervised data-driven ICA method is effective to explore the changes of FA in AD. This study assists us in understanding the mechanism of white matter covariant reductions in the development of AD.

  10. Scanning electron and atomic force microscopy, and raman and x-ray photoelectron spectroscopy characterization of near-isogenic soft and hard wheat kernels and corresponding flours

    USDA-ARS?s Scientific Manuscript database

    Atomic force microscopy (AFM), Raman spectroscopy and X-ray photoelectron spectroscopy (XPS) are used to investigate vitreous (hard) and non-vitreous (soft) wheat kernels and their corresponding wheat flours. AFM data reveal two different microstructures. The vitreous kernel reveals a granular text...

  11. Sensitivity of human auditory cortex to rapid frequency modulation revealed by multivariate representational similarity analysis.

    PubMed

    Joanisse, Marc F; DeSouza, Diedre D

    2014-01-01

    Functional Magnetic Resonance Imaging (fMRI) was used to investigate the extent, magnitude, and pattern of brain activity in response to rapid frequency-modulated sounds. We examined this by manipulating the direction (rise vs. fall) and the rate (fast vs. slow) of the apparent pitch of iterated rippled noise (IRN) bursts. Acoustic parameters were selected to capture features used in phoneme contrasts, however the stimuli themselves were not perceived as speech per se. Participants were scanned as they passively listened to sounds in an event-related paradigm. Univariate analyses revealed a greater level and extent of activation in bilateral auditory cortex in response to frequency-modulated sweeps compared to steady-state sounds. This effect was stronger in the left hemisphere. However, no regions showed selectivity for either rate or direction of frequency modulation. In contrast, multivoxel pattern analysis (MVPA) revealed feature-specific encoding for direction of modulation in auditory cortex bilaterally. Moreover, this effect was strongest when analyses were restricted to anatomical regions lying outside Heschl's gyrus. We found no support for feature-specific encoding of frequency modulation rate. Differential findings of modulation rate and direction of modulation are discussed with respect to their relevance to phonetic discrimination.

  12. X-ray photoelectron spectroscopic and morphologic studies of Ru nanoparticles deposited onto highly oriented pyrolytic graphite

    NASA Astrophysics Data System (ADS)

    Bavand, R.; Yelon, A.; Sacher, E.

    2015-11-01

    Ruthenium nanoparticles (Ru NPs) function as effective catalysts in specific reactions, such as methanation and Fischer-Tropsch syntheses. It is our purpose to physicochemically characterize their surfaces, at which catalysis occurs, by surface-sensitive X-ray photoelectron spectroscopy (XPS), using the symmetric peak component anaylsis technique developed in our laboratory to reveal previously hidden components. Ru NPs were deposited by evaporation (0.25-1.5 nm nominal deposition range) onto highly oriented pyrolytic graphite (HOPG). In addition to their surfaces being characterized by XPS, an indication of morphology was obtained from transmission electron microscopy (TEM). Our use of symmetric peak component XPS analysis has revealed detailed information on a previously unidentified surface oxide initially formed, as well as on the valence electronic structure and its variation with NP size, information that is of potential importance in the use of these NPs in catalysis. Each of the several Ru core XPS spectra characterized (3d, 3p and 3s) was found to be composed of three symmetric components. Together with two metal oxide O1s components, these give evidence of a rather complex, previously unidentified oxide that is initially formed. The Ru valence band (4d and 5s) spectra clearly demonstrate a loss of metallicity, a simultaneous increase of the Kubo gap, and an abrupt transfer in valence electron density from the 4d to the 5s orbitals (known as electron spill-over), as the NP size decreases below 0.5 nm. TEM photomicrographs, as a function of deposition rate, show that, at a rate that gives insufficient time for the NP condensation energy to dissipate, the initially well-separated NPs are capable of diffusing laterally and aggregating. This indicates weak NP bonding to the HOPG substrate. Carbide is formed, at both high and low deposition rates, at Ru deposition thicknesses greater than 0.25 nm, its formation explained by Ru NPs reacting with residual

  13. Comparative Analysis of Four Calypogeia Species Revealed Unexpected Change in Evolutionarily-Stable Liverwort Mitogenomes

    PubMed Central

    Ślipiko, Monika; Buczkowska-Chmielewska, Katarzyna; Bączkiewicz, Alina; Szczecińska, Monika; Sawicki, Jakub

    2017-01-01

    Liverwort mitogenomes are considered to be evolutionarily stable. A comparative analysis of four Calypogeia species revealed differences compared to previously sequenced liverwort mitogenomes. Such differences involve unexpected structural changes in the two genes, cox1 and atp1, which have lost three and two introns, respectively. The group I introns in the cox1 gene are proposed to have been lost by two-step localized retroprocessing, whereas one-step retroprocessing could be responsible for the disappearance of the group II introns in the atp1 gene. These cases represent the first identified losses of introns in mitogenomes of leafy liverworts (Jungermanniopsida) contrasting the stability of mitochondrial gene order with certain changes in the gene content and intron set in liverworts. PMID:29257096

  14. Effects of rare earth doping on multi-core iron oxide nanoparticles properties

    NASA Astrophysics Data System (ADS)

    Petran, Anca; Radu, Teodora; Borodi, Gheorghe; Nan, Alexandrina; Suciu, Maria; Turcu, Rodica

    2018-01-01

    New multi-core iron oxide magnetic nanoparticles doped with rare earth metals (Gd, Eu) were obtained by a one step synthesis procedure using a solvothermal method for potential biomedical applications. The obtained clusters were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), energy-dispersive X-ray microanalysis (EDX), X-ray photoelectron spectroscopy (XPS) and magnetization measurements. They possess high colloidal stability, a saturation magnetization of up to 52 emu/g, and nearly spherical shape. The presence of rare earth ions in the obtained samples was confirmed by EDX and XPS. XRD analysis proved the homogeneous distribution of the trivalent rare earth ions in the inverse-spinel structure of magnetite and the increase of crystal strain upon doping the samples. XPS study reveals the valence state and the cation distribution on the octahedral and tetrahedral sites of the analysed samples. The observed shift of the XPS valence band spectra maximum in the direction of higher binding energies after rare earth doping, as well as theoretical valence band calculations prove the presence of Gd and Eu ions in octahedral sites. The blood protein adsorption ability of the obtained samples surface, the most important factor of the interaction between biomaterials and body fluids, was assessed by interaction with bovine serum albumin (BSA). The rare earth doped clusters surface show higher afinity for binding BSA. In vitro cytotoxicity test results for the studied samples showed no cytotoxicity in low and medium doses, establishing a potential perspective for rare earth doped MNC to facilitate multiple therapies in a single formulation for cancer theranostics.

  15. The relationship between the surface composition and electrical properties of corrosion films formed on carbon steel in alkaline sour medium: an XPS and EIS study.

    PubMed

    Galicia, Policarpo; Batina, Nikola; González, Ignacio

    2006-07-27

    This work studies the evolution of 1018 carbon steel surfaces during 3-15 day immersion in alkaline sour medium 0.1 M (NH4)2S and 10 ppm CN(-) as (NaCN). During this period of time, surfaces were jointly characterized by electrochemical techniques in situ (electrochemical impedance spectroscopy, EIS) and spectroscopic techniques ex situ (X-ray photoelectron spectroscopy, XPS). The results obtained by these techniques allowed for a description of electrical and chemical properties of the films of corrosion products formed at the 1018 steel surface. There is an interconversion cycle of chemical species that form films of corrosion products whose conversion reactions favor two different types of diffusions inside the films: a chemical diffusion of iron cations and a typical diffusion of atomic hydrogen. These phenomena jointly control the passivity of the interface attacked by the corrosive medium.

  16. The effects of surface pretreatment and nitrogen tetroxide purification on the corrosion rate of Type 304L stainless steel

    NASA Technical Reports Server (NTRS)

    Blue, G. D.; Moran, C. M.

    1985-01-01

    Corrosion rates of 304L stainless steel coupons in MON-1 oxidizer have been measured as a function of cleaning procedures employed, surface layer positions, propellant impurity levels, and short-term exposure durations (14 to 90 days). Of special interest was propellant contamination by buildup of soluble iron, which may cause flow decay. Surface treatments employed were combinations of cleaning, pickling, and passivation procedures. Propellants used were MIL-SPEC MON-1 and several types of purified NTO (i.e., low water, low chloride) which may, at a later time, be specified as spacecraft grade. Pretest coupon surface analysis by X-ray photoelectron spectroscopy (XPS-ESCA) has revealed important differences, for the different cleaning procedures, in the make-up of the surface layer, both in composition and state of chemical combination of the elements involved. Comparisons will be made of XPS/ESCA data, for different cleaning procedures, for specimens before and after propellant exposure.

  17. Improved flotation performance of hematite fines using citric acid as a dispersant

    NASA Astrophysics Data System (ADS)

    Luo, Xi-mei; Yin, Wan-zhong; Sun, Chuan-yao; Wang, Nai-ling; Ma, Ying-qiang; Wang, Yun-fan

    2016-10-01

    In this study, citric acid was used as a dispersant to improve the flotation performance of hematite fines. The effect and mechanism of citric acid on the reverse flotation of hematite fines were investigated by flotation tests, sedimentation experiments, scanning electron microscopy (SEM), zeta-potential measurements, and X-ray photoelectron spectroscopy (XPS). The results of SEM analysis and flotation tests reveal that a strong heterocoagulation in the form of slime coating or coagulation in hematite fine slurry affects the beneficiation of hematite ores by froth flotation. The addition of a small amount of citric acid (less than 300 g/t) favorably affects the reverse flotation of hematite fines by improving particle dispersion. The results of sedimentation experiments, zeta-potential measurements, and XPS measurements demonstrate that citric acid adsorbs onto hematite and quartz surfaces via hydrogen bonding, thereby reducing the zeta potentials of mineral surfaces, strengthening the electrical double-layer repulsion between mineral particles, and dispersing the pulp particles.

  18. Effect of Electron Beam Irradiation on Structural and Optical Properties of Cu-Doped In2O3 Films Prepared by RF Magnetron Sputtering

    NASA Astrophysics Data System (ADS)

    Krishnan, R. Reshmi; Sanjeev, Ganesh; Prabhu, Radhakrishna; Pillai, V. P. Mahadevan

    2018-02-01

    Undoped and Cu-doped In2O3 films were prepared by radiofrequency magnetron sputtering technique. The effects of Cu doping and high-energy electron beam irradiation on the structural and optical properties of as-prepared films were investigated using techniques such as x-ray diffraction, x-ray photoelectron spectroscopy (XPS), lateral scanning electron microscopic image analysis, energy-dispersive x-ray (EDX) spectroscopy, micro-Raman, and ultraviolet-visible (UV-vis) spectroscopy. Moderate doping of Cu in In2O3 enhanced the intensity of (222) peak, indicating alignment of crystalline grains along <111>. Electron beam irradiation promoted orientation of crystalline grains along <111> in undoped and moderately Cu-doped films. EDX spectroscopic and XPS analyses revealed incorporation of Cu2+ ions in the lattice. The transmittance of Cu-doped films decreased with e-beam irradiation. Systematic reduction of the bandgap energy with increase in Cu doping concentration was seen in unirradiated and electron-beam-irradiated films.

  19. Electron-beam-induced post-grafting polymerization of acrylic acid onto the surface of Kevlar fibers

    NASA Astrophysics Data System (ADS)

    Xu, Lu; Hu, Jiangtao; Ma, Hongjuan; Wu, Guozhong

    2018-04-01

    The surface of Kevlar fibers was successfully modified by electron beam (EB)-induced post-grafting of acrylic acid (AA). The generation of radicals in the fibers was confirmed by electron spin resonance (ESR) measurements, and the concentration of radicals was shown to increase as the absorbed dose increased, but decrease with increasing temperature. The influence of the synthesis conditions on the degree of grafting was also investigated. The surface microstructure and chemical composition of the modified Kevlar fibers were characterized by scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). The SEM images revealed that the surface of the grafted fibers was rougher than those of the pristine and irradiated fibers. XPS analysis confirmed an increase in C(O)OH groups on the surface of the Kevlar fibers, suggesting successful grafting of AA. These results indicate that EB-induced post-grafting polymerization is effective for modifying the surface properties of Kevlar fibers.

  20. X-Ray photoelectron Spectroscopy Applications

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

    Engelhard, Mark H.; Droubay, Timothy C.; Du, Yingge

    2017-01-03

    With capability for obtaining quantitative elemental composition, chemical and electronic state, and overlayer thickness information from the top ~10 nm of a sample surface, X-ray Photoelectron Spectroscopy (XPS) or Electron Spectroscopy for Chemical Analysis (ESCA) is a versatile and widely used technique for analyzing surfaces. The technique is applied to a host of materials, from insulators to conductors in virtually every scientific field and sub-discipline. More recently, XPS has been extended under in-situ and operando conditions. Following a brief introduction to XPS principles and instrument components, this article exemplifies widely ranging XPS applications in material and life sciences.

  1. Genomic analysis of methanogenic archaea reveals a shift towards energy conservation

    DOE PAGES

    Gilmore, Sean P.; Henske, John K.; Sexton, Jessica A.; ...

    2017-08-21

    The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to other forms of respiration and is therefore critical to many anaerobic environments. Harnessing or altering methanogen metabolism has the potential to mitigate global warming and even be utilized for energy applications. Here, we report draft genome sequences for the isolated methanogens Methanobacterium bryantii, Methanosarcina spelaei, Methanosphaera cuniculi, and Methanocorpusculum parvum. These anaerobic, methane-producing archaea represent a diverse set of isolates, capable of methylotrophic, acetoclastic, and hydrogenotrophic methanogenesis. Assembly and analysis ofmore » the genomes allowed for simple and rapid reconstruction of metabolism in the four methanogens. Comparison of the distribution of Clusters of Orthologous Groups (COG) proteins to a sample of genomes from the RefSeq database revealed a trend towards energy conservation in genome composition of all methanogens sequenced. Further analysis of the predicted membrane proteins and transporters distinguished differing energy conservation methods utilized during methanogenesis, such as chemiosmotic coupling in Msar. spelaei and electron bifurcation linked to chemiosmotic coupling in Mbac. bryantii and Msph. cuniculi. Methanogens occupy a unique ecological niche, acting as the terminal electron acceptors in anaerobic environments, and their genomes display a significant shift towards energy conservation. The genome-enabled reconstructed metabolisms reported here have significance to diverse anaerobic communities and have led to proposed substrate utilization not previously reported in isolation, such as formate and methanol metabolism in Mbac. bryantii and CO 2 metabolism in Msph. cuniculi. The newly proposed substrates establish an important foundation with which to decipher how methanogens

  2. Genomic analysis of methanogenic archaea reveals a shift towards energy conservation

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

    Gilmore, Sean P.; Henske, John K.; Sexton, Jessica A.

    The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to other forms of respiration and is therefore critical to many anaerobic environments. Harnessing or altering methanogen metabolism has the potential to mitigate global warming and even be utilized for energy applications. Here, we report draft genome sequences for the isolated methanogens Methanobacterium bryantii, Methanosarcina spelaei, Methanosphaera cuniculi, and Methanocorpusculum parvum. These anaerobic, methane-producing archaea represent a diverse set of isolates, capable of methylotrophic, acetoclastic, and hydrogenotrophic methanogenesis. Assembly and analysis ofmore » the genomes allowed for simple and rapid reconstruction of metabolism in the four methanogens. Comparison of the distribution of Clusters of Orthologous Groups (COG) proteins to a sample of genomes from the RefSeq database revealed a trend towards energy conservation in genome composition of all methanogens sequenced. Further analysis of the predicted membrane proteins and transporters distinguished differing energy conservation methods utilized during methanogenesis, such as chemiosmotic coupling in Msar. spelaei and electron bifurcation linked to chemiosmotic coupling in Mbac. bryantii and Msph. cuniculi. Methanogens occupy a unique ecological niche, acting as the terminal electron acceptors in anaerobic environments, and their genomes display a significant shift towards energy conservation. The genome-enabled reconstructed metabolisms reported here have significance to diverse anaerobic communities and have led to proposed substrate utilization not previously reported in isolation, such as formate and methanol metabolism in Mbac. bryantii and CO 2 metabolism in Msph. cuniculi. The newly proposed substrates establish an important foundation with which to decipher how methanogens

  3. Note: Durability analysis of optical fiber hydrogen sensor based on Pd-Y alloy film.

    PubMed

    Huang, Peng-cheng; Chen, You-ping; Zhang, Gang; Song, Han; Liu, Yi

    2016-02-01

    The Pd-Y alloy sensing film has an excellent property for hydrogen detection, but just for one month, the sensing film's property decreases seriously. To study the failure of the sensing film, the XPS spectra analysis was used to explore the chemical content of the Pd-Y alloy film, and analysis results demonstrate that the yttrium was oxidized. The paper presented that such an oxidized process was the potential reason of the failure of the sensing film. By understanding the reason of the failure of the sensing film better, we could improve the manufacturing process to enhance the property of hydrogen sensor.

  4. Characterization of atmospheric pressure plasma treated wool/cashmere textiles: Treatment in nitrogen

    NASA Astrophysics Data System (ADS)

    Zanini, Stefano; Citterio, Attilio; Leonardi, Gabriella; Riccardi, Claudia

    2018-01-01

    We performed atmospheric pressure plasma treatments of wool/cashmere (15/85%) textiles with a dielectric barrier discharge (DBD) in nitrogen. The chemical properties of the plasma treated samples were investigated with attenuated total reflectance Fourier transform infrared (FTIR/ATR) spectroscopy, X-ray photoelectron microscopy (XPS), and fatty acid gas chromatographic analysis. Changes in mechanical properties and tactile performance of textiles after the plasma treatment were determined using the KES-F system. The analyses reveal significant surface modification of the treated fabrics, which enhances their surface wettability.

  5. A Systems-Level Analysis Reveals Circadian Regulation of Splicing in Colorectal Cancer.

    PubMed

    El-Athman, Rukeia; Fuhr, Luise; Relógio, Angela

    2018-06-20

    Accumulating evidence points to a significant role of the circadian clock in the regulation of splicing in various organisms, including mammals. Both dysregulated circadian rhythms and aberrant pre-mRNA splicing are frequently implicated in human disease, in particular in cancer. To investigate the role of the circadian clock in the regulation of splicing in a cancer progression context at the systems-level, we conducted a genome-wide analysis and compared the rhythmic transcriptional profiles of colon carcinoma cell lines SW480 and SW620, derived from primary and metastatic sites of the same patient, respectively. We identified spliceosome components and splicing factors with cell-specific circadian expression patterns including SRSF1, HNRNPLL, ESRP1, and RBM 8A, as well as altered alternative splicing events and circadian alternative splicing patterns of output genes (e.g., VEGFA, NCAM1, FGFR2, CD44) in our cellular model. Our data reveals a remarkable interplay between the circadian clock and pre-mRNA splicing with putative consequences in tumor progression and metastasis. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

  6. A near ambient pressure XPS study of subnanometer silver clusters on Al 2O 3 and TiO 2 ultrathin film supports

    DOE PAGES

    Mao, Bao -Hua; Chang, Rui; Shi, Lei; ...

    2014-10-29

    Here, we have investigated model systems of silver clusters with different sizes (3 and 15 atoms) deposited on alumina and titania supports using ambient pressure X-ray photoelectron spectroscopy. The electronic structures of silver clusters and support materials are studied upon exposure to various atmospheres (ultrahigh vacuum, O 2 and CO) at different temperatures. Compared to bulk silver, the binding energies of silver clusters are about 0.55 eV higher on TiO 2 and 0.95 eV higher on Al 2O 3 due to the final state effect and the interaction with supports. No clear size effect of the silver XPS peak ismore » observed on different silver clusters among these samples. Silver clusters on titania show better stability against sintering. Al 2p and Ti 2p core level peak positions of the alumina and titania support surfaces change upon exposure to oxygen while the Ag 3d core level position remains unchanged. We discuss the origin of these core level shifts and their implications for catalytic properties of Ag clusters.« less

  7. Genetic analysis of hyperemesis gravidarum reveals association with intracellular calcium release channel (RYR2).

    PubMed

    Fejzo, Marlena Schoenberg; Myhre, Ronny; Colodro-Conde, Lucía; MacGibbon, Kimber W; Sinsheimer, Janet S; Reddy, M V Prasad Linga; Pajukanta, Päivi; Nyholt, Dale R; Wright, Margaret J; Martin, Nicholas G; Engel, Stephanie M; Medland, Sarah E; Magnus, Per; Mullin, Patrick M

    2017-01-05

    Hyperemesis Gravidarum (HG), severe nausea/vomiting in pregnancy (NVP), can cause poor maternal/fetal outcomes. Genetic predisposition suggests the genetic component is essential in discovering an etiology. We performed whole-exome sequencing of 5 families followed by analysis of variants in 584 cases/431 controls. Variants in RYR2 segregated with disease in 2 families. The novel variant L3277R was not found in any case/control. The rare variant, G1886S was more common in cases (p = 0.046) and extreme cases (p = 0.023). Replication of G1886S using Norwegian/Australian data was supportive. Common variants rs790899 and rs1891246 were significantly associated with HG and weight loss. Copy-number analysis revealed a deletion in a patient. RYR2 encodes an intracellular calcium release channel involved in vomiting, cyclic-vomiting syndrome, and is a thyroid hormone target gene. Additionally, RYR2 is a downstream drug target of Inderal, used to treat HG and CVS. Thus, herein we provide genetic evidence for a pathway and therapy for HG. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  8. Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks.

    PubMed

    Pellacani, Davide; Bilenky, Misha; Kannan, Nagarajan; Heravi-Moussavi, Alireza; Knapp, David J H F; Gakkhar, Sitanshu; Moksa, Michelle; Carles, Annaick; Moore, Richard; Mungall, Andrew J; Marra, Marco A; Jones, Steven J M; Aparicio, Samuel; Hirst, Martin; Eaves, Connie J

    2016-11-15

    The normal adult human mammary gland is a continuous bilayered epithelial system. Bipotent and myoepithelial progenitors are prominent and unique components of the outer (basal) layer. The inner (luminal) layer includes both luminal-restricted progenitors and a phenotypically separable fraction that lacks progenitor activity. We now report an epigenomic comparison of these three subsets with one another, with their associated stromal cells, and with three immortalized, non-tumorigenic human mammary cell lines. Each genome-wide analysis contains profiles for six histone marks, methylated DNA, and RNA transcripts. Analysis of these datasets shows that each cell type has unique features, primarily within genomic regulatory regions, and that the cell lines group together. Analyses of the promoter and enhancer profiles place the luminal progenitors in between the basal cells and the non-progenitor luminal subset. Integrative analysis reveals networks of subset-specific transcription factors. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  9. EEG Cortical Connectivity Analysis of Working Memory Reveals Topological Reorganization in Theta and Alpha Bands

    PubMed Central

    Dai, Zhongxiang; de Souza, Joshua; Lim, Julian; Ho, Paul M.; Chen, Yu; Li, Junhua; Thakor, Nitish; Bezerianos, Anastasios; Sun, Yu

    2017-01-01

    Numerous studies have revealed various working memory (WM)-related brain activities that originate from various cortical regions and oscillate at different frequencies. However, multi-frequency band analysis of the brain network in WM in the cortical space remains largely unexplored. In this study, we employed a graph theoretical framework to characterize the topological properties of the brain functional network in the theta and alpha frequency bands during WM tasks. Twenty-eight subjects performed visual n-back tasks at two difficulty levels, i.e., 0-back (control task) and 2-back (WM task). After preprocessing, Electroencephalogram (EEG) signals were projected into the source space and 80 cortical brain regions were selected for further analysis. Subsequently, the theta- and alpha-band networks were constructed by calculating the Pearson correlation coefficients between the power series (obtained by concatenating the power values of all epochs in each session) of all pairs of brain regions. Graph theoretical approaches were then employed to estimate the topological properties of the brain networks at different WM tasks. We found higher functional integration in the theta band and lower functional segregation in the alpha band in the WM task compared with the control task. Moreover, compared to the 0-back task, altered regional centrality was revealed in the 2-back task in various brain regions that mainly resided in the frontal, temporal and occipital lobes, with distinct presentations in the theta and alpha bands. In addition, significant negative correlations were found between the reaction time with the average path length of the theta-band network and the local clustering of the alpha-band network, which demonstrates the potential for using the brain network metrics as biomarkers for predicting the task performance during WM tasks. PMID:28553215

  10. EEG Cortical Connectivity Analysis of Working Memory Reveals Topological Reorganization in Theta and Alpha Bands.

    PubMed

    Dai, Zhongxiang; de Souza, Joshua; Lim, Julian; Ho, Paul M; Chen, Yu; Li, Junhua; Thakor, Nitish; Bezerianos, Anastasios; Sun, Yu

    2017-01-01

    Numerous studies have revealed various working memory (WM)-related brain activities that originate from various cortical regions and oscillate at different frequencies. However, multi-frequency band analysis of the brain network in WM in the cortical space remains largely unexplored. In this study, we employed a graph theoretical framework to characterize the topological properties of the brain functional network in the theta and alpha frequency bands during WM tasks. Twenty-eight subjects performed visual n -back tasks at two difficulty levels, i.e., 0-back (control task) and 2-back (WM task). After preprocessing, Electroencephalogram (EEG) signals were projected into the source space and 80 cortical brain regions were selected for further analysis. Subsequently, the theta- and alpha-band networks were constructed by calculating the Pearson correlation coefficients between the power series (obtained by concatenating the power values of all epochs in each session) of all pairs of brain regions. Graph theoretical approaches were then employed to estimate the topological properties of the brain networks at different WM tasks. We found higher functional integration in the theta band and lower functional segregation in the alpha band in the WM task compared with the control task. Moreover, compared to the 0-back task, altered regional centrality was revealed in the 2-back task in various brain regions that mainly resided in the frontal, temporal and occipital lobes, with distinct presentations in the theta and alpha bands. In addition, significant negative correlations were found between the reaction time with the average path length of the theta-band network and the local clustering of the alpha-band network, which demonstrates the potential for using the brain network metrics as biomarkers for predicting the task performance during WM tasks.

  11. Phylogenetic Diversity and Genotypical Complexity of H9N2 Influenza A Viruses Revealed by Genomic Sequence Analysis

    PubMed Central

    Dong, Guoying; Luo, Jing; Zhang, Hong; Wang, Chengmin; Duan, Mingxing; Deliberto, Thomas Jude; Nolte, Dale Louis; Ji, Guangju; He, Hongxuan

    2011-01-01

    H9N2 influenza A viruses have become established worldwide in terrestrial poultry and wild birds, and are occasionally transmitted to mammals including humans and pigs. To comprehensively elucidate the genetic and evolutionary characteristics of H9N2 influenza viruses, we performed a large-scale sequence analysis of 571 viral genomes from the NCBI Influenza Virus Resource Database, representing the spectrum of H9N2 influenza viruses isolated from 1966 to 2009. Our study provides a panoramic framework for better understanding the genesis and evolution of H9N2 influenza viruses, and for describing the history of H9N2 viruses circulating in diverse hosts. Panorama phylogenetic analysis of the eight viral gene segments revealed the complexity and diversity of H9N2 influenza viruses. The 571 H9N2 viral genomes were classified into 74 separate lineages, which had marked host and geographical differences in phylogeny. Panorama genotypical analysis also revealed that H9N2 viruses include at least 98 genotypes, which were further divided according to their HA lineages into seven series (A–G). Phylogenetic analysis of the internal genes showed that H9N2 viruses are closely related to H3, H4, H5, H7, H10, and H14 subtype influenza viruses. Our results indicate that H9N2 viruses have undergone extensive reassortments to generate multiple reassortants and genotypes, suggesting that the continued circulation of multiple genotypical H9N2 viruses throughout the world in diverse hosts has the potential to cause future influenza outbreaks in poultry and epidemics in humans. We propose a nomenclature system for identifying and unifying all lineages and genotypes of H9N2 influenza viruses in order to facilitate international communication on the evolution, ecology and epidemiology of H9N2 influenza viruses. PMID:21386964

  12. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

    PubMed

    Preissl, Sebastian; Fang, Rongxin; Huang, Hui; Zhao, Yuan; Raviram, Ramya; Gorkin, David U; Zhang, Yanxiao; Sos, Brandon C; Afzal, Veena; Dickel, Diane E; Kuan, Samantha; Visel, Axel; Pennacchio, Len A; Zhang, Kun; Ren, Bing

    2018-03-01

    Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.

  13. Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins.

    PubMed

    Desdouits, Nathan; Nilges, Michael; Blondel, Arnaud

    2015-02-01

    Protein conformation has been recognized as the key feature determining biological function, as it determines the position of the essential groups specifically interacting with substrates. Hence, the shape of the cavities or grooves at the protein surface appears to drive those functions. However, only a few studies describe the geometrical evolution of protein cavities during molecular dynamics simulations (MD), usually with a crude representation. To unveil the dynamics of cavity geometry evolution, we developed an approach combining cavity detection and Principal Component Analysis (PCA). This approach was applied to four systems subjected to MD (lysozyme, sperm whale myoglobin, Dengue envelope protein and EF-CaM complex). PCA on cavities allows us to perform efficient analysis and classification of the geometry diversity explored by a cavity. Additionally, it reveals correlations between the evolutions of the cavities and structures, and can even suggest how to modify the protein conformation to induce a given cavity geometry. It also helps to perform fast and consensual clustering of conformations according to cavity geometry. Finally, using this approach, we show that both carbon monoxide (CO) location and transfer among the different xenon sites of myoglobin are correlated with few cavity evolution modes of high amplitude. This correlation illustrates the link between ligand diffusion and the dynamic network of internal cavities. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  14. Metabolomic analysis reveals altered metabolic pathways in a rat model of gastric carcinogenesis.

    PubMed

    Gu, Jinping; Hu, Xiaomin; Shao, Wei; Ji, Tianhai; Yang, Wensheng; Zhuo, Huiqin; Jin, Zeyu; Huang, Huiying; Chen, Jiacheng; Huang, Caihua; Lin, Donghai

    2016-09-13

    Gastric cancer (GC) is one of the most malignant tumors with a poor prognosis. Alterations in metabolic pathways are inextricably linked to GC progression. However, the underlying molecular mechanisms remain elusive. We performed NMR-based metabolomic analysis of sera derived from a rat model of gastric carcinogenesis, revealed significantly altered metabolic pathways correlated with the progression of gastric carcinogenesis. Rats were histologically classified into four pathological groups (gastritis, GS; low-grade gastric dysplasia, LGD; high-grade gastric dysplasia, HGD; GC) and the normal control group (CON). The metabolic profiles of the five groups were clearly distinguished from each other. Furthermore, significant inter-metabolite correlations were extracted and used to reconstruct perturbed metabolic networks associated with the four pathological stages compared with the normal stage. Then, significantly altered metabolic pathways were identified by pathway analysis. Our results showed that oxidative stress-related metabolic pathways, choline phosphorylation and fatty acid degradation were continually disturbed during gastric carcinogenesis. Moreover, amino acid metabolism was perturbed dramatically in gastric dysplasia and GC. The GC stage showed more changed metabolite levels and more altered metabolic pathways. Two activated pathways (glycolysis; glycine, serine and threonine metabolism) substantially contributed to the metabolic alterations in GC. These results lay the basis for addressing the molecular mechanisms underlying gastric carcinogenesis and extend our understanding of GC progression.

  15. Camelid genomes reveal evolution and adaptation to desert environments.

    PubMed

    Wu, Huiguang; Guang, Xuanmin; Al-Fageeh, Mohamed B; Cao, Junwei; Pan, Shengkai; Zhou, Huanmin; Zhang, Li; Abutarboush, Mohammed H; Xing, Yanping; Xie, Zhiyuan; Alshanqeeti, Ali S; Zhang, Yanru; Yao, Qiulin; Al-Shomrani, Badr M; Zhang, Dong; Li, Jiang; Manee, Manee M; Yang, Zili; Yang, Linfeng; Liu, Yiyi; Zhang, Jilin; Altammami, Musaad A; Wang, Shenyuan; Yu, Lili; Zhang, Wenbin; Liu, Sanyang; Ba, La; Liu, Chunxia; Yang, Xukui; Meng, Fanhua; Wang, Shaowei; Li, Lu; Li, Erli; Li, Xueqiong; Wu, Kaifeng; Zhang, Shu; Wang, Junyi; Yin, Ye; Yang, Huanming; Al-Swailem, Abdulaziz M; Wang, Jun

    2014-10-21

    Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments.

  16. Surface XPS characterization of NiTi shape memory alloy after advanced oxidation processes in UV/H 2O 2 photocatalytic system

    NASA Astrophysics Data System (ADS)

    Wang, R. M.; Chu, C. L.; Hu, T.; Dong, Y. S.; Guo, C.; Sheng, X. B.; Lin, P. H.; Chung, C. Y.; Chu, P. K.

    2007-08-01

    Surface structure of NiTi shape memory alloy (SMA) was modified by advanced oxidation processes (AOP) in an ultraviolet (UV)/H 2O 2 photocatalytic system, and then systematically characterized with x-ray photoelectron spectroscopy (XPS). It is found that the AOP in UV/H 2O 2 photocatalytic system leads to formation of titanium oxides film on NiTi substrate. Depth profiles of O, Ni and Ti show such a film possesses a graded interface structure to NiTi substrate and there is no intermediate Ni-rich layer like that produced in conventional high temperature oxidation. Except TiO 2 phase, some titanium suboxides (TiO, Ti 2O 3) may also exist in the titanium oxides film. Oxygen mainly presents in metal oxides and some chemisorbed water and OH - are found in titanium oxides film. Ni nearly reaches zero on the upper surface and relatively depleted in the whole titanium oxides film. The work indicates the AOP in UV/H 2O 2 photocatalytic system is a promising way to favor the widespread application of biomedical NiTi SMA by improving its biocompatibility.

  17. Expression analysis revealing destabilizing mutations in phosphomannomutase 2 deficiency (PMM2-CDG): expression analysis of PMM2-CDG mutations.

    PubMed

    Vega, Ana Isabel; Pérez-Cerdá, Celia; Abia, David; Gámez, Alejandra; Briones, Paz; Artuch, Rafael; Desviat, Lourdes R; Ugarte, Magdalena; Pérez, Belén

    2011-08-01

    Deficiency of phosphomannomutase (PMM2, MIM#601785) is the most common congenital disorder of glycosylation. Herein we report the genetic analysis of 22 Spanish PMM2 deficient patients and the functional analysis of 14 nucleotide changes in a prokaryotic expression system in order to elucidate their molecular pathogenesis. PMM2 activity assay revealed the presence of six protein changes with no enzymatic activities (p.R123Q, p.R141H, p.F157S, p.P184T, p.F207S and p.D209G) and seven mild protein changes with residual activities ranging from 16 to 54% (p.L32R, p.V44A p.D65Y, p.P113L p.T118S, p.T237M and p.C241S) and also one variant change with normal activity (p.E197A). The results obtained from Western blot analysis, degradation time courses of 11 protein changes and structural analysis of the PMM2 protein, suggest that the loss-of-function of most mutant proteins is based on their increased susceptibility to degradation or aggregation compared to the wild type protein, considering PMM2 deficiency as a conformational disease. We have identified exclusively catalytic protein change (p.D209G), catalytic protein changes affecting protein stability (p.R123Q and p.R141H), two protein changes disrupting the dimer interface (p.P113L and p.T118S) and several misfolding changes (p.L32R, p.V44A, p.D65Y, p.F157S, p.P184T, p.F207S, p.T237M and p.C241S). Our current work opens a promising therapeutic option using pharmacological chaperones to revert the effect of the characterized misfolding mutations identified in a wide range of PMM2 deficient patients.

  18. Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.

    PubMed

    Illeghems, Koen; De Vuyst, Luc; Papalexandratou, Zoi; Weckx, Stefan

    2012-01-01

    This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria) and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni). Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.

  19. Bioaccumulation characterization of uranium by a novel Streptomyces sporoverrucosus dwc-3.

    PubMed

    Li, Xiaolong; Ding, Congcong; Liao, Jiali; Du, Liang; Sun, Qun; Yang, Jijun; Yang, Yuanyou; Zhang, Dong; Tang, Jun; Liu, Ning

    2016-03-01

    The biosorption mechanisms of uranium on an aerobic bacterial strain Streptomyces sporoverrucosus dwc-3, isolated from a potential disposal site for (ultra-)low uraniferous radioactive waste in Southwest China, were evaluated by using transmission electron microscopy (TEM), energy dispersive X-ray (EDX) analysis, Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), proton induced X-ray emission (PIXE) and enhanced proton backscattering spectrometry (EPBS). Approximately 60% of total uranium at an initial concentration of 10mg/L uranium nitrate solution could be absorbed on 100mg S. sporoverrucosus dwc-3 with an adsorption capacity of more than 3.0mg/g (wet weight) after 12hr at room temperature at pH3.0. The dynamic biosorption process of S. sporoverrucosus dwc-3 for uranyl ions was well described by a pseudo second-order model. S. sporoverrucosus dwc-3 could accumulate uranium on cell walls and within the cell, as revealed by SEM and TEM analysis as well as EDX spectra. XPS and FT-IR analysis further suggested that the absorbed uranium was bound to amino, phosphate and carboxyl groups of the cells. Additionally, PIXE and EPBS results confirmed that ion exchange also contributed to the adsorption process of uranium. Copyright © 2015. Published by Elsevier B.V.

  20. Stable isotope analysis of vertebrae reveals ontogenetic changes in habitat in an endothermic pelagic shark

    PubMed Central

    Carlisle, Aaron B.; Goldman, Kenneth J.; Litvin, Steven Y.; Madigan, Daniel J.; Bigman, Jennifer S.; Swithenbank, Alan M.; Kline, Thomas C.; Block, Barbara A.

    2015-01-01

    Ontogenetic changes in habitat are driven by shifting life-history requirements and play an important role in population dynamics. However, large portions of the life history of many pelagic species are still poorly understood or unknown. We used a novel combination of stable isotope analysis of vertebral annuli, Bayesian mixing models, isoscapes and electronic tag data to reconstruct ontogenetic patterns of habitat and resource use in a pelagic apex predator, the salmon shark (Lamna ditropis). Results identified the North Pacific Transition Zone as the major nursery area for salmon sharks and revealed an ontogenetic shift around the age of maturity from oceanic to increased use of neritic habitats. The nursery habitat may reflect trade-offs between prey availability, predation pressure and thermal constraints on juvenile endothermic sharks. The ontogenetic shift in habitat coincided with a reduction of isotopic niche, possibly reflecting specialization upon particular prey or habitats. Using tagging data to inform Bayesian isotopic mixing models revealed that adult sharks primarily use neritic habitats of Alaska yet receive a trophic subsidy from oceanic habitats. Integrating the multiple methods used here provides a powerful approach to retrospectively study the ecology and life history of migratory species throughout their ontogeny. PMID:25621332

  1. XANES and EXAFS investigation of uranium incorporation on nZVI in the presence of phosphate.

    PubMed

    Qiu, Muqing; Wang, Min; Zhao, Qingzhou; Hu, Baowei; Zhu, Yuling

    2018-06-01

    Effect of phosphate on the reduction of U(VI) on nZVI was determined by batch, XPS, XANES and EXAFS techniques. The batch experiments showed that nZVI was quite effective for the removal of uranium under the anaerobic conditions, whereas the addition of phosphate enhanced uranium removal over wide pH range. At low pH, the reduction of U(VI) to U(IV) significantly decreased with increasing phosphate concentration by XPS and XANES analysis. According to EXAFS analysis, the occurrence of UU shell at 10 mg/L phosphate and pH 4.0 was similar to that of U (IV) O 2 (s), whereas the UP and UFe shells were observed at 50 mg/L phosphate, revealing that reductive co-precipitate (U (IV) O 2 (s)) and precipitation of uranyl-phosphate were observed at low and high phosphate, respectively. The findings are crucial for the prediction of the effect of phosphate on the speciation and binding of uranium by nZVI at low pH, which is significant in controlling the mobility of U(VI) in contaminated environments. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. UHV AFM based colloidal probe studies of adhesive properties of VAlN hard coatings

    NASA Astrophysics Data System (ADS)

    Wiesing, M.; de los Arcos, T.; Grundmeier, G.

    2018-01-01

    The adhesion of polystyrene (PS) on V0.27Al0.29N0.44 and the related influence of the oxidation states of both surfaces was investigated using X-Ray Photoelectron Spectroscopy (XPS) and Colloidal Force Spectroscopy (CFS) in Ultra-High Vacuum (UHV). Complementary, the intimate relation between the adhesion force, the chemical structure and surface polarizability was investigated by XPS valence band spectroscopy and the calculation of non-retarded Hamaker coefficients using Lifshitz theory based on optical data as derived from Reflection Electron Energy Loss Spectroscopy (REELS) spectra. The combined electron and force spectroscopic analysis of the interaction forces disclosed quantitatively the separation of the adhesion force in van der Waals and Lewis acid-base contributions. Further, the surface polarizability of VAlN was shown to be unaffected by oxygen incorporation due to the formation of an only gradually oxidized surface comprising a range of vanadium oxidation states. In contrast, the adhesion force analysis revealed additional Lewis acid-base interactions between the oxidized and non-oxidized VAlN surfaces and carboxyl groups present in the surface of PS after an oxidative oxygen beam treatment.

  3. Formation and stability of dense arrays of Au nanoclusters on hexagonal boron nitride/Rh(111)

    NASA Astrophysics Data System (ADS)

    Patterson, Matthew C.; Habenicht, Bradley F.; Kurtz, Richard L.; Liu, Li; Xu, Ye; Sprunger, Phillip T.

    2014-05-01

    We have studied the nucleation and growth of Au clusters at submonolayer and greater coverages on the h-BN nanomesh grown on Rh(111) by means of scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy (XPS), and density functional theory (DFT). STM reveals that submonolayer Au deposited at 115 K nucleates within the nanomesh pores and remains confined to the pores even after warming to room temperature. Whereas there is a propensity of monoatomic high islands at low temperature, upon annealing, bi- and multilayer Au clusters emerge. Deposition of higher coverages of Au similarly results in Au clusters primarily confined to the nanomesh pores at room temperature. XPS analysis of core-level electronic states in the deposited Au shows strong final-state effects induced by restricted particle size dominating for low Au coverage, with indications that larger Au clusters are negatively charged by interaction through the h-BN monolayer. DFT calculations suggest that the structure of the Au clusters transitions from monolayer to bilayer at a size between 30 and 37 atoms per cluster, in line with our experiment. Bader charge analysis supports the negative charge state of deposited Au.

  4. Characterization of tetraethylene glycol passivated iron nanoparticles

    NASA Astrophysics Data System (ADS)

    Nunes, Eloiza da Silva; Viali, Wesley Renato; da Silva, Sebastião William; Coaquira, José Antonio Huamaní; Garg, Vijayendra Kumar; de Oliveira, Aderbal Carlos; Morais, Paulo César; Jafelicci Júnior, Miguel

    2014-10-01

    The present study describes the synthesis and characterization of iron@iron oxide nanoparticles produced by passivation of metallic iron in tetraethylene glycol media. Structural and chemical characterizations were performed using transmission electron microscopy (TEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and Mössbauer spectroscopy. Pomegranate-like core@shell nanoparticulate material in the size range of 90-120 nm was obtained. According to quantitative phase analysis using Rietveld structure refinement the synthesized iron oxide was identified as magnetite (Fe3O4) whereas the iron to magnetite mass fractions was found to be 47:53. These findings are in good agreement with the data obtained from Mössbauer and thermal gravimetric analysis (TGA). The XPS data revealed the presence of a surface organic layer with higher hydrocarbon content, possibly due to the tetraethylene glycol thermal degradation correlated with iron oxidation. The room-temperature (300 K) saturation magnetization measured for the as-synthesized iron and for the iron-iron oxide were 145 emu g-1 and 131 emu g-1, respectively. The measured saturation magnetizations are in good agreement with data obtained from TEM, XRD and Mössbauer spectroscopy.

  5. Gene Set−Based Integrative Analysis Revealing Two Distinct Functional Regulation Patterns in Four Common Subtypes of Epithelial Ovarian Cancer

    PubMed Central

    Chang, Chia-Ming; Chuang, Chi-Mu; Wang, Mong-Lien; Yang, Yi-Ping; Chuang, Jen-Hua; Yang, Ming-Jie; Yen, Ming-Shyen; Chiou, Shih-Hwa; Chang, Cheng-Chang

    2016-01-01

    Clear cell (CCC), endometrioid (EC), mucinous (MC) and high-grade serous carcinoma (SC) are the four most common subtypes of epithelial ovarian carcinoma (EOC). The widely accepted dualistic model of ovarian carcinogenesis divided EOCs into type I and II categories based on the molecular features. However, this hypothesis has not been experimentally demonstrated. We carried out a gene set-based analysis by integrating the microarray gene expression profiles downloaded from the publicly available databases. These quantified biological functions of EOCs were defined by 1454 Gene Ontology (GO) term and 674 Reactome pathway gene sets. The pathogenesis of the four EOC subtypes was investigated by hierarchical clustering and exploratory factor analysis. The patterns of functional regulation among the four subtypes containing 1316 cases could be accurately classified by machine learning. The results revealed that the ERBB and PI3K-related pathways played important roles in the carcinogenesis of CCC, EC and MC; while deregulation of cell cycle was more predominant in SC. The study revealed that two different functional regulation patterns exist among the four EOC subtypes, which were compatible with the type I and II classifications proposed by the dualistic model of ovarian carcinogenesis. PMID:27527159

  6. Temporal analysis of mtDNA variation reveals decreased genetic diversity in least terns

    USGS Publications Warehouse

    Draheim, Hope M.; Baird, Patricia; Haig, Susan M.

    2012-01-01

    The Least Tern (Sternula antillarum) has undergone large population declines over the last century as a result of direct and indirect anthropogenic factors. The genetic implications of these declines are unknown. We used historical museum specimens (pre-1960) and contemporary (2001–2005) samples to examine range-wide phylogeographic patterns and investigate potential loss in the species' genetic variation. We obtained sequences (522 bp) of the mitochondrial gene for NADH dehydrogenase subunit 6 (ND6) from 268 individuals from across the species' range. Phylogeographic analysis revealed no association with geography or traditional subspecies designations. However, we detected potential reductions in genetic diversity in contemporary samples from California and the Atlantic coast Least Tern from that in historical samples, suggesting that current genetic diversity in Least Tern populations is lower than in their pre-1960 counterparts. Our results offer unique insights into changes in the Least Tern's genetic diversity over the past century and highlight the importance and utility of museum specimens in studies of conservation genetics.

  7. The dynamic evolutionary history of the bananaquit (Coereba flaveola) in the Caribbean revealed by a multigene analysis

    PubMed Central

    2008-01-01

    Background The bananaquit (Coereba flaveola) is a small nectivorous and frugivorous emberizine bird (order Passeriformes) that is an abundant resident throughout the Caribbean region. We used multi-gene analyses to investigate the evolutionary history of this species throughout its distribution in the West Indies and in South and Middle America. We sequenced six mitochondrial genes (3744 base pairs) and three nuclear genes (2049 base pairs) for forty-four bananaquits and three outgroup species. We infer the ancestral area of the present-day bananaquit populations, report on the species' phylogenetic, biogeographic and evolutionary history, and propose scenarios for its diversification and range expansion. Results Phylogenetic concordance between mitochondrial and nuclear genes at the base of the bananaquit phylogeny supported a West Indian origin for continental populations. Multi-gene analysis showing genetic remnants of successive colonization events in the Lesser Antilles reinforced earlier research demonstrating that bananaquits alternate periods of invasiveness and colonization with biogeographic quiescence. Although nuclear genes provided insufficient information at the tips of the tree to further evaluate relationships of closely allied but strongly supported mitochondrial DNA clades, the discrepancy between mitochondrial and nuclear data in the population of Dominican Republic suggested that the mitochondrial genome was recently acquired by introgression from Jamaica. Conclusion This study represents one of the most complete phylogeographic analyses of its kind and reveals three patterns that are not commonly appreciated in birds: (1) island to mainland colonization, (2) multiple expansion phases, and (3) mitochondrial genome replacement. The detail revealed by this analysis will guide evolutionary analyses of populations in archipelagos such as the West Indies, which include islands varying in size, age, and geological history. Our results suggest that

  8. Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots

    PubMed Central

    Fernández-Domínguez, Eva; Bertoncini, Stefania; Chimonas, Marios; Christofi, Vasilis; King, Jonathan; Budowle, Bruce; Manoli, Panayiotis

    2017-01-01

    Genetics can provide invaluable information on the ancestry of the current inhabitants of Cyprus. A Y-chromosome analysis was performed to (i) determine paternal ancestry among the Greek Cypriot (GCy) community in the context of the Central and Eastern Mediterranean and the Near East; and (ii) identify genetic similarities and differences between Greek Cypriots (GCy) and Turkish Cypriots (TCy). Our haplotype-based analysis has revealed that GCy and TCy patrilineages derive primarily from a single gene pool and show very close genetic affinity (low genetic differentiation) to Calabrian Italian and Lebanese patrilineages. In terms of more recent (past millennium) ancestry, as indicated by Y-haplotype sharing, GCy and TCy share much more haplotypes between them than with any surrounding population (7–8% of total haplotypes shared), while TCy also share around 3% of haplotypes with mainland Turks, and to a lesser extent with North Africans. In terms of Y-haplogroup frequencies, again GCy and TCy show very similar distributions, with the predominant haplogroups in both being J2a-M410, E-M78, and G2-P287. Overall, GCy also have a similar Y-haplogroup distribution to non-Turkic Anatolian and Southwest Caucasian populations, as well as Cretan Greeks. TCy show a slight shift towards Turkish populations, due to the presence of Eastern Eurasian (some of which of possible Ottoman origin) Y-haplogroups. Overall, the Y-chromosome analysis performed, using both Y-STR haplotype and binary Y-haplogroup data puts Cypriot in the middle of a genetic continuum stretching from the Levant to Southeast Europe and reveals that despite some differences in haplotype sharing and haplogroup structure, Greek Cypriots and Turkish Cypriots share primarily a common pre-Ottoman paternal ancestry. PMID:28622394

  9. Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots.

    PubMed

    Heraclides, Alexandros; Bashiardes, Evy; Fernández-Domínguez, Eva; Bertoncini, Stefania; Chimonas, Marios; Christofi, Vasilis; King, Jonathan; Budowle, Bruce; Manoli, Panayiotis; Cariolou, Marios A

    2017-01-01

    Genetics can provide invaluable information on the ancestry of the current inhabitants of Cyprus. A Y-chromosome analysis was performed to (i) determine paternal ancestry among the Greek Cypriot (GCy) community in the context of the Central and Eastern Mediterranean and the Near East; and (ii) identify genetic similarities and differences between Greek Cypriots (GCy) and Turkish Cypriots (TCy). Our haplotype-based analysis has revealed that GCy and TCy patrilineages derive primarily from a single gene pool and show very close genetic affinity (low genetic differentiation) to Calabrian Italian and Lebanese patrilineages. In terms of more recent (past millennium) ancestry, as indicated by Y-haplotype sharing, GCy and TCy share much more haplotypes between them than with any surrounding population (7-8% of total haplotypes shared), while TCy also share around 3% of haplotypes with mainland Turks, and to a lesser extent with North Africans. In terms of Y-haplogroup frequencies, again GCy and TCy show very similar distributions, with the predominant haplogroups in both being J2a-M410, E-M78, and G2-P287. Overall, GCy also have a similar Y-haplogroup distribution to non-Turkic Anatolian and Southwest Caucasian populations, as well as Cretan Greeks. TCy show a slight shift towards Turkish populations, due to the presence of Eastern Eurasian (some of which of possible Ottoman origin) Y-haplogroups. Overall, the Y-chromosome analysis performed, using both Y-STR haplotype and binary Y-haplogroup data puts Cypriot in the middle of a genetic continuum stretching from the Levant to Southeast Europe and reveals that despite some differences in haplotype sharing and haplogroup structure, Greek Cypriots and Turkish Cypriots share primarily a common pre-Ottoman paternal ancestry.

  10. Integrated lipidomics and transcriptomic analysis of peripheral blood reveals significantly enriched pathways in type 2 diabetes mellitus.

    PubMed

    Zhao, Chen; Mao, Jinghe; Ai, Junmei; Shenwu, Ming; Shi, Tieliu; Zhang, Daqing; Wang, Xiaonan; Wang, Yunliang; Deng, Youping

    2013-01-01

    Insulin resistance is a key element in the pathogenesis of type 2 diabetes mellitus. Plasma free fatty acids were assumed to mediate the insulin resistance, while the relationship between lipid and glucose disposal remains to be demonstrated across liver, skeletal muscle and blood. We profiled both lipidomics and gene expression of 144 total peripheral blood samples, 84 from patients with T2D and 60 from healthy controls. Then, factor and partial least squares models were used to perform a combined analysis of lipidomics and gene expression profiles to uncover the bioprocesses that are associated with lipidomic profiles in type 2 diabetes. According to factor analysis of the lipidomic profile, several species of lipids were found to be correlated with different phenotypes, including diabetes-related C23:2CE, C23:3CE, C23:4CE, ePE36:4, ePE36:5, ePE36:6; race-related (African-American) PI36:1; and sex-related PE34:1 and LPC18:2. The major variance of gene expression profile was not caused by known factors and no significant difference can be directly derived from differential gene expression profile. However, the combination of lipidomic and gene expression analyses allows us to reveal the correlation between the altered lipid profile with significantly enriched pathways, such as one carbon pool by folate, arachidonic acid metabolism, insulin signaling pathway, amino sugar and nucleotide sugar metabolism, propanoate metabolism, and starch and sucrose metabolism. The genes in these pathways showed a good capability to classify diabetes samples. Combined analysis of gene expression and lipidomic profiling reveals type 2 diabetes-associated lipid species and enriched biological pathways in peripheral blood, while gene expression profile does not show direct correlation. Our findings provide a new clue to better understand the mechanism of disordered lipid metabolism in association with type 2 diabetes.

  11. "Cooperative collapse" of the denatured state revealed through Clausius-Clapeyron analysis of protein denaturation phase diagrams.

    PubMed

    Tischer, Alexander; Machha, Venkata R; Rösgen, Jörg; Auton, Matthew

    2018-02-19

    Protein phase diagrams have a unique potential to identify the presence of additional thermodynamic states even when non-2-state character is not readily apparent from the experimental observables used to follow protein unfolding transitions. Two-state analysis of the von Willebrand factor A3 domain has previously revealed a discrepancy in the calorimetric enthalpy obtained from thermal unfolding transitions as compared with Gibbs-Helmholtz analysis of free energies obtained from the Linear Extrapolation Method (Tischer and Auton, Prot Sci 2013; 22(9):1147-60). We resolve this thermodynamic conundrum using a Clausius-Clapeyron analysis of the urea-temperature phase diagram that defines how ΔH and the urea m-value interconvert through the slope of c m versus T, (∂cm/∂T)=ΔH/(mT). This relationship permits the calculation of ΔH at low temperature from m-values obtained through iso-thermal urea denaturation and high temperature m-values from ΔH obtained through iso-urea thermal denaturation. Application of this equation uncovers sigmoid transitions in both cooperativity parameters as temperature is increased. Such residual thermal cooperativity of ΔH and the m-value confirms the presence of an additional state which is verified to result from a cooperative phase transition between urea-expanded and thermally-compact denatured states. Comparison of the equilibria between expanded and compact denatured ensembles of disulfide-intact and carboxyamidated A3 domains reveals that introducing a single disulfide crosslink does not affect the presence of the additional denatured state. It does, however, make a small thermodynamically favorable free energy (∼-13 ± 1 kJ/mol) contribution to the cooperative denatured state collapse transition as temperature is raised and urea concentration is lowered. The thermodynamics of this "cooperative collapse" of the denatured state retain significant compensations between the enthalpy and entropy contributions to the overall

  12. Comparative analysis of electrophysical properties of ceramic tantalum pentoxide coatings, deposited by electron beam evaporation and magnetron sputtering methods

    NASA Astrophysics Data System (ADS)

    Donkov, N.; Mateev, E.; Safonov, V.; Zykova, A.; Yakovin, S.; Kolesnikov, D.; Sudzhanskaya, I.; Goncharov, I.; Georgieva, V.

    2014-12-01

    Ta2O5 ceramic coatings have been deposited on glass substrates by e-beam evaporation and magnetron sputtering methods. For the magnetron sputtering process Ta target was used. X-ray diffraction measurements show that these coatings are amorphous. XPS survey spectra of the ceramic Ta2O5 coatings were obtained. All spectra consist of well-defined XPS lines of Ta 4f, 4d, 4p and 4s; O 1s; C 1s. Ta 4f doublets are typical for Ta2O5 coatings with two main peaks. Scanning electron microscopy and atomic force microscopy images of the e-beam evaporated and magnetron sputtered Ta2O5 ceramic coatings have revealed a relatively flat surface with no cracks. The dielectric properties of the tantalum pentoxide coatings have been investigated in the frequency range of 100 Hz to 1 MHz. The electrical behaviour of e-beam evaporated and magnetron sputtered Ta2O5 ceramic coatings have also been compared. The deposition process conditions principally effect the structure parameters and electrical properties of Ta2O5 ceramic coatings. The coatings deposited by different methods demonstrate the range of dielectric parameters due to the structural and stoichiometric composition changes

  13. HIDRA-MAT: A Material Analysis Tool for Fusion Devices

    NASA Astrophysics Data System (ADS)

    Andruczyk, Daniel; Rizkallah, Rabel; Bedoya, Felipe; Kapat, Aveek; Schamis, Hanna; Allain, Jean Paul

    2017-10-01

    The former WEGA stellarator which is now operating as HIDRA at the University of Illinois will be almost exclusively used to study the intimate relationship between the plasma interacting with surfaces of different materials. A Material Analysis Tool (HIDRA-MAT) is being designed and will be built based on the successful Material Analysis and Particle Probe (MAPP) which is currently used on NSTX-U at PPPL. This will be an in-situ material diagnostic probe, meaning that all analysis can be done without breaking vacuum. This allows surface changes to be studied in real-time. HIDRA-MAT will consist of several in-situ diagnostics including Langmuir probes (LP), Thermal Desorption Spectroscopy (TDS), X-ray Photo Spectroscopy (XPS) and Ion Scattering Spectroscopy (ISS). This presentation will outline the HIDRA-MAT diagnostic and initial design, as well as its integration into the HIDRA system.

  14. Population Genetic Analysis of Streptomyces albidoflavus Reveals Habitat Barriers to Homologous Recombination in the Diversification of Streptomycetes

    PubMed Central

    Cheng, Kun; Rong, Xiaoying; Pinto-Tomás, Adrián A.; Fernández-Villalobos, Marcela; Murillo-Cruz, Catalina

    2014-01-01

    Examining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains of Streptomyces albidoflavus derived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected in S. albidoflavus, supported by multiple lines of evidence from the pairwise homoplasy index (Φw) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination within Streptomyces species. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred for S. albidoflavus, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes. PMID:25416769

  15. Topological robustness analysis of protein interaction networks reveals key targets for overcoming chemotherapy resistance in glioma

    NASA Astrophysics Data System (ADS)

    Azevedo, Hátylas; Moreira-Filho, Carlos Alberto

    2015-11-01

    Biological networks display high robustness against random failures but are vulnerable to targeted attacks on central nodes. Thus, network topology analysis represents a powerful tool for investigating network susceptibility against targeted node removal. Here, we built protein interaction networks associated with chemoresistance to temozolomide, an alkylating agent used in glioma therapy, and analyzed their modular structure and robustness against intentional attack. These networks showed functional modules related to DNA repair, immunity, apoptosis, cell stress, proliferation and migration. Subsequently, network vulnerability was assessed by means of centrality-based attacks based on the removal of node fractions in descending orders of degree, betweenness, or the product of degree and betweenness. This analysis revealed that removing nodes with high degree and high betweenness was more effective in altering networks’ robustness parameters, suggesting that their corresponding proteins may be particularly relevant to target temozolomide resistance. In silico data was used for validation and confirmed that central nodes are more relevant for altering proliferation rates in temozolomide-resistant glioma cell lines and for predicting survival in glioma patients. Altogether, these results demonstrate how the analysis of network vulnerability to topological attack facilitates target prioritization for overcoming cancer chemoresistance.

  16. Casein mediated green synthesis and decoration of reduced graphene oxide

    NASA Astrophysics Data System (ADS)

    Maddinedi, Sireesh Babu; Mandal, Badal Kumar; Vankayala, Raviraj; Kalluru, Poliraju; Tammina, Sai Kumar; Kiran Kumar, H. A.

    This research is mainly focusing on one-step biosynthesis of graphene from graphene oxide and its stabilization using naturally occurring milk protein, casein. The synthesis of casein reduced graphene oxide (CRGO) was completed within 7 h under reflux at 90 °C with the formation of few layered fine graphene nanosheets. UV-Vis, XRD, XPS analysis data revealed the reduction process of the graphene oxide. Results of FT-IR, HPLC and TEM analysis have shown that the ensuing material consists of graphene decorated with casein molecules. Aspartic acid and glutamic acid residue present in casein molecules are responsible for the reduction of graphene oxide.

  17. Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

    PubMed

    Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

    2016-11-01

    Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

  18. Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

    PubMed Central

    Dewhurst, Henry; Sundararaman, Niveda

    2016-01-01

    Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

  19. Genome-Wide Transcriptome Analysis Reveals Conserved and Distinct Molecular Mechanisms of Al Resistance in Buckwheat (Fagopyrum esculentum Moench) Leaves

    PubMed Central

    Chen, Wei Wei; Xu, Jia Meng; Jin, Jian Feng; Lou, He Qiang; Fan, Wei

    2017-01-01

    Being an Al-accumulating crop, buckwheat detoxifies and tolerates Al not only in roots but also in leaves. While much progress has recently been made toward Al toxicity and resistance mechanisms in roots, little is known about the molecular basis responsible for detoxification and tolerance processes in leaves. Here, we carried out transcriptome analysis of buckwheat leaves in response to Al stress (20 µM, 24 h). We obtained 33,931 unigenes with 26,300 unigenes annotated in the NCBI database, and identified 1063 upregulated and 944 downregulated genes under Al stress. Functional category analysis revealed that genes related to protein translation, processing, degradation and metabolism comprised the biological processes most affected by Al, suggesting that buckwheat leaves maintain flexibility under Al stress by rapidly reprogramming their physiology and metabolism. Analysis of genes related to transcription regulation revealed that a large proportion of chromatin-regulation genes are specifically downregulated by Al stress, whereas transcription factor genes are overwhelmingly upregulated. Furthermore, we identified 78 upregulated and 22 downregulated genes that encode transporters. Intriguingly, only a few genes were overlapped with root Al-regulated transporter genes, which include homologs of AtMATE, ALS1, STAR1, ALS3 and a divalent ion symporter. In addition, we identified a subset of genes involved in development, in which genes associated with flowering regulation were important. Based on these data, it is proposed that buckwheat leaves develop conserved and distinct mechanisms to cope with Al toxicity. PMID:28846612

  20. Genome-Wide Transcriptome Analysis Reveals Conserved and Distinct Molecular Mechanisms of Al Resistance in Buckwheat (Fagopyrum esculentum Moench) Leaves.

    PubMed

    Chen, Wei Wei; Xu, Jia Meng; Jin, Jian Feng; Lou, He Qiang; Fan, Wei; Yang, Jian Li

    2017-08-27

    Being an Al-accumulating crop, buckwheat detoxifies and tolerates Al not only in roots but also in leaves. While much progress has recently been made toward Al toxicity and resistance mechanisms in roots, little is known about the molecular basis responsible for detoxification and tolerance processes in leaves. Here, we carried out transcriptome analysis of buckwheat leaves in response to Al stress (20 µM, 24 h). We obtained 33,931 unigenes with 26,300 unigenes annotated in the NCBI database, and identified 1063 upregulated and 944 downregulated genes under Al stress. Functional category analysis revealed that genes related to protein translation, processing, degradation and metabolism comprised the biological processes most affected by Al, suggesting that buckwheat leaves maintain flexibility under Al stress by rapidly reprogramming their physiology and metabolism. Analysis of genes related to transcription regulation revealed that a large proportion of chromatin-regulation genes are specifically downregulated by Al stress, whereas transcription factor genes are overwhelmingly upregulated. Furthermore, we identified 78 upregulated and 22 downregulated genes that encode transporters. Intriguingly, only a few genes were overlapped with root Al-regulated transporter genes, which include homologs of AtMATE , ALS1 , STAR1 , ALS3 and a divalent ion symporter. In addition, we identified a subset of genes involved in development, in which genes associated with flowering regulation were important. Based on these data, it is proposed that buckwheat leaves develop conserved and distinct mechanisms to cope with Al toxicity.

  1. Genomic and transcriptomic analysis of NDM-1 Klebsiella pneumoniae in spaceflight reveal mechanisms underlying environmental adaptability

    PubMed Central

    Li, Jia; Liu, Fei; Wang, Qi; Ge, Pupu; Woo, Patrick C. Y.; Yan, Jinghua; Zhao, Yanlin; Gao, George F.; Liu, Cui Hua; Liu, Changting

    2014-01-01

    The emergence and rapid spread of New Delhi Metallo-beta-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae strains has caused a great concern worldwide. To better understand the mechanisms underlying environmental adaptation of those highly drug-resistant K. pneumoniae strains, we took advantage of the China's Shenzhou 10 spacecraft mission to conduct comparative genomic and transcriptomic analysis of a NDM-1 K. pneumoniae strain (ATCC BAA-2146) being cultivated under different conditions. The samples were recovered from semisolid medium placed on the ground (D strain), in simulated space condition (M strain), or in Shenzhou 10 spacecraft (T strain) for analysis. Our data revealed multiple variations underlying pathogen adaptation into different environments in terms of changes in morphology, H2O2 tolerance and biofilm formation ability, genomic stability and regulation of metabolic pathways. Additionally, we found a few non-coding RNAs to be differentially regulated. The results are helpful for better understanding the adaptive mechanisms of drug-resistant bacterial pathogens. PMID:25163721

  2. Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis

    NASA Astrophysics Data System (ADS)

    Kaminski, Naftali; Allard, John D.; Pittet, Jean F.; Zuo, Fengrong; Griffiths, Mark J. D.; Morris, David; Huang, Xiaozhu; Sheppard, Dean; Heller, Renu A.

    2000-02-01

    The molecular mechanisms of pulmonary fibrosis are poorly understood. We have used oligonucleotide arrays to analyze the gene expression programs that underlie pulmonary fibrosis in response to bleomycin, a drug that causes lung inflammation and fibrosis, in two strains of susceptible mice (129 and C57BL/6). We then compared the gene expression patterns in these mice with 129 mice carrying a null mutation in the epithelial-restricted integrin 6 subunit (6/-), which develop inflammation but are protected from pulmonary fibrosis. Cluster analysis identified two distinct groups of genes involved in the inflammatory and fibrotic responses. Analysis of gene expression at multiple time points after bleomycin administration revealed sequential induction of subsets of genes that characterize each response. The availability of this comprehensive data set should accelerate the development of more effective strategies for intervention at the various stages in the development of fibrotic diseases of the lungs and other organs.

  3. Systematic Analysis of Two-Component Systems in Citrobacter rodentium Reveals Positive and Negative Roles in Virulence.

    PubMed

    Thomassin, Jenny-Lee; Leclerc, Jean-Mathieu; Giannakopoulou, Natalia; Zhu, Lei; Salmon, Kristiana; Portt, Andrea; Daigle, France; Le Moual, Hervé; Gruenheid, Samantha

    2017-02-01

    Citrobacter rodentium is a murine pathogen used to model intestinal infections caused by the human diarrheal pathogens enterohemorrhagic and enteropathogenic Escherichia coli During infection, bacteria use two-component systems (TCSs) to detect changing environmental cues within the host, allowing for rapid adaptation by altering the expression of specific genes. In this study, 26 TCSs were identified in C. rodentium, and quantitative PCR (qPCR) analysis showed that they are all expressed during murine infection. These TCSs were individually deleted, and the in vitro and in vivo effects were analyzed to determine the functional consequences. In vitro analyses only revealed minor differences, and surprisingly, type III secretion (T3S) was only affected in the ΔarcA strain. Murine infections identified 7 mutants with either attenuated or increased virulence. In agreement with the in vitro T3S assay, the ΔarcA strain was attenuated and defective in colonization and cell adherence. The ΔrcsB strain was among the most highly attenuated strains. The decrease in virulence of this strain may be associated with changes to the cell surface, as Congo red binding was altered, and qPCR revealed that expression of the wcaA gene, which has been implicated in colanic acid production in other bacteria, was drastically downregulated. The ΔuvrY strain exhibited increased virulence compared to the wild type, which was associated with a significant increase in bacterial burden within the mesenteric lymph nodes. The systematic analysis of virulence-associated TCSs and investigation of their functions during infection may open new avenues for drug development. Copyright © 2017 American Society for Microbiology.

  4. Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions

    PubMed Central

    Law, Yingyu; Kirkegaard, Rasmus Hansen; Cokro, Angel Anisa; Liu, Xianghui; Arumugam, Krithika; Xie, Chao; Stokholm-Bjerregaard, Mikkel; Drautz-Moses, Daniela I.; Nielsen, Per Halkjær; Wuertz, Stefan; Williams, Rohan B. H.

    2016-01-01

    Management of phosphorus discharge from human waste is essential for the control of eutrophication in surface waters. Enhanced biological phosphorus removal (EBPR) is a sustainable, efficient way of removing phosphorus from waste water without employing chemical precipitation, but is assumed unachievable in tropical temperatures due to conditions that favour glycogen accumulating organisms (GAOs) over polyphosphate accumulating organisms (PAOs). Here, we show these assumptions are unfounded by studying comparative community dynamics in a full-scale plant following systematic perturbation of operational conditions, which modified community abundance, function and physicochemical state. A statistically significant increase in the relative abundance of the PAO Accumulibacter was associated with improved EBPR activity. GAO relative abundance also increased, challenging the assumption of competition. An Accumulibacter bin-genome was identified from a whole community metagenomic survey, and comparative analysis against extant Accumulibacter genomes suggests a close relationship to Type II. Analysis of the associated metatranscriptome data revealed that genes encoding proteins involved in the tricarboxylic acid cycle and glycolysis pathways were highly expressed, consistent with metabolic modelling results. Our findings show that tropical EBPR is indeed possible, highlight the translational potential of studying competition dynamics in full-scale waste water communities and carry implications for plant design in tropical regions. PMID:27193869

  5. Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions

    NASA Astrophysics Data System (ADS)

    Law, Yingyu; Kirkegaard, Rasmus Hansen; Cokro, Angel Anisa; Liu, Xianghui; Arumugam, Krithika; Xie, Chao; Stokholm-Bjerregaard, Mikkel; Drautz-Moses, Daniela I.; Nielsen, Per Halkjær; Wuertz, Stefan; Williams, Rohan B. H.

    2016-05-01

    Management of phosphorus discharge from human waste is essential for the control of eutrophication in surface waters. Enhanced biological phosphorus removal (EBPR) is a sustainable, efficient way of removing phosphorus from waste water without employing chemical precipitation, but is assumed unachievable in tropical temperatures due to conditions that favour glycogen accumulating organisms (GAOs) over polyphosphate accumulating organisms (PAOs). Here, we show these assumptions are unfounded by studying comparative community dynamics in a full-scale plant following systematic perturbation of operational conditions, which modified community abundance, function and physicochemical state. A statistically significant increase in the relative abundance of the PAO Accumulibacter was associated with improved EBPR activity. GAO relative abundance also increased, challenging the assumption of competition. An Accumulibacter bin-genome was identified from a whole community metagenomic survey, and comparative analysis against extant Accumulibacter genomes suggests a close relationship to Type II. Analysis of the associated metatranscriptome data revealed that genes encoding proteins involved in the tricarboxylic acid cycle and glycolysis pathways were highly expressed, consistent with metabolic modelling results. Our findings show that tropical EBPR is indeed possible, highlight the translational potential of studying competition dynamics in full-scale waste water communities and carry implications for plant design in tropical regions.

  6. Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma.

    PubMed

    Naboulsi, Wael; Megger, Dominik A; Bracht, Thilo; Kohl, Michael; Turewicz, Michael; Eisenacher, Martin; Voss, Don Marvin; Schlaak, Jörg F; Hoffmann, Andreas-Claudius; Weber, Frank; Baba, Hideo A; Meyer, Helmut E; Sitek, Barbara

    2016-01-04

    Hepatocellular carcinoma (HCC) is one of the most aggressive tumors, and the treatment outcome of this disease is improved when the cancer is diagnosed at an early stage. This requires biomarkers allowing an accurate and early tumor diagnosis. To identify potential markers for such applications, we analyzed a patient cohort consisting of 50 patients (50 HCC and 50 adjacent nontumorous tissue samples as controls) using two independent proteomics approaches. We performed label-free discovery analysis on 19 HCC and corresponding tissue samples. The data were analyzed considering events known to take place in early events of HCC development, such as abnormal regulation of Wnt/b-catenin and activation of receptor tyrosine kinases (RTKs). 31 proteins were selected for verification experiments. For this analysis, the second set of the patient cohort (31 HCC and corresponding tissue samples) was analyzed using selected (multiple) reaction monitoring (SRM/MRM). We present the overexpression of ATP-dependent RNA helicase (DDX39), Fibulin-5 (FBLN5), myristoylated alanine-rich C-kinase substrate (MARCKS), and Serpin H1 (SERPINH1) in HCC for the first time. We demonstrate Versican core protein (VCAN) to be significantly associated with well differentiated and low-stage HCC. We revealed for the first time the evidence of VCAN as a potential biomarker for early-HCC diagnosis.

  7. Transcriptomic Analysis of Leaf in Tree Peony Reveals Differentially Expressed Pigments Genes.

    PubMed

    Luo, Jianrang; Shi, Qianqian; Niu, Lixin; Zhang, Yanlong

    2017-02-20

    Tree peony (Paeonia suffruticosa Andrews) is an important traditional flower in China. Besides its beautiful flower, the leaf of tree peony has also good ornamental value owing to its leaf color change in spring. So far, the molecular mechanism of leaf color change in tree peony is unclear. In this study, the pigment level and transcriptome of three different color stages of tree peony leaf were analyzed. The purplish red leaf was rich in anthocyanin, while yellowish green leaf was rich in chlorophyll and carotenoid. Transcriptome analysis revealed that 4302 differentially expressed genes (DEGs) were upregulated, and 4225 were downregulated in the purplish red leaf vs. yellowish green leaf. Among these DEGs, eight genes were predicted to participate in anthocyanin biosynthesis, eight genes were predicted involved in porphyrin and chlorophyll metabolism, and 10 genes were predicted to participate in carotenoid metabolism. In addition, 27 MYBs, 20 bHLHs, 36 WD40 genes were also identified from DEGs. Anthocyanidin synthase (ANS) is the key gene that controls the anthocyanin level in tree peony leaf. Protochlorophyllide oxido-reductase (POR) is the key gene which regulated the chlorophyll content in tree peony leaf.

  8. A Simple Geotracer Compositional Correlation Analysis Reveals Oil Charge and Migration Pathways

    NASA Astrophysics Data System (ADS)

    Yang, Yunlai; Arouri, Khaled

    2016-03-01

    A novel approach, based on geotracer compositional correlation analysis is reported, which reveals the oil charge sequence and migration pathways for five oil fields in Saudi Arabia. The geotracers utilised are carbazoles, a family of neutral pyrrolic nitrogen compounds known to occur naturally in crude oils. The approach is based on the concept that closely related fields, with respect to filling sequence, will show a higher carbazole compositional correlation, than those fields that are less related. That is, carbazole compositional correlation coefficients can quantify the charge and filling relationships among different fields. Consequently, oil migration pathways can be defined based on the established filling relationships. The compositional correlation coefficients of isomers of C1 and C2 carbazoles, and benzo[a]carbazole for all different combination pairs of the five fields were found to vary extremely widely (0.28 to 0.94). A wide range of compositional correlation coefficients allows adequate differentiation of separate filling relationships. Based on the established filling relationships, three distinct migration pathways were inferred, with each apparently being charged from a different part of a common source kitchen. The recognition of these charge and migration pathways will greatly aid the search for new accumulations.

  9. A Simple Geotracer Compositional Correlation Analysis Reveals Oil Charge and Migration Pathways.

    PubMed

    Yang, Yunlai; Arouri, Khaled

    2016-03-11

    A novel approach, based on geotracer compositional correlation analysis is reported, which reveals the oil charge sequence and migration pathways for five oil fields in Saudi Arabia. The geotracers utilised are carbazoles, a family of neutral pyrrolic nitrogen compounds known to occur naturally in crude oils. The approach is based on the concept that closely related fields, with respect to filling sequence, will show a higher carbazole compositional correlation, than those fields that are less related. That is, carbazole compositional correlation coefficients can quantify the charge and filling relationships among different fields. Consequently, oil migration pathways can be defined based on the established filling relationships. The compositional correlation coefficients of isomers of C1 and C2 carbazoles, and benzo[a]carbazole for all different combination pairs of the five fields were found to vary extremely widely (0.28 to 0.94). A wide range of compositional correlation coefficients allows adequate differentiation of separate filling relationships. Based on the established filling relationships, three distinct migration pathways were inferred, with each apparently being charged from a different part of a common source kitchen. The recognition of these charge and migration pathways will greatly aid the search for new accumulations.

  10. Phenotypic factor analysis of psychopathology reveals a new body-related transdiagnostic factor.

    PubMed

    Pezzoli, Patrizia; Antfolk, Jan; Santtila, Pekka

    2017-01-01

    Comorbidity challenges the notion of mental disorders as discrete categories. An increasing body of literature shows that symptoms cut across traditional diagnostic boundaries and interact in shaping the latent structure of psychopathology. Using exploratory and confirmatory factor analysis, we reveal the latent sources of covariation among nine measures of psychopathological functioning in a population-based sample of 13024 Finnish twins and their siblings. By implementing unidimensional, multidimensional, second-order, and bifactor models, we illustrate the relationships between observed variables, specific, and general latent factors. We also provide the first investigation to date of measurement invariance of the bifactor model of psychopathology across gender and age groups. Our main result is the identification of a distinct "Body" factor, alongside the previously identified Internalizing and Externalizing factors. We also report relevant cross-disorder associations, especially between body-related psychopathology and trait anger, as well as substantial sex and age differences in observed and latent means. The findings expand the meta-structure of psychopathology, with implications for empirical and clinical practice, and demonstrate shared mechanisms underlying attitudes towards nutrition, self-image, sexuality and anger, with gender- and age-specific features.

  11. Enhancing electrochemical water-splitting kinetics by polarization-driven formation of near-surface iron(0): an in situ XPS study on perovskite-type electrodes.

    PubMed

    Opitz, Alexander K; Nenning, Andreas; Rameshan, Christoph; Rameshan, Raffael; Blume, Raoul; Hävecker, Michael; Knop-Gericke, Axel; Rupprechter, Günther; Fleig, Jürgen; Klötzer, Bernhard

    2015-02-23

    In the search for optimized cathode materials for high-temperature electrolysis, mixed conducting oxides are highly promising candidates. This study deals with fundamentally novel insights into the relation between surface chemistry and electrocatalytic activity of lanthanum ferrite based electrolysis cathodes. For this means, near-ambient-pressure X-ray photoelectron spectroscopy (NAP-XPS) and impedance spectroscopy experiments were performed simultaneously on electrochemically polarized La0.6 Sr0.4 FeO3-δ (LSF) thin film electrodes. Under cathodic polarization the formation of Fe(0) on the LSF surface could be observed, which was accompanied by a strong improvement of the electrochemical water splitting activity of the electrodes. This correlation suggests a fundamentally different water splitting mechanism in presence of the metallic iron species and may open novel paths in the search for electrodes with increased water splitting activity. © 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

  12. Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups.

    PubMed

    Nourdin-Galindo, Guillermo; Sánchez, Patricio; Molina, Cristian F; Espinoza-Rojas, Daniela A; Oliver, Cristian; Ruiz, Pamela; Vargas-Chacoff, Luis; Cárcamo, Juan G; Figueroa, Jaime E; Mancilla, Marcos; Maracaja-Coutinho, Vinicius; Yañez, Alejandro J

    2017-01-01

    Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis , functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these genes could be

  13. Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups

    PubMed Central

    Nourdin-Galindo, Guillermo; Sánchez, Patricio; Molina, Cristian F.; Espinoza-Rojas, Daniela A.; Oliver, Cristian; Ruiz, Pamela; Vargas-Chacoff, Luis; Cárcamo, Juan G.; Figueroa, Jaime E.; Mancilla, Marcos; Maracaja-Coutinho, Vinicius; Yañez, Alejandro J.

    2017-01-01

    Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these genes could be

  14. Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus

    PubMed Central

    Pathania, Shivalika; Bagler, Ganesh; Ahuja, Paramvir S.

    2016-01-01

    Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Toward these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These genes may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of R. serpentina, and key genes that contribute toward diversification of specific metabolites. PMID:27588023

  15. Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus.

    PubMed

    Pathania, Shivalika; Bagler, Ganesh; Ahuja, Paramvir S

    2016-01-01

    Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Toward these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These genes may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of R. serpentina, and key genes that contribute toward diversification of specific metabolites.

  16. Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters.

    PubMed

    de Menezes, Alexandre B; Prendergast-Miller, Miranda T; Richardson, Alan E; Toscas, Peter; Farrell, Mark; Macdonald, Lynne M; Baker, Geoff; Wark, Tim; Thrall, Peter H

    2015-08-01

    Network and multivariate statistical analyses were performed to determine interactions between bacterial and fungal community terminal restriction length polymorphisms as well as soil properties in paired woodland and pasture sites. Canonical correspondence analysis (CCA) revealed that shifts in woodland community composition correlated with soil dissolved organic carbon, while changes in pasture community composition correlated with moisture, nitrogen and phosphorus. Weighted correlation network analysis detected two distinct microbial modules per land use. Bacterial and fungal ribotypes did not group separately, rather all modules comprised of both bacterial and fungal ribotypes. Woodland modules had a similar fungal : bacterial ribotype ratio, while in the pasture, one module was fungal dominated. There was no correspondence between pasture and woodland modules in their ribotype composition. The modules had different relationships to soil variables, and these contrasts were not detected without the use of network analysis. This study demonstrated that fungi and bacteria, components of the soil microbial communities usually treated as separate functional groups as in a CCA approach, were co-correlated and formed distinct associations in these adjacent habitats. Understanding these distinct modular associations may shed more light on their niche space in the soil environment, and allow a more realistic description of soil microbial ecology and function. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  17. Modern Material Analysis Instruments Add a New Dimension to Materials Characterization and Failure Analysis

    NASA Technical Reports Server (NTRS)

    Panda, Binayak

    2009-01-01

    Modern analytical tools can yield invaluable results during materials characterization and failure analysis. Scanning electron microscopes (SEMs) provide significant analytical capabilities, including angstrom-level resolution. These systems can be equipped with a silicon drift detector (SDD) for very fast yet precise analytical mapping of phases, as well as electron back-scattered diffraction (EBSD) units to map grain orientations, chambers that admit large samples, variable pressure for wet samples, and quantitative analysis software to examine phases. Advanced solid-state electronics have also improved surface and bulk analysis instruments: Secondary ion mass spectroscopy (SIMS) can quantitatively determine and map light elements such as hydrogen, lithium, and boron - with their isotopes. Its high sensitivity detects impurities at parts per billion (ppb) levels. X-ray photo-electron spectroscopy (XPS) can determine oxidation states of elements, as well as identifying polymers and measuring film thicknesses on coated composites. This technique is also known as electron spectroscopy for chemical analysis (ESCA). Scanning Auger electron spectroscopy (SAM) combines surface sensitivity, spatial lateral resolution (10 nm), and depth profiling capabilities to describe elemental compositions of near and below surface regions down to the chemical state of an atom.

  18. Social phobia subtypes in the general population revealed by cluster analysis.

    PubMed

    Furmark, T; Tillfors, M; Stattin, H; Ekselius, L; Fredrikson, M

    2000-11-01

    Epidemiological data on subtypes of social phobia are scarce and their defining features are debated. Hence, the present study explored the prevalence and descriptive characteristics of empirically derived social phobia subgroups in the general population. To reveal subtypes, data on social distress, functional impairment, number of social fears and criteria fulfilled for avoidant personality disorder were extracted from a previously published epidemiological study of 188 social phobics and entered into an hierarchical cluster analysis. Criterion validity was evaluated by comparing clusters on the Social Phobia Scale (SPS) and the Social Interaction Anxiety Scale (SIAS). Finally, profile analyses were performed in which clusters were compared on a set of sociodemographic and descriptive characteristics. Three clusters emerged, consisting of phobics scoring either high (generalized subtype), intermediate (non-generalized subtype) or low (discrete subtype) on all variables. Point prevalence rates were 2.0%, 5.9% and 7.7% respectively. All subtypes were distinguished on both SPS and SIAS. Generalized or severe social phobia tended to be over-represented among individuals with low levels of educational attainment and social support. Overall, public-speaking was the most common fear. Although categorical distinctions may be used, the present data suggest that social phobia subtypes in the general population mainly differ dimensionally along a mild moderate-severe continuum, and that the number of cases declines with increasing severity.

  19. Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria.

    PubMed

    Salzman, Nita H; de Jong, Hendrik; Paterson, Yvonne; Harmsen, Hermie J M; Welling, Gjalt W; Bos, Nicolaas A

    2002-11-01

    Total genomic DNA from samples of intact mouse small intestine, large intestine, caecum and faeces was used as template for PCR amplification of 16S rRNA gene sequences with conserved bacterial primers. Phylogenetic analysis of the amplification products revealed 40 unique 16S rDNA sequences. Of these sequences, 25% (10/40) corresponded to described intestinal organisms of the mouse, including Lactobacillus spp., Helicobacter spp., segmented filamentous bacteria and members of the altered Schaedler flora (ASF360, ASF361, ASF502 and ASF519); 75% (30/40) represented novel sequences. A large number (11/40) of the novel sequences revealed a new operational taxonomic unit (OTU) belonging to the Cytophaga-Flavobacter-Bacteroides phylum, which the authors named 'mouse intestinal bacteria'. 16S rRNA probes were developed for this new OTU. Upon analysis of the novel sequences, eight were found to cluster within the Eubacterium rectale-Clostridium coccoides group and three clustered within the Bacteroides group. One of the novel sequences was distantly related to Verrucomicrobium spinosum and one was distantly related to Bacillus mycoides. Oligonucleotide probes specific for the 16S rRNA of these novel clones were generated. Using a combination of four previously described and four newly designed probes, approximately 80% of bacteria recovered from the murine large intestine and 71% of bacteria recovered from the murine caecum could be identified by fluorescence in situ hybridization (FISH).

  20. REVEAL: Software Documentation and Platform Migration

    NASA Technical Reports Server (NTRS)

    Wilson, Michael A.; Veibell, Victoir T.

    2011-01-01

    The Research Environment for Vehicle Embedded Analysis on Linux (REVEAL) is reconfigurable data acquisition software designed for network-distributed test and measurement applications. In development since 2001, it has been successfully demonstrated in support of a number of actual missions within NASA's Suborbital Science Program. Improvements to software configuration control were needed to properly support both an ongoing transition to operational status and continued evolution of REVEAL capabilities. For this reason the project described in this report targets REVEAL software source documentation and deployment of the software on a small set of hardware platforms different from what is currently used in the baseline system implementation. This presentation specifically describes the actions taken over a ten week period by two undergraduate student interns and serves as an overview of the content of the final report for that internship.

  1. Atomic layer deposited TaCy metal gates: Impact on microstructure, electrical properties, and work function on HfO2 high-k dielectrics

    NASA Astrophysics Data System (ADS)

    Triyoso, D. H.; Gregory, R.; Schaeffer, J. K.; Werho, D.; Li, D.; Marcus, S.; Wilk, G. D.

    2007-11-01

    TaCy has been reported to have the appropriate work function for negative metal-oxide semiconductor metal in high-k metal-oxide field-effect transistors. As device size continues to shrink, a conformal deposition for metal gate electrodes is needed. In this work, we report on the development and characterization of a novel TaCy process by atomic layer deposition (ALD). Detailed physical properties of TaCy films are studied using ellipsometry, a four-point probe, Rutherford backscattering spectrometry (RBS), x-ray photoelectron spectroscopy (XPS), and x-ray diffraction (XRD). RBS and XPS analysis indicate that TaCy films are near-stoichiometric, nitrogen free, and have low oxygen impurities. Powder XRD spectra showed that ALD films have a cubic microstructure. XPS carbon bonding studies revealed that little or no glassy carbon is present in the bulk of the film. Excellent electrical properties are obtained using ALD TaCy as a metal gate electrode. Well-behaved capacitance-voltage characteristics with ALD HfO2 gate dielectrics are demonstrated for TaCy thicknesses of 50, 100, and 250 Å. A low fixed charge (˜2-4×10-11 cm-2) is observed for all ALD HfO2/ALD TaCy devices. Increasing the thickness of ALD TaCy results in a decrease in work function (4.77 to 4.54 eV) and lower threshold voltages.

  2. A study of the UV and VUV degradation of FEP

    NASA Technical Reports Server (NTRS)

    George, Graeme A.; Hill, David J. T.; Odonnell, James H.; Pomery, Peter J.; Rasoul, Firas A.

    1993-01-01

    UV and VUV degradation of fluorinated ethylene propylene (FEP) copolymer was studied using electron spin resonance (ESR) spectroscopy, x-ray photoelectron spectroscopy (XPS), and scanning electron microscopy (SEM). The ESR study revealed the formation of a terminal polymer radical. The stability of this radical was investigated under different environments. An XPS study of FEP film exposed to VUV and atomic oxygen showed that oxidation takes place on the polymer surface. The study revealed also that the percentage of CF2 in the polymer surface decreased with exposure time and the percentage of CF, CF3, and carbon attached to oxygen increased. SEM micrographs of FEP film exposed to VUV and atomic oxygen identified a rough surface with undulations similar to sand dunes.

  3. Network Analysis Reveals Putative Genes Affecting Meat Quality in Angus Cattle.

    PubMed

    Mateescu, Raluca G; Garrick, Dorian J; Reecy, James M

    2017-01-01

    Improvements in eating satisfaction will benefit consumers and should increase beef demand which is of interest to the beef industry. Tenderness, juiciness, and flavor are major determinants of the palatability of beef and are often used to reflect eating satisfaction. Carcass qualities are used as indicator traits for meat quality, with higher quality grade carcasses expected to relate to more tender and palatable meat. However, meat quality is a complex concept determined by many component traits making interpretation of genome-wide association studies (GWAS) on any one component challenging to interpret. Recent approaches combining traditional GWAS with gene network interactions theory could be more efficient in dissecting the genetic architecture of complex traits. Phenotypic measures of 23 traits reflecting carcass characteristics, components of meat quality, along with mineral and peptide concentrations were used along with Illumina 54k bovine SNP genotypes to derive an annotated gene network associated with meat quality in 2,110 Angus beef cattle. The efficient mixed model association (EMMAX) approach in combination with a genomic relationship matrix was used to directly estimate the associations between 54k SNP genotypes and each of the 23 component traits. Genomic correlated regions were identified by partial correlations which were further used along with an information theory algorithm to derive gene network clusters. Correlated SNP across 23 component traits were subjected to network scoring and visualization software to identify significant SNP. Significant pathways implicated in the meat quality complex through GO term enrichment analysis included angiogenesis, inflammation, transmembrane transporter activity, and receptor activity. These results suggest that network analysis using partial correlations and annotation of significant SNP can reveal the genetic architecture of complex traits and provide novel information regarding biological mechanisms

  4. Structure-Based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces.

    PubMed

    Engin, H Billur; Kreisberg, Jason F; Carter, Hannah

    2016-01-01

    Recently it has been shown that cancer mutations selectively target protein-protein interactions. We hypothesized that mutations affecting distinct protein interactions involving established cancer genes could contribute to tumor heterogeneity, and that novel mechanistic insights might be gained into tumorigenesis by investigating protein interactions under positive selection in cancer. To identify protein interactions under positive selection in cancer, we mapped over 1.2 million nonsynonymous somatic cancer mutations onto 4,896 experimentally determined protein structures and analyzed their spatial distribution. In total, 20% of mutations on the surface of known cancer genes perturbed protein-protein interactions (PPIs), and this enrichment for PPI interfaces was observed for both tumor suppressors (Odds Ratio 1.28, P-value < 10(-4)) and oncogenes (Odds Ratio 1.17, P-value < 10(-3)). To study this further, we constructed a bipartite network representing structurally resolved PPIs from all available human complexes in the Protein Data Bank (2,864 proteins, 3,072 PPIs). Analysis of frequently mutated cancer genes within this network revealed that tumor-suppressors, but not oncogenes, are significantly enriched with functional mutations in homo-oligomerization regions (Odds Ratio 3.68, P-Value < 10(-8)). We present two important examples, TP53 and beta-2-microglobulin, for which the patterns of somatic mutations at interfaces provide insights into specifically perturbed biological circuits. In patients with TP53 mutations, patient survival correlated with the specific interactions that were perturbed. Moreover, we investigated mutations at the interface of protein-nucleotide interactions and observed an unexpected number of missense mutations but not silent mutations occurring within DNA and RNA binding sites. Finally, we provide a resource of 3,072 PPI interfaces ranked according to their mutation rates. Analysis of this list highlights 282 novel candidate cancer

  5. The Immersive Virtual Reality Experience: A Typology of Users Revealed Through Multiple Correspondence Analysis Combined with Cluster Analysis Technique.

    PubMed

    Rosa, Pedro J; Morais, Diogo; Gamito, Pedro; Oliveira, Jorge; Saraiva, Tomaz

    2016-03-01

    Immersive virtual reality is thought to be advantageous by leading to higher levels of presence. However, and despite users getting actively involved in immersive three-dimensional virtual environments that incorporate sound and motion, there are individual factors, such as age, video game knowledge, and the predisposition to immersion, that may be associated with the quality of virtual reality experience. Moreover, one particular concern for users engaged in immersive virtual reality environments (VREs) is the possibility of side effects, such as cybersickness. The literature suggests that at least 60% of virtual reality users report having felt symptoms of cybersickness, which reduces the quality of the virtual reality experience. The aim of this study was thus to profile the right user to be involved in a VRE through head-mounted display. To examine which user characteristics are associated with the most effective virtual reality experience (lower cybersickness), a multiple correspondence analysis combined with cluster analysis technique was performed. Results revealed three distinct profiles, showing that the PC gamer profile is more associated with higher levels of virtual reality effectiveness, that is, higher predisposition to be immersed and reduced cybersickness symptoms in the VRE than console gamer and nongamer. These findings can be a useful orientation in clinical practice and future research as they help identify which users are more predisposed to benefit from immersive VREs.

  6. Location of Varying Hydrophobicity Zinc(II) Phthalocyanine-Type Photosensitizers in Methoxy Poly(ethylene oxide) and Poly(l-lactide) Block Copolymer Micelles Using 1H NMR and XPS Techniques.

    PubMed

    Lamch, Łukasz; Tylus, Włodzimierz; Jewgiński, Michał; Latajka, Rafał; Wilk, Kazimiera A

    2016-12-15

    Hydrophobic zinc(II) phthalocyanine-type derivatives, solubilized in polymeric micelles (PMs), provide a befitting group of so-called nanophotosensitizers, suitable for a variety of photodynamic therapy (PDT) protocols. The factors that influence the success of such products in PDT are the location of the active cargo in the PMs and the nanocarrier-enhanced ability to safely interact with biological systems and fulfill their therapeutic functions. Therefore, the aim of this work was to determine the solubilization loci of three phthalocyanines of varying hydrophobicity, i.e., zinc(II) phthalocyanine (ZnPc), along with its tetrasulfonic acid (ZnPc-sulfo 4 ) and perfluorinated (ZnPcF 16 ) derivatives, loaded in polymeric micelles of methoxy poly(ethylene oxide)-b-poly(l-lactide) (mPEG-b-PLLA), by means of 1 H nuclear magnetic resonance (NMR) and X-ray photoelectron spectroscopy (XPS) combined with ion sputtering. Furthermore, the microenvironment influence upon the chemical and physical status of the solubilized cargo in PMs, expressed by photobleaching and reactive oxygen species (ROS) generation comparing to the same properties of native cargoes in solution, was also evaluated and discussed in regards to the probing location data. The studied phthalocyanine-loaded PMs exhibited good physical stability, high drug-loading efficiency, and a size of less than ca. 150 nm with low polydispersity indices. The formation of polymeric micelles and the solubilization locus were investigated by 1 H NMR and XPS. ZnPc localized within the PM core, whereas both ZnPcF 16 and ZnPc-sulfo 4 - in the corona of PMs. We proved that the cargo locus is crucial for the photochemical properties of the studied phthalocyanines; the increase in photostability and ability to generate ROS in micellar solution compared to free photosensitizer was most significant for the photosensitizer in the PM core. Our results indicate the role of the cargo location in the PM microenvironment and demonstrate

  7. Analysis of an RNA-seq Strand-Specific Library from an East Timorese Cucumber Sample Reveals a Complete Cucurbit aphid-borne yellows virus Genome.

    PubMed

    Maina, Solomon; Edwards, Owain R; de Almeida, Luis; Ximenes, Abel; Jones, Roger A C

    2017-05-11

    Analysis of an RNA-seq library from cucumber leaf RNA extracted from a fast technology for analysis of nucleic acids (FTA) card revealed the first complete genome of Cucurbit aphid-borne yellows virus (CABYV) from East Timor. We compare it with 35 complete CABYV genomes from other world regions. It most resembled the genome of the South Korean isolate HD118. Copyright © 2017 Maina et al.

  8. Analysis of an RNA-seq Strand-Specific Library from an East Timorese Cucumber Sample Reveals a Complete Cucurbit aphid-borne yellows virus Genome

    PubMed Central

    Maina, Solomon; Edwards, Owain R.; de Almeida, Luis; Ximenes, Abel

    2017-01-01

    ABSTRACT Analysis of an RNA-seq library from cucumber leaf RNA extracted from a fast technology for analysis of nucleic acids (FTA) card revealed the first complete genome of Cucurbit aphid-borne yellows virus (CABYV) from East Timor. We compare it with 35 complete CABYV genomes from other world regions. It most resembled the genome of the South Korean isolate HD118. PMID:28495776

  9. Combined Metabolomic Analysis of Plasma and Urine Reveals AHBA, Tryptophan and Serotonin Metabolism as Potential Risk Factors in Gestational Diabetes Mellitus (GDM)

    PubMed Central

    Leitner, Miriam; Fragner, Lena; Danner, Sarah; Holeschofsky, Nastassja; Leitner, Karoline; Tischler, Sonja; Doerfler, Hannes; Bachmann, Gert; Sun, Xiaoliang; Jaeger, Walter; Kautzky-Willer, Alexandra; Weckwerth, Wolfram

    2017-01-01

    Gestational diabetes mellitus during pregnancy has severe implications for the health of the mother and the fetus. Therefore, early prediction and an understanding of the physiology are an important part of prenatal care. Metabolite profiling is a long established method for the analysis and prediction of metabolic diseases. Here, we applied untargeted and targeted metabolomic protocols to analyze plasma and urine samples of pregnant women with and without GDM. Univariate and multivariate statistical analyses of metabolomic profiles revealed markers such as 2-hydroxybutanoic acid (AHBA), 3-hydroxybutanoic acid (BHBA), amino acids valine and alanine, the glucose-alanine-cycle, but also plant-derived compounds like sitosterin as different between control and GDM patients. PLS-DA and VIP analysis revealed tryptophan as a strong variable separating control and GDM. As tryptophan is biotransformed to serotonin we hypothesized whether serotonin metabolism might also be altered in GDM. To test this hypothesis we applied a method for the analysis of serotonin, metabolic intermediates and dopamine in urine by stable isotope dilution direct infusion electrospray ionization mass spectrometry (SID-MS). Indeed, serotonin and related metabolites differ significantly between control and GDM patients confirming the involvement of serotonin metabolism in GDM. Clustered correlation coefficient visualization of metabolite correlation networks revealed the different metabolic signatures between control and GDM patients. Eventually, the combination of selected blood plasma and urine sample metabolites improved the AUC prediction accuracy to 0.99. The detected GDM candidate biomarkers and the related systemic metabolic signatures are discussed in their pathophysiological context. Further studies with larger cohorts are necessary to underpin these observations. PMID:29312952

  10. Metatranscriptome sequence analysis reveals diel periodicity of microbial community gene expression in the ocean's interior

    NASA Astrophysics Data System (ADS)

    Vislova, A.; Aylward, F.; Sosa, O.; DeLong, E.

    2016-02-01

    Previous work has revealed diel periodicity of gene expression in key metabolic pathways in both autotrophic and heterotrophic microbes in the surface ocean. In this study, we investigated patterns of diel periodicity of gene expression in depth profiles (25, 75, 125 and 250 meters). We postulated that microbial diel transcriptional signals would be increasingly dampened with depth, and that the timing of peak expression of specific transcripts would be shifted in time between depths, in accordance with depth-dependent diel light variability. Bacterioplankton were sampled from four depths every four hours at station ALOHA (22° 45' N 158° W) over 2 days. RNA was extracted from cells preserved on filters, converted to cDNA, and sequenced on the Illumina platform. Surprisingly, harmonic regression analysis revealed an increasing proportion of genes with diel periodic expression patterns with increasing depth between 25- 125 meters. At 250 meters, the proportion of genes exhibiting diel expression patterns decreased an order of magnitude compared to the photic zone. Community composition, functional gene categories, and diel patterns of gene expression were significantly different between the photic zone and 250 meter samples. The signals driving diel periodic gene expression in microbes at 250 meters is under further investigation. These data are now beginning provide a better understanding of the tempo and mode of microbial dynamics among specific taxa, throughout the ocean's interior.

  11. Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates

    PubMed Central

    Shenker, Sol; Mohammed, Jaaved; Lai, Eric C.

    2015-01-01

    Mirtrons are microRNA (miRNA) substrates that utilize the splicing machinery to bypass the necessity of Drosha cleavage for their biogenesis. Expanding our recent efforts for mammalian mirtron annotation, we use meta-analysis of aggregate datasets to identify ~500 novel mouse and human introns that confidently generate diced small RNA duplexes. These comprise nearly 1000 total loci distributed in four splicing-mediated biogenesis subclasses, with 5'-tailed mirtrons as, by far, the dominant subtype. Thus, mirtrons surprisingly comprise a substantial fraction of endogenous Dicer substrates in mammalian genomes. Although mirtron-derived small RNAs exhibit overall expression correlation with their host mRNAs, we observe a subset with substantial differences that suggest regulated processing or accumulation. We identify characteristic sequence, length, and structural features of mirtron loci that distinguish them from bulk introns, and find that mirtrons preferentially emerge from genes with larger numbers of introns. While mirtrons generate miRNA-class regulatory RNAs, we also find that mirtrons exhibit many features that distinguish them from canonical miRNAs. We observe that conventional mirtron hairpins are substantially longer than Drosha-generated pre-miRNAs, indicating that the characteristic length of canonical pre-miRNAs is not a general feature of Dicer substrate hairpins. In addition, mammalian mirtrons exhibit unique patterns of ordered 5' and 3' heterogeneity, which reveal hidden complexity in miRNA processing pathways. These include broad 3'-uridylation of mirtron hairpins, atypically heterogeneous 5' termini that may result from exonucleolytic processing, and occasionally robust decapitation of the 5' guanine (G) of mirtron-5p species defined by splicing. Altogether, this study reveals that this extensive class of non-canonical miRNA bears a multitude of characteristic properties, many of which raise general mechanistic questions regarding the processing

  12. Laminar and dorsoventral molecular organization of the medial entorhinal cortex revealed by large-scale anatomical analysis of gene expression.

    PubMed

    Ramsden, Helen L; Sürmeli, Gülşen; McDonagh, Steven G; Nolan, Matthew F

    2015-01-01

    Neural circuits in the medial entorhinal cortex (MEC) encode an animal's position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH) images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. We propose a new molecular basis for distinguishing the deep layers of the MEC and show that their similarity to corresponding layers of neocortex is greater than that of superficial layers. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. We also reveal laminar organization of genes related to disease pathology and suggest that a high metabolic demand predisposes layer II to neurodegenerative pathology. In principle, our computational pipeline can be applied to high-throughput analysis of many forms of neuroanatomical data. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations.

  13. Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression

    PubMed Central

    Ramsden, Helen L.; Sürmeli, Gülşen; McDonagh, Steven G.; Nolan, Matthew F.

    2015-01-01

    Neural circuits in the medial entorhinal cortex (MEC) encode an animal’s position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH) images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. We propose a new molecular basis for distinguishing the deep layers of the MEC and show that their similarity to corresponding layers of neocortex is greater than that of superficial layers. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. We also reveal laminar organization of genes related to disease pathology and suggest that a high metabolic demand predisposes layer II to neurodegenerative pathology. In principle, our computational pipeline can be applied to high-throughput analysis of many forms of neuroanatomical data. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations. PMID:25615592

  14. Phylogenetic analysis reveals two genotypes of the emerging fungus Mucor indicus, an opportunistic human pathogen in immunocompromised patients.

    PubMed

    Taj-Aldeen, Saad J; Almaslamani, Muna; Theelen, Bart; Boekhout, Teun

    2017-07-12

    Mucormycosis is a rare fungal infection caused by Mucor indicus. Phylogenetic analysis of many M. indicus isolates, mainly sampled from different clinical and environmental specimens collected worldwide, revealed two genotypes, I and II, based on ITS and D1/D2 LSU rDNA sequences. A retrospective review of the literature revealed 13 cases. Eight (76.9%) patients had disseminated infections, and the overall mortality rate was 30.7%. A pulmonary infection caused by M. indicus genotype I in a liver transplant recipient was disseminated to include the skin and was successfully treated with liposomal amphotericin B and aggressive surgery. M. indicus can infect a wide variety of patients with no real preference for the site of infection. We concluded that M. indicus has emerged as a significant cause of invasive mycosis in severely immunocompromised patients worldwide. Early diagnosis and initiation of appropriate therapy could enhance survival in these immunocompromised patient populations.

  15. Structural, optical and electronic properties of K2Ba(NO3)4 crystal

    NASA Astrophysics Data System (ADS)

    Isaenko, L. I.; Korzhneva, K. E.; Goryainov, S. V.; Goloshumova, A. A.; Sheludyakova, L. A.; Bekenev, V. L.; Khyzhun, O. Y.

    2018-02-01

    Nitrate crystals reveal nonlinear optical properties and could be considered as converters of laser radiation in the short-wave region. The conditions for obtaining and basic properties of K2Ba(NO3)4 double nitrate crystals were investigated. Crystal growth was implemented by slow cooling in the temperature range of 72-49 °C and low rate evaporation. The structural analysis of K2Ba(NO3)4 formation on the basis of two mixed simple nitrate structures is discussed. The main groups of oscillations in K2Ba(NO3)4 crystal were revealed using Raman and IR spectroscopy, and the table of vibrations for this compound was compiled. The electronic structure of K2Ba(NO3)4 was elucidated in the present work from both experimental and theoretical viewpoints. In particular, X-ray photoelectron spectroscopy (XPS) was employed in the present work to measure binding energies of the atoms constituting the titled compound and its XPS valence-band spectrum for both pristine and Ar+ ion-bombarded surfaces. Further, total and partial densities of states of constituent atoms of K2Ba(NO3)4 have been calculated. The calculations reveal that the O 2p states dominate in the total valence-band region of K2Ba(NO3)4 except of its bottom, where K 3p and Ba 5p states are the principal contributors, while the bottom of the conduction band is composed mainly of the unoccupied O 2p states, with somewhat smaller contributions of the N 2p∗ states as well. With respect to the occupation of the valence band by the O 2p states, the present band-structure calculations are confirmed by comparison on a common energy scale of the XPS valence-band spectrum and the X-ray emission O Kα band for the K2Ba(NO3)4 crystal under study. Furthermore, the present calculations indicate that the K2Ba(NO3)4 compound is a direct-gap material.

  16. Salivary gland proteome analysis reveals modulation of anopheline unique proteins in insensitive acetylcholinesterase resistant Anopheles gambiae mosquitoes.

    PubMed

    Cornelie, Sylvie; Rossignol, Marie; Seveno, Martial; Demettre, Edith; Mouchet, François; Djègbè, Innocent; Marin, Philippe; Chandre, Fabrice; Corbel, Vincent; Remoué, Franck; Mathieu-Daudé, Françoise

    2014-01-01

    Insensitive acetylcholinesterase resistance due to a mutation in the acetylcholinesterase (ace) encoding ace-1 gene confers cross-resistance to organophosphate and carbamate insecticides in Anopheles gambiae populations from Central and West Africa. This mutation is associated with a strong genetic cost revealed through alterations of some life history traits but little is known about the physiological and behavioural changes in insects bearing the ace-1(R) allele. Comparative analysis of the salivary gland contents between An. gambiae susceptible and ace-1(R) resistant strains was carried out to charaterize factors that could be involved in modifications of blood meal process, trophic behaviour or pathogen interaction in the insecticide-resistant mosquitoes. Differential analysis of the salivary gland protein profiles revealed differences in abundance for several proteins, two of them showing major differences between the two strains. These two proteins identified as saglin and TRIO are salivary gland-1 related proteins, a family unique to anopheline mosquitoes, one of them playing a crucial role in salivary gland invasion by Plasmodium falciparum sporozoites. Differential expression of two other proteins previously identified in the Anopheles sialome was also observed. The differentially regulated proteins are involved in pathogen invasion, blood feeding process, and protection against oxidation, relevant steps in the outcome of malaria infection. Further functional studies and insect behaviour experiments would confirm the impact of the modification of the sialome composition on blood feeding and pathogen transmission abilities of the resistant mosquitoes. The data supports the hypothesis of alterations linked to insecticide resistance in the biology of the primary vector of human malaria in Africa.

  17. Metabolomics analysis reveals 6‐benzylaminopurine as a stimulator for improving lipid and DHA accumulation of Aurantiochytriumsp.

    PubMed Central

    Yu, Xin‐Jun; Sun, Jie; Zheng, Jian‐Yong; Sun, Ya‐Qi

    2016-01-01

    Abstract BACKGROUND Phytohormones are chemical messengers that have a positive effect on biodiesel production of microalgae at low concentrations. However, the effect of phytohormone 6‐benzylaminopurine on lipid and docosahexaenoic acid (DHA) production in marine DHA‐producer Aurantiochytrium has never been reported. In this study, a GC‐MS‐based metabolomics method combined with a multivariate analysis is applied to reveal the metabolic mechanism of 6‐benzylaminopurine enhancing production of lipid and DHA in Aurantiochytrium sp.YLH70. RESULTS In total, 71 metabolites were identified by GC‐MS. The PCA model revealed that 76.9% of metabolite variation was related to 6‐benzylaminopurine treatment, and overall metabolomics profiles between the 6‐benzylaminopurine and control groups were clearly discriminated. Forty‐six metabolites identified by the PLS‐DA model were responsible for responding to 6‐benzylaminopurine. Metabolic analysis showed that 6‐benzylaminopurine could accelerate the rate of utilization of glucose in Aurantiochytrium sp. YLH70, and the metabolic flux from glycolysis, TCA cycle and mevalonate pathway to fatty acids biosynthesis was promoted. Moreover, the anti‐stress mechanism in Aurantiochytrium sp.YLH70 might be induced by 6‐benzylaminopurine. CONCLUSION Metabolomics is a suitable tool to discover the metabolic mechanism for improving lipid and DHA accumulation in a microorganism. 6‐benzylaminopurine has the potential to stimulate lipid and DHA production of Aurantiochytrium sp.YLH70 for industrial purposes. © 2015 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. PMID:27065509

  18. Integrated metagenomic analysis of the rumen microbiome of cattle reveals key biological mechanisms associated with methane traits.

    PubMed

    Wang, Haiying; Zheng, Huiru; Browne, Fiona; Roehe, Rainer; Dewhurst, Richard J; Engel, Felix; Hemmje, Matthias; Lu, Xiangwu; Walsh, Paul

    2017-07-15

    Methane is one of the major contributors to global warming. The rumen microbiota is directly involved in methane production in cattle. The link between variation in rumen microbial communities and host genetics has important applications and implications in bioscience. Having the potential to reveal the full extent of microbial gene diversity and complex microbial interactions, integrated metagenomics and network analysis holds great promise in this endeavour. This study investigates the rumen microbial community in cattle through the integration of metagenomic and network-based approaches. Based on the relative abundance of 1570 microbial genes identified in a metagenomics analysis, the co-abundance network was constructed and functional modules of microbial genes were identified. One of the main contributions is to develop a random matrix theory-based approach to automatically determining the correlation threshold used to construct the co-abundance network. The resulting network, consisting of 549 microbial genes and 3349 connections, exhibits a clear modular structure with certain trait-specific genes highly over-represented in modules. More specifically, all the 20 genes previously identified to be associated with methane emissions are found in a module (hypergeometric test, p<10 -11 ). One third of genes are involved in methane metabolism pathways. The further examination of abundance profiles across 8 samples of genes highlights that the revealed pattern of metagenomics abundance has a strong association with methane emissions. Furthermore, the module is significantly enriched with microbial genes encoding enzymes that are directly involved in methanogenesis (hypergeometric test, p<10 -9 ). Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Multi-omics analysis reveals that ornithine decarboxylase contributes to erlotinib resistance in pancreatic cancer cells

    PubMed Central

    Song, Sang-Hoon; Lee, Naeun; Kim, Dong-Joon; Lee, Sooyeun; Jeong, Chul-Ho

    2017-01-01

    Molecular and metabolic alterations in cancer cells are one of the leading causes of acquired resistance to chemotherapeutics. In this study, we explored an experimental strategy to identify which of these alterations can induce erlotinib resistance in human pancreatic cancer. Using genetically matched erlotinib-sensitive (BxPC-3) and erlotinib-resistant (BxPC-3ER) pancreatic cancer cells, we conducted a multi-omics analysis of metabolomes and transcriptomes in these cells. Untargeted and targeted metabolomic analyses revealed significant changes in metabolic pathways involved in the regulation of polyamines, amino acids, and fatty acids. Further transcriptomic analysis identified that ornithine decarboxylase (ODC) and its major metabolite, putrescine, contribute to the acquisition of erlotinib resistance in BxPC-3ER cells. Notably, either pharmacological or genetic blockage of ODC was able to restore erlotinib sensitivity, and this could be rescued by treatment with exogenous putrescine in erlotinib-resistant BxPC-3ER cells. Moreover, using a panel of cancer cells we demonstrated that ODC expression levels in cancer cells are inversely correlated with sensitivity to chemotherapeutics. Taken together, our findings will begin to uncover mechanisms of acquired drug resistance and ultimately help to identify potential therapeutic markers in cancer. PMID:29190951

  20. Exome-wide association analysis reveals novel coding sequence variants associated with lipid traits in Chinese.

    PubMed

    Tang, Clara S; Zhang, He; Cheung, Chloe Y Y; Xu, Ming; Ho, Jenny C Y; Zhou, Wei; Cherny, Stacey S; Zhang, Yan; Holmen, Oddgeir; Au, Ka-Wing; Yu, Haiyi; Xu, Lin; Jia, Jia; Porsch, Robert M; Sun, Lijie; Xu, Weixian; Zheng, Huiping; Wong, Lai-Yung; Mu, Yiming; Dou, Jingtao; Fong, Carol H Y; Wang, Shuyu; Hong, Xueyu; Dong, Liguang; Liao, Yanhua; Wang, Jiansong; Lam, Levina S M; Su, Xi; Yan, Hua; Yang, Min-Lee; Chen, Jin; Siu, Chung-Wah; Xie, Gaoqiang; Woo, Yu-Cho; Wu, Yangfeng; Tan, Kathryn C B; Hveem, Kristian; Cheung, Bernard M Y; Zöllner, Sebastian; Xu, Aimin; Eugene Chen, Y; Jiang, Chao Qiang; Zhang, Youyi; Lam, Tai-Hing; Ganesh, Santhi K; Huo, Yong; Sham, Pak C; Lam, Karen S L; Willer, Cristen J; Tse, Hung-Fat; Gao, Wei

    2015-12-22

    Blood lipids are important risk factors for coronary artery disease (CAD). Here we perform an exome-wide association study by genotyping 12,685 Chinese, using a custom Illumina HumanExome BeadChip, to identify additional loci influencing lipid levels. Single-variant association analysis on 65,671 single nucleotide polymorphisms reveals 19 loci associated with lipids at exome-wide significance (P<2.69 × 10(-7)), including three Asian-specific coding variants in known genes (CETP p.Asp459Gly, PCSK9 p.Arg93Cys and LDLR p.Arg257Trp). Furthermore, missense variants at two novel loci-PNPLA3 p.Ile148Met and PKD1L3 p.Thr429Ser-also influence levels of triglycerides and low-density lipoprotein cholesterol, respectively. Another novel gene, TEAD2, is found to be associated with high-density lipoprotein cholesterol through gene-based association analysis. Most of these newly identified coding variants show suggestive association (P<0.05) with CAD. These findings demonstrate that exome-wide genotyping on samples of non-European ancestry can identify additional population-specific possible causal variants, shedding light on novel lipid biology and CAD.

  1. Genome-Wide Analysis of Mycoplasma bovirhinis GS01 Reveals Potential Virulence Factors and Phylogenetic Relationships.

    PubMed

    Chen, Shengli; Hao, Huafang; Zhao, Ping; Liu, Yongsheng; Chu, Yuefeng

    2018-05-04

    Mycoplasma bovirhinis is a significant etiology in bovine pneumonia and mastitis, but our knowledge about the genetic and pathogenic mechanisms of M. bovirhinis is very limited. In this study, we sequenced the complete genome of M. bovirhinis strain GS01 isolated from the nasal swab of pneumonic calves in Gansu, China, and we found that its genome forms a 847,985 bp single circular chromosome with a GC content of 27.57% and with 707 protein-coding genes. The putative virulence determinants of M. bovirhinis were then analyzed. Results showed that three genomic islands and 16 putative virulence genes, including one adhesion gene enolase, seven surface lipoproteins, proteins involved in glycerol metabolism, and cation transporters, might be potential virulence factors. Glycerol and pyruvate metabolic pathways were defective. Comparative analysis revealed remarkable genome variations between GS01 and a recently reported HAZ141_2 strain, and extremely low homology with others mycoplasma species. Phylogenetic analysis demonstrated that M. bovirhinis was most genetically close to M. canis , distant from other bovine Mycoplasma species. Genomic dissection may provide useful information on the pathogenic mechanisms and genetics of M. bovirhinis . Copyright © 2018 Chen et al.

  2. Comparative analysis reveals genomic features of stress-induced transcriptional readthrough

    PubMed Central

    Vilborg, Anna; Sabath, Niv; Wiesel, Yuval; Nathans, Jenny; Levy-Adam, Flonia; Yario, Therese A.; Steitz, Joan A.; Shalgi, Reut

    2017-01-01

    Transcription is a highly regulated process, and stress-induced changes in gene transcription have been shown to play a major role in stress responses and adaptation. Genome-wide studies reveal prevalent transcription beyond known protein-coding gene loci, generating a variety of RNA classes, most of unknown function. One such class, termed downstream of gene-containing transcripts (DoGs), was reported to result from transcriptional readthrough upon osmotic stress in human cells. However, how widespread the readthrough phenomenon is, and what its causes and consequences are, remain elusive. Here we present a genome-wide mapping of transcriptional readthrough, using nuclear RNA-Seq, comparing heat shock, osmotic stress, and oxidative stress in NIH 3T3 mouse fibroblast cells. We observe massive induction of transcriptional readthrough, both in levels and length, under all stress conditions, with significant, yet not complete, overlap of readthrough-induced loci between different conditions. Importantly, our analyses suggest that stress-induced transcriptional readthrough is not a random failure process, but is rather differentially induced across different conditions. We explore potential regulators and find a role for HSF1 in the induction of a subset of heat shock-induced readthrough transcripts. Analysis of public datasets detected increases in polymerase II occupancy in DoG regions after heat shock, supporting our findings. Interestingly, DoGs tend to be produced in the vicinity of neighboring genes, leading to a marked increase in their antisense-generating potential. Finally, we examine genomic features of readthrough transcription and observe a unique chromatin signature typical of DoG-producing regions, suggesting that readthrough transcription is associated with the maintenance of an open chromatin state. PMID:28928151

  3. Gait phenotypes in paediatric hereditary spastic paraplegia revealed by dynamic time warping analysis and random forests

    PubMed Central

    Martín-Gonzalo, Juan Andrés; Rodríguez-Andonaegui, Irene; López-López, Javier; Pascual-Pascual, Samuel Ignacio

    2018-01-01

    The Hereditary Spastic Paraplegias (HSP) are a group of heterogeneous disorders with a wide spectrum of underlying neural pathology, and hence HSP patients express a variety of gait abnormalities. Classification of these phenotypes may help in monitoring disease progression and personalizing therapies. This is currently managed by measuring values of some kinematic and spatio-temporal parameters at certain moments during the gait cycle, either in the doctor´s surgery room or after very precise measurements produced by instrumental gait analysis (IGA). These methods, however, do not provide information about the whole structure of the gait cycle. Classification of the similarities among time series of IGA measured values of sagittal joint positions throughout the whole gait cycle can be achieved by hierarchical clustering analysis based on multivariate dynamic time warping (DTW). Random forests can estimate which are the most important isolated parameters to predict the classification revealed by DTW, since clinicians need to refer to them in their daily practice. We acquired time series of pelvic, hip, knee, ankle and forefoot sagittal angular positions from 26 HSP and 33 healthy children with an optokinetic IGA system. DTW revealed six gait patterns with different degrees of impairment of walking speed, cadence and gait cycle distribution and related with patient’s age, sex, GMFCS stage, concurrence of polyneuropathy and abnormal visual evoked potentials or corpus callosum. The most important parameters to differentiate patterns were mean pelvic tilt and hip flexion at initial contact. Longer time of support, decreased values of hip extension and increased knee flexion at initial contact can differentiate the mildest, near to normal HSP gait phenotype and the normal healthy one. Increased values of knee flexion at initial contact and delayed peak of knee flexion are important factors to distinguish GMFCS stages I from II-III and concurrence of polyneuropathy

  4. Bioinformatic analysis of the neprilysin (M13) family of peptidases reveals complex evolutionary and functional relationships.

    PubMed

    Bland, Nicholas D; Pinney, John W; Thomas, Josie E; Turner, Anthony J; Isaac, R Elwyn

    2008-01-23

    The neprilysin (M13) family of endopeptidases are zinc-metalloenzymes, the majority of which are type II integral membrane proteins. The best characterised of this family is neprilysin, which has important roles in inactivating signalling peptides involved in modulating neuronal activity, blood pressure and the immune system. Other family members include the endothelin converting enzymes (ECE-1 and ECE-2), which are responsible for the final step in the synthesis of potent vasoconstrictor endothelins. The ECEs, as well as neprilysin, are considered valuable therapeutic targets for treating cardiovascular disease. Other members of the M13 family have not been functionally characterised, but are also likely to have biological roles regulating peptide signalling. The recent sequencing of animal genomes has greatly increased the number of M13 family members in protein databases, information which can be used to reveal evolutionary relationships and to gain insight into conserved biological roles. The phylogenetic analysis successfully resolved vertebrate M13 peptidases into seven classes, one of which appears to be specific to mammals, and insect genes into five functional classes and a series of expansions, which may include inactive peptidases. Nematode genes primarily resolved into groups containing no other taxa, bar the two nematode genes associated with Drosophila DmeNEP1 and DmeNEP4. This analysis reconstructed only one relationship between chordate and invertebrate clusters, that of the ECE sub-group and the DmeNEP3 related genes. Analysis of amino acid utilisation in the active site of M13 peptidases reveals a basis for their biochemical properties. A relatively invariant S1' subsite gives the majority of M13 peptidases their strong preference for hydrophobic residues in P1' position. The greater variation in the S2' subsite may be instrumental in determining the specificity of M13 peptidases for their substrates and thus allows M13 peptidases to fulfil a

  5. Bioinformatic analysis of the neprilysin (M13) family of peptidases reveals complex evolutionary and functional relationships

    PubMed Central

    2008-01-01

    Background The neprilysin (M13) family of endopeptidases are zinc-metalloenzymes, the majority of which are type II integral membrane proteins. The best characterised of this family is neprilysin, which has important roles in inactivating signalling peptides involved in modulating neuronal activity, blood pressure and the immune system. Other family members include the endothelin converting enzymes (ECE-1 and ECE-2), which are responsible for the final step in the synthesis of potent vasoconstrictor endothelins. The ECEs, as well as neprilysin, are considered valuable therapeutic targets for treating cardiovascular disease. Other members of the M13 family have not been functionally characterised, but are also likely to have biological roles regulating peptide signalling. The recent sequencing of animal genomes has greatly increased the number of M13 family members in protein databases, information which can be used to reveal evolutionary relationships and to gain insight into conserved biological roles. Results The phylogenetic analysis successfully resolved vertebrate M13 peptidases into seven classes, one of which appears to be specific to mammals, and insect genes into five functional classes and a series of expansions, which may include inactive peptidases. Nematode genes primarily resolved into groups containing no other taxa, bar the two nematode genes associated with Drosophila DmeNEP1 and DmeNEP4. This analysis reconstructed only one relationship between chordate and invertebrate clusters, that of the ECE sub-group and the DmeNEP3 related genes. Analysis of amino acid utilisation in the active site of M13 peptidases reveals a basis for their biochemical properties. A relatively invariant S1' subsite gives the majority of M13 peptidases their strong preference for hydrophobic residues in P1' position. The greater variation in the S2' subsite may be instrumental in determining the specificity of M13 peptidases for their substrates and thus allows M13

  6. PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity

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

    Nelson, T.A.; Holmes, S.; Alekseyenko, A.V.

    Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease. Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS. Our results revealed a significantly increased compositionalmore » difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species. The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS.« less

  7. Toward a comprehensive understanding of solid-state core-level XPS linewidths: Experimental and theoretical studies on the Si2p and O1s linewidths in silicates

    NASA Astrophysics Data System (ADS)

    Bancroft, G. M.; Nesbitt, H. W.; Ho, R.; Shaw, D. M.; Tse, J. S.; Biesinger, M. C.

    2009-08-01

    High resolution X-ray Photoelectron Spectroscopy (XPS) core-level Si2p and O1s spectra of the nonconductors α-SiO2 (quartz) at 120 and 300 K and vitreous SiO2 at 300 K were obtained with a Kratos Axis Ultra XPS instrument (instrumental resolution of <0.4eV ) which incorporates a unique charge compensation system that minimizes differential charge broadening on nonconductors. The Si2p and O1s linewidths at 300 K ( ˜1.1 and ˜1.2eV , respectively) are similar for all silicates (and similar to previous thin film SiO2 spectra obtained previously), showing that differential charging does not contribute significantly to our spectra. At 120 K, there is a small decrease (0.04 eV) in the Si2p linewidth of α-SiO2 , but no measurable decrease in O1s linewidth. The O1s lines are generally and distinctly asymmetric. We consider all possible sources of line broadening and show that final state vibrational broadening (FSVB) and phonon broadening are the major causes of the broad and asymmetric lines. Previous high resolution gas phase XPS studies have identified large FSVB contributions to the Si2p spectra of SiCl4 , SiF4 , and Si(OCH3)4 molecules, and this vibrational structure leads total Si2p3/2 linewidths of up to ˜0.5eV , even with individual peak linewidths of <0.1eV . The Si atom of Si(OCH3)4 is an excellent analog for Si in crystalline SiO2 because the Si-O bond lengths and symmetric stretch frequencies are similar in both compounds. Similar vibrational contributions to the Si2p and O1s spectra of solid silicates are anticipated if the Si2p and O1s core-hole states produce similar changes to the Si-O bond length in both phases. To investigate the possibility, Car-Parrinello molecular dynamics calculations were performed and show that changes to Si-O bond lengths between ion and ground states (Δr) for both Si2p and O1s hole states are similar for both crystalline SiO2 and gaseous Si(OCH3)4 . Δr are -0.04Å for Si2p and ˜+0.05Å for O1s in both compounds. Indeed, the

  8. Genome-Wide Association Analysis Reveals Different Genetic Control in Panicle Architecture Between and Rice.

    PubMed

    Bai, Xufeng; Zhao, Hu; Huang, Yong; Xie, Weibo; Han, Zhongmin; Zhang, Bo; Guo, Zilong; Yang, Lin; Dong, Haijiao; Xue, Weiya; Li, Guangwei; Hu, Gang; Hu, Yong; Xing, Yongzhong

    2016-07-01

    Panicle architecture determines the number of spikelets per panicle (SPP) and is highly associated with grain yield in rice ( L.). Understanding the genetic basis of panicle architecture is important for improving the yield of rice grain. In this study, we dissected panicle architecture traits into eight components, which were phenotyped from a germplasm collection of 529 cultivars. Multiple regression analysis revealed that the number of secondary branch (NSB) was the major factor that contributed to SPP. Genome-wide association analysis was performed independently for the eight particle architecture traits observed in the and rice subpopulations compared with the whole rice population. In total, 30 loci were associated with these traits. Of these, 13 loci were closely linked to known panicle architecture genes, and 17 novel loci were repeatedly identified in different environments. An association signal cluster was identified for NSB and number of spikelets per secondary branch (NSSB) in the region of 31.6 to 31.7 Mb on chromosome 4. In addition to the common associations detected in both and subpopulations, many associated loci were unique to one subpopulation. For example, and were specifically associated with panicle length (PL) in and rice, respectively. Moreover, the -mediated flowering genes and were associated with the formation of panicle architecture in rice. These results suggest that different gene networks regulate panicle architecture in and rice. Copyright © 2016 Crop Science Society of America.

  9. Cellulose gum and copper nanoparticles based hydrogel as antimicrobial agents against urinary tract infection (UTI) pathogens.

    PubMed

    Al-Enizi, Abdullah M; Ahamad, Tansir; Al-Hajji, Abdullah Baker; Ahmed, Jahangeer; Chaudhary, Anis Ahmad; Alshehri, Saad M

    2018-04-01

    In the present study, stable copper nanoparticles (CuNPs) were successfully prepared in the hydrogel matrix. The prepared nanocomposite (HCuNPs) was characterized via x-ray diffraction (XRD), electron microscopy (TEM), and energy-dispersive (EDX) and x-ray photoelectron spectroscopic (XPS) studies. The wide scan XPS spectra support the presence of C, N and O in neat hydrogel; while, the XPS spectra of HCuNPs demonstrate the presence of Cu along with C, N, and O elements. TEM studies show the formation of spherical shaped CuNPs in the size range from 7 to 12nm. The rheology results reveal that the storage modulus (G') of the HCuNPs was found to be higher than the loss modulus (G"). Additionally, the antibacterial activities and cytotoxic were carried out against urinary tract infection (UTI) microbes and HeLa (cervical) cells respectively. The antibacterial results reveal that HCuNPs composites show higher zone of inhibition against these pathogens then that of corresponding hydrogel matrix. The cytotoxic effects suggest that the prepared nanocomposite could be used as promising candidates for biomedical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets.

    PubMed

    Lam, Max; Trampush, Joey W; Yu, Jin; Knowles, Emma; Davies, Gail; Liewald, David C; Starr, John M; Djurovic, Srdjan; Melle, Ingrid; Sundet, Kjetil; Christoforou, Andrea; Reinvang, Ivar; DeRosse, Pamela; Lundervold, Astri J; Steen, Vidar M; Espeseth, Thomas; Räikkönen, Katri; Widen, Elisabeth; Palotie, Aarno; Eriksson, Johan G; Giegling, Ina; Konte, Bettina; Roussos, Panos; Giakoumaki, Stella; Burdick, Katherine E; Payton, Antony; Ollier, William; Chiba-Falek, Ornit; Attix, Deborah K; Need, Anna C; Cirulli, Elizabeth T; Voineskos, Aristotle N; Stefanis, Nikos C; Avramopoulos, Dimitrios; Hatzimanolis, Alex; Arking, Dan E; Smyrnis, Nikolaos; Bilder, Robert M; Freimer, Nelson A; Cannon, Tyrone D; London, Edythe; Poldrack, Russell A; Sabb, Fred W; Congdon, Eliza; Conley, Emily Drabant; Scult, Matthew A; Dickinson, Dwight; Straub, Richard E; Donohoe, Gary; Morris, Derek; Corvin, Aiden; Gill, Michael; Hariri, Ahmad R; Weinberger, Daniel R; Pendleton, Neil; Bitsios, Panos; Rujescu, Dan; Lahti, Jari; Le Hellard, Stephanie; Keller, Matthew C; Andreassen, Ole A; Deary, Ian J; Glahn, David C; Malhotra, Anil K; Lencz, Todd

    2017-11-28

    Here, we present a large (n = 107,207) genome-wide association study (GWAS) of general cognitive ability ("g"), further enhanced by combining results with a large-scale GWAS of educational attainment. We identified 70 independent genomic loci associated with general cognitive ability. Results showed significant enrichment for genes causing Mendelian disorders with an intellectual disability phenotype. Competitive pathway analysis implicated the biological processes of neurogenesis and synaptic regulation, as well as the gene targets of two pharmacologic agents: cinnarizine, a T-type calcium channel blocker, and LY97241, a potassium channel inhibitor. Transcriptome-wide and epigenome-wide analysis revealed that the implicated loci were enriched for genes expressed across all brain regions (most strongly in the cerebellum). Enrichment was exclusive to genes expressed in neurons but not oligodendrocytes or astrocytes. Finally, we report genetic correlations between cognitive ability and disparate phenotypes including psychiatric disorders, several autoimmune disorders, longevity, and maternal age at first birth. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  11. Bach Is the Father of Harmony: Revealed by a 1/f Fluctuation Analysis across Musical Genres.

    PubMed

    Wu, Dan; Kendrick, Keith M; Levitin, Daniel J; Li, Chaoyi; Yao, Dezhong

    2015-01-01

    Harmony is a fundamental attribute of music. Close connections exist between music and mathematics since both pursue harmony and unity. In music, the consonance of notes played simultaneously partly determines our perception of harmony; associates with aesthetic responses; and influences the emotion expression. The consonance could be considered as a window to understand and analyze harmony. Here for the first time we used a 1/f fluctuation analysis to investigate whether the consonance fluctuation structure in music with a wide range of composers and genres followed the scale free pattern that has been found for pitch, melody, rhythm, human body movements, brain activity, natural images and geographical features. We then used a network graph approach to investigate which composers were the most influential both within and across genres. Our results showed that patterns of consonance in music did follow scale-free characteristics, suggesting that this feature is a universally evolved one in both music and the living world. Furthermore, our network analysis revealed that Bach's harmony patterns were having the most influence on those used by other composers, followed closely by Mozart.

  12. [Mastitis revealing Churg-Strauss syndrome].

    PubMed

    Dannepond, C; Le Fourn, E; de Muret, A; Ouldamer, L; Carmier, D; Machet, L

    2014-01-01

    Churg-Strauss syndrome often involves the skin, and this may sometimes reveal the disease. A 25-year-old woman was referred to a gynaecologist for inflammation of the right breast with breast discharge. Cytological analysis of the liquid showed numerous inflammatory cells, particularly polymorphonuclear eosinophils and neutrophils. Ultrasound examination of the breast was consistent with galactophoritis. CRP was normal, and hypereosinophilia was seen. The patient was subsequently referred to a dermatology unit. Skin examination revealed inflammation of the entire breast, which was painful, warm and erythematous; the border was oedematous with blisters. Necrotic lesions were also present on the thumbs and knees. Skin biopsy of the breast showed a dermal infiltrate with abundant infiltrate of polymorphonuclear eosinophils, including patchy necrosis and intraepidermal vesicles. Histological examination of a biopsy sample from a thumb revealed eosinophilic granuloma and leukocytoclastic vasculitis. The patient was also presenting asthma, pulmonary infiltrates and mononeuropathy at L3, consistent with Churg-Strauss syndrome. Breast involvement in Churg-Strauss syndrome is very rare (only one other case has been reported). This is the first case in which the breast condition revealed the disease. Cutaneous involvement of the breast is, however, also compatible with Wells' cellulitis. The lesions quickly disappeared with 1mg/kg/d oral prednisolone. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  13. Network analysis of ChIP-Seq data reveals key genes in prostate cancer.

    PubMed

    Zhang, Yu; Huang, Zhen; Zhu, Zhiqiang; Liu, Jianwei; Zheng, Xin; Zhang, Yuhai

    2014-09-03

    Prostate cancer (PC) is the second most common cancer among men in the United States, and it imposes a considerable threat to human health. A deep understanding of its underlying molecular mechanisms is the premise for developing effective targeted therapies. Recently, deep transcriptional sequencing has been used as an effective genomic assay to obtain insights into diseases and may be helpful in the study of PC. In present study, ChIP-Seq data for PC and normal samples were compared, and differential peaks identified, based upon fold changes (with P-values calculated with t-tests). Annotations of these peaks were performed. Protein-protein interaction (PPI) network analysis was performed with BioGRID and constructed with Cytoscape, following which the highly connected genes were screened. We obtained a total of 5,570 differential peaks, including 3,726 differentially enriched peaks in tumor samples and 1,844 differentially enriched peaks in normal samples. There were eight significant regions of the peaks. The intergenic region possessed the highest score (51%), followed by intronic (31%) and exonic (11%) regions. The analysis revealed the top 35 highly connected genes, which comprised 33 differential genes (such as YWHAQ, tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein and θ polypeptide) from ChIP-Seq data and 2 differential genes retrieved from the PPI network: UBA52 (ubiquitin A-52 residue ribosomal protein fusion product (1) and SUMO2 (SMT3 suppressor of mif two 3 homolog (2) . Our findings regarding potential PC-related genes increase the understanding of PC and provides direction for future research.

  14. Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano

    PubMed Central

    Banskar, Sunil; Bhute, Shrikant S.; Suryavanshi, Mangesh V.; Punekar, Sachin; Shouche, Yogesh S.

    2016-01-01

    Bats are crucial for proper functioning of an ecosystem. They provide various important services to ecosystem and environment. While, bats are well-known carrier of pathogenic viruses, their possible role as a potential carrier of pathogenic bacteria is under-explored. Here, using culture-based approach, employing multiple bacteriological media, over thousand bacteria were cultivated and identified from Rousettus leschenaultii (a frugivorous bat species), the majority of which were from the family Enterobacteriaceae and putative pathogens. Next, pathogenic potential of most frequently cultivated component of microbiome i.e. Escherichia coli was assessed to identify its known pathotypes which revealed the presence of virulent factors in many cultivated E. coli isolates. Applying in-depth bacterial community analysis using high-throughput 16 S rRNA gene sequencing, a high inter-individual variation was observed among the studied guano samples. Interestingly, a higher diversity of bacterial communities was observed in decaying guano representative. The search against human pathogenic bacteria database at 97% identity, a small proportion of sequences were found associated to well-known human pathogens. The present study thus indicates that this bat species may carry potential bacterial pathogens and advice to study the effect of these pathogens on bats itself and the probable mode of transmission to humans and other animals. PMID:27845426

  15. Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano.

    PubMed

    Banskar, Sunil; Bhute, Shrikant S; Suryavanshi, Mangesh V; Punekar, Sachin; Shouche, Yogesh S

    2016-11-15

    Bats are crucial for proper functioning of an ecosystem. They provide various important services to ecosystem and environment. While, bats are well-known carrier of pathogenic viruses, their possible role as a potential carrier of pathogenic bacteria is under-explored. Here, using culture-based approach, employing multiple bacteriological media, over thousand bacteria were cultivated and identified from Rousettus leschenaultii (a frugivorous bat species), the majority of which were from the family Enterobacteriaceae and putative pathogens. Next, pathogenic potential of most frequently cultivated component of microbiome i.e. Escherichia coli was assessed to identify its known pathotypes which revealed the presence of virulent factors in many cultivated E. coli isolates. Applying in-depth bacterial community analysis using high-throughput 16 S rRNA gene sequencing, a high inter-individual variation was observed among the studied guano samples. Interestingly, a higher diversity of bacterial communities was observed in decaying guano representative. The search against human pathogenic bacteria database at 97% identity, a small proportion of sequences were found associated to well-known human pathogens. The present study thus indicates that this bat species may carry potential bacterial pathogens and advice to study the effect of these pathogens on bats itself and the probable mode of transmission to humans and other animals.

  16. A Simple Geotracer Compositional Correlation Analysis Reveals Oil Charge and Migration Pathways

    PubMed Central

    Yang, Yunlai; Arouri, Khaled

    2016-01-01

    A novel approach, based on geotracer compositional correlation analysis is reported, which reveals the oil charge sequence and migration pathways for five oil fields in Saudi Arabia. The geotracers utilised are carbazoles, a family of neutral pyrrolic nitrogen compounds known to occur naturally in crude oils. The approach is based on the concept that closely related fields, with respect to filling sequence, will show a higher carbazole compositional correlation, than those fields that are less related. That is, carbazole compositional correlation coefficients can quantify the charge and filling relationships among different fields. Consequently, oil migration pathways can be defined based on the established filling relationships. The compositional correlation coefficients of isomers of C1 and C2 carbazoles, and benzo[a]carbazole for all different combination pairs of the five fields were found to vary extremely widely (0.28 to 0.94). A wide range of compositional correlation coefficients allows adequate differentiation of separate filling relationships. Based on the established filling relationships, three distinct migration pathways were inferred, with each apparently being charged from a different part of a common source kitchen. The recognition of these charge and migration pathways will greatly aid the search for new accumulations. PMID:26965479

  17. Sequence analysis of Jembrana disease virus strains reveals a genetically stable lentivirus.

    PubMed

    Desport, Moira; Stewart, Meredith E; Mikosza, Andrew S; Sheridan, Carol A; Peterson, Shane E; Chavand, Olivier; Hartaningsih, Nining; Wilcox, Graham E

    2007-06-01

    Jembrana disease virus (JDV) is a lentivirus associated with an acute disease syndrome with a 20% case fatality rate in Bos javanicus (Bali cattle) in Indonesia, occurring after a short incubation period and with no recurrence of the disease after recovery. Partial regions of gag and pol and the entire env were examined for sequence variation in DNA samples from cases of Jembrana disease obtained from Bali, Sumatra and South Kalimantan in Indonesian Borneo. A high level of nucleotide conservation (97-100%) was observed in gag sequences from samples taken in Bali and Sumatra, indicating that the source of JDV in Sumatra was most likely to have originated from Bali. The pol sequences and, unexpectedly, the env sequences from Bali samples were also well conserved with low nucleotide (96-99%) and amino acid substitutions (95-99%). However, the sample from South Kalimantan (JDV(KAL/01)) contained more divergent sequences, particularly in env (88% identity). Phylogenetic analysis revealed that the JDV(KAL/01)env sequences clustered with the sequence from the Pulukan sample (Bali) from 2001. JDV appears to be remarkably stable genetically and has undergone minor genetic changes over a period of nearly 20 years in Bali despite becoming endemic in the cattle population of the island.

  18. Superposed ruptile deformational events revealed by field and VOM structural analysis

    NASA Astrophysics Data System (ADS)

    Kumaira, Sissa; Guadagnin, Felipe; Keller Lautert, Maiara

    2017-04-01

    Virtual outcrop models (VOM) is becoming an important application in the analysis of geological structures due to the possibility of obtaining the geometry and in some cases kinematic aspects of analyzed structures in a tridimensional photorealistic space. These data are used to gain quantitative information on the deformational features which coupled with numeric models can assist in understands deformational processes. Old basement units commonly register superposed deformational events either ductile or ruptile along its evolution. The Porongos Belt, located at southern Brazil, have a complex deformational history registering at least five ductile and ruptile deformational events. In this study, we presents a structural analysis of a quarry in the Porongos Belt, coupling field and VOM structural information to understand process involved in the last two deformational events. Field information was acquired using traditional structural methods for analysis of ruptile structures, such as the descriptions, drawings, acquisition of orientation vectors and kinematic analysis. VOM was created from the image-based modeling method through photogrammetric data acquisition and orthorectification. Photogrammetric data acquisition was acquired using Sony a3500 camera and a total of 128 photographs were taken from ca. 10-20 m from the outcrop in different orientations. Thirty two control point coordinates were acquired using a combination of RTK dGPS surveying and total station work, providing a precision of few millimeters for x, y and z. Photographs were imported into the Photo Scan software to create a 3D dense point cloud from structure from-motion algorithm, which were triangulated and textured to generate the VOM. VOM was georreferenced (oriented and scaled) using the ground control points, and later analyzed in OpenPlot software to extract structural information. Data was imported in Wintensor software to obtain tensor orientations, and Move software to process and

  19. Active medulloblastoma enhancers reveal subgroup-specific cellular origins

    PubMed Central

    Lin, Charles Y.; Erkek, Serap; Tong, Yiai; Yin, Linlin; Federation, Alexander J.; Zapatka, Marc; Haldipur, Parthiv; Kawauchi, Daisuke; Risch, Thomas; Warnatz, Hans-Jörg; Worst, Barbara C.; Ju, Bensheng; Orr, Brent A.; Zeid, Rhamy; Polaski, Donald R.; Segura-Wang, Maia; Waszak, Sebastian M.; Jones, David T.W.; Kool, Marcel; Hovestadt, Volker; Buchhalter, Ivo; Sieber, Laura; Johann, Pascal; Chavez, Lukas; Gröschel, Stefan; Ryzhova, Marina; Korshunov, Andrey; Chen, Wenbiao; Chizhikov, Victor V.; Millen, Kathleen J.; Amstislavskiy, Vyacheslav; Lehrach, Hans; Yaspo, Marie-Laure; Eils, Roland; Lichter, Peter; Korbel, Jan O.; Pfister, Stefan M.; Bradner, James E.; Northcott, Paul A.

    2016-01-01

    Summary Medulloblastoma is a highly malignant paediatric brain tumour, often inflicting devastating consequences on the developing child. Genomic studies have revealed four distinct molecular subgroups with divergent biology and clinical behaviour. An understanding of the regulatory circuitry governing the transcriptional landscapes of medulloblastoma subgroups, and how this relates to their respective developmental origins, is lacking. Using H3K27ac and BRD4 ChIP-Seq, coupled with tissue-matched DNA methylation and transcriptome data, we describe the active cis-regulatory landscape across 28 primary medulloblastoma specimens. Analysis of differentially regulated enhancers and super-enhancers reinforced inter-subgroup heterogeneity and revealed novel, clinically relevant insights into medulloblastoma biology. Computational reconstruction of core regulatory circuitry identified a master set of transcription factors, validated by ChIP-Seq, that are responsible for subgroup divergence and implicate candidate cells-of-origin for Group 4. Our integrated analysis of enhancer elements in a large series of primary tumour samples reveals insights into cis-regulatory architecture, unrecognized dependencies, and cellular origins. PMID:26814967

  20. Novel Phage Group Infecting Lactobacillus delbrueckii subsp. lactis, as Revealed by Genomic and Proteomic Analysis of Bacteriophage Ldl1

    PubMed Central

    Casey, Eoghan; Mahony, Jennifer; Neve, Horst; Noben, Jean-Paul; Dal Bello, Fabio

    2014-01-01

    Ldl1 is a virulent phage infecting the dairy starter Lactobacillus delbrueckii subsp. lactis LdlS. Electron microscopy analysis revealed that this phage exhibits a large head and a long tail and bears little resemblance to other characterized phages infecting Lactobacillus delbrueckii. In vitro propagation of this phage revealed a latent period of 30 to 40 min and a burst size of 59.9 ± 1.9 phage particles. Comparative genomic and proteomic analyses showed remarkable similarity between the genome of Ldl1 and that of Lactobacillus plantarum phage ATCC 8014-B2. The genomic and proteomic characteristics of Ldl1 demonstrate that this phage does not belong to any of the four previously recognized L. delbrueckii phage groups, necessitating the creation of a new group, called group e, thus adding to the knowledge on the diversity of phages targeting strains of this industrially important lactic acid bacterial species. PMID:25501478

  1. Novel phage group infecting Lactobacillus delbrueckii subsp. lactis, as revealed by genomic and proteomic analysis of bacteriophage Ldl1.

    PubMed

    Casey, Eoghan; Mahony, Jennifer; Neve, Horst; Noben, Jean-Paul; Dal Bello, Fabio; van Sinderen, Douwe

    2015-02-01

    Ldl1 is a virulent phage infecting the dairy starter Lactobacillus delbrueckii subsp. lactis LdlS. Electron microscopy analysis revealed that this phage exhibits a large head and a long tail and bears little resemblance to other characterized phages infecting Lactobacillus delbrueckii. In vitro propagation of this phage revealed a latent period of 30 to 40 min and a burst size of 59.9 +/- 1.9 phage particles. Comparative genomic and proteomic analyses showed remarkable similarity between the genome of Ldl1 and that of Lactobacillus plantarum phage ATCC 8014-B2. The genomic and proteomic characteristics of Ldl1 demonstrate that this phage does not belong to any of the four previously recognized L. delbrueckii phage groups, necessitating the creation of a new group, called group e, thus adding to the knowledge on the diversity of phages targeting strains of this industrially important lactic acid bacterial species.

  2. Proteomics analysis reveals a dynamic diurnal pattern of photosynthesis-related pathways in maize leaves

    PubMed Central

    Lu, Tiegang; Zhang, Zhiguo

    2017-01-01

    Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions. Steady, single-peak and double-peak protein expression patterns were discovered in maize leaves, and antenna proteins in these leaves displayed a steady pattern. In contrast, the photosystem, carbon fixation and citrate pathways were highly controlled by diurnal light intensity. Most enzymes in the limiting steps of these pathways were major sites of regulation. Thus, maize leaves optimize photosynthesis and carbon fixation outside of light harvesting to adapt to the changes in diurnal light intensity at the protein level. PMID:28732011

  3. Proteomics analysis reveals a dynamic diurnal pattern of photosynthesis-related pathways in maize leaves.

    PubMed

    Feng, Dan; Wang, Yanwei; Lu, Tiegang; Zhang, Zhiguo; Han, Xiao

    2017-01-01

    Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions. Steady, single-peak and double-peak protein expression patterns were discovered in maize leaves, and antenna proteins in these leaves displayed a steady pattern. In contrast, the photosystem, carbon fixation and citrate pathways were highly controlled by diurnal light intensity. Most enzymes in the limiting steps of these pathways were major sites of regulation. Thus, maize leaves optimize photosynthesis and carbon fixation outside of light harvesting to adapt to the changes in diurnal light intensity at the protein level.

  4. Isotope analysis reveals foraging area dichotomy for atlantic leatherback turtles.

    PubMed

    Caut, Stéphane; Fossette, Sabrina; Guirlet, Elodie; Angulo, Elena; Das, Krishna; Girondot, Marc; Georges, Jean-Yves

    2008-03-26

    The leatherback turtle (Dermochelys coriacea) has undergone a dramatic decline over the last 25 years, and this is believed to be primarily the result of mortality associated with fisheries bycatch followed by egg and nesting female harvest. Atlantic leatherback turtles undertake long migrations across ocean basins from subtropical and tropical nesting beaches to productive frontal areas. Migration between two nesting seasons can last 2 or 3 years, a time period termed the remigration interval (RI). Recent satellite transmitter data revealed that Atlantic leatherbacks follow two major dispersion patterns after nesting season, through the North Gulf Stream area or more eastward across the North Equatorial Current. However, information on the whole RI is lacking, precluding the accurate identification of feeding areas where conservation measures may need to be applied. Using stable isotopes as dietary tracers we determined the characteristics of feeding grounds of leatherback females nesting in French Guiana. During migration, 3-year RI females differed from 2-year RI females in their isotope values, implying differences in their choice of feeding habitats (offshore vs. more coastal) and foraging latitude (North Atlantic vs. West African coasts, respectively). Egg-yolk and blood isotope values are correlated in nesting females, indicating that egg analysis is a useful tool for assessing isotope values in these turtles, including adults when not available. Our results complement previous data on turtle movements during the first year following the nesting season, integrating the diet consumed during the year before nesting. We suggest that the French Guiana leatherback population segregates into two distinct isotopic groupings, and highlight the urgent need to determine the feeding habitats of the turtle in the Atlantic in order to protect this species from incidental take by commercial fisheries. Our results also emphasize the use of eggs, a less-invasive sampling

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

    Sarkar, S.; Mondal, A.; Dey, K.

    Highlights: • Reduced graphene oxides (RGO) are prepared by two chemical routes. • Defects in RGO are characterized by Raman, FTIR and XPS studies. • Defects tailor colossal dielectricity in RGO. - Abstract: Reduced graphene oxide (RGO) is prepared in two different chemical routes where reduction of graphene oxide is performed by hydrazine hydrate and through high pressure in hydrothermal reactor. Samples are characterized by X-ray powdered diffraction (XRD), thermo gravimetric analysis (TGA), field emission scanning electron microscopy (FESEM) and tunneling electron microscopy (TEM). Types of defects are probed by Raman, FTIR spectroscopy and X-ray photoelectron spectroscopy (XPS). UV–vis absorptionmore » reveals different optical band gaps of the two RGOs. Conductivity mechanism is studied through I–V measurements displaying different characteristic features which are addressed due to the presence of defects appeared in different synthesis. Significantly high value (∼10{sup 4}) of dielectric permittivity at 10 MHz is attractive for technological application which could be tuned by the defects present in RGO.« less

  6. The synergistic effects of combining the high energy mechanical milling and wet milling on Si negative electrode materials for lithium ion battery

    NASA Astrophysics Data System (ADS)

    Hou, Shang-Chieh; Su, Yuh-Fan; Chang, Chia-Chin; Hu, Chih-Wei; Chen, Tsan-Yao; Yang, Shun-Min; Huang, Jow-Lay

    2017-05-01

    The submicro-sized and nanostructured Si aggregated powder is prepared by combinational routes of high energy mechanical milling (HEMM) and wet milling. Milled Si powder is investigated by particle size analyzer, SEM, TEM, XPS and XRD as well as the control ones. Its electrode is also investigated by in situ XRD and electrochemical performance. Morphology reveals that combining the high energy mechanical milling and wet milling not only fracture primary Si particles but also form submicro-sized Si aggregates constructed by amorphous and nanocrystalline phases. Moreover, XPS shows that wet milling in ethanol trigger Sisbnd Osbnd CH2CH3 bonding on Si surface might enhance the SEI formation. In situ XRD analysis shows negative electrode made of submicro-sized Si aggregated powder can effectively suppress formation of crystalline Li15Si4 during lithiation and delithiation due to amorphous and nanocrystalline construction. Thus, the submicro-sized Si powder with synergistic effects combining the high energy mechanical milling and wet milling in ethanol as negative electrode performs better capacity retention.

  7. A new method of nanocrystalline nickel powder formation by magnetron sputtering on the water-soluble substrates

    NASA Astrophysics Data System (ADS)

    Tučkutė, S.; Urbonavičius, M.; Lelis, M.; Maiorov, M.; Díaz Ordaz, J. R.; Milčius, D.

    2018-01-01

    Due to the accurate and relatively easy control magnetron sputtering is an attractive technique for the synthesis of metallic particles. This work describes a new method of nickel powder production by depositing nickel on the surface of sodium chloride particles which were used as the template and are soluble in water. Ni powder with flake-like structure was obtained after washing Ni coated salt particles in ultrasonic cleaner. Salt particles and nickel powder were characterized using scanning electron microscope (SEM), energy-dispersive x-ray spectrometer, XRD and X-ray photoelectron spectroscopy (XPS) techniques. SEM images showed that thickness of the received Ni particles varied in the nanoscale and depended on the magnetron deposition time but did not depend on the size of salt particles. On the other hand initial size of the salt particles was successfully employed a measure to control lateral dimensions of Ni powder. XRD and XPS analysis results revealed that Ni particles had metallic core and oxidized shell which was a cause of the slightly deteriorated magnetic properties.

  8. Hydrothermal-reduction synthesis of manganese oxide nanomaterials for electrochemical supercapacitors.

    PubMed

    Zhang, Xiong; Chen, Yao; Yu, Peng; Ma, Yanwei

    2010-11-01

    In the present work, amorphous manganese oxide nanomaterials have been synthesized by a common hydrothermal method based on the redox reaction between MnO4(-) and Fe(2+) under an acidic condition. The synthesized MnO2 samples were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), and electrochemical studies. XRD results showed that amorphous manganese oxide phase was obtained. XPS quantitative analysis revealed that the atomic ratio of Mn to Fe was 3.5 in the MnO2 samples. TEM images showed the porous structure of the samples. Electrochemical properties of the MnO2 electrodes were studied using cyclic voltammetry and galvanostatic charge-discharge cycling in 1 M Na2SO4 aqueous electrolyte, which showed excellent pseudocapacitance properties. A specific capacitance of 192 Fg(-1) at a current density of 0.5 Ag(-1) was obtained at the potential window from -0.1 to 0.9 V (vs. SCE).

  9. Comparative Proteomics Analysis Reveals L-Arginine Activates Ethanol Degradation Pathways in HepG2 Cells.

    PubMed

    Yan, Guokai; Lestari, Retno; Long, Baisheng; Fan, Qiwen; Wang, Zhichang; Guo, Xiaozhen; Yu, Jie; Hu, Jun; Yang, Xingya; Chen, Changqing; Liu, Lu; Li, Xiuzhi; Purnomoadi, Agung; Achmadi, Joelal; Yan, Xianghua

    2016-03-17

    L-Arginine (Arg) is a versatile amino acid that plays crucial roles in a wide range of physiological and pathological processes. In this study, to investigate the alteration induced by Arg supplementation in proteome scale, isobaric tags for relative and absolute quantification (iTRAQ) based proteomic approach was employed to comparatively characterize the differentially expressed proteins between Arg deprivation (Ctrl) and Arg supplementation (+Arg) treated human liver hepatocellular carcinoma (HepG2) cells. A total of 21 proteins were identified as differentially expressed proteins and these 21 proteins were all up-regulated by Arg supplementation. Six amino acid metabolism-related proteins, mostly metabolic enzymes, showed differential expressions. Intriguingly, Ingenuity Pathway Analysis (IPA) based pathway analysis suggested that the three ethanol degradation pathways were significantly altered between Ctrl and +Arg. Western blotting and enzymatic activity assays validated that the key enzymes ADH1C, ALDH1A1, and ALDH2, which are mainly involved in ethanol degradation pathways, were highly differentially expressed, and activated between Ctrl and +Arg in HepG2 cells. Furthermore, 10 mM Arg significantly attenuated the cytotoxicity induced by 100 mM ethanol treatment (P < 0.0001). This study is the first time to reveal that Arg activates ethanol degradation pathways in HepG2 cells.

  10. Revealing the Hidden Relationship by Sparse Modules in Complex Networks with a Large-Scale Analysis

    PubMed Central

    Jiao, Qing-Ju; Huang, Yan; Liu, Wei; Wang, Xiao-Fan; Chen, Xiao-Shuang; Shen, Hong-Bin

    2013-01-01

    One of the remarkable features of networks is module that can provide useful insights into not only network organizations but also functional behaviors between their components. Comprehensive efforts have been devoted to investigating cohesive modules in the past decade. However, it is still not clear whether there are important structural characteristics of the nodes that do not belong to any cohesive module. In order to answer this question, we performed a large-scale analysis on 25 complex networks with different types and scales using our recently developed BTS (bintree seeking) algorithm, which is able to detect both cohesive and sparse modules in the network. Our results reveal that the sparse modules composed by the cohesively isolated nodes widely co-exist with the cohesive modules. Detailed analysis shows that both types of modules provide better characterization for the division of a network into functional units than merely cohesive modules, because the sparse modules possibly re-organize the nodes in the so-called cohesive modules, which lack obvious modular significance, into meaningful groups. Compared with cohesive modules, the sizes of sparse ones are generally smaller. Sparse modules are also found to have preferences in social and biological networks than others. PMID:23762457

  11. Transcriptomic analysis of Ruditapes philippinarum hemocytes reveals cytoskeleton disruption after in vitro Vibrio tapetis challenge.

    PubMed

    Brulle, Franck; Jeffroy, Fanny; Madec, Stéphanie; Nicolas, Jean-Louis; Paillard, Christine

    2012-10-01

    The Manila clam, Ruditapes philippinarum, is an economically-important, commercial shellfish; harvests are diminished in some European waters by a pathogenic bacterium, Vibrio tapetis, that causes Brown Ring disease. To identify molecular characteristics associated with susceptibility or resistance to Brown Ring disease, Suppression Subtractive Hybridization (SSH) analyzes were performed to construct cDNA libraries enriched in up- or down-regulated transcripts from clam immune cells, hemocytes, after a 3-h in vitro challenge with cultured V. tapetis. Nine hundred and ninety eight sequences from the two libraries were sequenced, and an in silico analysis identified 235 unique genes. BLAST and "Gene ontology" classification analyzes revealed that 60.4% of the Expressed Sequence Tags (ESTs) have high similarities with genes involved in various physiological functions, such as immunity, apoptosis and cytoskeleton organization; whereas, 39.6% remain unidentified. From the 235 unique genes, we selected 22 candidates based upon physiological function and redundancy in the libraries. Then, Real-Time PCR analysis identified 3 genes related to cytoskeleton organization showing significant variation in expression attributable to V. tapetis exposure. Disruption in regulation of these genes is consistent with the etiologic agent of Brown Ring disease in Manila clams. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Plasma enhancement of in vitro attachment of rat bone-marrow-derived stem cells on cross-linked gelatin films.

    PubMed

    Prasertsung, I; Kanokpanont, S; Mongkolnavin, R; Wong, C S; Panpranot, J; Damrongsakkul, S

    2012-01-01

    In this work, nitrogen, oxygen and air glow discharges powered by 50 Hz AC power supply are used for the treatment of type-A gelatin film cross-linked by a dehydrothermal (DHT) process. The properties of cross-linked gelatin were characterized by contact angle measurement, atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS) analysis. The results showed that the water contact angle of gelatin films decrease with increasing plasma treatment time. The treatment of nitrogen, oxygen and air plasma up to 30 s had no effects on the surface roughness of the gelatin film as revealed by AFM results. The XPS analysis showed that the N-containing functional groups generated by nitrogen and air plasma, and O-containing functional groups generated by oxygen and air plasmas were incorporated onto the film surface, the functional groups were found to increase with increasing treatment time. An in vitro test using rat bone-marrow-mesenchym-derived stem cells (MSCs) revealed that the number of cells attached on plasma-treated gelatin films was significantly increased compared to untreated samples. The best enhancement of cell attachment was noticed when the film was treated with nitrogen plasma for 15-30 s, oxygen plasma for 3 s, and air plasma for 9 s. In addition, among the three types of plasmas used, nitrogen plasma treatment gave the best MSCs attachment on the gelatin surface. The results suggest that a type-A gelatin film with water contact angle of 27-28° and an O/N ratio of 1.4 is most suitable for MSCs attachment.

  13. Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species

    PubMed Central

    Xie, Jianbo; Shi, Haowen; Du, Zhenglin; Wang, Tianshu; Liu, Xiaomeng; Chen, Sanfeng

    2016-01-01

    Paenibacillus polymyxa has widely been studied as a model of plant-growth promoting rhizobacteria (PGPR). Here, the genome sequences of 9 P. polymyxa strains, together with 26 other sequenced Paenibacillus spp., were comparatively studied. Phylogenetic analysis of the concatenated 244 single-copy core genes suggests that the 9 P. polymyxa strains and 5 other Paenibacillus spp., isolated from diverse geographic regions and ecological niches, formed a closely related clade (here it is called Poly-clade). Analysis of single nucleotide polymorphisms (SNPs) reveals local diversification of the 14 Poly-clade genomes. SNPs were not evenly distributed throughout the 14 genomes and the regions with high SNP density contain the genes related to secondary metabolism, including genes coding for polyketide. Recombination played an important role in the genetic diversity of this clade, although the rate of recombination was clearly lower than mutation. Some genes relevant to plant-growth promoting traits, i.e. phosphate solubilization and IAA production, are well conserved, while some genes relevant to nitrogen fixation and antibiotics synthesis are evolved with diversity in this Poly-clade. This study reveals that both P. polymyxa and its closely related species have plant growth promoting traits and they have great potential uses in agriculture and horticulture as PGPR. PMID:26856413

  14. Novel applications of X-ray photoelectron spectroscopy on unsupported nanoparticles

    NASA Astrophysics Data System (ADS)

    Kostko, Oleg; Xu, Bo; Jacobs, Michael I.; Ahmed, Musahid

    X-ray photoelectron spectroscopy (XPS) is a powerful technique for chemical analysis of surfaces. We will present novel results of XPS on unsupported, gas-phase nanoparticles using a velocity-map imaging (VMI) spectrometer. This technique allows for probes of both the surfaces of nanoparticles via XPS as well as their interiors via near edge X-ray absorption fine structure (NEXAFS) spectroscopy. A recent application of this technique has confirmed that arginine's guanidinium group exists in a protonated state even in strongly basic solution. Moreover, the core-level photoelectron spectroscopy can provide information on the effective attenuation length (EAL) of low kinetic energy electrons. This contradictory value is important for determining the probing depth of XPS and in photolithography. A new method for determining EALs will be presented.

  15. Virtually Naked: Virtual Environment Reveals Sex-Dependent Nature of Skin Disclosure

    PubMed Central

    Lomanowska, Anna M.; Guitton, Matthieu J.

    2012-01-01

    The human tendency to reveal or cover naked skin reflects a competition between the individual propensity for social interactions related to sexual appeal and interpersonal touch versus climatic, environmental, physical, and cultural constraints. However, due to the ubiquitous nature of these constraints, isolating on a large scale the spontaneous human tendency to reveal naked skin has remained impossible. Using the online 3-dimensional virtual world of Second Life, we examined spontaneous human skin-covering behavior unhindered by real-world climatic, environmental, and physical variables. Analysis of hundreds of avatars revealed that virtual females disclose substantially more naked skin than virtual males. This phenomenon was not related to avatar hypersexualization as evaluated by measurement of sexually dimorphic body proportions. Furthermore, analysis of skin-covering behavior of a population of culturally homogeneous avatars indicated that the propensity of female avatars to reveal naked skin persisted despite explicit cultural norms promoting less revealing attire. These findings have implications for further understanding how sex-specific aspects of skin disclosure influence human social interactions in both virtual and real settings. PMID:23300580

  16. Virtually naked: virtual environment reveals sex-dependent nature of skin disclosure.

    PubMed

    Lomanowska, Anna M; Guitton, Matthieu J

    2012-01-01

    The human tendency to reveal or cover naked skin reflects a competition between the individual propensity for social interactions related to sexual appeal and interpersonal touch versus climatic, environmental, physical, and cultural constraints. However, due to the ubiquitous nature of these constraints, isolating on a large scale the spontaneous human tendency to reveal naked skin has remained impossible. Using the online 3-dimensional virtual world of Second Life, we examined spontaneous human skin-covering behavior unhindered by real-world climatic, environmental, and physical variables. Analysis of hundreds of avatars revealed that virtual females disclose substantially more naked skin than virtual males. This phenomenon was not related to avatar hypersexualization as evaluated by measurement of sexually dimorphic body proportions. Furthermore, analysis of skin-covering behavior of a population of culturally homogeneous avatars indicated that the propensity of female avatars to reveal naked skin persisted despite explicit cultural norms promoting less revealing attire. These findings have implications for further understanding how sex-specific aspects of skin disclosure influence human social interactions in both virtual and real settings.

  17. Growth, Crystal Structure, Theoretical Analysis and Properties of Te4+-Doped KTiOPO4

    NASA Astrophysics Data System (ADS)

    Liu, Lintao; Yao, Qian; Zhang, Junying; Dong, Weimin; Li, Jing; Wang, Jiyang; Boughton, Robert I.

    2018-04-01

    A single crystal of Te4+-doped KTiOPO4(Te:KTP) has been grown by the flux method. The electronic structure and density of states of KTiOPO4 (KTP) and Te:KTP were calculated from first principles. As the results reveal, there is no change in the space group or lattice structure of Te:KTP, but that some increase in lattice parameters occurred. The chemical composition of Te:KTP was analyzed using x-ray photoelectron spectroscopy (XPS). The possible existence of Ti3+ has been evaluated by measuring the electron paramagnetic resonance spectrum, and the results reveal that the ion is absent from this crystal. It was observed that Te4+ doping reduces the conductivity of the crystal from measurements of its conductivity at different temperatures and frequencies, indicating that Te:KTP has excellent electro-optical properties. The effect of Te4+ doping on the second harmonic generation in KTP was also studied. The thermal expansion, thermal diffusivity, thermal conductivity and specific heat capacity of KTP and Te:KTP were determined.

  18. Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis.

    PubMed

    Nguyen, Phuong H

    2006-12-01

    Employing the recently developed hierarchical nonlinear principal component analysis (NLPCA) method of Saegusa et al. (Neurocomputing 2004;61:57-70 and IEICE Trans Inf Syst 2005;E88-D:2242-2248), the complexities of the free energy landscapes of several peptides, including triglycine, hexaalanine, and the C-terminal beta-hairpin of protein G, were studied. First, the performance of this NLPCA method was compared with the standard linear principal component analysis (PCA). In particular, we compared two methods according to (1) the ability of the dimensionality reduction and (2) the efficient representation of peptide conformations in low-dimensional spaces spanned by the first few principal components. The study revealed that NLPCA reduces the dimensionality of the considered systems much better, than did PCA. For example, in order to get the similar error, which is due to representation of the original data of beta-hairpin in low dimensional space, one needs 4 and 21 principal components of NLPCA and PCA, respectively. Second, by representing the free energy landscapes of the considered systems as a function of the first two principal components obtained from PCA, we obtained the relatively well-structured free energy landscapes. In contrast, the free energy landscapes of NLPCA are much more complicated, exhibiting many states which are hidden in the PCA maps, especially in the unfolded regions. Furthermore, the study also showed that many states in the PCA maps are mixed up by several peptide conformations, while those of the NLPCA maps are more pure. This finding suggests that the NLPCA should be used to capture the essential features of the systems. (c) 2006 Wiley-Liss, Inc.

  19. Integrative Computational Network Analysis Reveals Site-Specific Mediators of Inflammation in Alzheimer's Disease.

    PubMed

    Ravichandran, Srikanth; Michelucci, Alessandro; Del Sol, Antonio

    2018-01-01

    Alzheimer's disease (AD) is a major neurodegenerative disease and is one of the most common cause of dementia in older adults. Among several factors, neuroinflammation is known to play a critical role in the pathogenesis of chronic neurodegenerative diseases. In particular, studies of brains affected by AD show a clear involvement of several inflammatory pathways. Furthermore, depending on the brain regions affected by the disease, the nature and the effect of inflammation can vary. Here, in order to shed more light on distinct and common features of inflammation in different brain regions affected by AD, we employed a computational approach to analyze gene expression data of six site-specific neuronal populations from AD patients. Our network based computational approach is driven by the concept that a sustained inflammatory environment could result in neurotoxicity leading to the disease. Thus, our method aims to infer intracellular signaling pathways/networks that are likely to be constantly activated or inhibited due to persistent inflammatory conditions. The computational analysis identified several inflammatory mediators, such as tumor necrosis factor alpha (TNF-a)-associated pathway, as key upstream receptors/ligands that are likely to transmit sustained inflammatory signals. Further, the analysis revealed that several inflammatory mediators were mainly region specific with few commonalities across different brain regions. Taken together, our results show that our integrative approach aids identification of inflammation-related signaling pathways that could be responsible for the onset or the progression of AD and can be applied to study other neurodegenerative diseases. Furthermore, such computational approaches can enable the translation of clinical omics data toward the development of novel therapeutic strategies for neurodegenerative diseases.

  20. Integrative Computational Network Analysis Reveals Site-Specific Mediators of Inflammation in Alzheimer's Disease

    PubMed Central

    Ravichandran, Srikanth; Michelucci, Alessandro; del Sol, Antonio

    2018-01-01

    Alzheimer's disease (AD) is a major neurodegenerative disease and is one of the most common cause of dementia in older adults. Among several factors, neuroinflammation is known to play a critical role in the pathogenesis of chronic neurodegenerative diseases. In particular, studies of brains affected by AD show a clear involvement of several inflammatory pathways. Furthermore, depending on the brain regions affected by the disease, the nature and the effect of inflammation can vary. Here, in order to shed more light on distinct and common features of inflammation in different brain regions affected by AD, we employed a computational approach to analyze gene expression data of six site-specific neuronal populations from AD patients. Our network based computational approach is driven by the concept that a sustained inflammatory environment could result in neurotoxicity leading to the disease. Thus, our method aims to infer intracellular signaling pathways/networks that are likely to be constantly activated or inhibited due to persistent inflammatory conditions. The computational analysis identified several inflammatory mediators, such as tumor necrosis factor alpha (TNF-a)-associated pathway, as key upstream receptors/ligands that are likely to transmit sustained inflammatory signals. Further, the analysis revealed that several inflammatory mediators were mainly region specific with few commonalities across different brain regions. Taken together, our results show that our integrative approach aids identification of inflammation-related signaling pathways that could be responsible for the onset or the progression of AD and can be applied to study other neurodegenerative diseases. Furthermore, such computational approaches can enable the translation of clinical omics data toward the development of novel therapeutic strategies for neurodegenerative diseases. PMID:29551980